diff --git a/nwb_linkml/adapters/adapter.py b/nwb_linkml/adapters/adapter.py index 475b32d..6d466c1 100644 --- a/nwb_linkml/adapters/adapter.py +++ b/nwb_linkml/adapters/adapter.py @@ -80,9 +80,11 @@ class Adapter(BaseModel): # do nothing, is a string or whatever pass - def walk_fields(self, input: BaseModel | list | dict, field: str): + def walk_fields(self, input: BaseModel | list | dict, field: str | Tuple[str, ...]): + if isinstance(field, str): + field = (field,) for item in self.walk(input): - if isinstance(item, tuple) and item[0] == field and item[1] is not None: + if isinstance(item, tuple) and item[0] in field and item[1] is not None: yield item[1] diff --git a/nwb_linkml/adapters/classes.py b/nwb_linkml/adapters/classes.py index b68fcc9..130d0eb 100644 --- a/nwb_linkml/adapters/classes.py +++ b/nwb_linkml/adapters/classes.py @@ -29,7 +29,7 @@ class ClassAdapter(Adapter): name_parts.append(self.parent._get_full_name()) name_parts.append(self.cls.name) - name = '_'.join(name_parts) + name = '__'.join(name_parts) elif self.cls.neurodata_type_inc is not None: # again, this is against the schema, but is common name = self.cls.neurodata_type_inc @@ -62,7 +62,9 @@ class ClassAdapter(Adapter): return name - def handle_arraylike(self, dataset: Dataset, name:Optional[str]=None) -> Optional[ClassDefinition]: + + + def handle_arraylike(self, dataset: Dataset, name:Optional[str]=None) -> Optional[ClassDefinition | SlotDefinition]: """ Handling the @@ -96,6 +98,11 @@ class ClassAdapter(Adapter): # need to have both if one is present! raise ValueError(f"A dataset needs both dims and shape to define an arraylike object") + # Special cases + if dataset.neurodata_type_inc == 'VectorData': + # Handle this in `handle_vectorlike` instead + return None + # The schema language doesn't have a way of specifying a dataset/group is "abstract" # and yet hdmf-common says you don't need a dtype if the dataset is "abstract" # so.... @@ -117,6 +124,18 @@ class ClassAdapter(Adapter): dims_shape = tuple(dict.fromkeys(dims_shape).keys()) + # if we only have one possible dimension, it's equivalent to a list, so we just return the slot + if len(dims_shape) == 1 and self.parent: + quantity = QUANTITY_MAP[dataset.quantity] + slot = SlotDefinition( + name=dataset.name, + range = dtype, + description=dataset.doc, + required=quantity['required'], + multivalued=True + ) + return slot + # now make slots for each of them slots = [] for dims, shape in dims_shape: @@ -140,6 +159,8 @@ class ClassAdapter(Adapter): range=dtype )) + + # and then the class is just a subclass of `Arraylike` (which is imported by default from `nwb.language.yaml`) if name: pass @@ -150,7 +171,7 @@ class ClassAdapter(Adapter): else: raise ValueError(f"Dataset has no name or type definition, what do call it?") - name = '_'.join([name, 'Array']) + name = '__'.join([name, 'Array']) array_class = ClassDefinition( name=name, @@ -203,13 +224,46 @@ class ClassAdapter(Adapter): nested_classes.extend([ClassAdapter(cls=grp, parent=self) for grp in cls.groups]) nested_res = BuildResult() for subclass in nested_classes: - this_slot = SlotDefinition( - name=subclass._get_name(), - description=subclass.cls.doc, - range=subclass._get_full_name(), - **QUANTITY_MAP[subclass.cls.quantity] - ) - nested_res.slots.append(this_slot) + # handle the special case where `VectorData` is subclasssed without any dims or attributes + # which just gets instantiated as a 1-d array in HDF5 + if subclass.cls.neurodata_type_inc == 'VectorData' and \ + not subclass.cls.dims and \ + not subclass.cls.shape and \ + not subclass.cls.attributes \ + and subclass.cls.name: + this_slot = SlotDefinition( + name=subclass.cls.name, + description=subclass.cls.doc, + range=self.handle_dtype(subclass.cls.dtype), + multivalued=True + ) + nested_res.slots.append(this_slot) + continue + + # Simplify datasets that are just a single value + elif isinstance(subclass.cls, Dataset) and \ + not subclass.cls.neurodata_type_inc and \ + not subclass.cls.attributes and \ + not subclass.cls.dims and \ + not subclass.cls.shape and \ + subclass.cls.name: + this_slot = SlotDefinition( + name=subclass.cls.name, + description=subclass.cls.doc, + range=self.handle_dtype(subclass.cls.dtype), + **QUANTITY_MAP[subclass.cls.quantity] + ) + nested_res.slots.append(this_slot) + continue + + else: + this_slot = SlotDefinition( + name=subclass._get_name(), + description=subclass.cls.doc, + range=subclass._get_full_name(), + **QUANTITY_MAP[subclass.cls.quantity] + ) + nested_res.slots.append(this_slot) if subclass.cls.name is None and subclass.cls.neurodata_type_def is None: # anonymous group that's just an inc, we only need the slot since the class is defined elsewhere @@ -246,14 +300,19 @@ class ClassAdapter(Adapter): nested_res = BuildResult() arraylike = self.handle_arraylike(self.cls, self._get_full_name()) if arraylike: - # make a slot for the arraylike class - attrs.append( - SlotDefinition( - name='array', - range=arraylike.name + # if the arraylike thing can only have one dimension, it's equivalent to a list, so + # we just add a multivalued slot + if isinstance(arraylike, SlotDefinition): + attrs.append(arraylike) + else: + # make a slot for the arraylike class + attrs.append( + SlotDefinition( + name='array', + range=arraylike.name + ) ) - ) - nested_res.classes.append(arraylike) + nested_res.classes.append(arraylike) cls = ClassDefinition( diff --git a/nwb_linkml/adapters/schema.py b/nwb_linkml/adapters/schema.py index 0556a04..1111beb 100644 --- a/nwb_linkml/adapters/schema.py +++ b/nwb_linkml/adapters/schema.py @@ -13,9 +13,15 @@ if TYPE_CHECKING: from nwb_linkml.adapters.namespaces import NamespacesAdapter from nwb_schema_language import Group, Dataset +from typing import NamedTuple from linkml_runtime.linkml_model import SchemaDefinition + +class SplitSchema(NamedTuple): + main: BuildResult + split: BuildResult + class SchemaAdapter(Adapter): """ An individual schema file in nwb_schema_language @@ -24,8 +30,13 @@ class SchemaAdapter(Adapter): groups: List[Group] = Field(default_factory=list) datasets: List[Dataset] = Field(default_factory=list) imports: List['SchemaAdapter'] = Field(default_factory=list) - namespace: Optional[str] = None - """Populated by NamespacesAdapter""" + namespace: Optional[str] = Field( + None, + description="""String of containing namespace. Populated by NamespacesAdapter""") + split: bool = Field( + True, + description="Split anonymous subclasses into a separate schema file" + ) @property def name(self) -> str: @@ -66,18 +77,69 @@ class SchemaAdapter(Adapter): else: built_results += cls.build() + if self.split: + sch_split = self.split_subclasses(built_results) + return sch_split - sch = SchemaDefinition( - name = self.name, - id = self.name, - imports = [i.name for i in self.imports], - classes=built_results.classes, - slots=built_results.slots, - types=built_results.types + else: + sch = SchemaDefinition( + name = self.name, + id = self.name, + imports = [i.name for i in self.imports], + classes=built_results.classes, + slots=built_results.slots, + types=built_results.types + ) + # every schema needs the language elements + sch.imports.append('nwb.language') + return BuildResult(schemas=[sch]) + + def split_subclasses(self, classes: BuildResult) -> BuildResult: + """ + Split the generated classes into top-level "main" classes and + nested/anonymous "split" classes. + + Args: + classes (BuildResult): A Build result object containing the classes + for the schema + + Returns: + :class:`.SplitSchema` + """ + # just split by the presence or absence of __ + main_classes = [c for c in classes.classes if '__' not in c.name] + split_classes = [c for c in classes.classes if '__' in c.name] + split_sch_name = '.'.join([self.name, 'include']) + + + imports = [i.name for i in self.imports] + imports.append('nwb.language') + # need to mutually import the two schemas because the subclasses + # could refer to the main classes + main_imports = imports + main_imports.append(split_sch_name) + imports.append(self.name) + main_sch = SchemaDefinition( + name=self.name, + id=self.name, + imports=main_imports, + classes=main_classes, + slots=classes.slots, + types=classes.types ) - # every schema needs the language elements - sch.imports.append('nwb.language') - return BuildResult(schemas=[sch]) + split_sch = SchemaDefinition( + name=split_sch_name, + id=split_sch_name, + imports=imports, + classes=split_classes, + slots=classes.slots, + types=classes.types + ) + res = BuildResult( + schemas=[main_sch, split_sch] + ) + return res + @property @@ -94,7 +156,8 @@ class SchemaAdapter(Adapter): - Need to also check classes used in links/references """ - type_incs = self.walk_fields(self, 'neurodata_type_inc') + type_incs = self.walk_fields(self, ('neurodata_type_inc', 'target_type')) + definitions = [c.neurodata_type_def for c in self.created_classes] need = [inc for inc in type_incs if inc not in definitions] return need diff --git a/nwb_linkml/generators/__init__.py b/nwb_linkml/generators/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/nwb_linkml/generators/pydantic.py b/nwb_linkml/generators/pydantic.py new file mode 100644 index 0000000..d9ef96d --- /dev/null +++ b/nwb_linkml/generators/pydantic.py @@ -0,0 +1,447 @@ +""" +Subclass of :class:`linkml.generators.PydanticGenerator` + +The pydantic generator is a subclass of +- :class:`linkml.utils.generator.Generator` +- :class:`linkml.generators.oocodegen.OOCodeGenerator` + +The default `__main__` method +- Instantiates the class +- Calls :meth:`~linkml.generators.PydanticGenerator.serialize` + +The `serialize` method +- Accepts an optional jinja-style template, otherwise it uses the default template +- Uses :class:`linkml_runtime.utils.schemaview.SchemaView` to interact with the schema +- Generates linkML Classes + - `generate_enums` runs first + +""" +import pdb +from typing import List, Dict, Set +from copy import deepcopy +import warnings + +from nwb_linkml.maps.dtype import flat_to_npytyping +from linkml.generators import PydanticGenerator +from linkml_runtime.linkml_model.meta import ( + Annotation, + ClassDefinition, + SchemaDefinition, + SlotDefinition, +SlotDefinitionName, + TypeDefinition, +ElementName +) +from linkml_runtime.utils.formatutils import camelcase, underscore +from linkml_runtime.utils.schemaview import SchemaView +from jinja2 import Template + + + +def default_template(pydantic_ver: str = "1") -> str: + """Constructs a default template for pydantic classes based on the version of pydantic""" + ### HEADER ### + template = """ +{#- + + Jinja2 Template for a pydantic classes +-#} +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + +{% for import_module, import_classes in imports.items() %} +from {{ import_module }} import ( + {{ import_classes | join(',\n ') }} +) +{% endfor %} + +metamodel_version = "{{metamodel_version}}" +version = "{{version if version else None}}" +""" + ### BASE MODEL ### + if pydantic_ver == "1": + template += """ +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = {% if allow_extra %}'allow'{% else %}'forbid'{% endif %}, + arbitrary_types_allowed = True, + use_enum_values = True): + pass +""" + else: + template += """ +class ConfiguredBaseModel(BaseModel, + validate_assignment = True, + validate_default = True, + extra = {% if allow_extra %}'allow'{% else %}'forbid'{% endif %}, + arbitrary_types_allowed = True, + use_enum_values = True): + pass +""" + ### ENUMS ### + template += """ +{% for e in enums.values() %} +class {{ e.name }}(str, Enum): + {% if e.description -%} + \"\"\" + {{ e.description }} + \"\"\" + {%- endif %} + {% for _, pv in e['values'].items() -%} + {% if pv.description -%} + # {{pv.description}} + {%- endif %} + {{pv.label}} = "{{pv.value}}" + {% endfor %} + {% if not e['values'] -%} + dummy = "dummy" + {% endif %} +{% endfor %} +""" + ### CLASSES ### + template += """ +{%- for c in schema.classes.values() %} +class {{ c.name }} + {%- if class_isa_plus_mixins[c.name] -%} + ({{class_isa_plus_mixins[c.name]|join(', ')}}) + {%- else -%} + (ConfiguredBaseModel) + {%- endif -%} + : + {% if c.description -%} + \"\"\" + {{ c.description }} + \"\"\" + {%- endif %} + {% for attr in c.attributes.values() if c.attributes -%} + {{attr.name}}: {{ attr.annotations['python_range'].value }} = Field( + {%- if predefined_slot_values[c.name][attr.name] -%} + {{ predefined_slot_values[c.name][attr.name] }} + {%- elif attr.required -%} + ... + {%- else -%} + None + {%- endif -%} + {%- if attr.title != None %}, title="{{attr.title}}"{% endif -%} + {%- if attr.description %}, description=\"\"\"{{attr.description}}\"\"\"{% endif -%} + {%- if attr.minimum_value != None %}, ge={{attr.minimum_value}}{% endif -%} + {%- if attr.maximum_value != None %}, le={{attr.maximum_value}}{% endif -%} + ) + {% else -%} + None + {% endfor %} +{% endfor %} +""" + ### FWD REFS / REBUILD MODEL ### + if pydantic_ver == "1": + template += """ +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +{% for c in schema.classes.values() -%} +{{ c.name }}.update_forward_refs() +{% endfor %} +""" + else: + template += """ +# Model rebuild +# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model +{% for c in schema.classes.values() -%} +{{ c.name }}.model_rebuild() +{% endfor %} +""" + return template + + + +class NWBPydanticGenerator(PydanticGenerator): + + SKIP_ENUM=('FlatDType',) + + def _get_imports(self, sv:SchemaView) -> Dict[str, List[str]]: + all_classes = sv.all_classes(imports=True) + local_classes = sv.all_classes(imports=False) + needed_classes = [] + # find needed classes - is_a and slot ranges + + for clsname, cls in local_classes.items(): + needed_classes.append(cls.is_a) + for slot_name, slot in cls.attributes.items(): + if slot.range in all_classes: + needed_classes.append(slot.range) + + needed_classes = [cls for cls in set(needed_classes) if cls is not None] + imports = {} + + # These classes are not generated by pydantic! + skips = ('AnyType',) + + for cls in needed_classes: + if cls in skips: + continue + # Find module that contains class + module_name = sv.element_by_schema_map()[ElementName(cls)] + # Don't get classes that are defined in this schema! + if module_name == self.schema.name: + continue + + local_mod_name = '.' + module_name.replace('.', '_').replace('-','_') + if local_mod_name not in imports: + imports[local_mod_name] = [camelcase(cls)] + else: + imports[local_mod_name].append(camelcase(cls)) + + return imports + + + def _get_classes(self, sv:SchemaView, imports: Dict[str, List[str]]) -> List[ClassDefinition]: + module_classes = sv.all_classes(imports=False).values() + imported_classes = [] + for classes in imports.values(): + imported_classes.extend(classes) + # pdb.set_trace() + sorted_classes = self.sort_classes(list(module_classes), imported_classes) + self.sorted_class_names = [camelcase(cname) for cname in imported_classes] + self.sorted_class_names += [camelcase(c.name) for c in sorted_classes] + + # Don't want to generate classes when class_uri is linkml:Any, will + # just swap in typing.Any instead down below + sorted_classes = [c for c in sorted_classes if c.class_uri != "linkml:Any"] + return sorted_classes + + def _build_class(self, class_original:ClassDefinition) -> ClassDefinition: + class_def: ClassDefinition + class_def = deepcopy(class_original) + class_def.name = camelcase(class_original.name) + if class_def.is_a: + class_def.is_a = camelcase(class_def.is_a) + class_def.mixins = [camelcase(p) for p in class_def.mixins] + if class_def.description: + class_def.description = class_def.description.replace('"', '\\"') + return class_def + + def _check_anyof(self, s:SlotDefinition, sn: SlotDefinitionName, sv:SchemaView): + # Confirm that the original slot range (ignoring the default that comes in from + # induced_slot) isn't in addition to setting any_of + if len(s.any_of) > 0 and sv.get_slot(sn).range is not None: + base_range_subsumes_any_of = False + base_range = sv.get_slot(sn).range + base_range_cls = sv.get_class(base_range, strict=False) + if base_range_cls is not None and base_range_cls.class_uri == "linkml:Any": + base_range_subsumes_any_of = True + if not base_range_subsumes_any_of: + raise ValueError("Slot cannot have both range and any_of defined") + + def _get_numpy_slot_range(self, cls:ClassDefinition) -> str: + # slot always starts with... + prefix='NDArray[' + + # and then we specify the shape: + shape_prefix = 'Shape["' + + # using the cardinality from the attributes + dim_pieces = [] + for attr in cls.attributes.values(): + + if attr.maximum_cardinality: + shape_part = str(attr.maximum_cardinality) + else: + shape_part = "*" + # do this cheaply instead of using regex because i want to see if this works at all first... + name_part = attr.name.replace(',', '_').replace(' ', '_').replace('__', '_') + + dim_pieces.append(' '.join([shape_part, name_part])) + + dimension = ', '.join(dim_pieces) + + shape_suffix = '"], ' + + # all dimensions should be the same dtype + try: + dtype = flat_to_npytyping[list(cls.attributes.values())[0].range] + except KeyError as e: + warnings.warn(e) + range = list(cls.attributes.values())[0].range + return f'List[{range}] | {range}' + suffix = "]" + + slot = ''.join([prefix, shape_prefix, dimension, shape_suffix, dtype, suffix]) + return slot + + + def sort_classes(self, clist: List[ClassDefinition], imports:List[str]) -> List[ClassDefinition]: + """ + sort classes such that if C is a child of P then C appears after P in the list + + Overridden method include mixin classes + + Modified from original to allow for imported classes + """ + clist = list(clist) + slist = [] # sorted + while len(clist) > 0: + can_add = False + for i in range(len(clist)): + candidate = clist[i] + can_add = False + if candidate.is_a: + candidates = [candidate.is_a] + candidate.mixins + else: + candidates = candidate.mixins + if not candidates: + can_add = True + + else: + if set(candidates) <= set([p.name for p in slist] + imports): + can_add = True + + if can_add: + slist = slist + [candidate] + del clist[i] + break + if not can_add: + raise ValueError( + f"could not find suitable element in {clist} that does not ref {slist}" + ) + return slist + + def get_class_slot_range(self, slot_range: str, inlined: bool, inlined_as_list: bool) -> str: + """ + Monkeypatch to convert Array typed slots and classes into npytyped hints + """ + sv = self.schemaview + range_cls = sv.get_class(slot_range) + if range_cls.is_a == "Arraylike": + return self._get_numpy_slot_range(range_cls) + else: + return super().get_class_slot_range(slot_range, inlined, inlined_as_list) + + def get_class_isa_plus_mixins(self) -> Dict[str, List[str]]: + """ + Generate the inheritance list for each class from is_a plus mixins + + Patched to only get local classes + + :return: + """ + sv = self.schemaview + parents = {} + for class_def in sv.all_classes(imports=False).values(): + class_parents = [] + if class_def.is_a: + class_parents.append(camelcase(class_def.is_a)) + if self.gen_mixin_inheritance and class_def.mixins: + class_parents.extend([camelcase(mixin) for mixin in class_def.mixins]) + if len(class_parents) > 0: + # Use the sorted list of classes to order the parent classes, but reversed to match MRO needs + class_parents.sort(key=lambda x: self.sorted_class_names.index(x)) + class_parents.reverse() + parents[camelcase(class_def.name)] = class_parents + return parents + + def serialize(self) -> str: + if self.template_file is not None: + with open(self.template_file) as template_file: + template_obj = Template(template_file.read()) + else: + template_obj = Template(default_template(self.pydantic_version)) + + sv: SchemaView + sv = self.schemaview + schema = sv.schema + pyschema = SchemaDefinition( + id=schema.id, + name=schema.name, + description=schema.description.replace('"', '\\"') if schema.description else None, + ) + enums = self.generate_enums(sv.all_enums()) + # filter skipped enums + enums = {k:v for k,v in enums.items() if k not in self.SKIP_ENUM} + + # import from local references, rather than serializing every class in every file + imports = self._get_imports(sv) + + sorted_classes = self._get_classes(sv, imports) + + for class_original in sorted_classes: + # Generate class definition + class_def = self._build_class(class_original) + pyschema.classes[class_def.name] = class_def + + # Not sure why this happens + for attribute in list(class_def.attributes.keys()): + del class_def.attributes[attribute] + + class_name = class_original.name + for sn in sv.class_slots(class_name): + # TODO: fix runtime, copy should not be necessary + s = deepcopy(sv.induced_slot(sn, class_name)) + # logging.error(f'Induced slot {class_name}.{sn} == {s.name} {s.range}') + s.name = underscore(s.name) + if s.description: + s.description = s.description.replace('"', '\\"') + class_def.attributes[s.name] = s + + slot_ranges: List[str] = [] + + self._check_anyof(s, sn, sv) + + if s.any_of is not None and len(s.any_of) > 0: + # list comprehension here is pulling ranges from within AnonymousSlotExpression + slot_ranges.extend([r.range for r in s.any_of]) + else: + slot_ranges.append(s.range) + + pyranges = [ + self.generate_python_range(slot_range, s, class_def) + for slot_range in slot_ranges + ] + + pyranges = list(set(pyranges)) # remove duplicates + pyranges.sort() + + if len(pyranges) == 1: + pyrange = pyranges[0] + elif len(pyranges) > 1: + pyrange = f"Union[{', '.join(pyranges)}]" + else: + raise Exception(f"Could not generate python range for {class_name}.{s.name}") + + if s.multivalued: + if s.inlined or s.inlined_as_list: + collection_key = self.generate_collection_key(slot_ranges, s, class_def) + else: + collection_key = None + if s.inlined is False or collection_key is None or s.inlined_as_list is True: + pyrange = f"List[{pyrange}]" + else: + pyrange = f"Dict[{collection_key}, {pyrange}]" + if not s.required and not s.designates_type: + pyrange = f"Optional[{pyrange}]" + ann = Annotation("python_range", pyrange) + s.annotations[ann.tag] = ann + code = template_obj.render( + imports=imports, + schema=pyschema, + underscore=underscore, + enums=enums, + predefined_slot_values=self.get_predefined_slot_values(), + allow_extra=self.allow_extra, + metamodel_version=self.schema.metamodel_version, + version=self.schema.version, + class_isa_plus_mixins=self.get_class_isa_plus_mixins(), + ) + return code \ No newline at end of file diff --git a/nwb_linkml/maps/dtype.py b/nwb_linkml/maps/dtype.py index 85b8dd8..008a05f 100644 --- a/nwb_linkml/maps/dtype.py +++ b/nwb_linkml/maps/dtype.py @@ -28,4 +28,32 @@ flat_to_linkml = { } """ Map between the flat data types and the simpler linkml base types -""" \ No newline at end of file +""" + +flat_to_npytyping = { + "float": "Float", + "float32": "Float32", + "double": "Double", + "float64": "Float64", + "long": "LongLong", + "int64": "Int64", + "int": "Int", + "int32": "Int32", + "int16": "Int16", + "short": "Short", + "int8": "Int8", + "uint": "UInt", + "uint32": "UInt32", + "uint16": "UInt16", + "uint8": "UInt8", + "uint64": "UInt64", + "numeric": "Number", + "text": "String", + "utf": "Unicode", + "utf8": "Unicode", + "utf_8": "Unicode", + "ascii": "String", + "bool": "Bool", + "isodatetime": "Datetime64", + 'AnyType': 'Any' +} \ No newline at end of file diff --git a/nwb_linkml/models/core.nwb.base.py b/nwb_linkml/models/core.nwb.base.py deleted file mode 100644 index c51f07a..0000000 --- a/nwb_linkml/models/core.nwb.base.py +++ /dev/null @@ -1,411 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): - pass - - -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - -class TimeSeriesData(ConfiguredBaseModel): - """ - Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file. - """ - conversion: Optional[float] = Field(None, description="""Scalar to multiply each element in data to convert it to the specified 'unit'. If the data are stored in acquisition system units or other units that require a conversion to be interpretable, multiply the data by 'conversion' to convert the data to the specified 'unit'. e.g. if the data acquisition system stores values in this object as signed 16-bit integers (int16 range -32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data acquisition system gain is 8000X, then the 'conversion' multiplier to get from raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9.""") - offset: Optional[float] = Field(None, description="""Scalar to add to the data after scaling by 'conversion' to finalize its coercion to the specified 'unit'. Two common examples of this include (a) data stored in an unsigned type that requires a shift after scaling to re-center the data, and (b) specialized recording devices that naturally cause a scalar offset with respect to the true units.""") - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data, stored in the specified by unit, e.g., the change in value of the least significant bit, or a larger number if signal noise is known to be present. If unknown, use -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - continuity: Optional[str] = Field(None, description="""Optionally describe the continuity of the data. Can be \"continuous\", \"instantaneous\", or \"step\". For example, a voltage trace would be \"continuous\", because samples are recorded from a continuous process. An array of lick times would be \"instantaneous\", because the data represents distinct moments in time. Times of image presentations would be \"step\" because the picture remains the same until the next timepoint. This field is optional, but is useful in providing information about the underlying data. It may inform the way this data is interpreted, the way it is visualized, and what analysis methods are applicable.""") - array: Optional[TimeSeriesDataArray] = Field(None) - - -class TimeSeriesStartingTime(ConfiguredBaseModel): - """ - Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute. - """ - rate: Optional[float] = Field(None, description="""Sampling rate, in Hz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement for time, which is fixed to 'seconds'.""") - - -class TimeSeriesTimestamps(ConfiguredBaseModel): - """ - Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. - """ - interval: Optional[int] = Field(None, description="""Value is '1'""") - unit: Optional[str] = Field(None, description="""Unit of measurement for timestamps, which is fixed to 'seconds'.""") - array: Optional[TimeSeriesTimestampsArray] = Field(None) - - -class TimeSeriesControl(ConfiguredBaseModel): - """ - Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data. - """ - array: Optional[TimeSeriesControlArray] = Field(None) - - -class TimeSeriesControlDescription(ConfiguredBaseModel): - """ - Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0. - """ - array: Optional[TimeSeriesControlDescriptionArray] = Field(None) - - -class TimeSeriesSync(ConfiguredBaseModel): - """ - Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes. - """ - None - - -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - -class ImageArray(Arraylike): - - x: float = Field(...) - y: float = Field(...) - r_g_b: Optional[float] = Field(None) - r_g_b_a: Optional[float] = Field(None) - - -class ImageReferencesArray(Arraylike): - - num_images: Image = Field(...) - - -class TimeSeriesDataArray(Arraylike): - - num_times: Any = Field(...) - num_DIM2: Optional[Any] = Field(None) - num_DIM3: Optional[Any] = Field(None) - num_DIM4: Optional[Any] = Field(None) - - -class TimeSeriesTimestampsArray(Arraylike): - - num_times: float = Field(...) - - -class TimeSeriesControlArray(Arraylike): - - num_times: int = Field(...) - - -class TimeSeriesControlDescriptionArray(Arraylike): - - num_control_values: str = Field(...) - - -class VectorDataArray(Arraylike): - - dim0: Any = Field(...) - dim1: Optional[Any] = Field(None) - dim2: Optional[Any] = Field(None) - dim3: Optional[Any] = Field(None) - - -class VectorIndexArray(Arraylike): - - num_rows: int = Field(...) - - -class ElementIdentifiersArray(Arraylike): - - num_elements: int = Field(...) - - -class DynamicTableRegionArray(Arraylike): - - num_rows: int = Field(...) - - -class DynamicTableIdArray(Arraylike): - - num_rows: int = Field(...) - - -class Data(ConfiguredBaseModel): - """ - An abstract data type for a dataset. - """ - None - - -class NWBData(Data): - """ - An abstract data type for a dataset. - """ - None - - -class Image(NWBData): - """ - An abstract data type for an image. Shape can be 2-D (x, y), or 3-D where the third dimension can have three or four elements, e.g. (x, y, (r, g, b)) or (x, y, (r, g, b, a)). - """ - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - array: Optional[ImageArray] = Field(None) - - -class ImageReferences(NWBData): - """ - Ordered dataset of references to Image objects. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class ImagesOrderOfImages(ImageReferences): - """ - Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class VectorData(Data): - """ - An n-dimensional dataset representing a column of a DynamicTable. If used without an accompanying VectorIndex, first dimension is along the rows of the DynamicTable and each step along the first dimension is a cell of the larger table. VectorData can also be used to represent a ragged array if paired with a VectorIndex. This allows for storing arrays of varying length in a single cell of the DynamicTable by indexing into this VectorData. The first vector is at VectorData[0:VectorIndex[0]]. The second vector is at VectorData[VectorIndex[0]:VectorIndex[1]], and so on. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class TimeSeriesReferenceVectorData(VectorData): - """ - Column storing references to a TimeSeries (rows). For each TimeSeries this VectorData column stores the start_index and count to indicate the range in time to be selected as well as an object reference to the TimeSeries. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class VectorIndex(VectorData): - """ - Used with VectorData to encode a ragged array. An array of indices into the first dimension of the target VectorData, and forming a map between the rows of a DynamicTable and the indices of the VectorData. The name of the VectorIndex is expected to be the name of the target VectorData object followed by \"_index\". - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ElementIdentifiers(Data): - """ - A list of unique identifiers for values within a dataset, e.g. rows of a DynamicTable. - """ - array: Optional[ElementIdentifiersArray] = Field(None) - - -class DynamicTableRegion(VectorData): - """ - DynamicTableRegion provides a link from one table to an index or region of another. The `table` attribute is a link to another `DynamicTable`, indicating which table is referenced, and the data is int(s) indicating the row(s) (0-indexed) of the target array. `DynamicTableRegion`s can be used to associate rows with repeated meta-data without data duplication. They can also be used to create hierarchical relationships between multiple `DynamicTable`s. `DynamicTableRegion` objects may be paired with a `VectorIndex` object to create ragged references, so a single cell of a `DynamicTable` can reference many rows of another `DynamicTable`. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DynamicTableId(ElementIdentifiers): - """ - Array of unique identifiers for the rows of this dynamic table. - """ - array: Optional[DynamicTableIdArray] = Field(None) - - -class Container(ConfiguredBaseModel): - """ - An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class NWBContainer(Container): - """ - An abstract data type for a generic container storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class NWBDataInterface(NWBContainer): - """ - An abstract data type for a generic container storing collections of data, as opposed to metadata. - """ - None - - -class TimeSeries(NWBDataInterface): - """ - General purpose time series. - """ - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - data: TimeSeriesData = Field(..., description="""Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class ProcessingModule(NWBContainer): - """ - A collection of processed data. - """ - description: Optional[str] = Field(None, description="""Description of this collection of processed data.""") - NWBDataInterface: Optional[List[NWBDataInterface]] = Field(default_factory=list, description="""Data objects stored in this collection.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tables stored in this collection.""") - - -class Images(NWBDataInterface): - """ - A collection of images with an optional way to specify the order of the images using the \"order_of_images\" dataset. An order must be specified if the images are referenced by index, e.g., from an IndexSeries. - """ - description: Optional[str] = Field(None, description="""Description of this collection of images.""") - Image: List[Image] = Field(default_factory=list, description="""Images stored in this collection.""") - order_of_images: Optional[ImagesOrderOfImages] = Field(None, description="""Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images.""") - - -class DynamicTable(Container): - """ - A group containing multiple datasets that are aligned on the first dimension (Currently, this requirement if left up to APIs to check and enforce). These datasets represent different columns in the table. Apart from a column that contains unique identifiers for each row, there are no other required datasets. Users are free to add any number of custom VectorData objects (columns) here. DynamicTable also supports ragged array columns, where each element can be of a different size. To add a ragged array column, use a VectorIndex type to index the corresponding VectorData type. See documentation for VectorData and VectorIndex for more details. Unlike a compound data type, which is analogous to storing an array-of-structs, a DynamicTable can be thought of as a struct-of-arrays. This provides an alternative structure to choose from when optimizing storage for anticipated access patterns. Additionally, this type provides a way of creating a table without having to define a compound type up front. Although this convenience may be attractive, users should think carefully about how data will be accessed. DynamicTable is more appropriate for column-centric access, whereas a dataset with a compound type would be more appropriate for row-centric access. Finally, data size should also be taken into account. For small tables, performance loss may be an acceptable trade-off for the flexibility of a DynamicTable. - """ - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class AlignedDynamicTable(DynamicTable): - """ - DynamicTable container that supports storing a collection of sub-tables. Each sub-table is a DynamicTable itself that is aligned with the main table by row index. I.e., all DynamicTables stored in this group MUST have the same number of rows. This type effectively defines a 2-level table in which the main data is stored in the main table implemented by this type and additional columns of the table are grouped into categories, with each category being represented by a separate DynamicTable stored within the group. - """ - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimpleMultiContainer(Container): - """ - A simple Container for holding onto multiple containers. - """ - Data: Optional[List[Data]] = Field(default_factory=list, description="""Data objects held within this SimpleMultiContainer.""") - Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") - - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -TimeSeriesData.update_forward_refs() -TimeSeriesStartingTime.update_forward_refs() -TimeSeriesTimestamps.update_forward_refs() -TimeSeriesControl.update_forward_refs() -TimeSeriesControlDescription.update_forward_refs() -TimeSeriesSync.update_forward_refs() -Arraylike.update_forward_refs() -ImageArray.update_forward_refs() -ImageReferencesArray.update_forward_refs() -TimeSeriesDataArray.update_forward_refs() -TimeSeriesTimestampsArray.update_forward_refs() -TimeSeriesControlArray.update_forward_refs() -TimeSeriesControlDescriptionArray.update_forward_refs() -VectorDataArray.update_forward_refs() -VectorIndexArray.update_forward_refs() -ElementIdentifiersArray.update_forward_refs() -DynamicTableRegionArray.update_forward_refs() -DynamicTableIdArray.update_forward_refs() -Data.update_forward_refs() -NWBData.update_forward_refs() -Image.update_forward_refs() -ImageReferences.update_forward_refs() -ImagesOrderOfImages.update_forward_refs() -VectorData.update_forward_refs() -TimeSeriesReferenceVectorData.update_forward_refs() -VectorIndex.update_forward_refs() -ElementIdentifiers.update_forward_refs() -DynamicTableRegion.update_forward_refs() -DynamicTableId.update_forward_refs() -Container.update_forward_refs() -NWBContainer.update_forward_refs() -NWBDataInterface.update_forward_refs() -TimeSeries.update_forward_refs() -ProcessingModule.update_forward_refs() -Images.update_forward_refs() -DynamicTable.update_forward_refs() -AlignedDynamicTable.update_forward_refs() -SimpleMultiContainer.update_forward_refs() diff --git a/nwb_linkml/models/core.nwb.behavior.py b/nwb_linkml/models/core.nwb.behavior.py deleted file mode 100644 index 767d8c2..0000000 --- a/nwb_linkml/models/core.nwb.behavior.py +++ /dev/null @@ -1,929 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): - pass - - -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - -class SpatialSeriesData(ConfiguredBaseModel): - """ - 1-D or 2-D array storing position or direction relative to some reference frame. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. The default value is 'meters'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - array: Optional[SpatialSeriesDataArray] = Field(None) - - -class SpatialSeriesReferenceFrame(ConfiguredBaseModel): - """ - Description defining what exactly 'straight-ahead' means. - """ - None - - -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - -class SpatialSeriesDataArray(Arraylike): - - num_times: float = Field(...) - x: Optional[float] = Field(None) - xy: Optional[float] = Field(None) - xyz: Optional[float] = Field(None) - - -class AbstractFeatureSeriesData(ConfiguredBaseModel): - """ - Values of each feature at each time. - """ - unit: Optional[str] = Field(None, description="""Since there can be different units for different features, store the units in 'feature_units'. The default value for this attribute is \"see 'feature_units'\".""") - array: Optional[AbstractFeatureSeriesDataArray] = Field(None) - - -class AbstractFeatureSeriesDataArray(Arraylike): - - num_times: float = Field(...) - num_features: Optional[float] = Field(None) - - -class AbstractFeatureSeriesFeatureUnits(ConfiguredBaseModel): - """ - Units of each feature. - """ - array: Optional[AbstractFeatureSeriesFeatureUnitsArray] = Field(None) - - -class AbstractFeatureSeriesFeatureUnitsArray(Arraylike): - - num_features: str = Field(...) - - -class AbstractFeatureSeriesFeatures(ConfiguredBaseModel): - """ - Description of the features represented in TimeSeries::data. - """ - array: Optional[AbstractFeatureSeriesFeaturesArray] = Field(None) - - -class AbstractFeatureSeriesFeaturesArray(Arraylike): - - num_features: str = Field(...) - - -class AnnotationSeriesData(ConfiguredBaseModel): - """ - Annotations made during an experiment. - """ - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data. Annotations have no units, so the value is fixed to -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Annotations have no units, so the value is fixed to 'n/a'.""") - array: Optional[AnnotationSeriesDataArray] = Field(None) - - -class AnnotationSeriesDataArray(Arraylike): - - num_times: str = Field(...) - - -class IntervalSeriesData(ConfiguredBaseModel): - """ - Use values >0 if interval started, <0 if interval ended. - """ - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data. Annotations have no units, so the value is fixed to -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Annotations have no units, so the value is fixed to 'n/a'.""") - array: Optional[IntervalSeriesDataArray] = Field(None) - - -class IntervalSeriesDataArray(Arraylike): - - num_times: int = Field(...) - - -class DecompositionSeriesData(ConfiguredBaseModel): - """ - Data decomposed into frequency bands. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion'.""") - array: Optional[DecompositionSeriesDataArray] = Field(None) - - -class DecompositionSeriesDataArray(Arraylike): - - num_times: Optional[float] = Field(None) - num_channels: Optional[float] = Field(None) - num_bands: Optional[float] = Field(None) - - -class DecompositionSeriesMetric(ConfiguredBaseModel): - """ - The metric used, e.g. phase, amplitude, power. - """ - None - - -class DecompositionSeriesBandsBandLimitsArray(Arraylike): - - num_bands: Optional[float] = Field(None) - low_high: Optional[float] = Field(None) - - -class DecompositionSeriesBandsBandMeanArray(Arraylike): - - num_bands: float = Field(...) - - -class DecompositionSeriesBandsBandStdevArray(Arraylike): - - num_bands: float = Field(...) - - -class UnitsObsIntervalsArray(Arraylike): - - num_intervals: Optional[float] = Field(None) - start|end: Optional[float] = Field(None) - - -class UnitsWaveformMeanArray(Arraylike): - - num_units: float = Field(...) - num_samples: float = Field(...) - num_electrodes: Optional[float] = Field(None) - - -class UnitsWaveformSdArray(Arraylike): - - num_units: float = Field(...) - num_samples: float = Field(...) - num_electrodes: Optional[float] = Field(None) - - -class UnitsWaveformsArray(Arraylike): - - num_waveforms: Optional[float] = Field(None) - num_samples: Optional[float] = Field(None) - - -class VectorDataArray(Arraylike): - - dim0: Any = Field(...) - dim1: Optional[Any] = Field(None) - dim2: Optional[Any] = Field(None) - dim3: Optional[Any] = Field(None) - - -class VectorIndexArray(Arraylike): - - num_rows: int = Field(...) - - -class ElementIdentifiersArray(Arraylike): - - num_elements: int = Field(...) - - -class DynamicTableRegionArray(Arraylike): - - num_rows: int = Field(...) - - -class DynamicTableIdArray(Arraylike): - - num_rows: int = Field(...) - - -class Data(ConfiguredBaseModel): - """ - An abstract data type for a dataset. - """ - None - - -class VectorData(Data): - """ - An n-dimensional dataset representing a column of a DynamicTable. If used without an accompanying VectorIndex, first dimension is along the rows of the DynamicTable and each step along the first dimension is a cell of the larger table. VectorData can also be used to represent a ragged array if paired with a VectorIndex. This allows for storing arrays of varying length in a single cell of the DynamicTable by indexing into this VectorData. The first vector is at VectorData[0:VectorIndex[0]]. The second vector is at VectorData[VectorIndex[0]:VectorIndex[1]], and so on. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class DecompositionSeriesBandsBandName(VectorData): - """ - Name of the band, e.g. theta. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class DecompositionSeriesBandsBandLimits(VectorData): - """ - Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center. - """ - array: Optional[DecompositionSeriesBandsBandLimitsArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class DecompositionSeriesBandsBandMean(VectorData): - """ - The mean Gaussian filters, in Hz. - """ - array: Optional[DecompositionSeriesBandsBandMeanArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class DecompositionSeriesBandsBandStdev(VectorData): - """ - The standard deviation of Gaussian filters, in Hz. - """ - array: Optional[DecompositionSeriesBandsBandStdevArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsSpikeTimes(VectorData): - """ - Spike times for each unit in seconds. - """ - resolution: Optional[float] = Field(None, description="""The smallest possible difference between two spike times. Usually 1 divided by the acquisition sampling rate from which spike times were extracted, but could be larger if the acquisition time series was downsampled or smaller if the acquisition time series was smoothed/interpolated and it is possible for the spike time to be between samples.""") - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class UnitsObsIntervals(VectorData): - """ - Observation intervals for each unit. - """ - array: Optional[UnitsObsIntervalsArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsElectrodeGroup(VectorData): - """ - Electrode group that each spike unit came from. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class UnitsWaveformMean(VectorData): - """ - Spike waveform mean for each spike unit. - """ - sampling_rate: Optional[float] = Field(None, description="""Sampling rate, in hertz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement. This value is fixed to 'volts'.""") - array: Optional[UnitsWaveformMeanArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsWaveformSd(VectorData): - """ - Spike waveform standard deviation for each spike unit. - """ - sampling_rate: Optional[float] = Field(None, description="""Sampling rate, in hertz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement. This value is fixed to 'volts'.""") - array: Optional[UnitsWaveformSdArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsWaveforms(VectorData): - """ - Individual waveforms for each spike on each electrode. This is a doubly indexed column. The 'waveforms_index' column indexes which waveforms in this column belong to the same spike event for a given unit, where each waveform was recorded from a different electrode. The 'waveforms_index_index' column indexes the 'waveforms_index' column to indicate which spike events belong to a given unit. For example, if the 'waveforms_index_index' column has values [2, 5, 6], then the first 2 elements of the 'waveforms_index' column correspond to the 2 spike events of the first unit, the next 3 elements of the 'waveforms_index' column correspond to the 3 spike events of the second unit, and the next 1 element of the 'waveforms_index' column corresponds to the 1 spike event of the third unit. If the 'waveforms_index' column has values [3, 6, 8, 10, 12, 13], then the first 3 elements of the 'waveforms' column contain the 3 spike waveforms that were recorded from 3 different electrodes for the first spike time of the first unit. See https://nwb-schema.readthedocs.io/en/stable/format_description.html#doubly-ragged-arrays for a graphical representation of this example. When there is only one electrode for each unit (i.e., each spike time is associated with a single waveform), then the 'waveforms_index' column will have values 1, 2, ..., N, where N is the number of spike events. The number of electrodes for each spike event should be the same within a given unit. The 'electrodes' column should be used to indicate which electrodes are associated with each unit, and the order of the waveforms within a given unit x spike event should be in the same order as the electrodes referenced in the 'electrodes' column of this table. The number of samples for each waveform must be the same. - """ - sampling_rate: Optional[float] = Field(None, description="""Sampling rate, in hertz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement. This value is fixed to 'volts'.""") - array: Optional[UnitsWaveformsArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class VectorIndex(VectorData): - """ - Used with VectorData to encode a ragged array. An array of indices into the first dimension of the target VectorData, and forming a map between the rows of a DynamicTable and the indices of the VectorData. The name of the VectorIndex is expected to be the name of the target VectorData object followed by \"_index\". - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsSpikeTimesIndex(VectorIndex): - """ - Index into the spike_times dataset. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsObsIntervalsIndex(VectorIndex): - """ - Index into the obs_intervals dataset. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsElectrodesIndex(VectorIndex): - """ - Index into electrodes. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsWaveformsIndex(VectorIndex): - """ - Index into the waveforms dataset. One value for every spike event. See 'waveforms' for more detail. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsWaveformsIndexIndex(VectorIndex): - """ - Index into the waveforms_index dataset. One value for every unit (row in the table). See 'waveforms' for more detail. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ElementIdentifiers(Data): - """ - A list of unique identifiers for values within a dataset, e.g. rows of a DynamicTable. - """ - array: Optional[ElementIdentifiersArray] = Field(None) - - -class DynamicTableRegion(VectorData): - """ - DynamicTableRegion provides a link from one table to an index or region of another. The `table` attribute is a link to another `DynamicTable`, indicating which table is referenced, and the data is int(s) indicating the row(s) (0-indexed) of the target array. `DynamicTableRegion`s can be used to associate rows with repeated meta-data without data duplication. They can also be used to create hierarchical relationships between multiple `DynamicTable`s. `DynamicTableRegion` objects may be paired with a `VectorIndex` object to create ragged references, so a single cell of a `DynamicTable` can reference many rows of another `DynamicTable`. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DecompositionSeriesSourceChannels(DynamicTableRegion): - """ - DynamicTableRegion pointer to the channels that this decomposition series was generated from. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class UnitsElectrodes(DynamicTableRegion): - """ - Electrode that each spike unit came from, specified using a DynamicTableRegion. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DynamicTableId(ElementIdentifiers): - """ - Array of unique identifiers for the rows of this dynamic table. - """ - array: Optional[DynamicTableIdArray] = Field(None) - - -class Container(ConfiguredBaseModel): - """ - An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class DynamicTable(Container): - """ - A group containing multiple datasets that are aligned on the first dimension (Currently, this requirement if left up to APIs to check and enforce). These datasets represent different columns in the table. Apart from a column that contains unique identifiers for each row, there are no other required datasets. Users are free to add any number of custom VectorData objects (columns) here. DynamicTable also supports ragged array columns, where each element can be of a different size. To add a ragged array column, use a VectorIndex type to index the corresponding VectorData type. See documentation for VectorData and VectorIndex for more details. Unlike a compound data type, which is analogous to storing an array-of-structs, a DynamicTable can be thought of as a struct-of-arrays. This provides an alternative structure to choose from when optimizing storage for anticipated access patterns. Additionally, this type provides a way of creating a table without having to define a compound type up front. Although this convenience may be attractive, users should think carefully about how data will be accessed. DynamicTable is more appropriate for column-centric access, whereas a dataset with a compound type would be more appropriate for row-centric access. Finally, data size should also be taken into account. For small tables, performance loss may be an acceptable trade-off for the flexibility of a DynamicTable. - """ - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class DecompositionSeriesBands(DynamicTable): - """ - Table for describing the bands that this series was generated from. There should be one row in this table for each band. - """ - band_name: DecompositionSeriesBandsBandName = Field(..., description="""Name of the band, e.g. theta.""") - band_limits: DecompositionSeriesBandsBandLimits = Field(..., description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""") - band_mean: DecompositionSeriesBandsBandMean = Field(..., description="""The mean Gaussian filters, in Hz.""") - band_stdev: DecompositionSeriesBandsBandStdev = Field(..., description="""The standard deviation of Gaussian filters, in Hz.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class Units(DynamicTable): - """ - Data about spiking units. Event times of observed units (e.g. cell, synapse, etc.) should be concatenated and stored in spike_times. - """ - spike_times_index: Optional[UnitsSpikeTimesIndex] = Field(None, description="""Index into the spike_times dataset.""") - spike_times: Optional[UnitsSpikeTimes] = Field(None, description="""Spike times for each unit in seconds.""") - obs_intervals_index: Optional[UnitsObsIntervalsIndex] = Field(None, description="""Index into the obs_intervals dataset.""") - obs_intervals: Optional[UnitsObsIntervals] = Field(None, description="""Observation intervals for each unit.""") - electrodes_index: Optional[UnitsElectrodesIndex] = Field(None, description="""Index into electrodes.""") - electrodes: Optional[UnitsElectrodes] = Field(None, description="""Electrode that each spike unit came from, specified using a DynamicTableRegion.""") - electrode_group: Optional[UnitsElectrodeGroup] = Field(None, description="""Electrode group that each spike unit came from.""") - waveform_mean: Optional[UnitsWaveformMean] = Field(None, description="""Spike waveform mean for each spike unit.""") - waveform_sd: Optional[UnitsWaveformSd] = Field(None, description="""Spike waveform standard deviation for each spike unit.""") - waveforms: Optional[UnitsWaveforms] = Field(None, description="""Individual waveforms for each spike on each electrode. This is a doubly indexed column. The 'waveforms_index' column indexes which waveforms in this column belong to the same spike event for a given unit, where each waveform was recorded from a different electrode. The 'waveforms_index_index' column indexes the 'waveforms_index' column to indicate which spike events belong to a given unit. For example, if the 'waveforms_index_index' column has values [2, 5, 6], then the first 2 elements of the 'waveforms_index' column correspond to the 2 spike events of the first unit, the next 3 elements of the 'waveforms_index' column correspond to the 3 spike events of the second unit, and the next 1 element of the 'waveforms_index' column corresponds to the 1 spike event of the third unit. If the 'waveforms_index' column has values [3, 6, 8, 10, 12, 13], then the first 3 elements of the 'waveforms' column contain the 3 spike waveforms that were recorded from 3 different electrodes for the first spike time of the first unit. See https://nwb-schema.readthedocs.io/en/stable/format_description.html#doubly-ragged-arrays for a graphical representation of this example. When there is only one electrode for each unit (i.e., each spike time is associated with a single waveform), then the 'waveforms_index' column will have values 1, 2, ..., N, where N is the number of spike events. The number of electrodes for each spike event should be the same within a given unit. The 'electrodes' column should be used to indicate which electrodes are associated with each unit, and the order of the waveforms within a given unit x spike event should be in the same order as the electrodes referenced in the 'electrodes' column of this table. The number of samples for each waveform must be the same.""") - waveforms_index: Optional[UnitsWaveformsIndex] = Field(None, description="""Index into the waveforms dataset. One value for every spike event. See 'waveforms' for more detail.""") - waveforms_index_index: Optional[UnitsWaveformsIndexIndex] = Field(None, description="""Index into the waveforms_index dataset. One value for every unit (row in the table). See 'waveforms' for more detail.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class AlignedDynamicTable(DynamicTable): - """ - DynamicTable container that supports storing a collection of sub-tables. Each sub-table is a DynamicTable itself that is aligned with the main table by row index. I.e., all DynamicTables stored in this group MUST have the same number of rows. This type effectively defines a 2-level table in which the main data is stored in the main table implemented by this type and additional columns of the table are grouped into categories, with each category being represented by a separate DynamicTable stored within the group. - """ - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimpleMultiContainer(Container): - """ - A simple Container for holding onto multiple containers. - """ - Data: Optional[List[Data]] = Field(default_factory=list, description="""Data objects held within this SimpleMultiContainer.""") - Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") - - -class NWBData(Data): - """ - An abstract data type for a dataset. - """ - None - - -class TimeSeriesReferenceVectorData(VectorData): - """ - Column storing references to a TimeSeries (rows). For each TimeSeries this VectorData column stores the start_index and count to indicate the range in time to be selected as well as an object reference to the TimeSeries. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class Image(NWBData): - """ - An abstract data type for an image. Shape can be 2-D (x, y), or 3-D where the third dimension can have three or four elements, e.g. (x, y, (r, g, b)) or (x, y, (r, g, b, a)). - """ - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - array: Optional[ImageArray] = Field(None) - - -class ImageArray(Arraylike): - - x: float = Field(...) - y: float = Field(...) - r_g_b: Optional[float] = Field(None) - r_g_b_a: Optional[float] = Field(None) - - -class ImageReferences(NWBData): - """ - Ordered dataset of references to Image objects. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class ImageReferencesArray(Arraylike): - - num_images: Image = Field(...) - - -class NWBContainer(Container): - """ - An abstract data type for a generic container storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class NWBDataInterface(NWBContainer): - """ - An abstract data type for a generic container storing collections of data, as opposed to metadata. - """ - None - - -class BehavioralEpochs(NWBDataInterface): - """ - TimeSeries for storing behavioral epochs. The objective of this and the other two Behavioral interfaces (e.g. BehavioralEvents and BehavioralTimeSeries) is to provide generic hooks for software tools/scripts. This allows a tool/script to take the output one specific interface (e.g., UnitTimes) and plot that data relative to another data modality (e.g., behavioral events) without having to define all possible modalities in advance. Declaring one of these interfaces means that one or more TimeSeries of the specified type is published. These TimeSeries should reside in a group having the same name as the interface. For example, if a BehavioralTimeSeries interface is declared, the module will have one or more TimeSeries defined in the module sub-group 'BehavioralTimeSeries'. BehavioralEpochs should use IntervalSeries. BehavioralEvents is used for irregular events. BehavioralTimeSeries is for continuous data. - """ - IntervalSeries: Optional[List[IntervalSeries]] = Field(default_factory=list, description="""IntervalSeries object containing start and stop times of epochs.""") - - -class BehavioralEvents(NWBDataInterface): - """ - TimeSeries for storing behavioral events. See description of BehavioralEpochs for more details. - """ - TimeSeries: Optional[List[TimeSeries]] = Field(default_factory=list, description="""TimeSeries object containing behavioral events.""") - - -class BehavioralTimeSeries(NWBDataInterface): - """ - TimeSeries for storing Behavoioral time series data. See description of BehavioralEpochs for more details. - """ - TimeSeries: Optional[List[TimeSeries]] = Field(default_factory=list, description="""TimeSeries object containing continuous behavioral data.""") - - -class PupilTracking(NWBDataInterface): - """ - Eye-tracking data, representing pupil size. - """ - TimeSeries: List[TimeSeries] = Field(default_factory=list, description="""TimeSeries object containing time series data on pupil size.""") - - -class EyeTracking(NWBDataInterface): - """ - Eye-tracking data, representing direction of gaze. - """ - SpatialSeries: Optional[List[SpatialSeries]] = Field(default_factory=list, description="""SpatialSeries object containing data measuring direction of gaze.""") - - -class CompassDirection(NWBDataInterface): - """ - With a CompassDirection interface, a module publishes a SpatialSeries object representing a floating point value for theta. The SpatialSeries::reference_frame field should indicate what direction corresponds to 0 and which is the direction of rotation (this should be clockwise). The si_unit for the SpatialSeries should be radians or degrees. - """ - SpatialSeries: Optional[List[SpatialSeries]] = Field(default_factory=list, description="""SpatialSeries object containing direction of gaze travel.""") - - -class Position(NWBDataInterface): - """ - Position data, whether along the x, x/y or x/y/z axis. - """ - SpatialSeries: List[SpatialSeries] = Field(default_factory=list, description="""SpatialSeries object containing position data.""") - - -class TimeSeries(NWBDataInterface): - """ - General purpose time series. - """ - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - data: TimeSeriesData = Field(..., description="""Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class SpatialSeries(TimeSeries): - """ - Direction, e.g., of gaze or travel, or position. The TimeSeries::data field is a 2D array storing position or direction relative to some reference frame. Array structure: [num measurements] [num dimensions]. Each SpatialSeries has a text dataset reference_frame that indicates the zero-position, or the zero-axes for direction. For example, if representing gaze direction, 'straight-ahead' might be a specific pixel on the monitor, or some other point in space. For position data, the 0,0 point might be the top-left corner of an enclosure, as viewed from the tracking camera. The unit of data will indicate how to interpret SpatialSeries values. - """ - data: SpatialSeriesData = Field(..., description="""1-D or 2-D array storing position or direction relative to some reference frame.""") - reference_frame: Optional[SpatialSeriesReferenceFrame] = Field(None, description="""Description defining what exactly 'straight-ahead' means.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class AbstractFeatureSeries(TimeSeries): - """ - Abstract features, such as quantitative descriptions of sensory stimuli. The TimeSeries::data field is a 2D array, storing those features (e.g., for visual grating stimulus this might be orientation, spatial frequency and contrast). Null stimuli (eg, uniform gray) can be marked as being an independent feature (eg, 1.0 for gray, 0.0 for actual stimulus) or by storing NaNs for feature values, or through use of the TimeSeries::control fields. A set of features is considered to persist until the next set of features is defined. The final set of features stored should be the null set. This is useful when storing the raw stimulus is impractical. - """ - data: AbstractFeatureSeriesData = Field(..., description="""Values of each feature at each time.""") - feature_units: Optional[AbstractFeatureSeriesFeatureUnits] = Field(None, description="""Units of each feature.""") - features: AbstractFeatureSeriesFeatures = Field(..., description="""Description of the features represented in TimeSeries::data.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class AnnotationSeries(TimeSeries): - """ - Stores user annotations made during an experiment. The data[] field stores a text array, and timestamps are stored for each annotation (ie, interval=1). This is largely an alias to a standard TimeSeries storing a text array but that is identifiable as storing annotations in a machine-readable way. - """ - data: AnnotationSeriesData = Field(..., description="""Annotations made during an experiment.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class IntervalSeries(TimeSeries): - """ - Stores intervals of data. The timestamps field stores the beginning and end of intervals. The data field stores whether the interval just started (>0 value) or ended (<0 value). Different interval types can be represented in the same series by using multiple key values (eg, 1 for feature A, 2 for feature B, 3 for feature C, etc). The field data stores an 8-bit integer. This is largely an alias of a standard TimeSeries but that is identifiable as representing time intervals in a machine-readable way. - """ - data: IntervalSeriesData = Field(..., description="""Use values >0 if interval started, <0 if interval ended.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class DecompositionSeries(TimeSeries): - """ - Spectral analysis of a time series, e.g. of an LFP or a speech signal. - """ - data: DecompositionSeriesData = Field(..., description="""Data decomposed into frequency bands.""") - metric: DecompositionSeriesMetric = Field(..., description="""The metric used, e.g. phase, amplitude, power.""") - source_channels: Optional[DecompositionSeriesSourceChannels] = Field(None, description="""DynamicTableRegion pointer to the channels that this decomposition series was generated from.""") - bands: DecompositionSeriesBands = Field(..., description="""Table for describing the bands that this series was generated from. There should be one row in this table for each band.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class TimeSeriesData(ConfiguredBaseModel): - """ - Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file. - """ - conversion: Optional[float] = Field(None, description="""Scalar to multiply each element in data to convert it to the specified 'unit'. If the data are stored in acquisition system units or other units that require a conversion to be interpretable, multiply the data by 'conversion' to convert the data to the specified 'unit'. e.g. if the data acquisition system stores values in this object as signed 16-bit integers (int16 range -32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data acquisition system gain is 8000X, then the 'conversion' multiplier to get from raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9.""") - offset: Optional[float] = Field(None, description="""Scalar to add to the data after scaling by 'conversion' to finalize its coercion to the specified 'unit'. Two common examples of this include (a) data stored in an unsigned type that requires a shift after scaling to re-center the data, and (b) specialized recording devices that naturally cause a scalar offset with respect to the true units.""") - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data, stored in the specified by unit, e.g., the change in value of the least significant bit, or a larger number if signal noise is known to be present. If unknown, use -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - continuity: Optional[str] = Field(None, description="""Optionally describe the continuity of the data. Can be \"continuous\", \"instantaneous\", or \"step\". For example, a voltage trace would be \"continuous\", because samples are recorded from a continuous process. An array of lick times would be \"instantaneous\", because the data represents distinct moments in time. Times of image presentations would be \"step\" because the picture remains the same until the next timepoint. This field is optional, but is useful in providing information about the underlying data. It may inform the way this data is interpreted, the way it is visualized, and what analysis methods are applicable.""") - array: Optional[TimeSeriesDataArray] = Field(None) - - -class TimeSeriesDataArray(Arraylike): - - num_times: Any = Field(...) - num_DIM2: Optional[Any] = Field(None) - num_DIM3: Optional[Any] = Field(None) - num_DIM4: Optional[Any] = Field(None) - - -class TimeSeriesStartingTime(ConfiguredBaseModel): - """ - Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute. - """ - rate: Optional[float] = Field(None, description="""Sampling rate, in Hz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement for time, which is fixed to 'seconds'.""") - - -class TimeSeriesTimestamps(ConfiguredBaseModel): - """ - Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. - """ - interval: Optional[int] = Field(None, description="""Value is '1'""") - unit: Optional[str] = Field(None, description="""Unit of measurement for timestamps, which is fixed to 'seconds'.""") - array: Optional[TimeSeriesTimestampsArray] = Field(None) - - -class TimeSeriesTimestampsArray(Arraylike): - - num_times: float = Field(...) - - -class TimeSeriesControl(ConfiguredBaseModel): - """ - Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data. - """ - array: Optional[TimeSeriesControlArray] = Field(None) - - -class TimeSeriesControlArray(Arraylike): - - num_times: int = Field(...) - - -class TimeSeriesControlDescription(ConfiguredBaseModel): - """ - Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0. - """ - array: Optional[TimeSeriesControlDescriptionArray] = Field(None) - - -class TimeSeriesControlDescriptionArray(Arraylike): - - num_control_values: str = Field(...) - - -class TimeSeriesSync(ConfiguredBaseModel): - """ - Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes. - """ - None - - -class ProcessingModule(NWBContainer): - """ - A collection of processed data. - """ - description: Optional[str] = Field(None, description="""Description of this collection of processed data.""") - NWBDataInterface: Optional[List[NWBDataInterface]] = Field(default_factory=list, description="""Data objects stored in this collection.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tables stored in this collection.""") - - -class Images(NWBDataInterface): - """ - A collection of images with an optional way to specify the order of the images using the \"order_of_images\" dataset. An order must be specified if the images are referenced by index, e.g., from an IndexSeries. - """ - description: Optional[str] = Field(None, description="""Description of this collection of images.""") - Image: List[Image] = Field(default_factory=list, description="""Images stored in this collection.""") - order_of_images: Optional[ImagesOrderOfImages] = Field(None, description="""Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images.""") - - -class ImagesOrderOfImages(ImageReferences): - """ - Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images. - """ - array: Optional[ImageReferencesArray] = Field(None) - - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -SpatialSeriesData.update_forward_refs() -SpatialSeriesReferenceFrame.update_forward_refs() -Arraylike.update_forward_refs() -SpatialSeriesDataArray.update_forward_refs() -AbstractFeatureSeriesData.update_forward_refs() -AbstractFeatureSeriesDataArray.update_forward_refs() -AbstractFeatureSeriesFeatureUnits.update_forward_refs() -AbstractFeatureSeriesFeatureUnitsArray.update_forward_refs() -AbstractFeatureSeriesFeatures.update_forward_refs() -AbstractFeatureSeriesFeaturesArray.update_forward_refs() -AnnotationSeriesData.update_forward_refs() -AnnotationSeriesDataArray.update_forward_refs() -IntervalSeriesData.update_forward_refs() -IntervalSeriesDataArray.update_forward_refs() -DecompositionSeriesData.update_forward_refs() -DecompositionSeriesDataArray.update_forward_refs() -DecompositionSeriesMetric.update_forward_refs() -DecompositionSeriesBandsBandLimitsArray.update_forward_refs() -DecompositionSeriesBandsBandMeanArray.update_forward_refs() -DecompositionSeriesBandsBandStdevArray.update_forward_refs() -UnitsObsIntervalsArray.update_forward_refs() -UnitsWaveformMeanArray.update_forward_refs() -UnitsWaveformSdArray.update_forward_refs() -UnitsWaveformsArray.update_forward_refs() -VectorDataArray.update_forward_refs() -VectorIndexArray.update_forward_refs() -ElementIdentifiersArray.update_forward_refs() -DynamicTableRegionArray.update_forward_refs() -DynamicTableIdArray.update_forward_refs() -Data.update_forward_refs() -VectorData.update_forward_refs() -DecompositionSeriesBandsBandName.update_forward_refs() -DecompositionSeriesBandsBandLimits.update_forward_refs() -DecompositionSeriesBandsBandMean.update_forward_refs() -DecompositionSeriesBandsBandStdev.update_forward_refs() -UnitsSpikeTimes.update_forward_refs() -UnitsObsIntervals.update_forward_refs() -UnitsElectrodeGroup.update_forward_refs() -UnitsWaveformMean.update_forward_refs() -UnitsWaveformSd.update_forward_refs() -UnitsWaveforms.update_forward_refs() -VectorIndex.update_forward_refs() -UnitsSpikeTimesIndex.update_forward_refs() -UnitsObsIntervalsIndex.update_forward_refs() -UnitsElectrodesIndex.update_forward_refs() -UnitsWaveformsIndex.update_forward_refs() -UnitsWaveformsIndexIndex.update_forward_refs() -ElementIdentifiers.update_forward_refs() -DynamicTableRegion.update_forward_refs() -DecompositionSeriesSourceChannels.update_forward_refs() -UnitsElectrodes.update_forward_refs() -DynamicTableId.update_forward_refs() -Container.update_forward_refs() -DynamicTable.update_forward_refs() -DecompositionSeriesBands.update_forward_refs() -Units.update_forward_refs() -AlignedDynamicTable.update_forward_refs() -SimpleMultiContainer.update_forward_refs() -NWBData.update_forward_refs() -TimeSeriesReferenceVectorData.update_forward_refs() -Image.update_forward_refs() -ImageArray.update_forward_refs() -ImageReferences.update_forward_refs() -ImageReferencesArray.update_forward_refs() -NWBContainer.update_forward_refs() -NWBDataInterface.update_forward_refs() -BehavioralEpochs.update_forward_refs() -BehavioralEvents.update_forward_refs() -BehavioralTimeSeries.update_forward_refs() -PupilTracking.update_forward_refs() -EyeTracking.update_forward_refs() -CompassDirection.update_forward_refs() -Position.update_forward_refs() -TimeSeries.update_forward_refs() -SpatialSeries.update_forward_refs() -AbstractFeatureSeries.update_forward_refs() -AnnotationSeries.update_forward_refs() -IntervalSeries.update_forward_refs() -DecompositionSeries.update_forward_refs() -TimeSeriesData.update_forward_refs() -TimeSeriesDataArray.update_forward_refs() -TimeSeriesStartingTime.update_forward_refs() -TimeSeriesTimestamps.update_forward_refs() -TimeSeriesTimestampsArray.update_forward_refs() -TimeSeriesControl.update_forward_refs() -TimeSeriesControlArray.update_forward_refs() -TimeSeriesControlDescription.update_forward_refs() -TimeSeriesControlDescriptionArray.update_forward_refs() -TimeSeriesSync.update_forward_refs() -ProcessingModule.update_forward_refs() -Images.update_forward_refs() -ImagesOrderOfImages.update_forward_refs() diff --git a/nwb_linkml/models/core.nwb.device.py b/nwb_linkml/models/core.nwb.device.py deleted file mode 100644 index 962201d..0000000 --- a/nwb_linkml/models/core.nwb.device.py +++ /dev/null @@ -1,420 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): - pass - - -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - -class ImageArray(Arraylike): - - x: float = Field(...) - y: float = Field(...) - r_g_b: Optional[float] = Field(None) - r_g_b_a: Optional[float] = Field(None) - - -class ImageReferencesArray(Arraylike): - - num_images: Image = Field(...) - - -class TimeSeriesData(ConfiguredBaseModel): - """ - Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file. - """ - conversion: Optional[float] = Field(None, description="""Scalar to multiply each element in data to convert it to the specified 'unit'. If the data are stored in acquisition system units or other units that require a conversion to be interpretable, multiply the data by 'conversion' to convert the data to the specified 'unit'. e.g. if the data acquisition system stores values in this object as signed 16-bit integers (int16 range -32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data acquisition system gain is 8000X, then the 'conversion' multiplier to get from raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9.""") - offset: Optional[float] = Field(None, description="""Scalar to add to the data after scaling by 'conversion' to finalize its coercion to the specified 'unit'. Two common examples of this include (a) data stored in an unsigned type that requires a shift after scaling to re-center the data, and (b) specialized recording devices that naturally cause a scalar offset with respect to the true units.""") - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data, stored in the specified by unit, e.g., the change in value of the least significant bit, or a larger number if signal noise is known to be present. If unknown, use -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - continuity: Optional[str] = Field(None, description="""Optionally describe the continuity of the data. Can be \"continuous\", \"instantaneous\", or \"step\". For example, a voltage trace would be \"continuous\", because samples are recorded from a continuous process. An array of lick times would be \"instantaneous\", because the data represents distinct moments in time. Times of image presentations would be \"step\" because the picture remains the same until the next timepoint. This field is optional, but is useful in providing information about the underlying data. It may inform the way this data is interpreted, the way it is visualized, and what analysis methods are applicable.""") - array: Optional[TimeSeriesDataArray] = Field(None) - - -class TimeSeriesDataArray(Arraylike): - - num_times: Any = Field(...) - num_DIM2: Optional[Any] = Field(None) - num_DIM3: Optional[Any] = Field(None) - num_DIM4: Optional[Any] = Field(None) - - -class TimeSeriesStartingTime(ConfiguredBaseModel): - """ - Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute. - """ - rate: Optional[float] = Field(None, description="""Sampling rate, in Hz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement for time, which is fixed to 'seconds'.""") - - -class TimeSeriesTimestamps(ConfiguredBaseModel): - """ - Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. - """ - interval: Optional[int] = Field(None, description="""Value is '1'""") - unit: Optional[str] = Field(None, description="""Unit of measurement for timestamps, which is fixed to 'seconds'.""") - array: Optional[TimeSeriesTimestampsArray] = Field(None) - - -class TimeSeriesTimestampsArray(Arraylike): - - num_times: float = Field(...) - - -class TimeSeriesControl(ConfiguredBaseModel): - """ - Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data. - """ - array: Optional[TimeSeriesControlArray] = Field(None) - - -class TimeSeriesControlArray(Arraylike): - - num_times: int = Field(...) - - -class TimeSeriesControlDescription(ConfiguredBaseModel): - """ - Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0. - """ - array: Optional[TimeSeriesControlDescriptionArray] = Field(None) - - -class TimeSeriesControlDescriptionArray(Arraylike): - - num_control_values: str = Field(...) - - -class TimeSeriesSync(ConfiguredBaseModel): - """ - Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes. - """ - None - - -class VectorDataArray(Arraylike): - - dim0: Any = Field(...) - dim1: Optional[Any] = Field(None) - dim2: Optional[Any] = Field(None) - dim3: Optional[Any] = Field(None) - - -class VectorIndexArray(Arraylike): - - num_rows: int = Field(...) - - -class ElementIdentifiersArray(Arraylike): - - num_elements: int = Field(...) - - -class DynamicTableRegionArray(Arraylike): - - num_rows: int = Field(...) - - -class DynamicTableIdArray(Arraylike): - - num_rows: int = Field(...) - - -class Data(ConfiguredBaseModel): - """ - An abstract data type for a dataset. - """ - None - - -class NWBData(Data): - """ - An abstract data type for a dataset. - """ - None - - -class Image(NWBData): - """ - An abstract data type for an image. Shape can be 2-D (x, y), or 3-D where the third dimension can have three or four elements, e.g. (x, y, (r, g, b)) or (x, y, (r, g, b, a)). - """ - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - array: Optional[ImageArray] = Field(None) - - -class ImageReferences(NWBData): - """ - Ordered dataset of references to Image objects. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class ImagesOrderOfImages(ImageReferences): - """ - Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class VectorData(Data): - """ - An n-dimensional dataset representing a column of a DynamicTable. If used without an accompanying VectorIndex, first dimension is along the rows of the DynamicTable and each step along the first dimension is a cell of the larger table. VectorData can also be used to represent a ragged array if paired with a VectorIndex. This allows for storing arrays of varying length in a single cell of the DynamicTable by indexing into this VectorData. The first vector is at VectorData[0:VectorIndex[0]]. The second vector is at VectorData[VectorIndex[0]:VectorIndex[1]], and so on. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class TimeSeriesReferenceVectorData(VectorData): - """ - Column storing references to a TimeSeries (rows). For each TimeSeries this VectorData column stores the start_index and count to indicate the range in time to be selected as well as an object reference to the TimeSeries. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class VectorIndex(VectorData): - """ - Used with VectorData to encode a ragged array. An array of indices into the first dimension of the target VectorData, and forming a map between the rows of a DynamicTable and the indices of the VectorData. The name of the VectorIndex is expected to be the name of the target VectorData object followed by \"_index\". - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ElementIdentifiers(Data): - """ - A list of unique identifiers for values within a dataset, e.g. rows of a DynamicTable. - """ - array: Optional[ElementIdentifiersArray] = Field(None) - - -class DynamicTableRegion(VectorData): - """ - DynamicTableRegion provides a link from one table to an index or region of another. The `table` attribute is a link to another `DynamicTable`, indicating which table is referenced, and the data is int(s) indicating the row(s) (0-indexed) of the target array. `DynamicTableRegion`s can be used to associate rows with repeated meta-data without data duplication. They can also be used to create hierarchical relationships between multiple `DynamicTable`s. `DynamicTableRegion` objects may be paired with a `VectorIndex` object to create ragged references, so a single cell of a `DynamicTable` can reference many rows of another `DynamicTable`. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DynamicTableId(ElementIdentifiers): - """ - Array of unique identifiers for the rows of this dynamic table. - """ - array: Optional[DynamicTableIdArray] = Field(None) - - -class Container(ConfiguredBaseModel): - """ - An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class NWBContainer(Container): - """ - An abstract data type for a generic container storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class Device(NWBContainer): - """ - Metadata about a data acquisition device, e.g., recording system, electrode, microscope. - """ - description: Optional[str] = Field(None, description="""Description of the device (e.g., model, firmware version, processing software version, etc.) as free-form text.""") - manufacturer: Optional[str] = Field(None, description="""The name of the manufacturer of the device.""") - - -class NWBDataInterface(NWBContainer): - """ - An abstract data type for a generic container storing collections of data, as opposed to metadata. - """ - None - - -class TimeSeries(NWBDataInterface): - """ - General purpose time series. - """ - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - data: TimeSeriesData = Field(..., description="""Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class ProcessingModule(NWBContainer): - """ - A collection of processed data. - """ - description: Optional[str] = Field(None, description="""Description of this collection of processed data.""") - NWBDataInterface: Optional[List[NWBDataInterface]] = Field(default_factory=list, description="""Data objects stored in this collection.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tables stored in this collection.""") - - -class Images(NWBDataInterface): - """ - A collection of images with an optional way to specify the order of the images using the \"order_of_images\" dataset. An order must be specified if the images are referenced by index, e.g., from an IndexSeries. - """ - description: Optional[str] = Field(None, description="""Description of this collection of images.""") - Image: List[Image] = Field(default_factory=list, description="""Images stored in this collection.""") - order_of_images: Optional[ImagesOrderOfImages] = Field(None, description="""Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images.""") - - -class DynamicTable(Container): - """ - A group containing multiple datasets that are aligned on the first dimension (Currently, this requirement if left up to APIs to check and enforce). These datasets represent different columns in the table. Apart from a column that contains unique identifiers for each row, there are no other required datasets. Users are free to add any number of custom VectorData objects (columns) here. DynamicTable also supports ragged array columns, where each element can be of a different size. To add a ragged array column, use a VectorIndex type to index the corresponding VectorData type. See documentation for VectorData and VectorIndex for more details. Unlike a compound data type, which is analogous to storing an array-of-structs, a DynamicTable can be thought of as a struct-of-arrays. This provides an alternative structure to choose from when optimizing storage for anticipated access patterns. Additionally, this type provides a way of creating a table without having to define a compound type up front. Although this convenience may be attractive, users should think carefully about how data will be accessed. DynamicTable is more appropriate for column-centric access, whereas a dataset with a compound type would be more appropriate for row-centric access. Finally, data size should also be taken into account. For small tables, performance loss may be an acceptable trade-off for the flexibility of a DynamicTable. - """ - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class AlignedDynamicTable(DynamicTable): - """ - DynamicTable container that supports storing a collection of sub-tables. Each sub-table is a DynamicTable itself that is aligned with the main table by row index. I.e., all DynamicTables stored in this group MUST have the same number of rows. This type effectively defines a 2-level table in which the main data is stored in the main table implemented by this type and additional columns of the table are grouped into categories, with each category being represented by a separate DynamicTable stored within the group. - """ - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimpleMultiContainer(Container): - """ - A simple Container for holding onto multiple containers. - """ - Data: Optional[List[Data]] = Field(default_factory=list, description="""Data objects held within this SimpleMultiContainer.""") - Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") - - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -Arraylike.update_forward_refs() -ImageArray.update_forward_refs() -ImageReferencesArray.update_forward_refs() -TimeSeriesData.update_forward_refs() -TimeSeriesDataArray.update_forward_refs() -TimeSeriesStartingTime.update_forward_refs() -TimeSeriesTimestamps.update_forward_refs() -TimeSeriesTimestampsArray.update_forward_refs() -TimeSeriesControl.update_forward_refs() -TimeSeriesControlArray.update_forward_refs() -TimeSeriesControlDescription.update_forward_refs() -TimeSeriesControlDescriptionArray.update_forward_refs() -TimeSeriesSync.update_forward_refs() -VectorDataArray.update_forward_refs() -VectorIndexArray.update_forward_refs() -ElementIdentifiersArray.update_forward_refs() -DynamicTableRegionArray.update_forward_refs() -DynamicTableIdArray.update_forward_refs() -Data.update_forward_refs() -NWBData.update_forward_refs() -Image.update_forward_refs() -ImageReferences.update_forward_refs() -ImagesOrderOfImages.update_forward_refs() -VectorData.update_forward_refs() -TimeSeriesReferenceVectorData.update_forward_refs() -VectorIndex.update_forward_refs() -ElementIdentifiers.update_forward_refs() -DynamicTableRegion.update_forward_refs() -DynamicTableId.update_forward_refs() -Container.update_forward_refs() -NWBContainer.update_forward_refs() -Device.update_forward_refs() -NWBDataInterface.update_forward_refs() -TimeSeries.update_forward_refs() -ProcessingModule.update_forward_refs() -Images.update_forward_refs() -DynamicTable.update_forward_refs() -AlignedDynamicTable.update_forward_refs() -SimpleMultiContainer.update_forward_refs() diff --git a/nwb_linkml/models/core.nwb.ecephys.py b/nwb_linkml/models/core.nwb.ecephys.py deleted file mode 100644 index 13e2d3d..0000000 --- a/nwb_linkml/models/core.nwb.ecephys.py +++ /dev/null @@ -1,785 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): - pass - - -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - -class ElectricalSeriesData(ConfiguredBaseModel): - """ - Recorded voltage data. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. This value is fixed to 'volts'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion', followed by 'channel_conversion' (if present), and then add 'offset'.""") - array: Optional[ElectricalSeriesDataArray] = Field(None) - - -class ElectricalSeriesChannelConversion(ConfiguredBaseModel): - """ - Channel-specific conversion factor. Multiply the data in the 'data' dataset by these values along the channel axis (as indicated by axis attribute) AND by the global conversion factor in the 'conversion' attribute of 'data' to get the data values in Volts, i.e, data in Volts = data * data.conversion * channel_conversion. This approach allows for both global and per-channel data conversion factors needed to support the storage of electrical recordings as native values generated by data acquisition systems. If this dataset is not present, then there is no channel-specific conversion factor, i.e. it is 1 for all channels. - """ - axis: Optional[int] = Field(None, description="""The zero-indexed axis of the 'data' dataset that the channel-specific conversion factor corresponds to. This value is fixed to 1.""") - array: Optional[ElectricalSeriesChannelConversionArray] = Field(None) - - -class SpikeEventSeriesData(ConfiguredBaseModel): - """ - Spike waveforms. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for waveforms, which is fixed to 'volts'.""") - array: Optional[SpikeEventSeriesDataArray] = Field(None) - - -class SpikeEventSeriesTimestamps(ConfiguredBaseModel): - """ - Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. Timestamps are required for the events. Unlike for TimeSeries, timestamps are required for SpikeEventSeries and are thus re-specified here. - """ - interval: Optional[int] = Field(None, description="""Value is '1'""") - unit: Optional[str] = Field(None, description="""Unit of measurement for timestamps, which is fixed to 'seconds'.""") - array: Optional[SpikeEventSeriesTimestampsArray] = Field(None) - - -class FeatureExtractionDescription(ConfiguredBaseModel): - """ - Description of features (eg, ''PC1'') for each of the extracted features. - """ - array: Optional[FeatureExtractionDescriptionArray] = Field(None) - - -class FeatureExtractionFeatures(ConfiguredBaseModel): - """ - Multi-dimensional array of features extracted from each event. - """ - array: Optional[FeatureExtractionFeaturesArray] = Field(None) - - -class FeatureExtractionTimes(ConfiguredBaseModel): - """ - Times of events that features correspond to (can be a link). - """ - array: Optional[FeatureExtractionTimesArray] = Field(None) - - -class EventDetectionDetectionMethod(ConfiguredBaseModel): - """ - Description of how events were detected, such as voltage threshold, or dV/dT threshold, as well as relevant values. - """ - None - - -class EventDetectionSourceIdx(ConfiguredBaseModel): - """ - Indices (zero-based) into source ElectricalSeries::data array corresponding to time of event. ''description'' should define what is meant by time of event (e.g., .25 ms before action potential peak, zero-crossing time, etc). The index points to each event from the raw data. - """ - array: Optional[EventDetectionSourceIdxArray] = Field(None) - - -class EventDetectionTimes(ConfiguredBaseModel): - """ - Timestamps of events, in seconds. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for event times, which is fixed to 'seconds'.""") - array: Optional[EventDetectionTimesArray] = Field(None) - - -class ElectrodeGroupPosition(ConfiguredBaseModel): - """ - stereotaxic or common framework coordinates - """ - None - - -class ClusterWaveformsWaveformFiltering(ConfiguredBaseModel): - """ - Filtering applied to data before generating mean/sd - """ - None - - -class ClusterWaveformsWaveformMean(ConfiguredBaseModel): - """ - The mean waveform for each cluster, using the same indices for each wave as cluster numbers in the associated Clustering module (i.e, cluster 3 is in array slot [3]). Waveforms corresponding to gaps in cluster sequence should be empty (e.g., zero- filled) - """ - array: Optional[ClusterWaveformsWaveformMeanArray] = Field(None) - - -class ClusterWaveformsWaveformSd(ConfiguredBaseModel): - """ - Stdev of waveforms for each cluster, using the same indices as in mean - """ - array: Optional[ClusterWaveformsWaveformSdArray] = Field(None) - - -class ClusteringDescription(ConfiguredBaseModel): - """ - Description of clusters or clustering, (e.g. cluster 0 is noise, clusters curated using Klusters, etc) - """ - None - - -class ClusteringNum(ConfiguredBaseModel): - """ - Cluster number of each event - """ - array: Optional[ClusteringNumArray] = Field(None) - - -class ClusteringPeakOverRms(ConfiguredBaseModel): - """ - Maximum ratio of waveform peak to RMS on any channel in the cluster (provides a basic clustering metric). - """ - array: Optional[ClusteringPeakOverRmsArray] = Field(None) - - -class ClusteringTimes(ConfiguredBaseModel): - """ - Times of clustered events, in seconds. This may be a link to times field in associated FeatureExtraction module. - """ - array: Optional[ClusteringTimesArray] = Field(None) - - -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - -class ElectricalSeriesDataArray(Arraylike): - - num_times: float = Field(...) - num_channels: Optional[float] = Field(None) - num_samples: Optional[float] = Field(None) - - -class ElectricalSeriesChannelConversionArray(Arraylike): - - num_channels: float = Field(...) - - -class SpikeEventSeriesDataArray(Arraylike): - - num_events: float = Field(...) - num_samples: float = Field(...) - num_channels: Optional[float] = Field(None) - - -class SpikeEventSeriesTimestampsArray(Arraylike): - - num_times: float = Field(...) - - -class FeatureExtractionDescriptionArray(Arraylike): - - num_features: str = Field(...) - - -class FeatureExtractionFeaturesArray(Arraylike): - - num_events: Optional[float] = Field(None) - num_channels: Optional[float] = Field(None) - num_features: Optional[float] = Field(None) - - -class FeatureExtractionTimesArray(Arraylike): - - num_events: float = Field(...) - - -class EventDetectionSourceIdxArray(Arraylike): - - num_events: int = Field(...) - - -class EventDetectionTimesArray(Arraylike): - - num_events: float = Field(...) - - -class ClusterWaveformsWaveformMeanArray(Arraylike): - - num_clusters: Optional[float] = Field(None) - num_samples: Optional[float] = Field(None) - - -class ClusterWaveformsWaveformSdArray(Arraylike): - - num_clusters: Optional[float] = Field(None) - num_samples: Optional[float] = Field(None) - - -class ClusteringNumArray(Arraylike): - - num_events: int = Field(...) - - -class ClusteringPeakOverRmsArray(Arraylike): - - num_clusters: float = Field(...) - - -class ClusteringTimesArray(Arraylike): - - num_events: float = Field(...) - - -class VectorDataArray(Arraylike): - - dim0: Any = Field(...) - dim1: Optional[Any] = Field(None) - dim2: Optional[Any] = Field(None) - dim3: Optional[Any] = Field(None) - - -class VectorIndexArray(Arraylike): - - num_rows: int = Field(...) - - -class ElementIdentifiersArray(Arraylike): - - num_elements: int = Field(...) - - -class DynamicTableRegionArray(Arraylike): - - num_rows: int = Field(...) - - -class DynamicTableIdArray(Arraylike): - - num_rows: int = Field(...) - - -class Data(ConfiguredBaseModel): - """ - An abstract data type for a dataset. - """ - None - - -class VectorData(Data): - """ - An n-dimensional dataset representing a column of a DynamicTable. If used without an accompanying VectorIndex, first dimension is along the rows of the DynamicTable and each step along the first dimension is a cell of the larger table. VectorData can also be used to represent a ragged array if paired with a VectorIndex. This allows for storing arrays of varying length in a single cell of the DynamicTable by indexing into this VectorData. The first vector is at VectorData[0:VectorIndex[0]]. The second vector is at VectorData[VectorIndex[0]:VectorIndex[1]], and so on. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class VectorIndex(VectorData): - """ - Used with VectorData to encode a ragged array. An array of indices into the first dimension of the target VectorData, and forming a map between the rows of a DynamicTable and the indices of the VectorData. The name of the VectorIndex is expected to be the name of the target VectorData object followed by \"_index\". - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ElementIdentifiers(Data): - """ - A list of unique identifiers for values within a dataset, e.g. rows of a DynamicTable. - """ - array: Optional[ElementIdentifiersArray] = Field(None) - - -class DynamicTableRegion(VectorData): - """ - DynamicTableRegion provides a link from one table to an index or region of another. The `table` attribute is a link to another `DynamicTable`, indicating which table is referenced, and the data is int(s) indicating the row(s) (0-indexed) of the target array. `DynamicTableRegion`s can be used to associate rows with repeated meta-data without data duplication. They can also be used to create hierarchical relationships between multiple `DynamicTable`s. `DynamicTableRegion` objects may be paired with a `VectorIndex` object to create ragged references, so a single cell of a `DynamicTable` can reference many rows of another `DynamicTable`. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class ElectricalSeriesElectrodes(DynamicTableRegion): - """ - DynamicTableRegion pointer to the electrodes that this time series was generated from. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class FeatureExtractionElectrodes(DynamicTableRegion): - """ - DynamicTableRegion pointer to the electrodes that this time series was generated from. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DynamicTableId(ElementIdentifiers): - """ - Array of unique identifiers for the rows of this dynamic table. - """ - array: Optional[DynamicTableIdArray] = Field(None) - - -class Container(ConfiguredBaseModel): - """ - An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class DynamicTable(Container): - """ - A group containing multiple datasets that are aligned on the first dimension (Currently, this requirement if left up to APIs to check and enforce). These datasets represent different columns in the table. Apart from a column that contains unique identifiers for each row, there are no other required datasets. Users are free to add any number of custom VectorData objects (columns) here. DynamicTable also supports ragged array columns, where each element can be of a different size. To add a ragged array column, use a VectorIndex type to index the corresponding VectorData type. See documentation for VectorData and VectorIndex for more details. Unlike a compound data type, which is analogous to storing an array-of-structs, a DynamicTable can be thought of as a struct-of-arrays. This provides an alternative structure to choose from when optimizing storage for anticipated access patterns. Additionally, this type provides a way of creating a table without having to define a compound type up front. Although this convenience may be attractive, users should think carefully about how data will be accessed. DynamicTable is more appropriate for column-centric access, whereas a dataset with a compound type would be more appropriate for row-centric access. Finally, data size should also be taken into account. For small tables, performance loss may be an acceptable trade-off for the flexibility of a DynamicTable. - """ - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class AlignedDynamicTable(DynamicTable): - """ - DynamicTable container that supports storing a collection of sub-tables. Each sub-table is a DynamicTable itself that is aligned with the main table by row index. I.e., all DynamicTables stored in this group MUST have the same number of rows. This type effectively defines a 2-level table in which the main data is stored in the main table implemented by this type and additional columns of the table are grouped into categories, with each category being represented by a separate DynamicTable stored within the group. - """ - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimpleMultiContainer(Container): - """ - A simple Container for holding onto multiple containers. - """ - Data: Optional[List[Data]] = Field(default_factory=list, description="""Data objects held within this SimpleMultiContainer.""") - Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") - - -class NWBData(Data): - """ - An abstract data type for a dataset. - """ - None - - -class TimeSeriesReferenceVectorData(VectorData): - """ - Column storing references to a TimeSeries (rows). For each TimeSeries this VectorData column stores the start_index and count to indicate the range in time to be selected as well as an object reference to the TimeSeries. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class Image(NWBData): - """ - An abstract data type for an image. Shape can be 2-D (x, y), or 3-D where the third dimension can have three or four elements, e.g. (x, y, (r, g, b)) or (x, y, (r, g, b, a)). - """ - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - array: Optional[ImageArray] = Field(None) - - -class ImageArray(Arraylike): - - x: float = Field(...) - y: float = Field(...) - r_g_b: Optional[float] = Field(None) - r_g_b_a: Optional[float] = Field(None) - - -class ImageReferences(NWBData): - """ - Ordered dataset of references to Image objects. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class ImageReferencesArray(Arraylike): - - num_images: Image = Field(...) - - -class NWBContainer(Container): - """ - An abstract data type for a generic container storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class ElectrodeGroup(NWBContainer): - """ - A physical grouping of electrodes, e.g. a shank of an array. - """ - description: Optional[str] = Field(None, description="""Description of this electrode group.""") - location: Optional[str] = Field(None, description="""Location of electrode group. Specify the area, layer, comments on estimation of area/layer, etc. Use standard atlas names for anatomical regions when possible.""") - position: Optional[ElectrodeGroupPosition] = Field(None, description="""stereotaxic or common framework coordinates""") - - -class NWBDataInterface(NWBContainer): - """ - An abstract data type for a generic container storing collections of data, as opposed to metadata. - """ - None - - -class FeatureExtraction(NWBDataInterface): - """ - Features, such as PC1 and PC2, that are extracted from signals stored in a SpikeEventSeries or other source. - """ - description: FeatureExtractionDescription = Field(..., description="""Description of features (eg, ''PC1'') for each of the extracted features.""") - features: FeatureExtractionFeatures = Field(..., description="""Multi-dimensional array of features extracted from each event.""") - times: FeatureExtractionTimes = Field(..., description="""Times of events that features correspond to (can be a link).""") - electrodes: FeatureExtractionElectrodes = Field(..., description="""DynamicTableRegion pointer to the electrodes that this time series was generated from.""") - - -class EventDetection(NWBDataInterface): - """ - Detected spike events from voltage trace(s). - """ - detection_method: EventDetectionDetectionMethod = Field(..., description="""Description of how events were detected, such as voltage threshold, or dV/dT threshold, as well as relevant values.""") - source_idx: EventDetectionSourceIdx = Field(..., description="""Indices (zero-based) into source ElectricalSeries::data array corresponding to time of event. ''description'' should define what is meant by time of event (e.g., .25 ms before action potential peak, zero-crossing time, etc). The index points to each event from the raw data.""") - times: EventDetectionTimes = Field(..., description="""Timestamps of events, in seconds.""") - - -class EventWaveform(NWBDataInterface): - """ - Represents either the waveforms of detected events, as extracted from a raw data trace in /acquisition, or the event waveforms that were stored during experiment acquisition. - """ - SpikeEventSeries: Optional[List[SpikeEventSeries]] = Field(default_factory=list, description="""SpikeEventSeries object(s) containing detected spike event waveforms.""") - - -class FilteredEphys(NWBDataInterface): - """ - Electrophysiology data from one or more channels that has been subjected to filtering. Examples of filtered data include Theta and Gamma (LFP has its own interface). FilteredEphys modules publish an ElectricalSeries for each filtered channel or set of channels. The name of each ElectricalSeries is arbitrary but should be informative. The source of the filtered data, whether this is from analysis of another time series or as acquired by hardware, should be noted in each's TimeSeries::description field. There is no assumed 1::1 correspondence between filtered ephys signals and electrodes, as a single signal can apply to many nearby electrodes, and one electrode may have different filtered (e.g., theta and/or gamma) signals represented. Filter properties should be noted in the ElectricalSeries 'filtering' attribute. - """ - ElectricalSeries: List[ElectricalSeries] = Field(default_factory=list, description="""ElectricalSeries object(s) containing filtered electrophysiology data.""") - - -class LFP(NWBDataInterface): - """ - LFP data from one or more channels. The electrode map in each published ElectricalSeries will identify which channels are providing LFP data. Filter properties should be noted in the ElectricalSeries 'filtering' attribute. - """ - ElectricalSeries: List[ElectricalSeries] = Field(default_factory=list, description="""ElectricalSeries object(s) containing LFP data for one or more channels.""") - - -class ClusterWaveforms(NWBDataInterface): - """ - DEPRECATED The mean waveform shape, including standard deviation, of the different clusters. Ideally, the waveform analysis should be performed on data that is only high-pass filtered. This is a separate module because it is expected to require updating. For example, IMEC probes may require different storage requirements to store/display mean waveforms, requiring a new interface or an extension of this one. - """ - waveform_filtering: ClusterWaveformsWaveformFiltering = Field(..., description="""Filtering applied to data before generating mean/sd""") - waveform_mean: ClusterWaveformsWaveformMean = Field(..., description="""The mean waveform for each cluster, using the same indices for each wave as cluster numbers in the associated Clustering module (i.e, cluster 3 is in array slot [3]). Waveforms corresponding to gaps in cluster sequence should be empty (e.g., zero- filled)""") - waveform_sd: ClusterWaveformsWaveformSd = Field(..., description="""Stdev of waveforms for each cluster, using the same indices as in mean""") - - -class Clustering(NWBDataInterface): - """ - DEPRECATED Clustered spike data, whether from automatic clustering tools (e.g., klustakwik) or as a result of manual sorting. - """ - description: ClusteringDescription = Field(..., description="""Description of clusters or clustering, (e.g. cluster 0 is noise, clusters curated using Klusters, etc)""") - num: ClusteringNum = Field(..., description="""Cluster number of each event""") - peak_over_rms: ClusteringPeakOverRms = Field(..., description="""Maximum ratio of waveform peak to RMS on any channel in the cluster (provides a basic clustering metric).""") - times: ClusteringTimes = Field(..., description="""Times of clustered events, in seconds. This may be a link to times field in associated FeatureExtraction module.""") - - -class TimeSeries(NWBDataInterface): - """ - General purpose time series. - """ - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - data: TimeSeriesData = Field(..., description="""Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class ElectricalSeries(TimeSeries): - """ - A time series of acquired voltage data from extracellular recordings. The data field is an int or float array storing data in volts. The first dimension should always represent time. The second dimension, if present, should represent channels. - """ - filtering: Optional[str] = Field(None, description="""Filtering applied to all channels of the data. For example, if this ElectricalSeries represents high-pass-filtered data (also known as AP Band), then this value could be \"High-pass 4-pole Bessel filter at 500 Hz\". If this ElectricalSeries represents low-pass-filtered LFP data and the type of filter is unknown, then this value could be \"Low-pass filter at 300 Hz\". If a non-standard filter type is used, provide as much detail about the filter properties as possible.""") - data: ElectricalSeriesData = Field(..., description="""Recorded voltage data.""") - electrodes: ElectricalSeriesElectrodes = Field(..., description="""DynamicTableRegion pointer to the electrodes that this time series was generated from.""") - channel_conversion: Optional[ElectricalSeriesChannelConversion] = Field(None, description="""Channel-specific conversion factor. Multiply the data in the 'data' dataset by these values along the channel axis (as indicated by axis attribute) AND by the global conversion factor in the 'conversion' attribute of 'data' to get the data values in Volts, i.e, data in Volts = data * data.conversion * channel_conversion. This approach allows for both global and per-channel data conversion factors needed to support the storage of electrical recordings as native values generated by data acquisition systems. If this dataset is not present, then there is no channel-specific conversion factor, i.e. it is 1 for all channels.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class SpikeEventSeries(ElectricalSeries): - """ - Stores snapshots/snippets of recorded spike events (i.e., threshold crossings). This may also be raw data, as reported by ephys hardware. If so, the TimeSeries::description field should describe how events were detected. All SpikeEventSeries should reside in a module (under EventWaveform interface) even if the spikes were reported and stored by hardware. All events span the same recording channels and store snapshots of equal duration. TimeSeries::data array structure: [num events] [num channels] [num samples] (or [num events] [num samples] for single electrode). - """ - data: SpikeEventSeriesData = Field(..., description="""Spike waveforms.""") - timestamps: SpikeEventSeriesTimestamps = Field(..., description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. Timestamps are required for the events. Unlike for TimeSeries, timestamps are required for SpikeEventSeries and are thus re-specified here.""") - filtering: Optional[str] = Field(None, description="""Filtering applied to all channels of the data. For example, if this ElectricalSeries represents high-pass-filtered data (also known as AP Band), then this value could be \"High-pass 4-pole Bessel filter at 500 Hz\". If this ElectricalSeries represents low-pass-filtered LFP data and the type of filter is unknown, then this value could be \"Low-pass filter at 300 Hz\". If a non-standard filter type is used, provide as much detail about the filter properties as possible.""") - electrodes: ElectricalSeriesElectrodes = Field(..., description="""DynamicTableRegion pointer to the electrodes that this time series was generated from.""") - channel_conversion: Optional[ElectricalSeriesChannelConversion] = Field(None, description="""Channel-specific conversion factor. Multiply the data in the 'data' dataset by these values along the channel axis (as indicated by axis attribute) AND by the global conversion factor in the 'conversion' attribute of 'data' to get the data values in Volts, i.e, data in Volts = data * data.conversion * channel_conversion. This approach allows for both global and per-channel data conversion factors needed to support the storage of electrical recordings as native values generated by data acquisition systems. If this dataset is not present, then there is no channel-specific conversion factor, i.e. it is 1 for all channels.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class TimeSeriesData(ConfiguredBaseModel): - """ - Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file. - """ - conversion: Optional[float] = Field(None, description="""Scalar to multiply each element in data to convert it to the specified 'unit'. If the data are stored in acquisition system units or other units that require a conversion to be interpretable, multiply the data by 'conversion' to convert the data to the specified 'unit'. e.g. if the data acquisition system stores values in this object as signed 16-bit integers (int16 range -32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data acquisition system gain is 8000X, then the 'conversion' multiplier to get from raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9.""") - offset: Optional[float] = Field(None, description="""Scalar to add to the data after scaling by 'conversion' to finalize its coercion to the specified 'unit'. Two common examples of this include (a) data stored in an unsigned type that requires a shift after scaling to re-center the data, and (b) specialized recording devices that naturally cause a scalar offset with respect to the true units.""") - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data, stored in the specified by unit, e.g., the change in value of the least significant bit, or a larger number if signal noise is known to be present. If unknown, use -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - continuity: Optional[str] = Field(None, description="""Optionally describe the continuity of the data. Can be \"continuous\", \"instantaneous\", or \"step\". For example, a voltage trace would be \"continuous\", because samples are recorded from a continuous process. An array of lick times would be \"instantaneous\", because the data represents distinct moments in time. Times of image presentations would be \"step\" because the picture remains the same until the next timepoint. This field is optional, but is useful in providing information about the underlying data. It may inform the way this data is interpreted, the way it is visualized, and what analysis methods are applicable.""") - array: Optional[TimeSeriesDataArray] = Field(None) - - -class TimeSeriesDataArray(Arraylike): - - num_times: Any = Field(...) - num_DIM2: Optional[Any] = Field(None) - num_DIM3: Optional[Any] = Field(None) - num_DIM4: Optional[Any] = Field(None) - - -class TimeSeriesStartingTime(ConfiguredBaseModel): - """ - Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute. - """ - rate: Optional[float] = Field(None, description="""Sampling rate, in Hz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement for time, which is fixed to 'seconds'.""") - - -class TimeSeriesTimestamps(ConfiguredBaseModel): - """ - Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. - """ - interval: Optional[int] = Field(None, description="""Value is '1'""") - unit: Optional[str] = Field(None, description="""Unit of measurement for timestamps, which is fixed to 'seconds'.""") - array: Optional[TimeSeriesTimestampsArray] = Field(None) - - -class TimeSeriesTimestampsArray(Arraylike): - - num_times: float = Field(...) - - -class TimeSeriesControl(ConfiguredBaseModel): - """ - Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data. - """ - array: Optional[TimeSeriesControlArray] = Field(None) - - -class TimeSeriesControlArray(Arraylike): - - num_times: int = Field(...) - - -class TimeSeriesControlDescription(ConfiguredBaseModel): - """ - Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0. - """ - array: Optional[TimeSeriesControlDescriptionArray] = Field(None) - - -class TimeSeriesControlDescriptionArray(Arraylike): - - num_control_values: str = Field(...) - - -class TimeSeriesSync(ConfiguredBaseModel): - """ - Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes. - """ - None - - -class ProcessingModule(NWBContainer): - """ - A collection of processed data. - """ - description: Optional[str] = Field(None, description="""Description of this collection of processed data.""") - NWBDataInterface: Optional[List[NWBDataInterface]] = Field(default_factory=list, description="""Data objects stored in this collection.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tables stored in this collection.""") - - -class Images(NWBDataInterface): - """ - A collection of images with an optional way to specify the order of the images using the \"order_of_images\" dataset. An order must be specified if the images are referenced by index, e.g., from an IndexSeries. - """ - description: Optional[str] = Field(None, description="""Description of this collection of images.""") - Image: List[Image] = Field(default_factory=list, description="""Images stored in this collection.""") - order_of_images: Optional[ImagesOrderOfImages] = Field(None, description="""Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images.""") - - -class ImagesOrderOfImages(ImageReferences): - """ - Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images. - """ - array: Optional[ImageReferencesArray] = Field(None) - - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -ElectricalSeriesData.update_forward_refs() -ElectricalSeriesChannelConversion.update_forward_refs() -SpikeEventSeriesData.update_forward_refs() -SpikeEventSeriesTimestamps.update_forward_refs() -FeatureExtractionDescription.update_forward_refs() -FeatureExtractionFeatures.update_forward_refs() -FeatureExtractionTimes.update_forward_refs() -EventDetectionDetectionMethod.update_forward_refs() -EventDetectionSourceIdx.update_forward_refs() -EventDetectionTimes.update_forward_refs() -ElectrodeGroupPosition.update_forward_refs() -ClusterWaveformsWaveformFiltering.update_forward_refs() -ClusterWaveformsWaveformMean.update_forward_refs() -ClusterWaveformsWaveformSd.update_forward_refs() -ClusteringDescription.update_forward_refs() -ClusteringNum.update_forward_refs() -ClusteringPeakOverRms.update_forward_refs() -ClusteringTimes.update_forward_refs() -Arraylike.update_forward_refs() -ElectricalSeriesDataArray.update_forward_refs() -ElectricalSeriesChannelConversionArray.update_forward_refs() -SpikeEventSeriesDataArray.update_forward_refs() -SpikeEventSeriesTimestampsArray.update_forward_refs() -FeatureExtractionDescriptionArray.update_forward_refs() -FeatureExtractionFeaturesArray.update_forward_refs() -FeatureExtractionTimesArray.update_forward_refs() -EventDetectionSourceIdxArray.update_forward_refs() -EventDetectionTimesArray.update_forward_refs() -ClusterWaveformsWaveformMeanArray.update_forward_refs() -ClusterWaveformsWaveformSdArray.update_forward_refs() -ClusteringNumArray.update_forward_refs() -ClusteringPeakOverRmsArray.update_forward_refs() -ClusteringTimesArray.update_forward_refs() -VectorDataArray.update_forward_refs() -VectorIndexArray.update_forward_refs() -ElementIdentifiersArray.update_forward_refs() -DynamicTableRegionArray.update_forward_refs() -DynamicTableIdArray.update_forward_refs() -Data.update_forward_refs() -VectorData.update_forward_refs() -VectorIndex.update_forward_refs() -ElementIdentifiers.update_forward_refs() -DynamicTableRegion.update_forward_refs() -ElectricalSeriesElectrodes.update_forward_refs() -FeatureExtractionElectrodes.update_forward_refs() -DynamicTableId.update_forward_refs() -Container.update_forward_refs() -DynamicTable.update_forward_refs() -AlignedDynamicTable.update_forward_refs() -SimpleMultiContainer.update_forward_refs() -NWBData.update_forward_refs() -TimeSeriesReferenceVectorData.update_forward_refs() -Image.update_forward_refs() -ImageArray.update_forward_refs() -ImageReferences.update_forward_refs() -ImageReferencesArray.update_forward_refs() -NWBContainer.update_forward_refs() -ElectrodeGroup.update_forward_refs() -NWBDataInterface.update_forward_refs() -FeatureExtraction.update_forward_refs() -EventDetection.update_forward_refs() -EventWaveform.update_forward_refs() -FilteredEphys.update_forward_refs() -LFP.update_forward_refs() -ClusterWaveforms.update_forward_refs() -Clustering.update_forward_refs() -TimeSeries.update_forward_refs() -ElectricalSeries.update_forward_refs() -SpikeEventSeries.update_forward_refs() -TimeSeriesData.update_forward_refs() -TimeSeriesDataArray.update_forward_refs() -TimeSeriesStartingTime.update_forward_refs() -TimeSeriesTimestamps.update_forward_refs() -TimeSeriesTimestampsArray.update_forward_refs() -TimeSeriesControl.update_forward_refs() -TimeSeriesControlArray.update_forward_refs() -TimeSeriesControlDescription.update_forward_refs() -TimeSeriesControlDescriptionArray.update_forward_refs() -TimeSeriesSync.update_forward_refs() -ProcessingModule.update_forward_refs() -Images.update_forward_refs() -ImagesOrderOfImages.update_forward_refs() diff --git a/nwb_linkml/models/core.nwb.epoch.py b/nwb_linkml/models/core.nwb.epoch.py deleted file mode 100644 index 0615738..0000000 --- a/nwb_linkml/models/core.nwb.epoch.py +++ /dev/null @@ -1,484 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): - pass - - -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - -class ImageArray(Arraylike): - - x: float = Field(...) - y: float = Field(...) - r_g_b: Optional[float] = Field(None) - r_g_b_a: Optional[float] = Field(None) - - -class ImageReferencesArray(Arraylike): - - num_images: Image = Field(...) - - -class TimeSeriesData(ConfiguredBaseModel): - """ - Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file. - """ - conversion: Optional[float] = Field(None, description="""Scalar to multiply each element in data to convert it to the specified 'unit'. If the data are stored in acquisition system units or other units that require a conversion to be interpretable, multiply the data by 'conversion' to convert the data to the specified 'unit'. e.g. if the data acquisition system stores values in this object as signed 16-bit integers (int16 range -32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data acquisition system gain is 8000X, then the 'conversion' multiplier to get from raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9.""") - offset: Optional[float] = Field(None, description="""Scalar to add to the data after scaling by 'conversion' to finalize its coercion to the specified 'unit'. Two common examples of this include (a) data stored in an unsigned type that requires a shift after scaling to re-center the data, and (b) specialized recording devices that naturally cause a scalar offset with respect to the true units.""") - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data, stored in the specified by unit, e.g., the change in value of the least significant bit, or a larger number if signal noise is known to be present. If unknown, use -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - continuity: Optional[str] = Field(None, description="""Optionally describe the continuity of the data. Can be \"continuous\", \"instantaneous\", or \"step\". For example, a voltage trace would be \"continuous\", because samples are recorded from a continuous process. An array of lick times would be \"instantaneous\", because the data represents distinct moments in time. Times of image presentations would be \"step\" because the picture remains the same until the next timepoint. This field is optional, but is useful in providing information about the underlying data. It may inform the way this data is interpreted, the way it is visualized, and what analysis methods are applicable.""") - array: Optional[TimeSeriesDataArray] = Field(None) - - -class TimeSeriesDataArray(Arraylike): - - num_times: Any = Field(...) - num_DIM2: Optional[Any] = Field(None) - num_DIM3: Optional[Any] = Field(None) - num_DIM4: Optional[Any] = Field(None) - - -class TimeSeriesStartingTime(ConfiguredBaseModel): - """ - Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute. - """ - rate: Optional[float] = Field(None, description="""Sampling rate, in Hz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement for time, which is fixed to 'seconds'.""") - - -class TimeSeriesTimestamps(ConfiguredBaseModel): - """ - Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. - """ - interval: Optional[int] = Field(None, description="""Value is '1'""") - unit: Optional[str] = Field(None, description="""Unit of measurement for timestamps, which is fixed to 'seconds'.""") - array: Optional[TimeSeriesTimestampsArray] = Field(None) - - -class TimeSeriesTimestampsArray(Arraylike): - - num_times: float = Field(...) - - -class TimeSeriesControl(ConfiguredBaseModel): - """ - Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data. - """ - array: Optional[TimeSeriesControlArray] = Field(None) - - -class TimeSeriesControlArray(Arraylike): - - num_times: int = Field(...) - - -class TimeSeriesControlDescription(ConfiguredBaseModel): - """ - Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0. - """ - array: Optional[TimeSeriesControlDescriptionArray] = Field(None) - - -class TimeSeriesControlDescriptionArray(Arraylike): - - num_control_values: str = Field(...) - - -class TimeSeriesSync(ConfiguredBaseModel): - """ - Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes. - """ - None - - -class VectorDataArray(Arraylike): - - dim0: Any = Field(...) - dim1: Optional[Any] = Field(None) - dim2: Optional[Any] = Field(None) - dim3: Optional[Any] = Field(None) - - -class VectorIndexArray(Arraylike): - - num_rows: int = Field(...) - - -class ElementIdentifiersArray(Arraylike): - - num_elements: int = Field(...) - - -class DynamicTableRegionArray(Arraylike): - - num_rows: int = Field(...) - - -class DynamicTableIdArray(Arraylike): - - num_rows: int = Field(...) - - -class Data(ConfiguredBaseModel): - """ - An abstract data type for a dataset. - """ - None - - -class NWBData(Data): - """ - An abstract data type for a dataset. - """ - None - - -class Image(NWBData): - """ - An abstract data type for an image. Shape can be 2-D (x, y), or 3-D where the third dimension can have three or four elements, e.g. (x, y, (r, g, b)) or (x, y, (r, g, b, a)). - """ - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - array: Optional[ImageArray] = Field(None) - - -class ImageReferences(NWBData): - """ - Ordered dataset of references to Image objects. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class ImagesOrderOfImages(ImageReferences): - """ - Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class VectorData(Data): - """ - An n-dimensional dataset representing a column of a DynamicTable. If used without an accompanying VectorIndex, first dimension is along the rows of the DynamicTable and each step along the first dimension is a cell of the larger table. VectorData can also be used to represent a ragged array if paired with a VectorIndex. This allows for storing arrays of varying length in a single cell of the DynamicTable by indexing into this VectorData. The first vector is at VectorData[0:VectorIndex[0]]. The second vector is at VectorData[VectorIndex[0]:VectorIndex[1]], and so on. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class TimeIntervalsStartTime(VectorData): - """ - Start time of epoch, in seconds. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class TimeIntervalsStopTime(VectorData): - """ - Stop time of epoch, in seconds. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class TimeIntervalsTags(VectorData): - """ - User-defined tags that identify or categorize events. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class TimeSeriesReferenceVectorData(VectorData): - """ - Column storing references to a TimeSeries (rows). For each TimeSeries this VectorData column stores the start_index and count to indicate the range in time to be selected as well as an object reference to the TimeSeries. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class TimeIntervalsTimeseries(TimeSeriesReferenceVectorData): - """ - An index into a TimeSeries object. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class VectorIndex(VectorData): - """ - Used with VectorData to encode a ragged array. An array of indices into the first dimension of the target VectorData, and forming a map between the rows of a DynamicTable and the indices of the VectorData. The name of the VectorIndex is expected to be the name of the target VectorData object followed by \"_index\". - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class TimeIntervalsTagsIndex(VectorIndex): - """ - Index for tags. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class TimeIntervalsTimeseriesIndex(VectorIndex): - """ - Index for timeseries. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ElementIdentifiers(Data): - """ - A list of unique identifiers for values within a dataset, e.g. rows of a DynamicTable. - """ - array: Optional[ElementIdentifiersArray] = Field(None) - - -class DynamicTableRegion(VectorData): - """ - DynamicTableRegion provides a link from one table to an index or region of another. The `table` attribute is a link to another `DynamicTable`, indicating which table is referenced, and the data is int(s) indicating the row(s) (0-indexed) of the target array. `DynamicTableRegion`s can be used to associate rows with repeated meta-data without data duplication. They can also be used to create hierarchical relationships between multiple `DynamicTable`s. `DynamicTableRegion` objects may be paired with a `VectorIndex` object to create ragged references, so a single cell of a `DynamicTable` can reference many rows of another `DynamicTable`. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DynamicTableId(ElementIdentifiers): - """ - Array of unique identifiers for the rows of this dynamic table. - """ - array: Optional[DynamicTableIdArray] = Field(None) - - -class Container(ConfiguredBaseModel): - """ - An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class NWBContainer(Container): - """ - An abstract data type for a generic container storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class NWBDataInterface(NWBContainer): - """ - An abstract data type for a generic container storing collections of data, as opposed to metadata. - """ - None - - -class TimeSeries(NWBDataInterface): - """ - General purpose time series. - """ - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - data: TimeSeriesData = Field(..., description="""Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class ProcessingModule(NWBContainer): - """ - A collection of processed data. - """ - description: Optional[str] = Field(None, description="""Description of this collection of processed data.""") - NWBDataInterface: Optional[List[NWBDataInterface]] = Field(default_factory=list, description="""Data objects stored in this collection.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tables stored in this collection.""") - - -class Images(NWBDataInterface): - """ - A collection of images with an optional way to specify the order of the images using the \"order_of_images\" dataset. An order must be specified if the images are referenced by index, e.g., from an IndexSeries. - """ - description: Optional[str] = Field(None, description="""Description of this collection of images.""") - Image: List[Image] = Field(default_factory=list, description="""Images stored in this collection.""") - order_of_images: Optional[ImagesOrderOfImages] = Field(None, description="""Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images.""") - - -class DynamicTable(Container): - """ - A group containing multiple datasets that are aligned on the first dimension (Currently, this requirement if left up to APIs to check and enforce). These datasets represent different columns in the table. Apart from a column that contains unique identifiers for each row, there are no other required datasets. Users are free to add any number of custom VectorData objects (columns) here. DynamicTable also supports ragged array columns, where each element can be of a different size. To add a ragged array column, use a VectorIndex type to index the corresponding VectorData type. See documentation for VectorData and VectorIndex for more details. Unlike a compound data type, which is analogous to storing an array-of-structs, a DynamicTable can be thought of as a struct-of-arrays. This provides an alternative structure to choose from when optimizing storage for anticipated access patterns. Additionally, this type provides a way of creating a table without having to define a compound type up front. Although this convenience may be attractive, users should think carefully about how data will be accessed. DynamicTable is more appropriate for column-centric access, whereas a dataset with a compound type would be more appropriate for row-centric access. Finally, data size should also be taken into account. For small tables, performance loss may be an acceptable trade-off for the flexibility of a DynamicTable. - """ - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class TimeIntervals(DynamicTable): - """ - A container for aggregating epoch data and the TimeSeries that each epoch applies to. - """ - start_time: TimeIntervalsStartTime = Field(..., description="""Start time of epoch, in seconds.""") - stop_time: TimeIntervalsStopTime = Field(..., description="""Stop time of epoch, in seconds.""") - tags: Optional[TimeIntervalsTags] = Field(None, description="""User-defined tags that identify or categorize events.""") - tags_index: Optional[TimeIntervalsTagsIndex] = Field(None, description="""Index for tags.""") - timeseries: Optional[TimeIntervalsTimeseries] = Field(None, description="""An index into a TimeSeries object.""") - timeseries_index: Optional[TimeIntervalsTimeseriesIndex] = Field(None, description="""Index for timeseries.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class AlignedDynamicTable(DynamicTable): - """ - DynamicTable container that supports storing a collection of sub-tables. Each sub-table is a DynamicTable itself that is aligned with the main table by row index. I.e., all DynamicTables stored in this group MUST have the same number of rows. This type effectively defines a 2-level table in which the main data is stored in the main table implemented by this type and additional columns of the table are grouped into categories, with each category being represented by a separate DynamicTable stored within the group. - """ - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimpleMultiContainer(Container): - """ - A simple Container for holding onto multiple containers. - """ - Data: Optional[List[Data]] = Field(default_factory=list, description="""Data objects held within this SimpleMultiContainer.""") - Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") - - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -Arraylike.update_forward_refs() -ImageArray.update_forward_refs() -ImageReferencesArray.update_forward_refs() -TimeSeriesData.update_forward_refs() -TimeSeriesDataArray.update_forward_refs() -TimeSeriesStartingTime.update_forward_refs() -TimeSeriesTimestamps.update_forward_refs() -TimeSeriesTimestampsArray.update_forward_refs() -TimeSeriesControl.update_forward_refs() -TimeSeriesControlArray.update_forward_refs() -TimeSeriesControlDescription.update_forward_refs() -TimeSeriesControlDescriptionArray.update_forward_refs() -TimeSeriesSync.update_forward_refs() -VectorDataArray.update_forward_refs() -VectorIndexArray.update_forward_refs() -ElementIdentifiersArray.update_forward_refs() -DynamicTableRegionArray.update_forward_refs() -DynamicTableIdArray.update_forward_refs() -Data.update_forward_refs() -NWBData.update_forward_refs() -Image.update_forward_refs() -ImageReferences.update_forward_refs() -ImagesOrderOfImages.update_forward_refs() -VectorData.update_forward_refs() -TimeIntervalsStartTime.update_forward_refs() -TimeIntervalsStopTime.update_forward_refs() -TimeIntervalsTags.update_forward_refs() -TimeSeriesReferenceVectorData.update_forward_refs() -TimeIntervalsTimeseries.update_forward_refs() -VectorIndex.update_forward_refs() -TimeIntervalsTagsIndex.update_forward_refs() -TimeIntervalsTimeseriesIndex.update_forward_refs() -ElementIdentifiers.update_forward_refs() -DynamicTableRegion.update_forward_refs() -DynamicTableId.update_forward_refs() -Container.update_forward_refs() -NWBContainer.update_forward_refs() -NWBDataInterface.update_forward_refs() -TimeSeries.update_forward_refs() -ProcessingModule.update_forward_refs() -Images.update_forward_refs() -DynamicTable.update_forward_refs() -TimeIntervals.update_forward_refs() -AlignedDynamicTable.update_forward_refs() -SimpleMultiContainer.update_forward_refs() diff --git a/nwb_linkml/models/core.nwb.file.py b/nwb_linkml/models/core.nwb.file.py deleted file mode 100644 index ce352ef..0000000 --- a/nwb_linkml/models/core.nwb.file.py +++ /dev/null @@ -1,3431 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): - pass - - -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - -class NWBFileFileCreateDate(ConfiguredBaseModel): - """ - A record of the date the file was created and of subsequent modifications. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted strings: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in \"Z\" with no timezone offset. Date accuracy is up to milliseconds. The file can be created after the experiment was run, so this may differ from the experiment start time. Each modification to the nwb file adds a new entry to the array. - """ - array: Optional[NWBFileFileCreateDateArray] = Field(None) - - -class NWBFileIdentifier(ConfiguredBaseModel): - """ - A unique text identifier for the file. For example, concatenated lab name, file creation date/time and experimentalist, or a hash of these and/or other values. The goal is that the string should be unique to all other files. - """ - None - - -class NWBFileSessionDescription(ConfiguredBaseModel): - """ - A description of the experimental session and data in the file. - """ - None - - -class NWBFileSessionStartTime(ConfiguredBaseModel): - """ - Date and time of the experiment/session start. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted string: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in \"Z\" with no timezone offset. Date accuracy is up to milliseconds. - """ - None - - -class NWBFileTimestampsReferenceTime(ConfiguredBaseModel): - """ - Date and time corresponding to time zero of all timestamps. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted string: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in \"Z\" with no timezone offset. Date accuracy is up to milliseconds. All times stored in the file use this time as reference (i.e., time zero). - """ - None - - -class NWBFileAcquisition(ConfiguredBaseModel): - """ - Data streams recorded from the system, including ephys, ophys, tracking, etc. This group should be read-only after the experiment is completed and timestamps are corrected to a common timebase. The data stored here may be links to raw data stored in external NWB files. This will allow keeping bulky raw data out of the file while preserving the option of keeping some/all in the file. Acquired data includes tracking and experimental data streams (i.e., everything measured from the system). If bulky data is stored in the /acquisition group, the data can exist in a separate NWB file that is linked to by the file being used for processing and analysis. - """ - NWBDataInterface: Optional[List[NWBDataInterface]] = Field(default_factory=list, description="""Acquired, raw data.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tabular data that is relevant to acquisition""") - - -class NWBFileAnalysis(ConfiguredBaseModel): - """ - Lab-specific and custom scientific analysis of data. There is no defined format for the content of this group - the format is up to the individual user/lab. To facilitate sharing analysis data between labs, the contents here should be stored in standard types (e.g., neurodata_types) and appropriately documented. The file can store lab-specific and custom data analysis without restriction on its form or schema, reducing data formatting restrictions on end users. Such data should be placed in the analysis group. The analysis data should be documented so that it could be shared with other labs. - """ - NWBContainer: Optional[List[NWBContainer]] = Field(default_factory=list, description="""Custom analysis results.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tabular data that is relevant to data stored in analysis""") - - -class NWBFileScratch(ConfiguredBaseModel): - """ - A place to store one-off analysis results. Data placed here is not intended for sharing. By placing data here, users acknowledge that there is no guarantee that their data meets any standard. - """ - ScratchData: Optional[List[ScratchData]] = Field(default_factory=list, description="""Any one-off datasets""") - NWBContainer: Optional[List[NWBContainer]] = Field(default_factory=list, description="""Any one-off containers""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Any one-off tables""") - - -class NWBFileProcessing(ConfiguredBaseModel): - """ - The home for ProcessingModules. These modules perform intermediate analysis of data that is necessary to perform before scientific analysis. Examples include spike clustering, extracting position from tracking data, stitching together image slices. ProcessingModules can be large and express many data sets from relatively complex analysis (e.g., spike detection and clustering) or small, representing extraction of position information from tracking video, or even binary lick/no-lick decisions. Common software tools (e.g., klustakwik, MClust) are expected to read/write data here. 'Processing' refers to intermediate analysis of the acquired data to make it more amenable to scientific analysis. - """ - ProcessingModule: Optional[List[ProcessingModule]] = Field(default_factory=list, description="""Intermediate analysis of acquired data.""") - - -class NWBFileStimulus(ConfiguredBaseModel): - """ - Data pushed into the system (eg, video stimulus, sound, voltage, etc) and secondary representations of that data (eg, measurements of something used as a stimulus). This group should be made read-only after experiment complete and timestamps are corrected to common timebase. Stores both presented stimuli and stimulus templates, the latter in case the same stimulus is presented multiple times, or is pulled from an external stimulus library. Stimuli are here defined as any signal that is pushed into the system as part of the experiment (eg, sound, video, voltage, etc). Many different experiments can use the same stimuli, and stimuli can be re-used during an experiment. The stimulus group is organized so that one version of template stimuli can be stored and these be used multiple times. These templates can exist in the present file or can be linked to a remote library file. - """ - presentation: NWBFileStimulusPresentation = Field(..., description="""Stimuli presented during the experiment.""") - templates: NWBFileStimulusTemplates = Field(..., description="""Template stimuli. Timestamps in templates are based on stimulus design and are relative to the beginning of the stimulus. When templates are used, the stimulus instances must convert presentation times to the experiment`s time reference frame.""") - - -class NWBFileStimulusPresentation(ConfiguredBaseModel): - """ - Stimuli presented during the experiment. - """ - TimeSeries: Optional[List[TimeSeries]] = Field(default_factory=list, description="""TimeSeries objects containing data of presented stimuli.""") - - -class NWBFileStimulusTemplates(ConfiguredBaseModel): - """ - Template stimuli. Timestamps in templates are based on stimulus design and are relative to the beginning of the stimulus. When templates are used, the stimulus instances must convert presentation times to the experiment`s time reference frame. - """ - TimeSeries: Optional[List[TimeSeries]] = Field(default_factory=list, description="""TimeSeries objects containing template data of presented stimuli.""") - Images: Optional[List[Images]] = Field(default_factory=list, description="""Images objects containing images of presented stimuli.""") - - -class NWBFileGeneral(ConfiguredBaseModel): - """ - Experimental metadata, including protocol, notes and description of hardware device(s). The metadata stored in this section should be used to describe the experiment. Metadata necessary for interpreting the data is stored with the data. General experimental metadata, including animal strain, experimental protocols, experimenter, devices, etc, are stored under 'general'. Core metadata (e.g., that required to interpret data fields) is stored with the data itself, and implicitly defined by the file specification (e.g., time is in seconds). The strategy used here for storing non-core metadata is to use free-form text fields, such as would appear in sentences or paragraphs from a Methods section. Metadata fields are text to enable them to be more general, for example to represent ranges instead of numerical values. Machine-readable metadata is stored as attributes to these free-form datasets. All entries in the below table are to be included when data is present. Unused groups (e.g., intracellular_ephys in an optophysiology experiment) should not be created unless there is data to store within them. - """ - data_collection: Optional[NWBFileGeneralDataCollection] = Field(None, description="""Notes about data collection and analysis.""") - experiment_description: Optional[NWBFileGeneralExperimentDescription] = Field(None, description="""General description of the experiment.""") - experimenter: Optional[NWBFileGeneralExperimenter] = Field(None, description="""Name of person(s) who performed the experiment. Can also specify roles of different people involved.""") - institution: Optional[NWBFileGeneralInstitution] = Field(None, description="""Institution(s) where experiment was performed.""") - keywords: Optional[NWBFileGeneralKeywords] = Field(None, description="""Terms to search over.""") - lab: Optional[NWBFileGeneralLab] = Field(None, description="""Laboratory where experiment was performed.""") - notes: Optional[NWBFileGeneralNotes] = Field(None, description="""Notes about the experiment.""") - pharmacology: Optional[NWBFileGeneralPharmacology] = Field(None, description="""Description of drugs used, including how and when they were administered. Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc.""") - protocol: Optional[NWBFileGeneralProtocol] = Field(None, description="""Experimental protocol, if applicable. e.g., include IACUC protocol number.""") - related_publications: Optional[NWBFileGeneralRelatedPublications] = Field(None, description="""Publication information. PMID, DOI, URL, etc.""") - session_id: Optional[NWBFileGeneralSessionId] = Field(None, description="""Lab-specific ID for the session.""") - slices: Optional[NWBFileGeneralSlices] = Field(None, description="""Description of slices, including information about preparation thickness, orientation, temperature, and bath solution.""") - source_script: Optional[NWBFileGeneralSourceScript] = Field(None, description="""Script file or link to public source code used to create this NWB file.""") - stimulus: Optional[NWBFileGeneralStimulus] = Field(None, description="""Notes about stimuli, such as how and where they were presented.""") - surgery: Optional[NWBFileGeneralSurgery] = Field(None, description="""Narrative description about surgery/surgeries, including date(s) and who performed surgery.""") - virus: Optional[NWBFileGeneralVirus] = Field(None, description="""Information about virus(es) used in experiments, including virus ID, source, date made, injection location, volume, etc.""") - LabMetaData: Optional[List[LabMetaData]] = Field(default_factory=list, description="""Place-holder than can be extended so that lab-specific meta-data can be placed in /general.""") - devices: Optional[NWBFileGeneralDevices] = Field(None, description="""Description of hardware devices used during experiment, e.g., monitors, ADC boards, microscopes, etc.""") - subject: Optional[NWBFileGeneralSubject] = Field(None, description="""Information about the animal or person from which the data was measured.""") - extracellular_ephys: Optional[NWBFileGeneralExtracellularEphys] = Field(None, description="""Metadata related to extracellular electrophysiology.""") - intracellular_ephys: Optional[NWBFileGeneralIntracellularEphys] = Field(None, description="""Metadata related to intracellular electrophysiology.""") - optogenetics: Optional[NWBFileGeneralOptogenetics] = Field(None, description="""Metadata describing optogenetic stimuluation.""") - optophysiology: Optional[NWBFileGeneralOptophysiology] = Field(None, description="""Metadata related to optophysiology.""") - - -class NWBFileGeneralDataCollection(ConfiguredBaseModel): - """ - Notes about data collection and analysis. - """ - None - - -class NWBFileGeneralExperimentDescription(ConfiguredBaseModel): - """ - General description of the experiment. - """ - None - - -class NWBFileGeneralExperimenter(ConfiguredBaseModel): - """ - Name of person(s) who performed the experiment. Can also specify roles of different people involved. - """ - array: Optional[NWBFileGeneralExperimenterArray] = Field(None) - - -class NWBFileGeneralInstitution(ConfiguredBaseModel): - """ - Institution(s) where experiment was performed. - """ - None - - -class NWBFileGeneralKeywords(ConfiguredBaseModel): - """ - Terms to search over. - """ - array: Optional[NWBFileGeneralKeywordsArray] = Field(None) - - -class NWBFileGeneralLab(ConfiguredBaseModel): - """ - Laboratory where experiment was performed. - """ - None - - -class NWBFileGeneralNotes(ConfiguredBaseModel): - """ - Notes about the experiment. - """ - None - - -class NWBFileGeneralPharmacology(ConfiguredBaseModel): - """ - Description of drugs used, including how and when they were administered. Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc. - """ - None - - -class NWBFileGeneralProtocol(ConfiguredBaseModel): - """ - Experimental protocol, if applicable. e.g., include IACUC protocol number. - """ - None - - -class NWBFileGeneralRelatedPublications(ConfiguredBaseModel): - """ - Publication information. PMID, DOI, URL, etc. - """ - array: Optional[NWBFileGeneralRelatedPublicationsArray] = Field(None) - - -class NWBFileGeneralSessionId(ConfiguredBaseModel): - """ - Lab-specific ID for the session. - """ - None - - -class NWBFileGeneralSlices(ConfiguredBaseModel): - """ - Description of slices, including information about preparation thickness, orientation, temperature, and bath solution. - """ - None - - -class NWBFileGeneralSourceScript(ConfiguredBaseModel): - """ - Script file or link to public source code used to create this NWB file. - """ - file_name: Optional[str] = Field(None, description="""Name of script file.""") - - -class NWBFileGeneralStimulus(ConfiguredBaseModel): - """ - Notes about stimuli, such as how and where they were presented. - """ - None - - -class NWBFileGeneralSurgery(ConfiguredBaseModel): - """ - Narrative description about surgery/surgeries, including date(s) and who performed surgery. - """ - None - - -class NWBFileGeneralVirus(ConfiguredBaseModel): - """ - Information about virus(es) used in experiments, including virus ID, source, date made, injection location, volume, etc. - """ - None - - -class NWBFileGeneralDevices(ConfiguredBaseModel): - """ - Description of hardware devices used during experiment, e.g., monitors, ADC boards, microscopes, etc. - """ - Device: Optional[List[Device]] = Field(default_factory=list, description="""Data acquisition devices.""") - - -class NWBFileGeneralExtracellularEphys(ConfiguredBaseModel): - """ - Metadata related to extracellular electrophysiology. - """ - ElectrodeGroup: Optional[List[ElectrodeGroup]] = Field(default_factory=list, description="""Physical group of electrodes.""") - electrodes: Optional[NWBFileGeneralExtracellularEphysElectrodes] = Field(None, description="""A table of all electrodes (i.e. channels) used for recording.""") - - -class NWBFileGeneralIntracellularEphys(ConfiguredBaseModel): - """ - Metadata related to intracellular electrophysiology. - """ - filtering: Optional[NWBFileGeneralIntracellularEphysFiltering] = Field(None, description="""[DEPRECATED] Use IntracellularElectrode.filtering instead. Description of filtering used. Includes filtering type and parameters, frequency fall-off, etc. If this changes between TimeSeries, filter description should be stored as a text attribute for each TimeSeries.""") - IntracellularElectrode: Optional[List[IntracellularElectrode]] = Field(default_factory=list, description="""An intracellular electrode.""") - sweep_table: Optional[NWBFileGeneralIntracellularEphysSweepTable] = Field(None, description="""[DEPRECATED] Table used to group different PatchClampSeries. SweepTable is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable tables. Additional SequentialRecordingsTable, RepetitionsTable and ExperimentalConditions tables provide enhanced support for experiment metadata.""") - intracellular_recordings: Optional[NWBFileGeneralIntracellularEphysIntracellularRecordings] = Field(None, description="""A table to group together a stimulus and response from a single electrode and a single simultaneous recording. Each row in the table represents a single recording consisting typically of a stimulus and a corresponding response. In some cases, however, only a stimulus or a response are recorded as as part of an experiment. In this case both, the stimulus and response will point to the same TimeSeries while the idx_start and count of the invalid column will be set to -1, thus, indicating that no values have been recorded for the stimulus or response, respectively. Note, a recording MUST contain at least a stimulus or a response. Typically the stimulus and response are PatchClampSeries. However, the use of AD/DA channels that are not associated to an electrode is also common in intracellular electrophysiology, in which case other TimeSeries may be used.""") - simultaneous_recordings: Optional[NWBFileGeneralIntracellularEphysSimultaneousRecordings] = Field(None, description="""A table for grouping different intracellular recordings from the IntracellularRecordingsTable table together that were recorded simultaneously from different electrodes""") - sequential_recordings: Optional[NWBFileGeneralIntracellularEphysSequentialRecordings] = Field(None, description="""A table for grouping different sequential recordings from the SimultaneousRecordingsTable table together. This is typically used to group together sequential recordings where the a sequence of stimuli of the same type with varying parameters have been presented in a sequence.""") - repetitions: Optional[NWBFileGeneralIntracellularEphysRepetitions] = Field(None, description="""A table for grouping different sequential intracellular recordings together. With each SequentialRecording typically representing a particular type of stimulus, the RepetitionsTable table is typically used to group sets of stimuli applied in sequence.""") - experimental_conditions: Optional[NWBFileGeneralIntracellularEphysExperimentalConditions] = Field(None, description="""A table for grouping different intracellular recording repetitions together that belong to the same experimental experimental_conditions.""") - - -class NWBFileGeneralIntracellularEphysFiltering(ConfiguredBaseModel): - """ - [DEPRECATED] Use IntracellularElectrode.filtering instead. Description of filtering used. Includes filtering type and parameters, frequency fall-off, etc. If this changes between TimeSeries, filter description should be stored as a text attribute for each TimeSeries. - """ - None - - -class NWBFileGeneralOptogenetics(ConfiguredBaseModel): - """ - Metadata describing optogenetic stimuluation. - """ - OptogeneticStimulusSite: Optional[List[OptogeneticStimulusSite]] = Field(default_factory=list, description="""An optogenetic stimulation site.""") - - -class NWBFileGeneralOptophysiology(ConfiguredBaseModel): - """ - Metadata related to optophysiology. - """ - ImagingPlane: Optional[List[ImagingPlane]] = Field(default_factory=list, description="""An imaging plane.""") - - -class NWBFileIntervals(ConfiguredBaseModel): - """ - Experimental intervals, whether that be logically distinct sub-experiments having a particular scientific goal, trials (see trials subgroup) during an experiment, or epochs (see epochs subgroup) deriving from analysis of data. - """ - epochs: Optional[NWBFileIntervalsEpochs] = Field(None, description="""Divisions in time marking experimental stages or sub-divisions of a single recording session.""") - trials: Optional[NWBFileIntervalsTrials] = Field(None, description="""Repeated experimental events that have a logical grouping.""") - invalid_times: Optional[NWBFileIntervalsInvalidTimes] = Field(None, description="""Time intervals that should be removed from analysis.""") - TimeIntervals: Optional[List[TimeIntervals]] = Field(default_factory=list, description="""Optional additional table(s) for describing other experimental time intervals.""") - - -class SubjectAge(ConfiguredBaseModel): - """ - Age of subject. Can be supplied instead of 'date_of_birth'. - """ - reference: Optional[str] = Field(None, description="""Age is with reference to this event. Can be 'birth' or 'gestational'. If reference is omitted, 'birth' is implied.""") - - -class SubjectDateOfBirth(ConfiguredBaseModel): - """ - Date of birth of subject. Can be supplied instead of 'age'. - """ - None - - -class SubjectDescription(ConfiguredBaseModel): - """ - Description of subject and where subject came from (e.g., breeder, if animal). - """ - None - - -class SubjectGenotype(ConfiguredBaseModel): - """ - Genetic strain. If absent, assume Wild Type (WT). - """ - None - - -class SubjectSex(ConfiguredBaseModel): - """ - Gender of subject. - """ - None - - -class SubjectSpecies(ConfiguredBaseModel): - """ - Species of subject. - """ - None - - -class SubjectStrain(ConfiguredBaseModel): - """ - Strain of subject. - """ - None - - -class SubjectSubjectId(ConfiguredBaseModel): - """ - ID of animal/person used/participating in experiment (lab convention). - """ - None - - -class SubjectWeight(ConfiguredBaseModel): - """ - Weight at time of experiment, at time of surgery and at other important times. - """ - None - - -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - -class NWBFileFileCreateDateArray(Arraylike): - - num_modifications: date = Field(...) - - -class NWBFileGeneralExperimenterArray(Arraylike): - - num_experimenters: str = Field(...) - - -class NWBFileGeneralKeywordsArray(Arraylike): - - num_keywords: str = Field(...) - - -class NWBFileGeneralRelatedPublicationsArray(Arraylike): - - num_publications: str = Field(...) - - -class AbstractFeatureSeriesData(ConfiguredBaseModel): - """ - Values of each feature at each time. - """ - unit: Optional[str] = Field(None, description="""Since there can be different units for different features, store the units in 'feature_units'. The default value for this attribute is \"see 'feature_units'\".""") - array: Optional[AbstractFeatureSeriesDataArray] = Field(None) - - -class AbstractFeatureSeriesDataArray(Arraylike): - - num_times: float = Field(...) - num_features: Optional[float] = Field(None) - - -class AbstractFeatureSeriesFeatureUnits(ConfiguredBaseModel): - """ - Units of each feature. - """ - array: Optional[AbstractFeatureSeriesFeatureUnitsArray] = Field(None) - - -class AbstractFeatureSeriesFeatureUnitsArray(Arraylike): - - num_features: str = Field(...) - - -class AbstractFeatureSeriesFeatures(ConfiguredBaseModel): - """ - Description of the features represented in TimeSeries::data. - """ - array: Optional[AbstractFeatureSeriesFeaturesArray] = Field(None) - - -class AbstractFeatureSeriesFeaturesArray(Arraylike): - - num_features: str = Field(...) - - -class AnnotationSeriesData(ConfiguredBaseModel): - """ - Annotations made during an experiment. - """ - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data. Annotations have no units, so the value is fixed to -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Annotations have no units, so the value is fixed to 'n/a'.""") - array: Optional[AnnotationSeriesDataArray] = Field(None) - - -class AnnotationSeriesDataArray(Arraylike): - - num_times: str = Field(...) - - -class IntervalSeriesData(ConfiguredBaseModel): - """ - Use values >0 if interval started, <0 if interval ended. - """ - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data. Annotations have no units, so the value is fixed to -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Annotations have no units, so the value is fixed to 'n/a'.""") - array: Optional[IntervalSeriesDataArray] = Field(None) - - -class IntervalSeriesDataArray(Arraylike): - - num_times: int = Field(...) - - -class DecompositionSeriesData(ConfiguredBaseModel): - """ - Data decomposed into frequency bands. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion'.""") - array: Optional[DecompositionSeriesDataArray] = Field(None) - - -class DecompositionSeriesDataArray(Arraylike): - - num_times: Optional[float] = Field(None) - num_channels: Optional[float] = Field(None) - num_bands: Optional[float] = Field(None) - - -class DecompositionSeriesMetric(ConfiguredBaseModel): - """ - The metric used, e.g. phase, amplitude, power. - """ - None - - -class DecompositionSeriesBandsBandLimitsArray(Arraylike): - - num_bands: Optional[float] = Field(None) - low_high: Optional[float] = Field(None) - - -class DecompositionSeriesBandsBandMeanArray(Arraylike): - - num_bands: float = Field(...) - - -class DecompositionSeriesBandsBandStdevArray(Arraylike): - - num_bands: float = Field(...) - - -class UnitsObsIntervalsArray(Arraylike): - - num_intervals: Optional[float] = Field(None) - start|end: Optional[float] = Field(None) - - -class UnitsWaveformMeanArray(Arraylike): - - num_units: float = Field(...) - num_samples: float = Field(...) - num_electrodes: Optional[float] = Field(None) - - -class UnitsWaveformSdArray(Arraylike): - - num_units: float = Field(...) - num_samples: float = Field(...) - num_electrodes: Optional[float] = Field(None) - - -class UnitsWaveformsArray(Arraylike): - - num_waveforms: Optional[float] = Field(None) - num_samples: Optional[float] = Field(None) - - -class VectorDataArray(Arraylike): - - dim0: Any = Field(...) - dim1: Optional[Any] = Field(None) - dim2: Optional[Any] = Field(None) - dim3: Optional[Any] = Field(None) - - -class VectorIndexArray(Arraylike): - - num_rows: int = Field(...) - - -class ElementIdentifiersArray(Arraylike): - - num_elements: int = Field(...) - - -class DynamicTableRegionArray(Arraylike): - - num_rows: int = Field(...) - - -class DynamicTableIdArray(Arraylike): - - num_rows: int = Field(...) - - -class Data(ConfiguredBaseModel): - """ - An abstract data type for a dataset. - """ - None - - -class VectorData(Data): - """ - An n-dimensional dataset representing a column of a DynamicTable. If used without an accompanying VectorIndex, first dimension is along the rows of the DynamicTable and each step along the first dimension is a cell of the larger table. VectorData can also be used to represent a ragged array if paired with a VectorIndex. This allows for storing arrays of varying length in a single cell of the DynamicTable by indexing into this VectorData. The first vector is at VectorData[0:VectorIndex[0]]. The second vector is at VectorData[VectorIndex[0]:VectorIndex[1]], and so on. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesX(VectorData): - """ - x coordinate of the channel location in the brain (+x is posterior). - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesY(VectorData): - """ - y coordinate of the channel location in the brain (+y is inferior). - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesZ(VectorData): - """ - z coordinate of the channel location in the brain (+z is right). - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesImp(VectorData): - """ - Impedance of the channel, in ohms. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesLocation(VectorData): - """ - Location of the electrode (channel). Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesFiltering(VectorData): - """ - Description of hardware filtering, including the filter name and frequency cutoffs. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesGroup(VectorData): - """ - Reference to the ElectrodeGroup this electrode is a part of. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesGroupName(VectorData): - """ - Name of the ElectrodeGroup this electrode is a part of. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesRelX(VectorData): - """ - x coordinate in electrode group - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesRelY(VectorData): - """ - y coordinate in electrode group - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesRelZ(VectorData): - """ - z coordinate in electrode group - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesReference(VectorData): - """ - Description of the reference electrode and/or reference scheme used for this electrode, e.g., \"stainless steel skull screw\" or \"online common average referencing\". - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class DecompositionSeriesBandsBandName(VectorData): - """ - Name of the band, e.g. theta. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class DecompositionSeriesBandsBandLimits(VectorData): - """ - Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center. - """ - array: Optional[DecompositionSeriesBandsBandLimitsArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class DecompositionSeriesBandsBandMean(VectorData): - """ - The mean Gaussian filters, in Hz. - """ - array: Optional[DecompositionSeriesBandsBandMeanArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class DecompositionSeriesBandsBandStdev(VectorData): - """ - The standard deviation of Gaussian filters, in Hz. - """ - array: Optional[DecompositionSeriesBandsBandStdevArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsSpikeTimes(VectorData): - """ - Spike times for each unit in seconds. - """ - resolution: Optional[float] = Field(None, description="""The smallest possible difference between two spike times. Usually 1 divided by the acquisition sampling rate from which spike times were extracted, but could be larger if the acquisition time series was downsampled or smaller if the acquisition time series was smoothed/interpolated and it is possible for the spike time to be between samples.""") - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class UnitsObsIntervals(VectorData): - """ - Observation intervals for each unit. - """ - array: Optional[UnitsObsIntervalsArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsElectrodeGroup(VectorData): - """ - Electrode group that each spike unit came from. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class UnitsWaveformMean(VectorData): - """ - Spike waveform mean for each spike unit. - """ - sampling_rate: Optional[float] = Field(None, description="""Sampling rate, in hertz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement. This value is fixed to 'volts'.""") - array: Optional[UnitsWaveformMeanArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsWaveformSd(VectorData): - """ - Spike waveform standard deviation for each spike unit. - """ - sampling_rate: Optional[float] = Field(None, description="""Sampling rate, in hertz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement. This value is fixed to 'volts'.""") - array: Optional[UnitsWaveformSdArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsWaveforms(VectorData): - """ - Individual waveforms for each spike on each electrode. This is a doubly indexed column. The 'waveforms_index' column indexes which waveforms in this column belong to the same spike event for a given unit, where each waveform was recorded from a different electrode. The 'waveforms_index_index' column indexes the 'waveforms_index' column to indicate which spike events belong to a given unit. For example, if the 'waveforms_index_index' column has values [2, 5, 6], then the first 2 elements of the 'waveforms_index' column correspond to the 2 spike events of the first unit, the next 3 elements of the 'waveforms_index' column correspond to the 3 spike events of the second unit, and the next 1 element of the 'waveforms_index' column corresponds to the 1 spike event of the third unit. If the 'waveforms_index' column has values [3, 6, 8, 10, 12, 13], then the first 3 elements of the 'waveforms' column contain the 3 spike waveforms that were recorded from 3 different electrodes for the first spike time of the first unit. See https://nwb-schema.readthedocs.io/en/stable/format_description.html#doubly-ragged-arrays for a graphical representation of this example. When there is only one electrode for each unit (i.e., each spike time is associated with a single waveform), then the 'waveforms_index' column will have values 1, 2, ..., N, where N is the number of spike events. The number of electrodes for each spike event should be the same within a given unit. The 'electrodes' column should be used to indicate which electrodes are associated with each unit, and the order of the waveforms within a given unit x spike event should be in the same order as the electrodes referenced in the 'electrodes' column of this table. The number of samples for each waveform must be the same. - """ - sampling_rate: Optional[float] = Field(None, description="""Sampling rate, in hertz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement. This value is fixed to 'volts'.""") - array: Optional[UnitsWaveformsArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class VectorIndex(VectorData): - """ - Used with VectorData to encode a ragged array. An array of indices into the first dimension of the target VectorData, and forming a map between the rows of a DynamicTable and the indices of the VectorData. The name of the VectorIndex is expected to be the name of the target VectorData object followed by \"_index\". - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsSpikeTimesIndex(VectorIndex): - """ - Index into the spike_times dataset. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsObsIntervalsIndex(VectorIndex): - """ - Index into the obs_intervals dataset. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsElectrodesIndex(VectorIndex): - """ - Index into electrodes. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsWaveformsIndex(VectorIndex): - """ - Index into the waveforms dataset. One value for every spike event. See 'waveforms' for more detail. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsWaveformsIndexIndex(VectorIndex): - """ - Index into the waveforms_index dataset. One value for every unit (row in the table). See 'waveforms' for more detail. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ElementIdentifiers(Data): - """ - A list of unique identifiers for values within a dataset, e.g. rows of a DynamicTable. - """ - array: Optional[ElementIdentifiersArray] = Field(None) - - -class DynamicTableRegion(VectorData): - """ - DynamicTableRegion provides a link from one table to an index or region of another. The `table` attribute is a link to another `DynamicTable`, indicating which table is referenced, and the data is int(s) indicating the row(s) (0-indexed) of the target array. `DynamicTableRegion`s can be used to associate rows with repeated meta-data without data duplication. They can also be used to create hierarchical relationships between multiple `DynamicTable`s. `DynamicTableRegion` objects may be paired with a `VectorIndex` object to create ragged references, so a single cell of a `DynamicTable` can reference many rows of another `DynamicTable`. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DecompositionSeriesSourceChannels(DynamicTableRegion): - """ - DynamicTableRegion pointer to the channels that this decomposition series was generated from. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class UnitsElectrodes(DynamicTableRegion): - """ - Electrode that each spike unit came from, specified using a DynamicTableRegion. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DynamicTableId(ElementIdentifiers): - """ - Array of unique identifiers for the rows of this dynamic table. - """ - array: Optional[DynamicTableIdArray] = Field(None) - - -class Container(ConfiguredBaseModel): - """ - An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class DynamicTable(Container): - """ - A group containing multiple datasets that are aligned on the first dimension (Currently, this requirement if left up to APIs to check and enforce). These datasets represent different columns in the table. Apart from a column that contains unique identifiers for each row, there are no other required datasets. Users are free to add any number of custom VectorData objects (columns) here. DynamicTable also supports ragged array columns, where each element can be of a different size. To add a ragged array column, use a VectorIndex type to index the corresponding VectorData type. See documentation for VectorData and VectorIndex for more details. Unlike a compound data type, which is analogous to storing an array-of-structs, a DynamicTable can be thought of as a struct-of-arrays. This provides an alternative structure to choose from when optimizing storage for anticipated access patterns. Additionally, this type provides a way of creating a table without having to define a compound type up front. Although this convenience may be attractive, users should think carefully about how data will be accessed. DynamicTable is more appropriate for column-centric access, whereas a dataset with a compound type would be more appropriate for row-centric access. Finally, data size should also be taken into account. For small tables, performance loss may be an acceptable trade-off for the flexibility of a DynamicTable. - """ - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileGeneralExtracellularEphysElectrodes(DynamicTable): - """ - A table of all electrodes (i.e. channels) used for recording. - """ - x: Optional[NWBFileGeneralExtracellularEphysElectrodesX] = Field(None, description="""x coordinate of the channel location in the brain (+x is posterior).""") - y: Optional[NWBFileGeneralExtracellularEphysElectrodesY] = Field(None, description="""y coordinate of the channel location in the brain (+y is inferior).""") - z: Optional[NWBFileGeneralExtracellularEphysElectrodesZ] = Field(None, description="""z coordinate of the channel location in the brain (+z is right).""") - imp: Optional[NWBFileGeneralExtracellularEphysElectrodesImp] = Field(None, description="""Impedance of the channel, in ohms.""") - location: NWBFileGeneralExtracellularEphysElectrodesLocation = Field(..., description="""Location of the electrode (channel). Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible.""") - filtering: Optional[NWBFileGeneralExtracellularEphysElectrodesFiltering] = Field(None, description="""Description of hardware filtering, including the filter name and frequency cutoffs.""") - group: NWBFileGeneralExtracellularEphysElectrodesGroup = Field(..., description="""Reference to the ElectrodeGroup this electrode is a part of.""") - group_name: NWBFileGeneralExtracellularEphysElectrodesGroupName = Field(..., description="""Name of the ElectrodeGroup this electrode is a part of.""") - rel_x: Optional[NWBFileGeneralExtracellularEphysElectrodesRelX] = Field(None, description="""x coordinate in electrode group""") - rel_y: Optional[NWBFileGeneralExtracellularEphysElectrodesRelY] = Field(None, description="""y coordinate in electrode group""") - rel_z: Optional[NWBFileGeneralExtracellularEphysElectrodesRelZ] = Field(None, description="""z coordinate in electrode group""") - reference: Optional[NWBFileGeneralExtracellularEphysElectrodesReference] = Field(None, description="""Description of the reference electrode and/or reference scheme used for this electrode, e.g., \"stainless steel skull screw\" or \"online common average referencing\".""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class DecompositionSeriesBands(DynamicTable): - """ - Table for describing the bands that this series was generated from. There should be one row in this table for each band. - """ - band_name: DecompositionSeriesBandsBandName = Field(..., description="""Name of the band, e.g. theta.""") - band_limits: DecompositionSeriesBandsBandLimits = Field(..., description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""") - band_mean: DecompositionSeriesBandsBandMean = Field(..., description="""The mean Gaussian filters, in Hz.""") - band_stdev: DecompositionSeriesBandsBandStdev = Field(..., description="""The standard deviation of Gaussian filters, in Hz.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class Units(DynamicTable): - """ - Data about spiking units. Event times of observed units (e.g. cell, synapse, etc.) should be concatenated and stored in spike_times. - """ - spike_times_index: Optional[UnitsSpikeTimesIndex] = Field(None, description="""Index into the spike_times dataset.""") - spike_times: Optional[UnitsSpikeTimes] = Field(None, description="""Spike times for each unit in seconds.""") - obs_intervals_index: Optional[UnitsObsIntervalsIndex] = Field(None, description="""Index into the obs_intervals dataset.""") - obs_intervals: Optional[UnitsObsIntervals] = Field(None, description="""Observation intervals for each unit.""") - electrodes_index: Optional[UnitsElectrodesIndex] = Field(None, description="""Index into electrodes.""") - electrodes: Optional[UnitsElectrodes] = Field(None, description="""Electrode that each spike unit came from, specified using a DynamicTableRegion.""") - electrode_group: Optional[UnitsElectrodeGroup] = Field(None, description="""Electrode group that each spike unit came from.""") - waveform_mean: Optional[UnitsWaveformMean] = Field(None, description="""Spike waveform mean for each spike unit.""") - waveform_sd: Optional[UnitsWaveformSd] = Field(None, description="""Spike waveform standard deviation for each spike unit.""") - waveforms: Optional[UnitsWaveforms] = Field(None, description="""Individual waveforms for each spike on each electrode. This is a doubly indexed column. The 'waveforms_index' column indexes which waveforms in this column belong to the same spike event for a given unit, where each waveform was recorded from a different electrode. The 'waveforms_index_index' column indexes the 'waveforms_index' column to indicate which spike events belong to a given unit. For example, if the 'waveforms_index_index' column has values [2, 5, 6], then the first 2 elements of the 'waveforms_index' column correspond to the 2 spike events of the first unit, the next 3 elements of the 'waveforms_index' column correspond to the 3 spike events of the second unit, and the next 1 element of the 'waveforms_index' column corresponds to the 1 spike event of the third unit. If the 'waveforms_index' column has values [3, 6, 8, 10, 12, 13], then the first 3 elements of the 'waveforms' column contain the 3 spike waveforms that were recorded from 3 different electrodes for the first spike time of the first unit. See https://nwb-schema.readthedocs.io/en/stable/format_description.html#doubly-ragged-arrays for a graphical representation of this example. When there is only one electrode for each unit (i.e., each spike time is associated with a single waveform), then the 'waveforms_index' column will have values 1, 2, ..., N, where N is the number of spike events. The number of electrodes for each spike event should be the same within a given unit. The 'electrodes' column should be used to indicate which electrodes are associated with each unit, and the order of the waveforms within a given unit x spike event should be in the same order as the electrodes referenced in the 'electrodes' column of this table. The number of samples for each waveform must be the same.""") - waveforms_index: Optional[UnitsWaveformsIndex] = Field(None, description="""Index into the waveforms dataset. One value for every spike event. See 'waveforms' for more detail.""") - waveforms_index_index: Optional[UnitsWaveformsIndexIndex] = Field(None, description="""Index into the waveforms_index dataset. One value for every unit (row in the table). See 'waveforms' for more detail.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileUnits(Units): - """ - Data about sorted spike units. - """ - spike_times_index: Optional[UnitsSpikeTimesIndex] = Field(None, description="""Index into the spike_times dataset.""") - spike_times: Optional[UnitsSpikeTimes] = Field(None, description="""Spike times for each unit in seconds.""") - obs_intervals_index: Optional[UnitsObsIntervalsIndex] = Field(None, description="""Index into the obs_intervals dataset.""") - obs_intervals: Optional[UnitsObsIntervals] = Field(None, description="""Observation intervals for each unit.""") - electrodes_index: Optional[UnitsElectrodesIndex] = Field(None, description="""Index into electrodes.""") - electrodes: Optional[UnitsElectrodes] = Field(None, description="""Electrode that each spike unit came from, specified using a DynamicTableRegion.""") - electrode_group: Optional[UnitsElectrodeGroup] = Field(None, description="""Electrode group that each spike unit came from.""") - waveform_mean: Optional[UnitsWaveformMean] = Field(None, description="""Spike waveform mean for each spike unit.""") - waveform_sd: Optional[UnitsWaveformSd] = Field(None, description="""Spike waveform standard deviation for each spike unit.""") - waveforms: Optional[UnitsWaveforms] = Field(None, description="""Individual waveforms for each spike on each electrode. This is a doubly indexed column. The 'waveforms_index' column indexes which waveforms in this column belong to the same spike event for a given unit, where each waveform was recorded from a different electrode. The 'waveforms_index_index' column indexes the 'waveforms_index' column to indicate which spike events belong to a given unit. For example, if the 'waveforms_index_index' column has values [2, 5, 6], then the first 2 elements of the 'waveforms_index' column correspond to the 2 spike events of the first unit, the next 3 elements of the 'waveforms_index' column correspond to the 3 spike events of the second unit, and the next 1 element of the 'waveforms_index' column corresponds to the 1 spike event of the third unit. If the 'waveforms_index' column has values [3, 6, 8, 10, 12, 13], then the first 3 elements of the 'waveforms' column contain the 3 spike waveforms that were recorded from 3 different electrodes for the first spike time of the first unit. See https://nwb-schema.readthedocs.io/en/stable/format_description.html#doubly-ragged-arrays for a graphical representation of this example. When there is only one electrode for each unit (i.e., each spike time is associated with a single waveform), then the 'waveforms_index' column will have values 1, 2, ..., N, where N is the number of spike events. The number of electrodes for each spike event should be the same within a given unit. The 'electrodes' column should be used to indicate which electrodes are associated with each unit, and the order of the waveforms within a given unit x spike event should be in the same order as the electrodes referenced in the 'electrodes' column of this table. The number of samples for each waveform must be the same.""") - waveforms_index: Optional[UnitsWaveformsIndex] = Field(None, description="""Index into the waveforms dataset. One value for every spike event. See 'waveforms' for more detail.""") - waveforms_index_index: Optional[UnitsWaveformsIndexIndex] = Field(None, description="""Index into the waveforms_index dataset. One value for every unit (row in the table). See 'waveforms' for more detail.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class AlignedDynamicTable(DynamicTable): - """ - DynamicTable container that supports storing a collection of sub-tables. Each sub-table is a DynamicTable itself that is aligned with the main table by row index. I.e., all DynamicTables stored in this group MUST have the same number of rows. This type effectively defines a 2-level table in which the main data is stored in the main table implemented by this type and additional columns of the table are grouped into categories, with each category being represented by a separate DynamicTable stored within the group. - """ - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimpleMultiContainer(Container): - """ - A simple Container for holding onto multiple containers. - """ - Data: Optional[List[Data]] = Field(default_factory=list, description="""Data objects held within this SimpleMultiContainer.""") - Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") - - -class NWBData(Data): - """ - An abstract data type for a dataset. - """ - None - - -class ScratchData(NWBData): - """ - Any one-off datasets - """ - notes: Optional[str] = Field(None, description="""Any notes the user has about the dataset being stored""") - - -class TimeSeriesReferenceVectorData(VectorData): - """ - Column storing references to a TimeSeries (rows). For each TimeSeries this VectorData column stores the start_index and count to indicate the range in time to be selected as well as an object reference to the TimeSeries. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class Image(NWBData): - """ - An abstract data type for an image. Shape can be 2-D (x, y), or 3-D where the third dimension can have three or four elements, e.g. (x, y, (r, g, b)) or (x, y, (r, g, b, a)). - """ - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - array: Optional[ImageArray] = Field(None) - - -class ImageArray(Arraylike): - - x: float = Field(...) - y: float = Field(...) - r_g_b: Optional[float] = Field(None) - r_g_b_a: Optional[float] = Field(None) - - -class ImageReferences(NWBData): - """ - Ordered dataset of references to Image objects. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class ImageReferencesArray(Arraylike): - - num_images: Image = Field(...) - - -class NWBContainer(Container): - """ - An abstract data type for a generic container storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class NWBFile(NWBContainer): - """ - An NWB file storing cellular-based neurophysiology data from a single experimental session. - """ - nwb_version: Optional[str] = Field(None, description="""File version string. Use semantic versioning, e.g. 1.2.1. This will be the name of the format with trailing major, minor and patch numbers.""") - file_create_date: NWBFileFileCreateDate = Field(..., description="""A record of the date the file was created and of subsequent modifications. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted strings: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in \"Z\" with no timezone offset. Date accuracy is up to milliseconds. The file can be created after the experiment was run, so this may differ from the experiment start time. Each modification to the nwb file adds a new entry to the array.""") - identifier: NWBFileIdentifier = Field(..., description="""A unique text identifier for the file. For example, concatenated lab name, file creation date/time and experimentalist, or a hash of these and/or other values. The goal is that the string should be unique to all other files.""") - session_description: NWBFileSessionDescription = Field(..., description="""A description of the experimental session and data in the file.""") - session_start_time: NWBFileSessionStartTime = Field(..., description="""Date and time of the experiment/session start. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted string: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in \"Z\" with no timezone offset. Date accuracy is up to milliseconds.""") - timestamps_reference_time: NWBFileTimestampsReferenceTime = Field(..., description="""Date and time corresponding to time zero of all timestamps. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted string: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in \"Z\" with no timezone offset. Date accuracy is up to milliseconds. All times stored in the file use this time as reference (i.e., time zero).""") - acquisition: NWBFileAcquisition = Field(..., description="""Data streams recorded from the system, including ephys, ophys, tracking, etc. This group should be read-only after the experiment is completed and timestamps are corrected to a common timebase. The data stored here may be links to raw data stored in external NWB files. This will allow keeping bulky raw data out of the file while preserving the option of keeping some/all in the file. Acquired data includes tracking and experimental data streams (i.e., everything measured from the system). If bulky data is stored in the /acquisition group, the data can exist in a separate NWB file that is linked to by the file being used for processing and analysis.""") - analysis: NWBFileAnalysis = Field(..., description="""Lab-specific and custom scientific analysis of data. There is no defined format for the content of this group - the format is up to the individual user/lab. To facilitate sharing analysis data between labs, the contents here should be stored in standard types (e.g., neurodata_types) and appropriately documented. The file can store lab-specific and custom data analysis without restriction on its form or schema, reducing data formatting restrictions on end users. Such data should be placed in the analysis group. The analysis data should be documented so that it could be shared with other labs.""") - scratch: Optional[NWBFileScratch] = Field(None, description="""A place to store one-off analysis results. Data placed here is not intended for sharing. By placing data here, users acknowledge that there is no guarantee that their data meets any standard.""") - processing: NWBFileProcessing = Field(..., description="""The home for ProcessingModules. These modules perform intermediate analysis of data that is necessary to perform before scientific analysis. Examples include spike clustering, extracting position from tracking data, stitching together image slices. ProcessingModules can be large and express many data sets from relatively complex analysis (e.g., spike detection and clustering) or small, representing extraction of position information from tracking video, or even binary lick/no-lick decisions. Common software tools (e.g., klustakwik, MClust) are expected to read/write data here. 'Processing' refers to intermediate analysis of the acquired data to make it more amenable to scientific analysis.""") - stimulus: NWBFileStimulus = Field(..., description="""Data pushed into the system (eg, video stimulus, sound, voltage, etc) and secondary representations of that data (eg, measurements of something used as a stimulus). This group should be made read-only after experiment complete and timestamps are corrected to common timebase. Stores both presented stimuli and stimulus templates, the latter in case the same stimulus is presented multiple times, or is pulled from an external stimulus library. Stimuli are here defined as any signal that is pushed into the system as part of the experiment (eg, sound, video, voltage, etc). Many different experiments can use the same stimuli, and stimuli can be re-used during an experiment. The stimulus group is organized so that one version of template stimuli can be stored and these be used multiple times. These templates can exist in the present file or can be linked to a remote library file.""") - general: NWBFileGeneral = Field(..., description="""Experimental metadata, including protocol, notes and description of hardware device(s). The metadata stored in this section should be used to describe the experiment. Metadata necessary for interpreting the data is stored with the data. General experimental metadata, including animal strain, experimental protocols, experimenter, devices, etc, are stored under 'general'. Core metadata (e.g., that required to interpret data fields) is stored with the data itself, and implicitly defined by the file specification (e.g., time is in seconds). The strategy used here for storing non-core metadata is to use free-form text fields, such as would appear in sentences or paragraphs from a Methods section. Metadata fields are text to enable them to be more general, for example to represent ranges instead of numerical values. Machine-readable metadata is stored as attributes to these free-form datasets. All entries in the below table are to be included when data is present. Unused groups (e.g., intracellular_ephys in an optophysiology experiment) should not be created unless there is data to store within them.""") - intervals: Optional[NWBFileIntervals] = Field(None, description="""Experimental intervals, whether that be logically distinct sub-experiments having a particular scientific goal, trials (see trials subgroup) during an experiment, or epochs (see epochs subgroup) deriving from analysis of data.""") - units: Optional[NWBFileUnits] = Field(None, description="""Data about sorted spike units.""") - - -class LabMetaData(NWBContainer): - """ - Lab-specific meta-data. - """ - None - - -class Subject(NWBContainer): - """ - Information about the animal or person from which the data was measured. - """ - age: Optional[SubjectAge] = Field(None, description="""Age of subject. Can be supplied instead of 'date_of_birth'.""") - date_of_birth: Optional[SubjectDateOfBirth] = Field(None, description="""Date of birth of subject. Can be supplied instead of 'age'.""") - description: Optional[SubjectDescription] = Field(None, description="""Description of subject and where subject came from (e.g., breeder, if animal).""") - genotype: Optional[SubjectGenotype] = Field(None, description="""Genetic strain. If absent, assume Wild Type (WT).""") - sex: Optional[SubjectSex] = Field(None, description="""Gender of subject.""") - species: Optional[SubjectSpecies] = Field(None, description="""Species of subject.""") - strain: Optional[SubjectStrain] = Field(None, description="""Strain of subject.""") - subject_id: Optional[SubjectSubjectId] = Field(None, description="""ID of animal/person used/participating in experiment (lab convention).""") - weight: Optional[SubjectWeight] = Field(None, description="""Weight at time of experiment, at time of surgery and at other important times.""") - - -class NWBFileGeneralSubject(Subject): - """ - Information about the animal or person from which the data was measured. - """ - age: Optional[SubjectAge] = Field(None, description="""Age of subject. Can be supplied instead of 'date_of_birth'.""") - date_of_birth: Optional[SubjectDateOfBirth] = Field(None, description="""Date of birth of subject. Can be supplied instead of 'age'.""") - description: Optional[SubjectDescription] = Field(None, description="""Description of subject and where subject came from (e.g., breeder, if animal).""") - genotype: Optional[SubjectGenotype] = Field(None, description="""Genetic strain. If absent, assume Wild Type (WT).""") - sex: Optional[SubjectSex] = Field(None, description="""Gender of subject.""") - species: Optional[SubjectSpecies] = Field(None, description="""Species of subject.""") - strain: Optional[SubjectStrain] = Field(None, description="""Strain of subject.""") - subject_id: Optional[SubjectSubjectId] = Field(None, description="""ID of animal/person used/participating in experiment (lab convention).""") - weight: Optional[SubjectWeight] = Field(None, description="""Weight at time of experiment, at time of surgery and at other important times.""") - - -class NWBDataInterface(NWBContainer): - """ - An abstract data type for a generic container storing collections of data, as opposed to metadata. - """ - None - - -class TimeSeries(NWBDataInterface): - """ - General purpose time series. - """ - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - data: TimeSeriesData = Field(..., description="""Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class AbstractFeatureSeries(TimeSeries): - """ - Abstract features, such as quantitative descriptions of sensory stimuli. The TimeSeries::data field is a 2D array, storing those features (e.g., for visual grating stimulus this might be orientation, spatial frequency and contrast). Null stimuli (eg, uniform gray) can be marked as being an independent feature (eg, 1.0 for gray, 0.0 for actual stimulus) or by storing NaNs for feature values, or through use of the TimeSeries::control fields. A set of features is considered to persist until the next set of features is defined. The final set of features stored should be the null set. This is useful when storing the raw stimulus is impractical. - """ - data: AbstractFeatureSeriesData = Field(..., description="""Values of each feature at each time.""") - feature_units: Optional[AbstractFeatureSeriesFeatureUnits] = Field(None, description="""Units of each feature.""") - features: AbstractFeatureSeriesFeatures = Field(..., description="""Description of the features represented in TimeSeries::data.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class AnnotationSeries(TimeSeries): - """ - Stores user annotations made during an experiment. The data[] field stores a text array, and timestamps are stored for each annotation (ie, interval=1). This is largely an alias to a standard TimeSeries storing a text array but that is identifiable as storing annotations in a machine-readable way. - """ - data: AnnotationSeriesData = Field(..., description="""Annotations made during an experiment.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class IntervalSeries(TimeSeries): - """ - Stores intervals of data. The timestamps field stores the beginning and end of intervals. The data field stores whether the interval just started (>0 value) or ended (<0 value). Different interval types can be represented in the same series by using multiple key values (eg, 1 for feature A, 2 for feature B, 3 for feature C, etc). The field data stores an 8-bit integer. This is largely an alias of a standard TimeSeries but that is identifiable as representing time intervals in a machine-readable way. - """ - data: IntervalSeriesData = Field(..., description="""Use values >0 if interval started, <0 if interval ended.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class DecompositionSeries(TimeSeries): - """ - Spectral analysis of a time series, e.g. of an LFP or a speech signal. - """ - data: DecompositionSeriesData = Field(..., description="""Data decomposed into frequency bands.""") - metric: DecompositionSeriesMetric = Field(..., description="""The metric used, e.g. phase, amplitude, power.""") - source_channels: Optional[DecompositionSeriesSourceChannels] = Field(None, description="""DynamicTableRegion pointer to the channels that this decomposition series was generated from.""") - bands: DecompositionSeriesBands = Field(..., description="""Table for describing the bands that this series was generated from. There should be one row in this table for each band.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class TimeSeriesData(ConfiguredBaseModel): - """ - Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file. - """ - conversion: Optional[float] = Field(None, description="""Scalar to multiply each element in data to convert it to the specified 'unit'. If the data are stored in acquisition system units or other units that require a conversion to be interpretable, multiply the data by 'conversion' to convert the data to the specified 'unit'. e.g. if the data acquisition system stores values in this object as signed 16-bit integers (int16 range -32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data acquisition system gain is 8000X, then the 'conversion' multiplier to get from raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9.""") - offset: Optional[float] = Field(None, description="""Scalar to add to the data after scaling by 'conversion' to finalize its coercion to the specified 'unit'. Two common examples of this include (a) data stored in an unsigned type that requires a shift after scaling to re-center the data, and (b) specialized recording devices that naturally cause a scalar offset with respect to the true units.""") - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data, stored in the specified by unit, e.g., the change in value of the least significant bit, or a larger number if signal noise is known to be present. If unknown, use -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - continuity: Optional[str] = Field(None, description="""Optionally describe the continuity of the data. Can be \"continuous\", \"instantaneous\", or \"step\". For example, a voltage trace would be \"continuous\", because samples are recorded from a continuous process. An array of lick times would be \"instantaneous\", because the data represents distinct moments in time. Times of image presentations would be \"step\" because the picture remains the same until the next timepoint. This field is optional, but is useful in providing information about the underlying data. It may inform the way this data is interpreted, the way it is visualized, and what analysis methods are applicable.""") - array: Optional[TimeSeriesDataArray] = Field(None) - - -class TimeSeriesDataArray(Arraylike): - - num_times: Any = Field(...) - num_DIM2: Optional[Any] = Field(None) - num_DIM3: Optional[Any] = Field(None) - num_DIM4: Optional[Any] = Field(None) - - -class TimeSeriesStartingTime(ConfiguredBaseModel): - """ - Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute. - """ - rate: Optional[float] = Field(None, description="""Sampling rate, in Hz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement for time, which is fixed to 'seconds'.""") - - -class TimeSeriesTimestamps(ConfiguredBaseModel): - """ - Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. - """ - interval: Optional[int] = Field(None, description="""Value is '1'""") - unit: Optional[str] = Field(None, description="""Unit of measurement for timestamps, which is fixed to 'seconds'.""") - array: Optional[TimeSeriesTimestampsArray] = Field(None) - - -class TimeSeriesTimestampsArray(Arraylike): - - num_times: float = Field(...) - - -class TimeSeriesControl(ConfiguredBaseModel): - """ - Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data. - """ - array: Optional[TimeSeriesControlArray] = Field(None) - - -class TimeSeriesControlArray(Arraylike): - - num_times: int = Field(...) - - -class TimeSeriesControlDescription(ConfiguredBaseModel): - """ - Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0. - """ - array: Optional[TimeSeriesControlDescriptionArray] = Field(None) - - -class TimeSeriesControlDescriptionArray(Arraylike): - - num_control_values: str = Field(...) - - -class TimeSeriesSync(ConfiguredBaseModel): - """ - Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes. - """ - None - - -class ProcessingModule(NWBContainer): - """ - A collection of processed data. - """ - description: Optional[str] = Field(None, description="""Description of this collection of processed data.""") - NWBDataInterface: Optional[List[NWBDataInterface]] = Field(default_factory=list, description="""Data objects stored in this collection.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tables stored in this collection.""") - - -class Images(NWBDataInterface): - """ - A collection of images with an optional way to specify the order of the images using the \"order_of_images\" dataset. An order must be specified if the images are referenced by index, e.g., from an IndexSeries. - """ - description: Optional[str] = Field(None, description="""Description of this collection of images.""") - Image: List[Image] = Field(default_factory=list, description="""Images stored in this collection.""") - order_of_images: Optional[ImagesOrderOfImages] = Field(None, description="""Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images.""") - - -class ImagesOrderOfImages(ImageReferences): - """ - Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class TimeIntervals(DynamicTable): - """ - A container for aggregating epoch data and the TimeSeries that each epoch applies to. - """ - start_time: TimeIntervalsStartTime = Field(..., description="""Start time of epoch, in seconds.""") - stop_time: TimeIntervalsStopTime = Field(..., description="""Stop time of epoch, in seconds.""") - tags: Optional[TimeIntervalsTags] = Field(None, description="""User-defined tags that identify or categorize events.""") - tags_index: Optional[TimeIntervalsTagsIndex] = Field(None, description="""Index for tags.""") - timeseries: Optional[TimeIntervalsTimeseries] = Field(None, description="""An index into a TimeSeries object.""") - timeseries_index: Optional[TimeIntervalsTimeseriesIndex] = Field(None, description="""Index for timeseries.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileIntervalsEpochs(TimeIntervals): - """ - Divisions in time marking experimental stages or sub-divisions of a single recording session. - """ - start_time: TimeIntervalsStartTime = Field(..., description="""Start time of epoch, in seconds.""") - stop_time: TimeIntervalsStopTime = Field(..., description="""Stop time of epoch, in seconds.""") - tags: Optional[TimeIntervalsTags] = Field(None, description="""User-defined tags that identify or categorize events.""") - tags_index: Optional[TimeIntervalsTagsIndex] = Field(None, description="""Index for tags.""") - timeseries: Optional[TimeIntervalsTimeseries] = Field(None, description="""An index into a TimeSeries object.""") - timeseries_index: Optional[TimeIntervalsTimeseriesIndex] = Field(None, description="""Index for timeseries.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileIntervalsTrials(TimeIntervals): - """ - Repeated experimental events that have a logical grouping. - """ - start_time: TimeIntervalsStartTime = Field(..., description="""Start time of epoch, in seconds.""") - stop_time: TimeIntervalsStopTime = Field(..., description="""Stop time of epoch, in seconds.""") - tags: Optional[TimeIntervalsTags] = Field(None, description="""User-defined tags that identify or categorize events.""") - tags_index: Optional[TimeIntervalsTagsIndex] = Field(None, description="""Index for tags.""") - timeseries: Optional[TimeIntervalsTimeseries] = Field(None, description="""An index into a TimeSeries object.""") - timeseries_index: Optional[TimeIntervalsTimeseriesIndex] = Field(None, description="""Index for timeseries.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileIntervalsInvalidTimes(TimeIntervals): - """ - Time intervals that should be removed from analysis. - """ - start_time: TimeIntervalsStartTime = Field(..., description="""Start time of epoch, in seconds.""") - stop_time: TimeIntervalsStopTime = Field(..., description="""Stop time of epoch, in seconds.""") - tags: Optional[TimeIntervalsTags] = Field(None, description="""User-defined tags that identify or categorize events.""") - tags_index: Optional[TimeIntervalsTagsIndex] = Field(None, description="""Index for tags.""") - timeseries: Optional[TimeIntervalsTimeseries] = Field(None, description="""An index into a TimeSeries object.""") - timeseries_index: Optional[TimeIntervalsTimeseriesIndex] = Field(None, description="""Index for timeseries.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class TimeIntervalsStartTime(VectorData): - """ - Start time of epoch, in seconds. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class TimeIntervalsStopTime(VectorData): - """ - Stop time of epoch, in seconds. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class TimeIntervalsTags(VectorData): - """ - User-defined tags that identify or categorize events. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class TimeIntervalsTagsIndex(VectorIndex): - """ - Index for tags. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class TimeIntervalsTimeseries(TimeSeriesReferenceVectorData): - """ - An index into a TimeSeries object. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class TimeIntervalsTimeseriesIndex(VectorIndex): - """ - Index for timeseries. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class TwoPhotonSeriesFieldOfView(ConfiguredBaseModel): - """ - Width, height and depth of image, or imaged area, in meters. - """ - array: Optional[TwoPhotonSeriesFieldOfViewArray] = Field(None) - - -class TwoPhotonSeriesFieldOfViewArray(Arraylike): - - width|height: Optional[float] = Field(None) - width|height|depth: Optional[float] = Field(None) - - -class RoiResponseSeries(TimeSeries): - """ - ROI responses over an imaging plane. The first dimension represents time. The second dimension, if present, represents ROIs. - """ - data: RoiResponseSeriesData = Field(..., description="""Signals from ROIs.""") - rois: RoiResponseSeriesRois = Field(..., description="""DynamicTableRegion referencing into an ROITable containing information on the ROIs stored in this timeseries.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class RoiResponseSeriesData(ConfiguredBaseModel): - """ - Signals from ROIs. - """ - array: Optional[RoiResponseSeriesDataArray] = Field(None) - - -class RoiResponseSeriesDataArray(Arraylike): - - num_times: float = Field(...) - num_ROIs: Optional[float] = Field(None) - - -class RoiResponseSeriesRois(DynamicTableRegion): - """ - DynamicTableRegion referencing into an ROITable containing information on the ROIs stored in this timeseries. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DfOverF(NWBDataInterface): - """ - dF/F information about a region of interest (ROI). Storage hierarchy of dF/F should be the same as for segmentation (i.e., same names for ROIs and for image planes). - """ - RoiResponseSeries: List[RoiResponseSeries] = Field(default_factory=list, description="""RoiResponseSeries object(s) containing dF/F for a ROI.""") - - -class Fluorescence(NWBDataInterface): - """ - Fluorescence information about a region of interest (ROI). Storage hierarchy of fluorescence should be the same as for segmentation (ie, same names for ROIs and for image planes). - """ - RoiResponseSeries: List[RoiResponseSeries] = Field(default_factory=list, description="""RoiResponseSeries object(s) containing fluorescence data for a ROI.""") - - -class ImageSegmentation(NWBDataInterface): - """ - Stores pixels in an image that represent different regions of interest (ROIs) or masks. All segmentation for a given imaging plane is stored together, with storage for multiple imaging planes (masks) supported. Each ROI is stored in its own subgroup, with the ROI group containing both a 2D mask and a list of pixels that make up this mask. Segments can also be used for masking neuropil. If segmentation is allowed to change with time, a new imaging plane (or module) is required and ROI names should remain consistent between them. - """ - PlaneSegmentation: List[PlaneSegmentation] = Field(default_factory=list, description="""Results from image segmentation of a specific imaging plane.""") - - -class PlaneSegmentation(DynamicTable): - """ - Results from image segmentation of a specific imaging plane. - """ - image_mask: Optional[PlaneSegmentationImageMask] = Field(None, description="""ROI masks for each ROI. Each image mask is the size of the original imaging plane (or volume) and members of the ROI are finite non-zero.""") - pixel_mask_index: Optional[PlaneSegmentationPixelMaskIndex] = Field(None, description="""Index into pixel_mask.""") - pixel_mask: Optional[PlaneSegmentationPixelMask] = Field(None, description="""Pixel masks for each ROI: a list of indices and weights for the ROI. Pixel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation""") - voxel_mask_index: Optional[PlaneSegmentationVoxelMaskIndex] = Field(None, description="""Index into voxel_mask.""") - voxel_mask: Optional[PlaneSegmentationVoxelMask] = Field(None, description="""Voxel masks for each ROI: a list of indices and weights for the ROI. Voxel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation""") - reference_images: PlaneSegmentationReferenceImages = Field(..., description="""Image stacks that the segmentation masks apply to.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class PlaneSegmentationImageMask(VectorData): - """ - ROI masks for each ROI. Each image mask is the size of the original imaging plane (or volume) and members of the ROI are finite non-zero. - """ - array: Optional[PlaneSegmentationImageMaskArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class PlaneSegmentationImageMaskArray(Arraylike): - - num_roi: Any = Field(...) - num_x: Any = Field(...) - num_y: Any = Field(...) - num_z: Optional[Any] = Field(None) - - -class PlaneSegmentationPixelMaskIndex(VectorIndex): - """ - Index into pixel_mask. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class PlaneSegmentationPixelMask(VectorData): - """ - Pixel masks for each ROI: a list of indices and weights for the ROI. Pixel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class PlaneSegmentationVoxelMaskIndex(VectorIndex): - """ - Index into voxel_mask. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class PlaneSegmentationVoxelMask(VectorData): - """ - Voxel masks for each ROI: a list of indices and weights for the ROI. Voxel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class PlaneSegmentationReferenceImages(ConfiguredBaseModel): - """ - Image stacks that the segmentation masks apply to. - """ - ImageSeries: Optional[List[ImageSeries]] = Field(default_factory=list, description="""One or more image stacks that the masks apply to (can be one-element stack).""") - - -class ImagingPlane(NWBContainer): - """ - An imaging plane and its metadata. - """ - description: Optional[ImagingPlaneDescription] = Field(None, description="""Description of the imaging plane.""") - excitation_lambda: ImagingPlaneExcitationLambda = Field(..., description="""Excitation wavelength, in nm.""") - imaging_rate: Optional[ImagingPlaneImagingRate] = Field(None, description="""Rate that images are acquired, in Hz. If the corresponding TimeSeries is present, the rate should be stored there instead.""") - indicator: ImagingPlaneIndicator = Field(..., description="""Calcium indicator.""") - location: ImagingPlaneLocation = Field(..., description="""Location of the imaging plane. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible.""") - manifold: Optional[ImagingPlaneManifold] = Field(None, description="""DEPRECATED Physical position of each pixel. 'xyz' represents the position of the pixel relative to the defined coordinate space. Deprecated in favor of origin_coords and grid_spacing.""") - origin_coords: Optional[ImagingPlaneOriginCoords] = Field(None, description="""Physical location of the first element of the imaging plane (0, 0) for 2-D data or (0, 0, 0) for 3-D data. See also reference_frame for what the physical location is relative to (e.g., bregma).""") - grid_spacing: Optional[ImagingPlaneGridSpacing] = Field(None, description="""Space between pixels in (x, y) or voxels in (x, y, z) directions, in the specified unit. Assumes imaging plane is a regular grid. See also reference_frame to interpret the grid.""") - reference_frame: Optional[ImagingPlaneReferenceFrame] = Field(None, description="""Describes reference frame of origin_coords and grid_spacing. For example, this can be a text description of the anatomical location and orientation of the grid defined by origin_coords and grid_spacing or the vectors needed to transform or rotate the grid to a common anatomical axis (e.g., AP/DV/ML). This field is necessary to interpret origin_coords and grid_spacing. If origin_coords and grid_spacing are not present, then this field is not required. For example, if the microscope takes 10 x 10 x 2 images, where the first value of the data matrix (index (0, 0, 0)) corresponds to (-1.2, -0.6, -2) mm relative to bregma, the spacing between pixels is 0.2 mm in x, 0.2 mm in y and 0.5 mm in z, and larger numbers in x means more anterior, larger numbers in y means more rightward, and larger numbers in z means more ventral, then enter the following -- origin_coords = (-1.2, -0.6, -2) grid_spacing = (0.2, 0.2, 0.5) reference_frame = \"Origin coordinates are relative to bregma. First dimension corresponds to anterior-posterior axis (larger index = more anterior). Second dimension corresponds to medial-lateral axis (larger index = more rightward). Third dimension corresponds to dorsal-ventral axis (larger index = more ventral).\"""") - OpticalChannel: List[OpticalChannel] = Field(default_factory=list, description="""An optical channel used to record from an imaging plane.""") - - -class ImagingPlaneDescription(ConfiguredBaseModel): - """ - Description of the imaging plane. - """ - None - - -class ImagingPlaneExcitationLambda(ConfiguredBaseModel): - """ - Excitation wavelength, in nm. - """ - None - - -class ImagingPlaneImagingRate(ConfiguredBaseModel): - """ - Rate that images are acquired, in Hz. If the corresponding TimeSeries is present, the rate should be stored there instead. - """ - None - - -class ImagingPlaneIndicator(ConfiguredBaseModel): - """ - Calcium indicator. - """ - None - - -class ImagingPlaneLocation(ConfiguredBaseModel): - """ - Location of the imaging plane. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible. - """ - None - - -class ImagingPlaneManifold(ConfiguredBaseModel): - """ - DEPRECATED Physical position of each pixel. 'xyz' represents the position of the pixel relative to the defined coordinate space. Deprecated in favor of origin_coords and grid_spacing. - """ - conversion: Optional[float] = Field(None, description="""Scalar to multiply each element in data to convert it to the specified 'unit'. If the data are stored in acquisition system units or other units that require a conversion to be interpretable, multiply the data by 'conversion' to convert the data to the specified 'unit'. e.g. if the data acquisition system stores values in this object as pixels from x = -500 to 499, y = -500 to 499 that correspond to a 2 m x 2 m range, then the 'conversion' multiplier to get from raw data acquisition pixel units to meters is 2/1000.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. The default value is 'meters'.""") - array: Optional[ImagingPlaneManifoldArray] = Field(None) - - -class ImagingPlaneManifoldArray(Arraylike): - - height: float = Field(...) - width: float = Field(...) - x_y_z: float = Field(...) - depth: Optional[float] = Field(None) - - -class ImagingPlaneOriginCoords(ConfiguredBaseModel): - """ - Physical location of the first element of the imaging plane (0, 0) for 2-D data or (0, 0, 0) for 3-D data. See also reference_frame for what the physical location is relative to (e.g., bregma). - """ - unit: Optional[str] = Field(None, description="""Measurement units for origin_coords. The default value is 'meters'.""") - array: Optional[ImagingPlaneOriginCoordsArray] = Field(None) - - -class ImagingPlaneOriginCoordsArray(Arraylike): - - x_y: Optional[float] = Field(None) - x_y_z: Optional[float] = Field(None) - - -class ImagingPlaneGridSpacing(ConfiguredBaseModel): - """ - Space between pixels in (x, y) or voxels in (x, y, z) directions, in the specified unit. Assumes imaging plane is a regular grid. See also reference_frame to interpret the grid. - """ - unit: Optional[str] = Field(None, description="""Measurement units for grid_spacing. The default value is 'meters'.""") - array: Optional[ImagingPlaneGridSpacingArray] = Field(None) - - -class ImagingPlaneGridSpacingArray(Arraylike): - - x_y: Optional[float] = Field(None) - x_y_z: Optional[float] = Field(None) - - -class ImagingPlaneReferenceFrame(ConfiguredBaseModel): - """ - Describes reference frame of origin_coords and grid_spacing. For example, this can be a text description of the anatomical location and orientation of the grid defined by origin_coords and grid_spacing or the vectors needed to transform or rotate the grid to a common anatomical axis (e.g., AP/DV/ML). This field is necessary to interpret origin_coords and grid_spacing. If origin_coords and grid_spacing are not present, then this field is not required. For example, if the microscope takes 10 x 10 x 2 images, where the first value of the data matrix (index (0, 0, 0)) corresponds to (-1.2, -0.6, -2) mm relative to bregma, the spacing between pixels is 0.2 mm in x, 0.2 mm in y and 0.5 mm in z, and larger numbers in x means more anterior, larger numbers in y means more rightward, and larger numbers in z means more ventral, then enter the following -- origin_coords = (-1.2, -0.6, -2) grid_spacing = (0.2, 0.2, 0.5) reference_frame = \"Origin coordinates are relative to bregma. First dimension corresponds to anterior-posterior axis (larger index = more anterior). Second dimension corresponds to medial-lateral axis (larger index = more rightward). Third dimension corresponds to dorsal-ventral axis (larger index = more ventral).\" - """ - None - - -class OpticalChannel(NWBContainer): - """ - An optical channel used to record from an imaging plane. - """ - description: OpticalChannelDescription = Field(..., description="""Description or other notes about the channel.""") - emission_lambda: OpticalChannelEmissionLambda = Field(..., description="""Emission wavelength for channel, in nm.""") - - -class OpticalChannelDescription(ConfiguredBaseModel): - """ - Description or other notes about the channel. - """ - None - - -class OpticalChannelEmissionLambda(ConfiguredBaseModel): - """ - Emission wavelength for channel, in nm. - """ - None - - -class MotionCorrection(NWBDataInterface): - """ - An image stack where all frames are shifted (registered) to a common coordinate system, to account for movement and drift between frames. Note: each frame at each point in time is assumed to be 2-D (has only x & y dimensions). - """ - CorrectedImageStack: List[CorrectedImageStack] = Field(default_factory=list, description="""Reuslts from motion correction of an image stack.""") - - -class CorrectedImageStack(NWBDataInterface): - """ - Reuslts from motion correction of an image stack. - """ - corrected: CorrectedImageStackCorrected = Field(..., description="""Image stack with frames shifted to the common coordinates.""") - xy_translation: CorrectedImageStackXyTranslation = Field(..., description="""Stores the x,y delta necessary to align each frame to the common coordinates, for example, to align each frame to a reference image.""") - - -class CorrectedImageStackXyTranslation(TimeSeries): - """ - Stores the x,y delta necessary to align each frame to the common coordinates, for example, to align each frame to a reference image. - """ - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - data: TimeSeriesData = Field(..., description="""Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class GrayscaleImage(Image): - """ - A grayscale image. - """ - array: Optional[GrayscaleImageArray] = Field(None) - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - - -class GrayscaleImageArray(Arraylike): - - x: Optional[float] = Field(None) - y: Optional[float] = Field(None) - - -class RGBImage(Image): - """ - A color image. - """ - array: Optional[RGBImageArray] = Field(None) - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - - -class RGBImageArray(Arraylike): - - x: Optional[float] = Field(None) - y: Optional[float] = Field(None) - r_g_b: Optional[float] = Field(None) - - -class RGBAImage(Image): - """ - A color image with transparency. - """ - array: Optional[RGBAImageArray] = Field(None) - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - - -class RGBAImageArray(Arraylike): - - x: Optional[float] = Field(None) - y: Optional[float] = Field(None) - r_g_b_a: Optional[float] = Field(None) - - -class ImageSeries(TimeSeries): - """ - General image data that is common between acquisition and stimulus time series. Sometimes the image data is stored in the file in a raw format while other times it will be stored as a series of external image files in the host file system. The data field will either be binary data, if the data is stored in the NWB file, or empty, if the data is stored in an external image stack. [frame][x][y] or [frame][x][y][z]. - """ - data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class OnePhotonSeries(ImageSeries): - """ - Image stack recorded over time from 1-photon microscope. - """ - pmt_gain: Optional[float] = Field(None, description="""Photomultiplier gain.""") - scan_line_rate: Optional[float] = Field(None, description="""Lines imaged per second. This is also stored in /general/optophysiology but is kept here as it is useful information for analysis, and so good to be stored w/ the actual data.""") - exposure_time: Optional[float] = Field(None, description="""Exposure time of the sample; often the inverse of the frequency.""") - binning: Optional[int] = Field(None, description="""Amount of pixels combined into 'bins'; could be 1, 2, 4, 8, etc.""") - power: Optional[float] = Field(None, description="""Power of the excitation in mW, if known.""") - intensity: Optional[float] = Field(None, description="""Intensity of the excitation in mW/mm^2, if known.""") - data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class TwoPhotonSeries(ImageSeries): - """ - Image stack recorded over time from 2-photon microscope. - """ - pmt_gain: Optional[float] = Field(None, description="""Photomultiplier gain.""") - scan_line_rate: Optional[float] = Field(None, description="""Lines imaged per second. This is also stored in /general/optophysiology but is kept here as it is useful information for analysis, and so good to be stored w/ the actual data.""") - field_of_view: Optional[TwoPhotonSeriesFieldOfView] = Field(None, description="""Width, height and depth of image, or imaged area, in meters.""") - data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class CorrectedImageStackCorrected(ImageSeries): - """ - Image stack with frames shifted to the common coordinates. - """ - data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class ImageSeriesData(ConfiguredBaseModel): - """ - Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array. - """ - array: Optional[ImageSeriesDataArray] = Field(None) - - -class ImageSeriesDataArray(Arraylike): - - frame: float = Field(...) - x: float = Field(...) - y: float = Field(...) - z: Optional[float] = Field(None) - - -class ImageSeriesDimension(ConfiguredBaseModel): - """ - Number of pixels on x, y, (and z) axes. - """ - array: Optional[ImageSeriesDimensionArray] = Field(None) - - -class ImageSeriesDimensionArray(Arraylike): - - rank: int = Field(...) - - -class ImageSeriesExternalFile(ConfiguredBaseModel): - """ - Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file. - """ - starting_frame: Optional[int] = Field(None, description="""Each external image may contain one or more consecutive frames of the full ImageSeries. This attribute serves as an index to indicate which frames each file contains, to facilitate random access. The 'starting_frame' attribute, hence, contains a list of frame numbers within the full ImageSeries of the first frame of each file listed in the parent 'external_file' dataset. Zero-based indexing is used (hence, the first element will always be zero). For example, if the 'external_file' dataset has three paths to files and the first file has 5 frames, the second file has 10 frames, and the third file has 20 frames, then this attribute will have values [0, 5, 15]. If there is a single external file that holds all of the frames of the ImageSeries (and so there is a single element in the 'external_file' dataset), then this attribute should have value [0].""") - array: Optional[ImageSeriesExternalFileArray] = Field(None) - - -class ImageSeriesExternalFileArray(Arraylike): - - num_files: str = Field(...) - - -class ImageSeriesFormat(ConfiguredBaseModel): - """ - Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed. - """ - None - - -class ImageMaskSeries(ImageSeries): - """ - An alpha mask that is applied to a presented visual stimulus. The 'data' array contains an array of mask values that are applied to the displayed image. Mask values are stored as RGBA. Mask can vary with time. The timestamps array indicates the starting time of a mask, and that mask pattern continues until it's explicitly changed. - """ - data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class OpticalSeries(ImageSeries): - """ - Image data that is presented or recorded. A stimulus template movie will be stored only as an image. When the image is presented as stimulus, additional data is required, such as field of view (e.g., how much of the visual field the image covers, or how what is the area of the target being imaged). If the OpticalSeries represents acquired imaging data, orientation is also important. - """ - distance: Optional[OpticalSeriesDistance] = Field(None, description="""Distance from camera/monitor to target/eye.""") - field_of_view: Optional[OpticalSeriesFieldOfView] = Field(None, description="""Width, height and depth of image, or imaged area, in meters.""") - data: OpticalSeriesData = Field(..., description="""Images presented to subject, either grayscale or RGB""") - orientation: Optional[OpticalSeriesOrientation] = Field(None, description="""Description of image relative to some reference frame (e.g., which way is up). Must also specify frame of reference.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class OpticalSeriesDistance(ConfiguredBaseModel): - """ - Distance from camera/monitor to target/eye. - """ - None - - -class OpticalSeriesFieldOfView(ConfiguredBaseModel): - """ - Width, height and depth of image, or imaged area, in meters. - """ - array: Optional[OpticalSeriesFieldOfViewArray] = Field(None) - - -class OpticalSeriesFieldOfViewArray(Arraylike): - - width_height: Optional[float] = Field(None) - width_height_depth: Optional[float] = Field(None) - - -class OpticalSeriesData(ConfiguredBaseModel): - """ - Images presented to subject, either grayscale or RGB - """ - array: Optional[OpticalSeriesDataArray] = Field(None) - - -class OpticalSeriesDataArray(Arraylike): - - frame: float = Field(...) - x: float = Field(...) - y: float = Field(...) - r_g_b: Optional[float] = Field(None) - - -class OpticalSeriesOrientation(ConfiguredBaseModel): - """ - Description of image relative to some reference frame (e.g., which way is up). Must also specify frame of reference. - """ - None - - -class IndexSeries(TimeSeries): - """ - Stores indices to image frames stored in an ImageSeries. The purpose of the IndexSeries is to allow a static image stack to be stored in an Images object, and the images in the stack to be referenced out-of-order. This can be for the display of individual images, or of movie segments (as a movie is simply a series of images). The data field stores the index of the frame in the referenced Images object, and the timestamps array indicates when that image was displayed. - """ - data: IndexSeriesData = Field(..., description="""Index of the image (using zero-indexing) in the linked Images object.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class IndexSeriesData(ConfiguredBaseModel): - """ - Index of the image (using zero-indexing) in the linked Images object. - """ - conversion: Optional[float] = Field(None, description="""This field is unused by IndexSeries.""") - resolution: Optional[float] = Field(None, description="""This field is unused by IndexSeries.""") - offset: Optional[float] = Field(None, description="""This field is unused by IndexSeries.""") - unit: Optional[str] = Field(None, description="""This field is unused by IndexSeries and has the value N/A.""") - array: Optional[IndexSeriesDataArray] = Field(None) - - -class IndexSeriesDataArray(Arraylike): - - num_times: int = Field(...) - - -class OptogeneticSeries(TimeSeries): - """ - An optogenetic stimulus. - """ - data: OptogeneticSeriesData = Field(..., description="""Applied power for optogenetic stimulus, in watts.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class OptogeneticSeriesData(ConfiguredBaseModel): - """ - Applied power for optogenetic stimulus, in watts. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for data, which is fixed to 'watts'.""") - array: Optional[OptogeneticSeriesDataArray] = Field(None) - - -class OptogeneticSeriesDataArray(Arraylike): - - num_times: float = Field(...) - - -class OptogeneticStimulusSite(NWBContainer): - """ - A site of optogenetic stimulation. - """ - description: OptogeneticStimulusSiteDescription = Field(..., description="""Description of stimulation site.""") - excitation_lambda: OptogeneticStimulusSiteExcitationLambda = Field(..., description="""Excitation wavelength, in nm.""") - location: OptogeneticStimulusSiteLocation = Field(..., description="""Location of the stimulation site. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible.""") - - -class OptogeneticStimulusSiteDescription(ConfiguredBaseModel): - """ - Description of stimulation site. - """ - None - - -class OptogeneticStimulusSiteExcitationLambda(ConfiguredBaseModel): - """ - Excitation wavelength, in nm. - """ - None - - -class OptogeneticStimulusSiteLocation(ConfiguredBaseModel): - """ - Location of the stimulation site. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible. - """ - None - - -class PatchClampSeries(TimeSeries): - """ - An abstract base class for patch-clamp data - stimulus or response, current or voltage. - """ - stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") - sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") - data: PatchClampSeriesData = Field(..., description="""Recorded voltage or current.""") - gain: Optional[PatchClampSeriesGain] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class PatchClampSeriesData(ConfiguredBaseModel): - """ - Recorded voltage or current. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - array: Optional[PatchClampSeriesDataArray] = Field(None) - - -class PatchClampSeriesDataArray(Arraylike): - - num_times: float = Field(...) - - -class PatchClampSeriesGain(ConfiguredBaseModel): - """ - Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp). - """ - None - - -class CurrentClampSeries(PatchClampSeries): - """ - Voltage data from an intracellular current-clamp recording. A corresponding CurrentClampStimulusSeries (stored separately as a stimulus) is used to store the current injected. - """ - data: CurrentClampSeriesData = Field(..., description="""Recorded voltage.""") - bias_current: Optional[CurrentClampSeriesBiasCurrent] = Field(None, description="""Bias current, in amps.""") - bridge_balance: Optional[CurrentClampSeriesBridgeBalance] = Field(None, description="""Bridge balance, in ohms.""") - capacitance_compensation: Optional[CurrentClampSeriesCapacitanceCompensation] = Field(None, description="""Capacitance compensation, in farads.""") - stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") - sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") - gain: Optional[PatchClampSeriesGain] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class CurrentClampSeriesData(ConfiguredBaseModel): - """ - Recorded voltage. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'volts'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - - -class CurrentClampSeriesBiasCurrent(ConfiguredBaseModel): - """ - Bias current, in amps. - """ - None - - -class CurrentClampSeriesBridgeBalance(ConfiguredBaseModel): - """ - Bridge balance, in ohms. - """ - None - - -class CurrentClampSeriesCapacitanceCompensation(ConfiguredBaseModel): - """ - Capacitance compensation, in farads. - """ - None - - -class IZeroClampSeries(CurrentClampSeries): - """ - Voltage data from an intracellular recording when all current and amplifier settings are off (i.e., CurrentClampSeries fields will be zero). There is no CurrentClampStimulusSeries associated with an IZero series because the amplifier is disconnected and no stimulus can reach the cell. - """ - stimulus_description: Optional[str] = Field(None, description="""An IZeroClampSeries has no stimulus, so this attribute is automatically set to \"N/A\"""") - bias_current: IZeroClampSeriesBiasCurrent = Field(..., description="""Bias current, in amps, fixed to 0.0.""") - bridge_balance: IZeroClampSeriesBridgeBalance = Field(..., description="""Bridge balance, in ohms, fixed to 0.0.""") - capacitance_compensation: IZeroClampSeriesCapacitanceCompensation = Field(..., description="""Capacitance compensation, in farads, fixed to 0.0.""") - data: CurrentClampSeriesData = Field(..., description="""Recorded voltage.""") - sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") - gain: Optional[PatchClampSeriesGain] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class IZeroClampSeriesBiasCurrent(ConfiguredBaseModel): - """ - Bias current, in amps, fixed to 0.0. - """ - None - - -class IZeroClampSeriesBridgeBalance(ConfiguredBaseModel): - """ - Bridge balance, in ohms, fixed to 0.0. - """ - None - - -class IZeroClampSeriesCapacitanceCompensation(ConfiguredBaseModel): - """ - Capacitance compensation, in farads, fixed to 0.0. - """ - None - - -class CurrentClampStimulusSeries(PatchClampSeries): - """ - Stimulus current applied during current clamp recording. - """ - data: CurrentClampStimulusSeriesData = Field(..., description="""Stimulus current applied.""") - stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") - sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") - gain: Optional[PatchClampSeriesGain] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class CurrentClampStimulusSeriesData(ConfiguredBaseModel): - """ - Stimulus current applied. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'amperes'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - - -class VoltageClampSeries(PatchClampSeries): - """ - Current data from an intracellular voltage-clamp recording. A corresponding VoltageClampStimulusSeries (stored separately as a stimulus) is used to store the voltage injected. - """ - data: VoltageClampSeriesData = Field(..., description="""Recorded current.""") - capacitance_fast: Optional[VoltageClampSeriesCapacitanceFast] = Field(None, description="""Fast capacitance, in farads.""") - capacitance_slow: Optional[VoltageClampSeriesCapacitanceSlow] = Field(None, description="""Slow capacitance, in farads.""") - resistance_comp_bandwidth: Optional[VoltageClampSeriesResistanceCompBandwidth] = Field(None, description="""Resistance compensation bandwidth, in hertz.""") - resistance_comp_correction: Optional[VoltageClampSeriesResistanceCompCorrection] = Field(None, description="""Resistance compensation correction, in percent.""") - resistance_comp_prediction: Optional[VoltageClampSeriesResistanceCompPrediction] = Field(None, description="""Resistance compensation prediction, in percent.""") - whole_cell_capacitance_comp: Optional[VoltageClampSeriesWholeCellCapacitanceComp] = Field(None, description="""Whole cell capacitance compensation, in farads.""") - whole_cell_series_resistance_comp: Optional[VoltageClampSeriesWholeCellSeriesResistanceComp] = Field(None, description="""Whole cell series resistance compensation, in ohms.""") - stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") - sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") - gain: Optional[PatchClampSeriesGain] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class VoltageClampSeriesData(ConfiguredBaseModel): - """ - Recorded current. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'amperes'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - - -class VoltageClampSeriesCapacitanceFast(ConfiguredBaseModel): - """ - Fast capacitance, in farads. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for capacitance_fast, which is fixed to 'farads'.""") - - -class VoltageClampSeriesCapacitanceSlow(ConfiguredBaseModel): - """ - Slow capacitance, in farads. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for capacitance_fast, which is fixed to 'farads'.""") - - -class VoltageClampSeriesResistanceCompBandwidth(ConfiguredBaseModel): - """ - Resistance compensation bandwidth, in hertz. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for resistance_comp_bandwidth, which is fixed to 'hertz'.""") - - -class VoltageClampSeriesResistanceCompCorrection(ConfiguredBaseModel): - """ - Resistance compensation correction, in percent. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for resistance_comp_correction, which is fixed to 'percent'.""") - - -class VoltageClampSeriesResistanceCompPrediction(ConfiguredBaseModel): - """ - Resistance compensation prediction, in percent. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for resistance_comp_prediction, which is fixed to 'percent'.""") - - -class VoltageClampSeriesWholeCellCapacitanceComp(ConfiguredBaseModel): - """ - Whole cell capacitance compensation, in farads. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for whole_cell_capacitance_comp, which is fixed to 'farads'.""") - - -class VoltageClampSeriesWholeCellSeriesResistanceComp(ConfiguredBaseModel): - """ - Whole cell series resistance compensation, in ohms. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for whole_cell_series_resistance_comp, which is fixed to 'ohms'.""") - - -class VoltageClampStimulusSeries(PatchClampSeries): - """ - Stimulus voltage applied during a voltage clamp recording. - """ - data: VoltageClampStimulusSeriesData = Field(..., description="""Stimulus voltage applied.""") - stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") - sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") - gain: Optional[PatchClampSeriesGain] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class VoltageClampStimulusSeriesData(ConfiguredBaseModel): - """ - Stimulus voltage applied. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'volts'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - - -class IntracellularElectrode(NWBContainer): - """ - An intracellular electrode and its metadata. - """ - cell_id: Optional[IntracellularElectrodeCellId] = Field(None, description="""unique ID of the cell""") - description: IntracellularElectrodeDescription = Field(..., description="""Description of electrode (e.g., whole-cell, sharp, etc.).""") - filtering: Optional[IntracellularElectrodeFiltering] = Field(None, description="""Electrode specific filtering.""") - initial_access_resistance: Optional[IntracellularElectrodeInitialAccessResistance] = Field(None, description="""Initial access resistance.""") - location: Optional[IntracellularElectrodeLocation] = Field(None, description="""Location of the electrode. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible.""") - resistance: Optional[IntracellularElectrodeResistance] = Field(None, description="""Electrode resistance, in ohms.""") - seal: Optional[IntracellularElectrodeSeal] = Field(None, description="""Information about seal used for recording.""") - slice: Optional[IntracellularElectrodeSlice] = Field(None, description="""Information about slice used for recording.""") - - -class IntracellularElectrodeCellId(ConfiguredBaseModel): - """ - unique ID of the cell - """ - None - - -class IntracellularElectrodeDescription(ConfiguredBaseModel): - """ - Description of electrode (e.g., whole-cell, sharp, etc.). - """ - None - - -class IntracellularElectrodeFiltering(ConfiguredBaseModel): - """ - Electrode specific filtering. - """ - None - - -class IntracellularElectrodeInitialAccessResistance(ConfiguredBaseModel): - """ - Initial access resistance. - """ - None - - -class IntracellularElectrodeLocation(ConfiguredBaseModel): - """ - Location of the electrode. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible. - """ - None - - -class IntracellularElectrodeResistance(ConfiguredBaseModel): - """ - Electrode resistance, in ohms. - """ - None - - -class IntracellularElectrodeSeal(ConfiguredBaseModel): - """ - Information about seal used for recording. - """ - None - - -class IntracellularElectrodeSlice(ConfiguredBaseModel): - """ - Information about slice used for recording. - """ - None - - -class SweepTable(DynamicTable): - """ - [DEPRECATED] Table used to group different PatchClampSeries. SweepTable is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable tables. Additional SequentialRecordingsTable, RepetitionsTable, and ExperimentalConditions tables provide enhanced support for experiment metadata. - """ - sweep_number: SweepTableSweepNumber = Field(..., description="""Sweep number of the PatchClampSeries in that row.""") - series: SweepTableSeries = Field(..., description="""The PatchClampSeries with the sweep number in that row.""") - series_index: SweepTableSeriesIndex = Field(..., description="""Index for series.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileGeneralIntracellularEphysSweepTable(SweepTable): - """ - [DEPRECATED] Table used to group different PatchClampSeries. SweepTable is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable tables. Additional SequentialRecordingsTable, RepetitionsTable and ExperimentalConditions tables provide enhanced support for experiment metadata. - """ - sweep_number: SweepTableSweepNumber = Field(..., description="""Sweep number of the PatchClampSeries in that row.""") - series: SweepTableSeries = Field(..., description="""The PatchClampSeries with the sweep number in that row.""") - series_index: SweepTableSeriesIndex = Field(..., description="""Index for series.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SweepTableSweepNumber(VectorData): - """ - Sweep number of the PatchClampSeries in that row. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class SweepTableSeries(VectorData): - """ - The PatchClampSeries with the sweep number in that row. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class SweepTableSeriesIndex(VectorIndex): - """ - Index for series. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class IntracellularElectrodesTable(DynamicTable): - """ - Table for storing intracellular electrode related metadata. - """ - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - electrode: IntracellularElectrodesTableElectrode = Field(..., description="""Column for storing the reference to the intracellular electrode.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class IntracellularElectrodesTableElectrode(VectorData): - """ - Column for storing the reference to the intracellular electrode. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class IntracellularStimuliTable(DynamicTable): - """ - Table for storing intracellular stimulus related metadata. - """ - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - stimulus: IntracellularStimuliTableStimulus = Field(..., description="""Column storing the reference to the recorded stimulus for the recording (rows).""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class IntracellularStimuliTableStimulus(TimeSeriesReferenceVectorData): - """ - Column storing the reference to the recorded stimulus for the recording (rows). - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class IntracellularResponsesTable(DynamicTable): - """ - Table for storing intracellular response related metadata. - """ - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - response: IntracellularResponsesTableResponse = Field(..., description="""Column storing the reference to the recorded response for the recording (rows)""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class IntracellularResponsesTableResponse(TimeSeriesReferenceVectorData): - """ - Column storing the reference to the recorded response for the recording (rows) - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class IntracellularRecordingsTable(AlignedDynamicTable): - """ - A table to group together a stimulus and response from a single electrode and a single simultaneous recording. Each row in the table represents a single recording consisting typically of a stimulus and a corresponding response. In some cases, however, only a stimulus or a response is recorded as part of an experiment. In this case, both the stimulus and response will point to the same TimeSeries while the idx_start and count of the invalid column will be set to -1, thus, indicating that no values have been recorded for the stimulus or response, respectively. Note, a recording MUST contain at least a stimulus or a response. Typically the stimulus and response are PatchClampSeries. However, the use of AD/DA channels that are not associated to an electrode is also common in intracellular electrophysiology, in which case other TimeSeries may be used. - """ - description: Optional[str] = Field(None, description="""Description of the contents of this table. Inherited from AlignedDynamicTable and overwritten here to fix the value of the attribute.""") - electrodes: IntracellularRecordingsTableElectrodes = Field(..., description="""Table for storing intracellular electrode related metadata.""") - stimuli: IntracellularRecordingsTableStimuli = Field(..., description="""Table for storing intracellular stimulus related metadata.""") - responses: IntracellularRecordingsTableResponses = Field(..., description="""Table for storing intracellular response related metadata.""") - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileGeneralIntracellularEphysIntracellularRecordings(IntracellularRecordingsTable): - """ - A table to group together a stimulus and response from a single electrode and a single simultaneous recording. Each row in the table represents a single recording consisting typically of a stimulus and a corresponding response. In some cases, however, only a stimulus or a response are recorded as as part of an experiment. In this case both, the stimulus and response will point to the same TimeSeries while the idx_start and count of the invalid column will be set to -1, thus, indicating that no values have been recorded for the stimulus or response, respectively. Note, a recording MUST contain at least a stimulus or a response. Typically the stimulus and response are PatchClampSeries. However, the use of AD/DA channels that are not associated to an electrode is also common in intracellular electrophysiology, in which case other TimeSeries may be used. - """ - description: Optional[str] = Field(None, description="""Description of the contents of this table. Inherited from AlignedDynamicTable and overwritten here to fix the value of the attribute.""") - electrodes: IntracellularRecordingsTableElectrodes = Field(..., description="""Table for storing intracellular electrode related metadata.""") - stimuli: IntracellularRecordingsTableStimuli = Field(..., description="""Table for storing intracellular stimulus related metadata.""") - responses: IntracellularRecordingsTableResponses = Field(..., description="""Table for storing intracellular response related metadata.""") - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class IntracellularRecordingsTableElectrodes(IntracellularElectrodesTable): - """ - Table for storing intracellular electrode related metadata. - """ - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - electrode: IntracellularElectrodesTableElectrode = Field(..., description="""Column for storing the reference to the intracellular electrode.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class IntracellularRecordingsTableStimuli(IntracellularStimuliTable): - """ - Table for storing intracellular stimulus related metadata. - """ - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - stimulus: IntracellularStimuliTableStimulus = Field(..., description="""Column storing the reference to the recorded stimulus for the recording (rows).""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class IntracellularRecordingsTableResponses(IntracellularResponsesTable): - """ - Table for storing intracellular response related metadata. - """ - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - response: IntracellularResponsesTableResponse = Field(..., description="""Column storing the reference to the recorded response for the recording (rows)""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimultaneousRecordingsTable(DynamicTable): - """ - A table for grouping different intracellular recordings from the IntracellularRecordingsTable table together that were recorded simultaneously from different electrodes. - """ - recordings: SimultaneousRecordingsTableRecordings = Field(..., description="""A reference to one or more rows in the IntracellularRecordingsTable table.""") - recordings_index: SimultaneousRecordingsTableRecordingsIndex = Field(..., description="""Index dataset for the recordings column.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileGeneralIntracellularEphysSimultaneousRecordings(SimultaneousRecordingsTable): - """ - A table for grouping different intracellular recordings from the IntracellularRecordingsTable table together that were recorded simultaneously from different electrodes - """ - recordings: SimultaneousRecordingsTableRecordings = Field(..., description="""A reference to one or more rows in the IntracellularRecordingsTable table.""") - recordings_index: SimultaneousRecordingsTableRecordingsIndex = Field(..., description="""Index dataset for the recordings column.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimultaneousRecordingsTableRecordings(DynamicTableRegion): - """ - A reference to one or more rows in the IntracellularRecordingsTable table. - """ - table: Optional[IntracellularRecordingsTable] = Field(None, description="""Reference to the IntracellularRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class SimultaneousRecordingsTableRecordingsIndex(VectorIndex): - """ - Index dataset for the recordings column. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class SequentialRecordingsTable(DynamicTable): - """ - A table for grouping different sequential recordings from the SimultaneousRecordingsTable table together. This is typically used to group together sequential recordings where a sequence of stimuli of the same type with varying parameters have been presented in a sequence. - """ - simultaneous_recordings: SequentialRecordingsTableSimultaneousRecordings = Field(..., description="""A reference to one or more rows in the SimultaneousRecordingsTable table.""") - simultaneous_recordings_index: SequentialRecordingsTableSimultaneousRecordingsIndex = Field(..., description="""Index dataset for the simultaneous_recordings column.""") - stimulus_type: SequentialRecordingsTableStimulusType = Field(..., description="""The type of stimulus used for the sequential recording.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileGeneralIntracellularEphysSequentialRecordings(SequentialRecordingsTable): - """ - A table for grouping different sequential recordings from the SimultaneousRecordingsTable table together. This is typically used to group together sequential recordings where the a sequence of stimuli of the same type with varying parameters have been presented in a sequence. - """ - simultaneous_recordings: SequentialRecordingsTableSimultaneousRecordings = Field(..., description="""A reference to one or more rows in the SimultaneousRecordingsTable table.""") - simultaneous_recordings_index: SequentialRecordingsTableSimultaneousRecordingsIndex = Field(..., description="""Index dataset for the simultaneous_recordings column.""") - stimulus_type: SequentialRecordingsTableStimulusType = Field(..., description="""The type of stimulus used for the sequential recording.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SequentialRecordingsTableSimultaneousRecordings(DynamicTableRegion): - """ - A reference to one or more rows in the SimultaneousRecordingsTable table. - """ - table: Optional[SimultaneousRecordingsTable] = Field(None, description="""Reference to the SimultaneousRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class SequentialRecordingsTableSimultaneousRecordingsIndex(VectorIndex): - """ - Index dataset for the simultaneous_recordings column. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class SequentialRecordingsTableStimulusType(VectorData): - """ - The type of stimulus used for the sequential recording. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class RepetitionsTable(DynamicTable): - """ - A table for grouping different sequential intracellular recordings together. With each SequentialRecording typically representing a particular type of stimulus, the RepetitionsTable table is typically used to group sets of stimuli applied in sequence. - """ - sequential_recordings: RepetitionsTableSequentialRecordings = Field(..., description="""A reference to one or more rows in the SequentialRecordingsTable table.""") - sequential_recordings_index: RepetitionsTableSequentialRecordingsIndex = Field(..., description="""Index dataset for the sequential_recordings column.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileGeneralIntracellularEphysRepetitions(RepetitionsTable): - """ - A table for grouping different sequential intracellular recordings together. With each SequentialRecording typically representing a particular type of stimulus, the RepetitionsTable table is typically used to group sets of stimuli applied in sequence. - """ - sequential_recordings: RepetitionsTableSequentialRecordings = Field(..., description="""A reference to one or more rows in the SequentialRecordingsTable table.""") - sequential_recordings_index: RepetitionsTableSequentialRecordingsIndex = Field(..., description="""Index dataset for the sequential_recordings column.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class RepetitionsTableSequentialRecordings(DynamicTableRegion): - """ - A reference to one or more rows in the SequentialRecordingsTable table. - """ - table: Optional[SequentialRecordingsTable] = Field(None, description="""Reference to the SequentialRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class RepetitionsTableSequentialRecordingsIndex(VectorIndex): - """ - Index dataset for the sequential_recordings column. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ExperimentalConditionsTable(DynamicTable): - """ - A table for grouping different intracellular recording repetitions together that belong to the same experimental condition. - """ - repetitions: ExperimentalConditionsTableRepetitions = Field(..., description="""A reference to one or more rows in the RepetitionsTable table.""") - repetitions_index: ExperimentalConditionsTableRepetitionsIndex = Field(..., description="""Index dataset for the repetitions column.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileGeneralIntracellularEphysExperimentalConditions(ExperimentalConditionsTable): - """ - A table for grouping different intracellular recording repetitions together that belong to the same experimental experimental_conditions. - """ - repetitions: ExperimentalConditionsTableRepetitions = Field(..., description="""A reference to one or more rows in the RepetitionsTable table.""") - repetitions_index: ExperimentalConditionsTableRepetitionsIndex = Field(..., description="""Index dataset for the repetitions column.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class ExperimentalConditionsTableRepetitions(DynamicTableRegion): - """ - A reference to one or more rows in the RepetitionsTable table. - """ - table: Optional[RepetitionsTable] = Field(None, description="""Reference to the RepetitionsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class ExperimentalConditionsTableRepetitionsIndex(VectorIndex): - """ - Index dataset for the repetitions column. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ElectricalSeries(TimeSeries): - """ - A time series of acquired voltage data from extracellular recordings. The data field is an int or float array storing data in volts. The first dimension should always represent time. The second dimension, if present, should represent channels. - """ - filtering: Optional[str] = Field(None, description="""Filtering applied to all channels of the data. For example, if this ElectricalSeries represents high-pass-filtered data (also known as AP Band), then this value could be \"High-pass 4-pole Bessel filter at 500 Hz\". If this ElectricalSeries represents low-pass-filtered LFP data and the type of filter is unknown, then this value could be \"Low-pass filter at 300 Hz\". If a non-standard filter type is used, provide as much detail about the filter properties as possible.""") - data: ElectricalSeriesData = Field(..., description="""Recorded voltage data.""") - electrodes: ElectricalSeriesElectrodes = Field(..., description="""DynamicTableRegion pointer to the electrodes that this time series was generated from.""") - channel_conversion: Optional[ElectricalSeriesChannelConversion] = Field(None, description="""Channel-specific conversion factor. Multiply the data in the 'data' dataset by these values along the channel axis (as indicated by axis attribute) AND by the global conversion factor in the 'conversion' attribute of 'data' to get the data values in Volts, i.e, data in Volts = data * data.conversion * channel_conversion. This approach allows for both global and per-channel data conversion factors needed to support the storage of electrical recordings as native values generated by data acquisition systems. If this dataset is not present, then there is no channel-specific conversion factor, i.e. it is 1 for all channels.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class ElectricalSeriesData(ConfiguredBaseModel): - """ - Recorded voltage data. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. This value is fixed to 'volts'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion', followed by 'channel_conversion' (if present), and then add 'offset'.""") - array: Optional[ElectricalSeriesDataArray] = Field(None) - - -class ElectricalSeriesDataArray(Arraylike): - - num_times: float = Field(...) - num_channels: Optional[float] = Field(None) - num_samples: Optional[float] = Field(None) - - -class ElectricalSeriesElectrodes(DynamicTableRegion): - """ - DynamicTableRegion pointer to the electrodes that this time series was generated from. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class ElectricalSeriesChannelConversion(ConfiguredBaseModel): - """ - Channel-specific conversion factor. Multiply the data in the 'data' dataset by these values along the channel axis (as indicated by axis attribute) AND by the global conversion factor in the 'conversion' attribute of 'data' to get the data values in Volts, i.e, data in Volts = data * data.conversion * channel_conversion. This approach allows for both global and per-channel data conversion factors needed to support the storage of electrical recordings as native values generated by data acquisition systems. If this dataset is not present, then there is no channel-specific conversion factor, i.e. it is 1 for all channels. - """ - axis: Optional[int] = Field(None, description="""The zero-indexed axis of the 'data' dataset that the channel-specific conversion factor corresponds to. This value is fixed to 1.""") - array: Optional[ElectricalSeriesChannelConversionArray] = Field(None) - - -class ElectricalSeriesChannelConversionArray(Arraylike): - - num_channels: float = Field(...) - - -class SpikeEventSeries(ElectricalSeries): - """ - Stores snapshots/snippets of recorded spike events (i.e., threshold crossings). This may also be raw data, as reported by ephys hardware. If so, the TimeSeries::description field should describe how events were detected. All SpikeEventSeries should reside in a module (under EventWaveform interface) even if the spikes were reported and stored by hardware. All events span the same recording channels and store snapshots of equal duration. TimeSeries::data array structure: [num events] [num channels] [num samples] (or [num events] [num samples] for single electrode). - """ - data: SpikeEventSeriesData = Field(..., description="""Spike waveforms.""") - timestamps: SpikeEventSeriesTimestamps = Field(..., description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. Timestamps are required for the events. Unlike for TimeSeries, timestamps are required for SpikeEventSeries and are thus re-specified here.""") - filtering: Optional[str] = Field(None, description="""Filtering applied to all channels of the data. For example, if this ElectricalSeries represents high-pass-filtered data (also known as AP Band), then this value could be \"High-pass 4-pole Bessel filter at 500 Hz\". If this ElectricalSeries represents low-pass-filtered LFP data and the type of filter is unknown, then this value could be \"Low-pass filter at 300 Hz\". If a non-standard filter type is used, provide as much detail about the filter properties as possible.""") - electrodes: ElectricalSeriesElectrodes = Field(..., description="""DynamicTableRegion pointer to the electrodes that this time series was generated from.""") - channel_conversion: Optional[ElectricalSeriesChannelConversion] = Field(None, description="""Channel-specific conversion factor. Multiply the data in the 'data' dataset by these values along the channel axis (as indicated by axis attribute) AND by the global conversion factor in the 'conversion' attribute of 'data' to get the data values in Volts, i.e, data in Volts = data * data.conversion * channel_conversion. This approach allows for both global and per-channel data conversion factors needed to support the storage of electrical recordings as native values generated by data acquisition systems. If this dataset is not present, then there is no channel-specific conversion factor, i.e. it is 1 for all channels.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class SpikeEventSeriesData(ConfiguredBaseModel): - """ - Spike waveforms. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for waveforms, which is fixed to 'volts'.""") - array: Optional[SpikeEventSeriesDataArray] = Field(None) - - -class SpikeEventSeriesDataArray(Arraylike): - - num_events: float = Field(...) - num_samples: float = Field(...) - num_channels: Optional[float] = Field(None) - - -class SpikeEventSeriesTimestamps(ConfiguredBaseModel): - """ - Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. Timestamps are required for the events. Unlike for TimeSeries, timestamps are required for SpikeEventSeries and are thus re-specified here. - """ - interval: Optional[int] = Field(None, description="""Value is '1'""") - unit: Optional[str] = Field(None, description="""Unit of measurement for timestamps, which is fixed to 'seconds'.""") - array: Optional[SpikeEventSeriesTimestampsArray] = Field(None) - - -class SpikeEventSeriesTimestampsArray(Arraylike): - - num_times: float = Field(...) - - -class FeatureExtraction(NWBDataInterface): - """ - Features, such as PC1 and PC2, that are extracted from signals stored in a SpikeEventSeries or other source. - """ - description: FeatureExtractionDescription = Field(..., description="""Description of features (eg, ''PC1'') for each of the extracted features.""") - features: FeatureExtractionFeatures = Field(..., description="""Multi-dimensional array of features extracted from each event.""") - times: FeatureExtractionTimes = Field(..., description="""Times of events that features correspond to (can be a link).""") - electrodes: FeatureExtractionElectrodes = Field(..., description="""DynamicTableRegion pointer to the electrodes that this time series was generated from.""") - - -class FeatureExtractionDescription(ConfiguredBaseModel): - """ - Description of features (eg, ''PC1'') for each of the extracted features. - """ - array: Optional[FeatureExtractionDescriptionArray] = Field(None) - - -class FeatureExtractionDescriptionArray(Arraylike): - - num_features: str = Field(...) - - -class FeatureExtractionFeatures(ConfiguredBaseModel): - """ - Multi-dimensional array of features extracted from each event. - """ - array: Optional[FeatureExtractionFeaturesArray] = Field(None) - - -class FeatureExtractionFeaturesArray(Arraylike): - - num_events: Optional[float] = Field(None) - num_channels: Optional[float] = Field(None) - num_features: Optional[float] = Field(None) - - -class FeatureExtractionTimes(ConfiguredBaseModel): - """ - Times of events that features correspond to (can be a link). - """ - array: Optional[FeatureExtractionTimesArray] = Field(None) - - -class FeatureExtractionTimesArray(Arraylike): - - num_events: float = Field(...) - - -class FeatureExtractionElectrodes(DynamicTableRegion): - """ - DynamicTableRegion pointer to the electrodes that this time series was generated from. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class EventDetection(NWBDataInterface): - """ - Detected spike events from voltage trace(s). - """ - detection_method: EventDetectionDetectionMethod = Field(..., description="""Description of how events were detected, such as voltage threshold, or dV/dT threshold, as well as relevant values.""") - source_idx: EventDetectionSourceIdx = Field(..., description="""Indices (zero-based) into source ElectricalSeries::data array corresponding to time of event. ''description'' should define what is meant by time of event (e.g., .25 ms before action potential peak, zero-crossing time, etc). The index points to each event from the raw data.""") - times: EventDetectionTimes = Field(..., description="""Timestamps of events, in seconds.""") - - -class EventDetectionDetectionMethod(ConfiguredBaseModel): - """ - Description of how events were detected, such as voltage threshold, or dV/dT threshold, as well as relevant values. - """ - None - - -class EventDetectionSourceIdx(ConfiguredBaseModel): - """ - Indices (zero-based) into source ElectricalSeries::data array corresponding to time of event. ''description'' should define what is meant by time of event (e.g., .25 ms before action potential peak, zero-crossing time, etc). The index points to each event from the raw data. - """ - array: Optional[EventDetectionSourceIdxArray] = Field(None) - - -class EventDetectionSourceIdxArray(Arraylike): - - num_events: int = Field(...) - - -class EventDetectionTimes(ConfiguredBaseModel): - """ - Timestamps of events, in seconds. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for event times, which is fixed to 'seconds'.""") - array: Optional[EventDetectionTimesArray] = Field(None) - - -class EventDetectionTimesArray(Arraylike): - - num_events: float = Field(...) - - -class EventWaveform(NWBDataInterface): - """ - Represents either the waveforms of detected events, as extracted from a raw data trace in /acquisition, or the event waveforms that were stored during experiment acquisition. - """ - SpikeEventSeries: Optional[List[SpikeEventSeries]] = Field(default_factory=list, description="""SpikeEventSeries object(s) containing detected spike event waveforms.""") - - -class FilteredEphys(NWBDataInterface): - """ - Electrophysiology data from one or more channels that has been subjected to filtering. Examples of filtered data include Theta and Gamma (LFP has its own interface). FilteredEphys modules publish an ElectricalSeries for each filtered channel or set of channels. The name of each ElectricalSeries is arbitrary but should be informative. The source of the filtered data, whether this is from analysis of another time series or as acquired by hardware, should be noted in each's TimeSeries::description field. There is no assumed 1::1 correspondence between filtered ephys signals and electrodes, as a single signal can apply to many nearby electrodes, and one electrode may have different filtered (e.g., theta and/or gamma) signals represented. Filter properties should be noted in the ElectricalSeries 'filtering' attribute. - """ - ElectricalSeries: List[ElectricalSeries] = Field(default_factory=list, description="""ElectricalSeries object(s) containing filtered electrophysiology data.""") - - -class LFP(NWBDataInterface): - """ - LFP data from one or more channels. The electrode map in each published ElectricalSeries will identify which channels are providing LFP data. Filter properties should be noted in the ElectricalSeries 'filtering' attribute. - """ - ElectricalSeries: List[ElectricalSeries] = Field(default_factory=list, description="""ElectricalSeries object(s) containing LFP data for one or more channels.""") - - -class ElectrodeGroup(NWBContainer): - """ - A physical grouping of electrodes, e.g. a shank of an array. - """ - description: Optional[str] = Field(None, description="""Description of this electrode group.""") - location: Optional[str] = Field(None, description="""Location of electrode group. Specify the area, layer, comments on estimation of area/layer, etc. Use standard atlas names for anatomical regions when possible.""") - position: Optional[ElectrodeGroupPosition] = Field(None, description="""stereotaxic or common framework coordinates""") - - -class ElectrodeGroupPosition(ConfiguredBaseModel): - """ - stereotaxic or common framework coordinates - """ - None - - -class ClusterWaveforms(NWBDataInterface): - """ - DEPRECATED The mean waveform shape, including standard deviation, of the different clusters. Ideally, the waveform analysis should be performed on data that is only high-pass filtered. This is a separate module because it is expected to require updating. For example, IMEC probes may require different storage requirements to store/display mean waveforms, requiring a new interface or an extension of this one. - """ - waveform_filtering: ClusterWaveformsWaveformFiltering = Field(..., description="""Filtering applied to data before generating mean/sd""") - waveform_mean: ClusterWaveformsWaveformMean = Field(..., description="""The mean waveform for each cluster, using the same indices for each wave as cluster numbers in the associated Clustering module (i.e, cluster 3 is in array slot [3]). Waveforms corresponding to gaps in cluster sequence should be empty (e.g., zero- filled)""") - waveform_sd: ClusterWaveformsWaveformSd = Field(..., description="""Stdev of waveforms for each cluster, using the same indices as in mean""") - - -class ClusterWaveformsWaveformFiltering(ConfiguredBaseModel): - """ - Filtering applied to data before generating mean/sd - """ - None - - -class ClusterWaveformsWaveformMean(ConfiguredBaseModel): - """ - The mean waveform for each cluster, using the same indices for each wave as cluster numbers in the associated Clustering module (i.e, cluster 3 is in array slot [3]). Waveforms corresponding to gaps in cluster sequence should be empty (e.g., zero- filled) - """ - array: Optional[ClusterWaveformsWaveformMeanArray] = Field(None) - - -class ClusterWaveformsWaveformMeanArray(Arraylike): - - num_clusters: Optional[float] = Field(None) - num_samples: Optional[float] = Field(None) - - -class ClusterWaveformsWaveformSd(ConfiguredBaseModel): - """ - Stdev of waveforms for each cluster, using the same indices as in mean - """ - array: Optional[ClusterWaveformsWaveformSdArray] = Field(None) - - -class ClusterWaveformsWaveformSdArray(Arraylike): - - num_clusters: Optional[float] = Field(None) - num_samples: Optional[float] = Field(None) - - -class Clustering(NWBDataInterface): - """ - DEPRECATED Clustered spike data, whether from automatic clustering tools (e.g., klustakwik) or as a result of manual sorting. - """ - description: ClusteringDescription = Field(..., description="""Description of clusters or clustering, (e.g. cluster 0 is noise, clusters curated using Klusters, etc)""") - num: ClusteringNum = Field(..., description="""Cluster number of each event""") - peak_over_rms: ClusteringPeakOverRms = Field(..., description="""Maximum ratio of waveform peak to RMS on any channel in the cluster (provides a basic clustering metric).""") - times: ClusteringTimes = Field(..., description="""Times of clustered events, in seconds. This may be a link to times field in associated FeatureExtraction module.""") - - -class ClusteringDescription(ConfiguredBaseModel): - """ - Description of clusters or clustering, (e.g. cluster 0 is noise, clusters curated using Klusters, etc) - """ - None - - -class ClusteringNum(ConfiguredBaseModel): - """ - Cluster number of each event - """ - array: Optional[ClusteringNumArray] = Field(None) - - -class ClusteringNumArray(Arraylike): - - num_events: int = Field(...) - - -class ClusteringPeakOverRms(ConfiguredBaseModel): - """ - Maximum ratio of waveform peak to RMS on any channel in the cluster (provides a basic clustering metric). - """ - array: Optional[ClusteringPeakOverRmsArray] = Field(None) - - -class ClusteringPeakOverRmsArray(Arraylike): - - num_clusters: float = Field(...) - - -class ClusteringTimes(ConfiguredBaseModel): - """ - Times of clustered events, in seconds. This may be a link to times field in associated FeatureExtraction module. - """ - array: Optional[ClusteringTimesArray] = Field(None) - - -class ClusteringTimesArray(Arraylike): - - num_events: float = Field(...) - - -class Device(NWBContainer): - """ - Metadata about a data acquisition device, e.g., recording system, electrode, microscope. - """ - description: Optional[str] = Field(None, description="""Description of the device (e.g., model, firmware version, processing software version, etc.) as free-form text.""") - manufacturer: Optional[str] = Field(None, description="""The name of the manufacturer of the device.""") - - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -NWBFileFileCreateDate.update_forward_refs() -NWBFileIdentifier.update_forward_refs() -NWBFileSessionDescription.update_forward_refs() -NWBFileSessionStartTime.update_forward_refs() -NWBFileTimestampsReferenceTime.update_forward_refs() -NWBFileAcquisition.update_forward_refs() -NWBFileAnalysis.update_forward_refs() -NWBFileScratch.update_forward_refs() -NWBFileProcessing.update_forward_refs() -NWBFileStimulus.update_forward_refs() -NWBFileStimulusPresentation.update_forward_refs() -NWBFileStimulusTemplates.update_forward_refs() -NWBFileGeneral.update_forward_refs() -NWBFileGeneralDataCollection.update_forward_refs() -NWBFileGeneralExperimentDescription.update_forward_refs() -NWBFileGeneralExperimenter.update_forward_refs() -NWBFileGeneralInstitution.update_forward_refs() -NWBFileGeneralKeywords.update_forward_refs() -NWBFileGeneralLab.update_forward_refs() -NWBFileGeneralNotes.update_forward_refs() -NWBFileGeneralPharmacology.update_forward_refs() -NWBFileGeneralProtocol.update_forward_refs() -NWBFileGeneralRelatedPublications.update_forward_refs() -NWBFileGeneralSessionId.update_forward_refs() -NWBFileGeneralSlices.update_forward_refs() -NWBFileGeneralSourceScript.update_forward_refs() -NWBFileGeneralStimulus.update_forward_refs() -NWBFileGeneralSurgery.update_forward_refs() -NWBFileGeneralVirus.update_forward_refs() -NWBFileGeneralDevices.update_forward_refs() -NWBFileGeneralExtracellularEphys.update_forward_refs() -NWBFileGeneralIntracellularEphys.update_forward_refs() -NWBFileGeneralIntracellularEphysFiltering.update_forward_refs() -NWBFileGeneralOptogenetics.update_forward_refs() -NWBFileGeneralOptophysiology.update_forward_refs() -NWBFileIntervals.update_forward_refs() -SubjectAge.update_forward_refs() -SubjectDateOfBirth.update_forward_refs() -SubjectDescription.update_forward_refs() -SubjectGenotype.update_forward_refs() -SubjectSex.update_forward_refs() -SubjectSpecies.update_forward_refs() -SubjectStrain.update_forward_refs() -SubjectSubjectId.update_forward_refs() -SubjectWeight.update_forward_refs() -Arraylike.update_forward_refs() -NWBFileFileCreateDateArray.update_forward_refs() -NWBFileGeneralExperimenterArray.update_forward_refs() -NWBFileGeneralKeywordsArray.update_forward_refs() -NWBFileGeneralRelatedPublicationsArray.update_forward_refs() -AbstractFeatureSeriesData.update_forward_refs() -AbstractFeatureSeriesDataArray.update_forward_refs() -AbstractFeatureSeriesFeatureUnits.update_forward_refs() -AbstractFeatureSeriesFeatureUnitsArray.update_forward_refs() -AbstractFeatureSeriesFeatures.update_forward_refs() -AbstractFeatureSeriesFeaturesArray.update_forward_refs() -AnnotationSeriesData.update_forward_refs() -AnnotationSeriesDataArray.update_forward_refs() -IntervalSeriesData.update_forward_refs() -IntervalSeriesDataArray.update_forward_refs() -DecompositionSeriesData.update_forward_refs() -DecompositionSeriesDataArray.update_forward_refs() -DecompositionSeriesMetric.update_forward_refs() -DecompositionSeriesBandsBandLimitsArray.update_forward_refs() -DecompositionSeriesBandsBandMeanArray.update_forward_refs() -DecompositionSeriesBandsBandStdevArray.update_forward_refs() -UnitsObsIntervalsArray.update_forward_refs() -UnitsWaveformMeanArray.update_forward_refs() -UnitsWaveformSdArray.update_forward_refs() -UnitsWaveformsArray.update_forward_refs() -VectorDataArray.update_forward_refs() -VectorIndexArray.update_forward_refs() -ElementIdentifiersArray.update_forward_refs() -DynamicTableRegionArray.update_forward_refs() -DynamicTableIdArray.update_forward_refs() -Data.update_forward_refs() -VectorData.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesX.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesY.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesZ.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesImp.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesLocation.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesFiltering.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesGroup.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesGroupName.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesRelX.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesRelY.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesRelZ.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesReference.update_forward_refs() -DecompositionSeriesBandsBandName.update_forward_refs() -DecompositionSeriesBandsBandLimits.update_forward_refs() -DecompositionSeriesBandsBandMean.update_forward_refs() -DecompositionSeriesBandsBandStdev.update_forward_refs() -UnitsSpikeTimes.update_forward_refs() -UnitsObsIntervals.update_forward_refs() -UnitsElectrodeGroup.update_forward_refs() -UnitsWaveformMean.update_forward_refs() -UnitsWaveformSd.update_forward_refs() -UnitsWaveforms.update_forward_refs() -VectorIndex.update_forward_refs() -UnitsSpikeTimesIndex.update_forward_refs() -UnitsObsIntervalsIndex.update_forward_refs() -UnitsElectrodesIndex.update_forward_refs() -UnitsWaveformsIndex.update_forward_refs() -UnitsWaveformsIndexIndex.update_forward_refs() -ElementIdentifiers.update_forward_refs() -DynamicTableRegion.update_forward_refs() -DecompositionSeriesSourceChannels.update_forward_refs() -UnitsElectrodes.update_forward_refs() -DynamicTableId.update_forward_refs() -Container.update_forward_refs() -DynamicTable.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodes.update_forward_refs() -DecompositionSeriesBands.update_forward_refs() -Units.update_forward_refs() -NWBFileUnits.update_forward_refs() -AlignedDynamicTable.update_forward_refs() -SimpleMultiContainer.update_forward_refs() -NWBData.update_forward_refs() -ScratchData.update_forward_refs() -TimeSeriesReferenceVectorData.update_forward_refs() -Image.update_forward_refs() -ImageArray.update_forward_refs() -ImageReferences.update_forward_refs() -ImageReferencesArray.update_forward_refs() -NWBContainer.update_forward_refs() -NWBFile.update_forward_refs() -LabMetaData.update_forward_refs() -Subject.update_forward_refs() -NWBFileGeneralSubject.update_forward_refs() -NWBDataInterface.update_forward_refs() -TimeSeries.update_forward_refs() -AbstractFeatureSeries.update_forward_refs() -AnnotationSeries.update_forward_refs() -IntervalSeries.update_forward_refs() -DecompositionSeries.update_forward_refs() -TimeSeriesData.update_forward_refs() -TimeSeriesDataArray.update_forward_refs() -TimeSeriesStartingTime.update_forward_refs() -TimeSeriesTimestamps.update_forward_refs() -TimeSeriesTimestampsArray.update_forward_refs() -TimeSeriesControl.update_forward_refs() -TimeSeriesControlArray.update_forward_refs() -TimeSeriesControlDescription.update_forward_refs() -TimeSeriesControlDescriptionArray.update_forward_refs() -TimeSeriesSync.update_forward_refs() -ProcessingModule.update_forward_refs() -Images.update_forward_refs() -ImagesOrderOfImages.update_forward_refs() -TimeIntervals.update_forward_refs() -NWBFileIntervalsEpochs.update_forward_refs() -NWBFileIntervalsTrials.update_forward_refs() -NWBFileIntervalsInvalidTimes.update_forward_refs() -TimeIntervalsStartTime.update_forward_refs() -TimeIntervalsStopTime.update_forward_refs() -TimeIntervalsTags.update_forward_refs() -TimeIntervalsTagsIndex.update_forward_refs() -TimeIntervalsTimeseries.update_forward_refs() -TimeIntervalsTimeseriesIndex.update_forward_refs() -TwoPhotonSeriesFieldOfView.update_forward_refs() -TwoPhotonSeriesFieldOfViewArray.update_forward_refs() -RoiResponseSeries.update_forward_refs() -RoiResponseSeriesData.update_forward_refs() -RoiResponseSeriesDataArray.update_forward_refs() -RoiResponseSeriesRois.update_forward_refs() -DfOverF.update_forward_refs() -Fluorescence.update_forward_refs() -ImageSegmentation.update_forward_refs() -PlaneSegmentation.update_forward_refs() -PlaneSegmentationImageMask.update_forward_refs() -PlaneSegmentationImageMaskArray.update_forward_refs() -PlaneSegmentationPixelMaskIndex.update_forward_refs() -PlaneSegmentationPixelMask.update_forward_refs() -PlaneSegmentationVoxelMaskIndex.update_forward_refs() -PlaneSegmentationVoxelMask.update_forward_refs() -PlaneSegmentationReferenceImages.update_forward_refs() -ImagingPlane.update_forward_refs() -ImagingPlaneDescription.update_forward_refs() -ImagingPlaneExcitationLambda.update_forward_refs() -ImagingPlaneImagingRate.update_forward_refs() -ImagingPlaneIndicator.update_forward_refs() -ImagingPlaneLocation.update_forward_refs() -ImagingPlaneManifold.update_forward_refs() -ImagingPlaneManifoldArray.update_forward_refs() -ImagingPlaneOriginCoords.update_forward_refs() -ImagingPlaneOriginCoordsArray.update_forward_refs() -ImagingPlaneGridSpacing.update_forward_refs() -ImagingPlaneGridSpacingArray.update_forward_refs() -ImagingPlaneReferenceFrame.update_forward_refs() -OpticalChannel.update_forward_refs() -OpticalChannelDescription.update_forward_refs() -OpticalChannelEmissionLambda.update_forward_refs() -MotionCorrection.update_forward_refs() -CorrectedImageStack.update_forward_refs() -CorrectedImageStackXyTranslation.update_forward_refs() -GrayscaleImage.update_forward_refs() -GrayscaleImageArray.update_forward_refs() -RGBImage.update_forward_refs() -RGBImageArray.update_forward_refs() -RGBAImage.update_forward_refs() -RGBAImageArray.update_forward_refs() -ImageSeries.update_forward_refs() -OnePhotonSeries.update_forward_refs() -TwoPhotonSeries.update_forward_refs() -CorrectedImageStackCorrected.update_forward_refs() -ImageSeriesData.update_forward_refs() -ImageSeriesDataArray.update_forward_refs() -ImageSeriesDimension.update_forward_refs() -ImageSeriesDimensionArray.update_forward_refs() -ImageSeriesExternalFile.update_forward_refs() -ImageSeriesExternalFileArray.update_forward_refs() -ImageSeriesFormat.update_forward_refs() -ImageMaskSeries.update_forward_refs() -OpticalSeries.update_forward_refs() -OpticalSeriesDistance.update_forward_refs() -OpticalSeriesFieldOfView.update_forward_refs() -OpticalSeriesFieldOfViewArray.update_forward_refs() -OpticalSeriesData.update_forward_refs() -OpticalSeriesDataArray.update_forward_refs() -OpticalSeriesOrientation.update_forward_refs() -IndexSeries.update_forward_refs() -IndexSeriesData.update_forward_refs() -IndexSeriesDataArray.update_forward_refs() -OptogeneticSeries.update_forward_refs() -OptogeneticSeriesData.update_forward_refs() -OptogeneticSeriesDataArray.update_forward_refs() -OptogeneticStimulusSite.update_forward_refs() -OptogeneticStimulusSiteDescription.update_forward_refs() -OptogeneticStimulusSiteExcitationLambda.update_forward_refs() -OptogeneticStimulusSiteLocation.update_forward_refs() -PatchClampSeries.update_forward_refs() -PatchClampSeriesData.update_forward_refs() -PatchClampSeriesDataArray.update_forward_refs() -PatchClampSeriesGain.update_forward_refs() -CurrentClampSeries.update_forward_refs() -CurrentClampSeriesData.update_forward_refs() -CurrentClampSeriesBiasCurrent.update_forward_refs() -CurrentClampSeriesBridgeBalance.update_forward_refs() -CurrentClampSeriesCapacitanceCompensation.update_forward_refs() -IZeroClampSeries.update_forward_refs() -IZeroClampSeriesBiasCurrent.update_forward_refs() -IZeroClampSeriesBridgeBalance.update_forward_refs() -IZeroClampSeriesCapacitanceCompensation.update_forward_refs() -CurrentClampStimulusSeries.update_forward_refs() -CurrentClampStimulusSeriesData.update_forward_refs() -VoltageClampSeries.update_forward_refs() -VoltageClampSeriesData.update_forward_refs() -VoltageClampSeriesCapacitanceFast.update_forward_refs() -VoltageClampSeriesCapacitanceSlow.update_forward_refs() -VoltageClampSeriesResistanceCompBandwidth.update_forward_refs() -VoltageClampSeriesResistanceCompCorrection.update_forward_refs() -VoltageClampSeriesResistanceCompPrediction.update_forward_refs() -VoltageClampSeriesWholeCellCapacitanceComp.update_forward_refs() -VoltageClampSeriesWholeCellSeriesResistanceComp.update_forward_refs() -VoltageClampStimulusSeries.update_forward_refs() -VoltageClampStimulusSeriesData.update_forward_refs() -IntracellularElectrode.update_forward_refs() -IntracellularElectrodeCellId.update_forward_refs() -IntracellularElectrodeDescription.update_forward_refs() -IntracellularElectrodeFiltering.update_forward_refs() -IntracellularElectrodeInitialAccessResistance.update_forward_refs() -IntracellularElectrodeLocation.update_forward_refs() -IntracellularElectrodeResistance.update_forward_refs() -IntracellularElectrodeSeal.update_forward_refs() -IntracellularElectrodeSlice.update_forward_refs() -SweepTable.update_forward_refs() -NWBFileGeneralIntracellularEphysSweepTable.update_forward_refs() -SweepTableSweepNumber.update_forward_refs() -SweepTableSeries.update_forward_refs() -SweepTableSeriesIndex.update_forward_refs() -IntracellularElectrodesTable.update_forward_refs() -IntracellularElectrodesTableElectrode.update_forward_refs() -IntracellularStimuliTable.update_forward_refs() -IntracellularStimuliTableStimulus.update_forward_refs() -IntracellularResponsesTable.update_forward_refs() -IntracellularResponsesTableResponse.update_forward_refs() -IntracellularRecordingsTable.update_forward_refs() -NWBFileGeneralIntracellularEphysIntracellularRecordings.update_forward_refs() -IntracellularRecordingsTableElectrodes.update_forward_refs() -IntracellularRecordingsTableStimuli.update_forward_refs() -IntracellularRecordingsTableResponses.update_forward_refs() -SimultaneousRecordingsTable.update_forward_refs() -NWBFileGeneralIntracellularEphysSimultaneousRecordings.update_forward_refs() -SimultaneousRecordingsTableRecordings.update_forward_refs() -SimultaneousRecordingsTableRecordingsIndex.update_forward_refs() -SequentialRecordingsTable.update_forward_refs() -NWBFileGeneralIntracellularEphysSequentialRecordings.update_forward_refs() -SequentialRecordingsTableSimultaneousRecordings.update_forward_refs() -SequentialRecordingsTableSimultaneousRecordingsIndex.update_forward_refs() -SequentialRecordingsTableStimulusType.update_forward_refs() -RepetitionsTable.update_forward_refs() -NWBFileGeneralIntracellularEphysRepetitions.update_forward_refs() -RepetitionsTableSequentialRecordings.update_forward_refs() -RepetitionsTableSequentialRecordingsIndex.update_forward_refs() -ExperimentalConditionsTable.update_forward_refs() -NWBFileGeneralIntracellularEphysExperimentalConditions.update_forward_refs() -ExperimentalConditionsTableRepetitions.update_forward_refs() -ExperimentalConditionsTableRepetitionsIndex.update_forward_refs() -ElectricalSeries.update_forward_refs() -ElectricalSeriesData.update_forward_refs() -ElectricalSeriesDataArray.update_forward_refs() -ElectricalSeriesElectrodes.update_forward_refs() -ElectricalSeriesChannelConversion.update_forward_refs() -ElectricalSeriesChannelConversionArray.update_forward_refs() -SpikeEventSeries.update_forward_refs() -SpikeEventSeriesData.update_forward_refs() -SpikeEventSeriesDataArray.update_forward_refs() -SpikeEventSeriesTimestamps.update_forward_refs() -SpikeEventSeriesTimestampsArray.update_forward_refs() -FeatureExtraction.update_forward_refs() -FeatureExtractionDescription.update_forward_refs() -FeatureExtractionDescriptionArray.update_forward_refs() -FeatureExtractionFeatures.update_forward_refs() -FeatureExtractionFeaturesArray.update_forward_refs() -FeatureExtractionTimes.update_forward_refs() -FeatureExtractionTimesArray.update_forward_refs() -FeatureExtractionElectrodes.update_forward_refs() -EventDetection.update_forward_refs() -EventDetectionDetectionMethod.update_forward_refs() -EventDetectionSourceIdx.update_forward_refs() -EventDetectionSourceIdxArray.update_forward_refs() -EventDetectionTimes.update_forward_refs() -EventDetectionTimesArray.update_forward_refs() -EventWaveform.update_forward_refs() -FilteredEphys.update_forward_refs() -LFP.update_forward_refs() -ElectrodeGroup.update_forward_refs() -ElectrodeGroupPosition.update_forward_refs() -ClusterWaveforms.update_forward_refs() -ClusterWaveformsWaveformFiltering.update_forward_refs() -ClusterWaveformsWaveformMean.update_forward_refs() -ClusterWaveformsWaveformMeanArray.update_forward_refs() -ClusterWaveformsWaveformSd.update_forward_refs() -ClusterWaveformsWaveformSdArray.update_forward_refs() -Clustering.update_forward_refs() -ClusteringDescription.update_forward_refs() -ClusteringNum.update_forward_refs() -ClusteringNumArray.update_forward_refs() -ClusteringPeakOverRms.update_forward_refs() -ClusteringPeakOverRmsArray.update_forward_refs() -ClusteringTimes.update_forward_refs() -ClusteringTimesArray.update_forward_refs() -Device.update_forward_refs() diff --git a/nwb_linkml/models/core.nwb.icephys.py b/nwb_linkml/models/core.nwb.icephys.py deleted file mode 100644 index 68885cc..0000000 --- a/nwb_linkml/models/core.nwb.icephys.py +++ /dev/null @@ -1,1069 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): - pass - - -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - -class PatchClampSeriesData(ConfiguredBaseModel): - """ - Recorded voltage or current. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - array: Optional[PatchClampSeriesDataArray] = Field(None) - - -class PatchClampSeriesGain(ConfiguredBaseModel): - """ - Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp). - """ - None - - -class CurrentClampSeriesData(ConfiguredBaseModel): - """ - Recorded voltage. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'volts'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - - -class CurrentClampSeriesBiasCurrent(ConfiguredBaseModel): - """ - Bias current, in amps. - """ - None - - -class CurrentClampSeriesBridgeBalance(ConfiguredBaseModel): - """ - Bridge balance, in ohms. - """ - None - - -class CurrentClampSeriesCapacitanceCompensation(ConfiguredBaseModel): - """ - Capacitance compensation, in farads. - """ - None - - -class IZeroClampSeriesBiasCurrent(ConfiguredBaseModel): - """ - Bias current, in amps, fixed to 0.0. - """ - None - - -class IZeroClampSeriesBridgeBalance(ConfiguredBaseModel): - """ - Bridge balance, in ohms, fixed to 0.0. - """ - None - - -class IZeroClampSeriesCapacitanceCompensation(ConfiguredBaseModel): - """ - Capacitance compensation, in farads, fixed to 0.0. - """ - None - - -class CurrentClampStimulusSeriesData(ConfiguredBaseModel): - """ - Stimulus current applied. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'amperes'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - - -class VoltageClampSeriesData(ConfiguredBaseModel): - """ - Recorded current. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'amperes'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - - -class VoltageClampSeriesCapacitanceFast(ConfiguredBaseModel): - """ - Fast capacitance, in farads. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for capacitance_fast, which is fixed to 'farads'.""") - - -class VoltageClampSeriesCapacitanceSlow(ConfiguredBaseModel): - """ - Slow capacitance, in farads. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for capacitance_fast, which is fixed to 'farads'.""") - - -class VoltageClampSeriesResistanceCompBandwidth(ConfiguredBaseModel): - """ - Resistance compensation bandwidth, in hertz. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for resistance_comp_bandwidth, which is fixed to 'hertz'.""") - - -class VoltageClampSeriesResistanceCompCorrection(ConfiguredBaseModel): - """ - Resistance compensation correction, in percent. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for resistance_comp_correction, which is fixed to 'percent'.""") - - -class VoltageClampSeriesResistanceCompPrediction(ConfiguredBaseModel): - """ - Resistance compensation prediction, in percent. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for resistance_comp_prediction, which is fixed to 'percent'.""") - - -class VoltageClampSeriesWholeCellCapacitanceComp(ConfiguredBaseModel): - """ - Whole cell capacitance compensation, in farads. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for whole_cell_capacitance_comp, which is fixed to 'farads'.""") - - -class VoltageClampSeriesWholeCellSeriesResistanceComp(ConfiguredBaseModel): - """ - Whole cell series resistance compensation, in ohms. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for whole_cell_series_resistance_comp, which is fixed to 'ohms'.""") - - -class VoltageClampStimulusSeriesData(ConfiguredBaseModel): - """ - Stimulus voltage applied. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'volts'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - - -class IntracellularElectrodeCellId(ConfiguredBaseModel): - """ - unique ID of the cell - """ - None - - -class IntracellularElectrodeDescription(ConfiguredBaseModel): - """ - Description of electrode (e.g., whole-cell, sharp, etc.). - """ - None - - -class IntracellularElectrodeFiltering(ConfiguredBaseModel): - """ - Electrode specific filtering. - """ - None - - -class IntracellularElectrodeInitialAccessResistance(ConfiguredBaseModel): - """ - Initial access resistance. - """ - None - - -class IntracellularElectrodeLocation(ConfiguredBaseModel): - """ - Location of the electrode. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible. - """ - None - - -class IntracellularElectrodeResistance(ConfiguredBaseModel): - """ - Electrode resistance, in ohms. - """ - None - - -class IntracellularElectrodeSeal(ConfiguredBaseModel): - """ - Information about seal used for recording. - """ - None - - -class IntracellularElectrodeSlice(ConfiguredBaseModel): - """ - Information about slice used for recording. - """ - None - - -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - -class PatchClampSeriesDataArray(Arraylike): - - num_times: float = Field(...) - - -class VectorDataArray(Arraylike): - - dim0: Any = Field(...) - dim1: Optional[Any] = Field(None) - dim2: Optional[Any] = Field(None) - dim3: Optional[Any] = Field(None) - - -class VectorIndexArray(Arraylike): - - num_rows: int = Field(...) - - -class ElementIdentifiersArray(Arraylike): - - num_elements: int = Field(...) - - -class DynamicTableRegionArray(Arraylike): - - num_rows: int = Field(...) - - -class DynamicTableIdArray(Arraylike): - - num_rows: int = Field(...) - - -class Data(ConfiguredBaseModel): - """ - An abstract data type for a dataset. - """ - None - - -class VectorData(Data): - """ - An n-dimensional dataset representing a column of a DynamicTable. If used without an accompanying VectorIndex, first dimension is along the rows of the DynamicTable and each step along the first dimension is a cell of the larger table. VectorData can also be used to represent a ragged array if paired with a VectorIndex. This allows for storing arrays of varying length in a single cell of the DynamicTable by indexing into this VectorData. The first vector is at VectorData[0:VectorIndex[0]]. The second vector is at VectorData[VectorIndex[0]:VectorIndex[1]], and so on. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class SweepTableSweepNumber(VectorData): - """ - Sweep number of the PatchClampSeries in that row. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class SweepTableSeries(VectorData): - """ - The PatchClampSeries with the sweep number in that row. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class IntracellularElectrodesTableElectrode(VectorData): - """ - Column for storing the reference to the intracellular electrode. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class SequentialRecordingsTableStimulusType(VectorData): - """ - The type of stimulus used for the sequential recording. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class VectorIndex(VectorData): - """ - Used with VectorData to encode a ragged array. An array of indices into the first dimension of the target VectorData, and forming a map between the rows of a DynamicTable and the indices of the VectorData. The name of the VectorIndex is expected to be the name of the target VectorData object followed by \"_index\". - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class SweepTableSeriesIndex(VectorIndex): - """ - Index for series. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class SimultaneousRecordingsTableRecordingsIndex(VectorIndex): - """ - Index dataset for the recordings column. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class SequentialRecordingsTableSimultaneousRecordingsIndex(VectorIndex): - """ - Index dataset for the simultaneous_recordings column. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class RepetitionsTableSequentialRecordingsIndex(VectorIndex): - """ - Index dataset for the sequential_recordings column. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ExperimentalConditionsTableRepetitionsIndex(VectorIndex): - """ - Index dataset for the repetitions column. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ElementIdentifiers(Data): - """ - A list of unique identifiers for values within a dataset, e.g. rows of a DynamicTable. - """ - array: Optional[ElementIdentifiersArray] = Field(None) - - -class DynamicTableRegion(VectorData): - """ - DynamicTableRegion provides a link from one table to an index or region of another. The `table` attribute is a link to another `DynamicTable`, indicating which table is referenced, and the data is int(s) indicating the row(s) (0-indexed) of the target array. `DynamicTableRegion`s can be used to associate rows with repeated meta-data without data duplication. They can also be used to create hierarchical relationships between multiple `DynamicTable`s. `DynamicTableRegion` objects may be paired with a `VectorIndex` object to create ragged references, so a single cell of a `DynamicTable` can reference many rows of another `DynamicTable`. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class SimultaneousRecordingsTableRecordings(DynamicTableRegion): - """ - A reference to one or more rows in the IntracellularRecordingsTable table. - """ - table: Optional[IntracellularRecordingsTable] = Field(None, description="""Reference to the IntracellularRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class SequentialRecordingsTableSimultaneousRecordings(DynamicTableRegion): - """ - A reference to one or more rows in the SimultaneousRecordingsTable table. - """ - table: Optional[SimultaneousRecordingsTable] = Field(None, description="""Reference to the SimultaneousRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class RepetitionsTableSequentialRecordings(DynamicTableRegion): - """ - A reference to one or more rows in the SequentialRecordingsTable table. - """ - table: Optional[SequentialRecordingsTable] = Field(None, description="""Reference to the SequentialRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class ExperimentalConditionsTableRepetitions(DynamicTableRegion): - """ - A reference to one or more rows in the RepetitionsTable table. - """ - table: Optional[RepetitionsTable] = Field(None, description="""Reference to the RepetitionsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DynamicTableId(ElementIdentifiers): - """ - Array of unique identifiers for the rows of this dynamic table. - """ - array: Optional[DynamicTableIdArray] = Field(None) - - -class Container(ConfiguredBaseModel): - """ - An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class DynamicTable(Container): - """ - A group containing multiple datasets that are aligned on the first dimension (Currently, this requirement if left up to APIs to check and enforce). These datasets represent different columns in the table. Apart from a column that contains unique identifiers for each row, there are no other required datasets. Users are free to add any number of custom VectorData objects (columns) here. DynamicTable also supports ragged array columns, where each element can be of a different size. To add a ragged array column, use a VectorIndex type to index the corresponding VectorData type. See documentation for VectorData and VectorIndex for more details. Unlike a compound data type, which is analogous to storing an array-of-structs, a DynamicTable can be thought of as a struct-of-arrays. This provides an alternative structure to choose from when optimizing storage for anticipated access patterns. Additionally, this type provides a way of creating a table without having to define a compound type up front. Although this convenience may be attractive, users should think carefully about how data will be accessed. DynamicTable is more appropriate for column-centric access, whereas a dataset with a compound type would be more appropriate for row-centric access. Finally, data size should also be taken into account. For small tables, performance loss may be an acceptable trade-off for the flexibility of a DynamicTable. - """ - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SweepTable(DynamicTable): - """ - [DEPRECATED] Table used to group different PatchClampSeries. SweepTable is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable tables. Additional SequentialRecordingsTable, RepetitionsTable, and ExperimentalConditions tables provide enhanced support for experiment metadata. - """ - sweep_number: SweepTableSweepNumber = Field(..., description="""Sweep number of the PatchClampSeries in that row.""") - series: SweepTableSeries = Field(..., description="""The PatchClampSeries with the sweep number in that row.""") - series_index: SweepTableSeriesIndex = Field(..., description="""Index for series.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class IntracellularElectrodesTable(DynamicTable): - """ - Table for storing intracellular electrode related metadata. - """ - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - electrode: IntracellularElectrodesTableElectrode = Field(..., description="""Column for storing the reference to the intracellular electrode.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class IntracellularStimuliTable(DynamicTable): - """ - Table for storing intracellular stimulus related metadata. - """ - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - stimulus: IntracellularStimuliTableStimulus = Field(..., description="""Column storing the reference to the recorded stimulus for the recording (rows).""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class IntracellularResponsesTable(DynamicTable): - """ - Table for storing intracellular response related metadata. - """ - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - response: IntracellularResponsesTableResponse = Field(..., description="""Column storing the reference to the recorded response for the recording (rows)""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class IntracellularRecordingsTableElectrodes(IntracellularElectrodesTable): - """ - Table for storing intracellular electrode related metadata. - """ - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - electrode: IntracellularElectrodesTableElectrode = Field(..., description="""Column for storing the reference to the intracellular electrode.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class IntracellularRecordingsTableStimuli(IntracellularStimuliTable): - """ - Table for storing intracellular stimulus related metadata. - """ - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - stimulus: IntracellularStimuliTableStimulus = Field(..., description="""Column storing the reference to the recorded stimulus for the recording (rows).""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class IntracellularRecordingsTableResponses(IntracellularResponsesTable): - """ - Table for storing intracellular response related metadata. - """ - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - response: IntracellularResponsesTableResponse = Field(..., description="""Column storing the reference to the recorded response for the recording (rows)""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimultaneousRecordingsTable(DynamicTable): - """ - A table for grouping different intracellular recordings from the IntracellularRecordingsTable table together that were recorded simultaneously from different electrodes. - """ - recordings: SimultaneousRecordingsTableRecordings = Field(..., description="""A reference to one or more rows in the IntracellularRecordingsTable table.""") - recordings_index: SimultaneousRecordingsTableRecordingsIndex = Field(..., description="""Index dataset for the recordings column.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SequentialRecordingsTable(DynamicTable): - """ - A table for grouping different sequential recordings from the SimultaneousRecordingsTable table together. This is typically used to group together sequential recordings where a sequence of stimuli of the same type with varying parameters have been presented in a sequence. - """ - simultaneous_recordings: SequentialRecordingsTableSimultaneousRecordings = Field(..., description="""A reference to one or more rows in the SimultaneousRecordingsTable table.""") - simultaneous_recordings_index: SequentialRecordingsTableSimultaneousRecordingsIndex = Field(..., description="""Index dataset for the simultaneous_recordings column.""") - stimulus_type: SequentialRecordingsTableStimulusType = Field(..., description="""The type of stimulus used for the sequential recording.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class RepetitionsTable(DynamicTable): - """ - A table for grouping different sequential intracellular recordings together. With each SequentialRecording typically representing a particular type of stimulus, the RepetitionsTable table is typically used to group sets of stimuli applied in sequence. - """ - sequential_recordings: RepetitionsTableSequentialRecordings = Field(..., description="""A reference to one or more rows in the SequentialRecordingsTable table.""") - sequential_recordings_index: RepetitionsTableSequentialRecordingsIndex = Field(..., description="""Index dataset for the sequential_recordings column.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class ExperimentalConditionsTable(DynamicTable): - """ - A table for grouping different intracellular recording repetitions together that belong to the same experimental condition. - """ - repetitions: ExperimentalConditionsTableRepetitions = Field(..., description="""A reference to one or more rows in the RepetitionsTable table.""") - repetitions_index: ExperimentalConditionsTableRepetitionsIndex = Field(..., description="""Index dataset for the repetitions column.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class AlignedDynamicTable(DynamicTable): - """ - DynamicTable container that supports storing a collection of sub-tables. Each sub-table is a DynamicTable itself that is aligned with the main table by row index. I.e., all DynamicTables stored in this group MUST have the same number of rows. This type effectively defines a 2-level table in which the main data is stored in the main table implemented by this type and additional columns of the table are grouped into categories, with each category being represented by a separate DynamicTable stored within the group. - """ - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class IntracellularRecordingsTable(AlignedDynamicTable): - """ - A table to group together a stimulus and response from a single electrode and a single simultaneous recording. Each row in the table represents a single recording consisting typically of a stimulus and a corresponding response. In some cases, however, only a stimulus or a response is recorded as part of an experiment. In this case, both the stimulus and response will point to the same TimeSeries while the idx_start and count of the invalid column will be set to -1, thus, indicating that no values have been recorded for the stimulus or response, respectively. Note, a recording MUST contain at least a stimulus or a response. Typically the stimulus and response are PatchClampSeries. However, the use of AD/DA channels that are not associated to an electrode is also common in intracellular electrophysiology, in which case other TimeSeries may be used. - """ - description: Optional[str] = Field(None, description="""Description of the contents of this table. Inherited from AlignedDynamicTable and overwritten here to fix the value of the attribute.""") - electrodes: IntracellularRecordingsTableElectrodes = Field(..., description="""Table for storing intracellular electrode related metadata.""") - stimuli: IntracellularRecordingsTableStimuli = Field(..., description="""Table for storing intracellular stimulus related metadata.""") - responses: IntracellularRecordingsTableResponses = Field(..., description="""Table for storing intracellular response related metadata.""") - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimpleMultiContainer(Container): - """ - A simple Container for holding onto multiple containers. - """ - Data: Optional[List[Data]] = Field(default_factory=list, description="""Data objects held within this SimpleMultiContainer.""") - Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") - - -class NWBData(Data): - """ - An abstract data type for a dataset. - """ - None - - -class TimeSeriesReferenceVectorData(VectorData): - """ - Column storing references to a TimeSeries (rows). For each TimeSeries this VectorData column stores the start_index and count to indicate the range in time to be selected as well as an object reference to the TimeSeries. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class IntracellularStimuliTableStimulus(TimeSeriesReferenceVectorData): - """ - Column storing the reference to the recorded stimulus for the recording (rows). - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class IntracellularResponsesTableResponse(TimeSeriesReferenceVectorData): - """ - Column storing the reference to the recorded response for the recording (rows) - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class Image(NWBData): - """ - An abstract data type for an image. Shape can be 2-D (x, y), or 3-D where the third dimension can have three or four elements, e.g. (x, y, (r, g, b)) or (x, y, (r, g, b, a)). - """ - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - array: Optional[ImageArray] = Field(None) - - -class ImageArray(Arraylike): - - x: float = Field(...) - y: float = Field(...) - r_g_b: Optional[float] = Field(None) - r_g_b_a: Optional[float] = Field(None) - - -class ImageReferences(NWBData): - """ - Ordered dataset of references to Image objects. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class ImageReferencesArray(Arraylike): - - num_images: Image = Field(...) - - -class NWBContainer(Container): - """ - An abstract data type for a generic container storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class IntracellularElectrode(NWBContainer): - """ - An intracellular electrode and its metadata. - """ - cell_id: Optional[IntracellularElectrodeCellId] = Field(None, description="""unique ID of the cell""") - description: IntracellularElectrodeDescription = Field(..., description="""Description of electrode (e.g., whole-cell, sharp, etc.).""") - filtering: Optional[IntracellularElectrodeFiltering] = Field(None, description="""Electrode specific filtering.""") - initial_access_resistance: Optional[IntracellularElectrodeInitialAccessResistance] = Field(None, description="""Initial access resistance.""") - location: Optional[IntracellularElectrodeLocation] = Field(None, description="""Location of the electrode. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible.""") - resistance: Optional[IntracellularElectrodeResistance] = Field(None, description="""Electrode resistance, in ohms.""") - seal: Optional[IntracellularElectrodeSeal] = Field(None, description="""Information about seal used for recording.""") - slice: Optional[IntracellularElectrodeSlice] = Field(None, description="""Information about slice used for recording.""") - - -class NWBDataInterface(NWBContainer): - """ - An abstract data type for a generic container storing collections of data, as opposed to metadata. - """ - None - - -class TimeSeries(NWBDataInterface): - """ - General purpose time series. - """ - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - data: TimeSeriesData = Field(..., description="""Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class PatchClampSeries(TimeSeries): - """ - An abstract base class for patch-clamp data - stimulus or response, current or voltage. - """ - stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") - sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") - data: PatchClampSeriesData = Field(..., description="""Recorded voltage or current.""") - gain: Optional[PatchClampSeriesGain] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class CurrentClampSeries(PatchClampSeries): - """ - Voltage data from an intracellular current-clamp recording. A corresponding CurrentClampStimulusSeries (stored separately as a stimulus) is used to store the current injected. - """ - data: CurrentClampSeriesData = Field(..., description="""Recorded voltage.""") - bias_current: Optional[CurrentClampSeriesBiasCurrent] = Field(None, description="""Bias current, in amps.""") - bridge_balance: Optional[CurrentClampSeriesBridgeBalance] = Field(None, description="""Bridge balance, in ohms.""") - capacitance_compensation: Optional[CurrentClampSeriesCapacitanceCompensation] = Field(None, description="""Capacitance compensation, in farads.""") - stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") - sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") - gain: Optional[PatchClampSeriesGain] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class IZeroClampSeries(CurrentClampSeries): - """ - Voltage data from an intracellular recording when all current and amplifier settings are off (i.e., CurrentClampSeries fields will be zero). There is no CurrentClampStimulusSeries associated with an IZero series because the amplifier is disconnected and no stimulus can reach the cell. - """ - stimulus_description: Optional[str] = Field(None, description="""An IZeroClampSeries has no stimulus, so this attribute is automatically set to \"N/A\"""") - bias_current: IZeroClampSeriesBiasCurrent = Field(..., description="""Bias current, in amps, fixed to 0.0.""") - bridge_balance: IZeroClampSeriesBridgeBalance = Field(..., description="""Bridge balance, in ohms, fixed to 0.0.""") - capacitance_compensation: IZeroClampSeriesCapacitanceCompensation = Field(..., description="""Capacitance compensation, in farads, fixed to 0.0.""") - data: CurrentClampSeriesData = Field(..., description="""Recorded voltage.""") - sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") - gain: Optional[PatchClampSeriesGain] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class CurrentClampStimulusSeries(PatchClampSeries): - """ - Stimulus current applied during current clamp recording. - """ - data: CurrentClampStimulusSeriesData = Field(..., description="""Stimulus current applied.""") - stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") - sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") - gain: Optional[PatchClampSeriesGain] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class VoltageClampSeries(PatchClampSeries): - """ - Current data from an intracellular voltage-clamp recording. A corresponding VoltageClampStimulusSeries (stored separately as a stimulus) is used to store the voltage injected. - """ - data: VoltageClampSeriesData = Field(..., description="""Recorded current.""") - capacitance_fast: Optional[VoltageClampSeriesCapacitanceFast] = Field(None, description="""Fast capacitance, in farads.""") - capacitance_slow: Optional[VoltageClampSeriesCapacitanceSlow] = Field(None, description="""Slow capacitance, in farads.""") - resistance_comp_bandwidth: Optional[VoltageClampSeriesResistanceCompBandwidth] = Field(None, description="""Resistance compensation bandwidth, in hertz.""") - resistance_comp_correction: Optional[VoltageClampSeriesResistanceCompCorrection] = Field(None, description="""Resistance compensation correction, in percent.""") - resistance_comp_prediction: Optional[VoltageClampSeriesResistanceCompPrediction] = Field(None, description="""Resistance compensation prediction, in percent.""") - whole_cell_capacitance_comp: Optional[VoltageClampSeriesWholeCellCapacitanceComp] = Field(None, description="""Whole cell capacitance compensation, in farads.""") - whole_cell_series_resistance_comp: Optional[VoltageClampSeriesWholeCellSeriesResistanceComp] = Field(None, description="""Whole cell series resistance compensation, in ohms.""") - stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") - sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") - gain: Optional[PatchClampSeriesGain] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class VoltageClampStimulusSeries(PatchClampSeries): - """ - Stimulus voltage applied during a voltage clamp recording. - """ - data: VoltageClampStimulusSeriesData = Field(..., description="""Stimulus voltage applied.""") - stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") - sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") - gain: Optional[PatchClampSeriesGain] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class TimeSeriesData(ConfiguredBaseModel): - """ - Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file. - """ - conversion: Optional[float] = Field(None, description="""Scalar to multiply each element in data to convert it to the specified 'unit'. If the data are stored in acquisition system units or other units that require a conversion to be interpretable, multiply the data by 'conversion' to convert the data to the specified 'unit'. e.g. if the data acquisition system stores values in this object as signed 16-bit integers (int16 range -32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data acquisition system gain is 8000X, then the 'conversion' multiplier to get from raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9.""") - offset: Optional[float] = Field(None, description="""Scalar to add to the data after scaling by 'conversion' to finalize its coercion to the specified 'unit'. Two common examples of this include (a) data stored in an unsigned type that requires a shift after scaling to re-center the data, and (b) specialized recording devices that naturally cause a scalar offset with respect to the true units.""") - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data, stored in the specified by unit, e.g., the change in value of the least significant bit, or a larger number if signal noise is known to be present. If unknown, use -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - continuity: Optional[str] = Field(None, description="""Optionally describe the continuity of the data. Can be \"continuous\", \"instantaneous\", or \"step\". For example, a voltage trace would be \"continuous\", because samples are recorded from a continuous process. An array of lick times would be \"instantaneous\", because the data represents distinct moments in time. Times of image presentations would be \"step\" because the picture remains the same until the next timepoint. This field is optional, but is useful in providing information about the underlying data. It may inform the way this data is interpreted, the way it is visualized, and what analysis methods are applicable.""") - array: Optional[TimeSeriesDataArray] = Field(None) - - -class TimeSeriesDataArray(Arraylike): - - num_times: Any = Field(...) - num_DIM2: Optional[Any] = Field(None) - num_DIM3: Optional[Any] = Field(None) - num_DIM4: Optional[Any] = Field(None) - - -class TimeSeriesStartingTime(ConfiguredBaseModel): - """ - Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute. - """ - rate: Optional[float] = Field(None, description="""Sampling rate, in Hz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement for time, which is fixed to 'seconds'.""") - - -class TimeSeriesTimestamps(ConfiguredBaseModel): - """ - Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. - """ - interval: Optional[int] = Field(None, description="""Value is '1'""") - unit: Optional[str] = Field(None, description="""Unit of measurement for timestamps, which is fixed to 'seconds'.""") - array: Optional[TimeSeriesTimestampsArray] = Field(None) - - -class TimeSeriesTimestampsArray(Arraylike): - - num_times: float = Field(...) - - -class TimeSeriesControl(ConfiguredBaseModel): - """ - Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data. - """ - array: Optional[TimeSeriesControlArray] = Field(None) - - -class TimeSeriesControlArray(Arraylike): - - num_times: int = Field(...) - - -class TimeSeriesControlDescription(ConfiguredBaseModel): - """ - Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0. - """ - array: Optional[TimeSeriesControlDescriptionArray] = Field(None) - - -class TimeSeriesControlDescriptionArray(Arraylike): - - num_control_values: str = Field(...) - - -class TimeSeriesSync(ConfiguredBaseModel): - """ - Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes. - """ - None - - -class ProcessingModule(NWBContainer): - """ - A collection of processed data. - """ - description: Optional[str] = Field(None, description="""Description of this collection of processed data.""") - NWBDataInterface: Optional[List[NWBDataInterface]] = Field(default_factory=list, description="""Data objects stored in this collection.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tables stored in this collection.""") - - -class Images(NWBDataInterface): - """ - A collection of images with an optional way to specify the order of the images using the \"order_of_images\" dataset. An order must be specified if the images are referenced by index, e.g., from an IndexSeries. - """ - description: Optional[str] = Field(None, description="""Description of this collection of images.""") - Image: List[Image] = Field(default_factory=list, description="""Images stored in this collection.""") - order_of_images: Optional[ImagesOrderOfImages] = Field(None, description="""Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images.""") - - -class ImagesOrderOfImages(ImageReferences): - """ - Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images. - """ - array: Optional[ImageReferencesArray] = Field(None) - - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -PatchClampSeriesData.update_forward_refs() -PatchClampSeriesGain.update_forward_refs() -CurrentClampSeriesData.update_forward_refs() -CurrentClampSeriesBiasCurrent.update_forward_refs() -CurrentClampSeriesBridgeBalance.update_forward_refs() -CurrentClampSeriesCapacitanceCompensation.update_forward_refs() -IZeroClampSeriesBiasCurrent.update_forward_refs() -IZeroClampSeriesBridgeBalance.update_forward_refs() -IZeroClampSeriesCapacitanceCompensation.update_forward_refs() -CurrentClampStimulusSeriesData.update_forward_refs() -VoltageClampSeriesData.update_forward_refs() -VoltageClampSeriesCapacitanceFast.update_forward_refs() -VoltageClampSeriesCapacitanceSlow.update_forward_refs() -VoltageClampSeriesResistanceCompBandwidth.update_forward_refs() -VoltageClampSeriesResistanceCompCorrection.update_forward_refs() -VoltageClampSeriesResistanceCompPrediction.update_forward_refs() -VoltageClampSeriesWholeCellCapacitanceComp.update_forward_refs() -VoltageClampSeriesWholeCellSeriesResistanceComp.update_forward_refs() -VoltageClampStimulusSeriesData.update_forward_refs() -IntracellularElectrodeCellId.update_forward_refs() -IntracellularElectrodeDescription.update_forward_refs() -IntracellularElectrodeFiltering.update_forward_refs() -IntracellularElectrodeInitialAccessResistance.update_forward_refs() -IntracellularElectrodeLocation.update_forward_refs() -IntracellularElectrodeResistance.update_forward_refs() -IntracellularElectrodeSeal.update_forward_refs() -IntracellularElectrodeSlice.update_forward_refs() -Arraylike.update_forward_refs() -PatchClampSeriesDataArray.update_forward_refs() -VectorDataArray.update_forward_refs() -VectorIndexArray.update_forward_refs() -ElementIdentifiersArray.update_forward_refs() -DynamicTableRegionArray.update_forward_refs() -DynamicTableIdArray.update_forward_refs() -Data.update_forward_refs() -VectorData.update_forward_refs() -SweepTableSweepNumber.update_forward_refs() -SweepTableSeries.update_forward_refs() -IntracellularElectrodesTableElectrode.update_forward_refs() -SequentialRecordingsTableStimulusType.update_forward_refs() -VectorIndex.update_forward_refs() -SweepTableSeriesIndex.update_forward_refs() -SimultaneousRecordingsTableRecordingsIndex.update_forward_refs() -SequentialRecordingsTableSimultaneousRecordingsIndex.update_forward_refs() -RepetitionsTableSequentialRecordingsIndex.update_forward_refs() -ExperimentalConditionsTableRepetitionsIndex.update_forward_refs() -ElementIdentifiers.update_forward_refs() -DynamicTableRegion.update_forward_refs() -SimultaneousRecordingsTableRecordings.update_forward_refs() -SequentialRecordingsTableSimultaneousRecordings.update_forward_refs() -RepetitionsTableSequentialRecordings.update_forward_refs() -ExperimentalConditionsTableRepetitions.update_forward_refs() -DynamicTableId.update_forward_refs() -Container.update_forward_refs() -DynamicTable.update_forward_refs() -SweepTable.update_forward_refs() -IntracellularElectrodesTable.update_forward_refs() -IntracellularStimuliTable.update_forward_refs() -IntracellularResponsesTable.update_forward_refs() -IntracellularRecordingsTableElectrodes.update_forward_refs() -IntracellularRecordingsTableStimuli.update_forward_refs() -IntracellularRecordingsTableResponses.update_forward_refs() -SimultaneousRecordingsTable.update_forward_refs() -SequentialRecordingsTable.update_forward_refs() -RepetitionsTable.update_forward_refs() -ExperimentalConditionsTable.update_forward_refs() -AlignedDynamicTable.update_forward_refs() -IntracellularRecordingsTable.update_forward_refs() -SimpleMultiContainer.update_forward_refs() -NWBData.update_forward_refs() -TimeSeriesReferenceVectorData.update_forward_refs() -IntracellularStimuliTableStimulus.update_forward_refs() -IntracellularResponsesTableResponse.update_forward_refs() -Image.update_forward_refs() -ImageArray.update_forward_refs() -ImageReferences.update_forward_refs() -ImageReferencesArray.update_forward_refs() -NWBContainer.update_forward_refs() -IntracellularElectrode.update_forward_refs() -NWBDataInterface.update_forward_refs() -TimeSeries.update_forward_refs() -PatchClampSeries.update_forward_refs() -CurrentClampSeries.update_forward_refs() -IZeroClampSeries.update_forward_refs() -CurrentClampStimulusSeries.update_forward_refs() -VoltageClampSeries.update_forward_refs() -VoltageClampStimulusSeries.update_forward_refs() -TimeSeriesData.update_forward_refs() -TimeSeriesDataArray.update_forward_refs() -TimeSeriesStartingTime.update_forward_refs() -TimeSeriesTimestamps.update_forward_refs() -TimeSeriesTimestampsArray.update_forward_refs() -TimeSeriesControl.update_forward_refs() -TimeSeriesControlArray.update_forward_refs() -TimeSeriesControlDescription.update_forward_refs() -TimeSeriesControlDescriptionArray.update_forward_refs() -TimeSeriesSync.update_forward_refs() -ProcessingModule.update_forward_refs() -Images.update_forward_refs() -ImagesOrderOfImages.update_forward_refs() diff --git a/nwb_linkml/models/core.nwb.image.py b/nwb_linkml/models/core.nwb.image.py deleted file mode 100644 index adc8afb..0000000 --- a/nwb_linkml/models/core.nwb.image.py +++ /dev/null @@ -1,656 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): - pass - - -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - -class ImageSeriesData(ConfiguredBaseModel): - """ - Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array. - """ - array: Optional[ImageSeriesDataArray] = Field(None) - - -class ImageSeriesDimension(ConfiguredBaseModel): - """ - Number of pixels on x, y, (and z) axes. - """ - array: Optional[ImageSeriesDimensionArray] = Field(None) - - -class ImageSeriesExternalFile(ConfiguredBaseModel): - """ - Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file. - """ - starting_frame: Optional[int] = Field(None, description="""Each external image may contain one or more consecutive frames of the full ImageSeries. This attribute serves as an index to indicate which frames each file contains, to facilitate random access. The 'starting_frame' attribute, hence, contains a list of frame numbers within the full ImageSeries of the first frame of each file listed in the parent 'external_file' dataset. Zero-based indexing is used (hence, the first element will always be zero). For example, if the 'external_file' dataset has three paths to files and the first file has 5 frames, the second file has 10 frames, and the third file has 20 frames, then this attribute will have values [0, 5, 15]. If there is a single external file that holds all of the frames of the ImageSeries (and so there is a single element in the 'external_file' dataset), then this attribute should have value [0].""") - array: Optional[ImageSeriesExternalFileArray] = Field(None) - - -class ImageSeriesFormat(ConfiguredBaseModel): - """ - Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed. - """ - None - - -class OpticalSeriesDistance(ConfiguredBaseModel): - """ - Distance from camera/monitor to target/eye. - """ - None - - -class OpticalSeriesFieldOfView(ConfiguredBaseModel): - """ - Width, height and depth of image, or imaged area, in meters. - """ - array: Optional[OpticalSeriesFieldOfViewArray] = Field(None) - - -class OpticalSeriesData(ConfiguredBaseModel): - """ - Images presented to subject, either grayscale or RGB - """ - array: Optional[OpticalSeriesDataArray] = Field(None) - - -class OpticalSeriesOrientation(ConfiguredBaseModel): - """ - Description of image relative to some reference frame (e.g., which way is up). Must also specify frame of reference. - """ - None - - -class IndexSeriesData(ConfiguredBaseModel): - """ - Index of the image (using zero-indexing) in the linked Images object. - """ - conversion: Optional[float] = Field(None, description="""This field is unused by IndexSeries.""") - resolution: Optional[float] = Field(None, description="""This field is unused by IndexSeries.""") - offset: Optional[float] = Field(None, description="""This field is unused by IndexSeries.""") - unit: Optional[str] = Field(None, description="""This field is unused by IndexSeries and has the value N/A.""") - array: Optional[IndexSeriesDataArray] = Field(None) - - -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - -class GrayscaleImageArray(Arraylike): - - x: Optional[float] = Field(None) - y: Optional[float] = Field(None) - - -class RGBImageArray(Arraylike): - - x: Optional[float] = Field(None) - y: Optional[float] = Field(None) - r_g_b: Optional[float] = Field(None) - - -class RGBAImageArray(Arraylike): - - x: Optional[float] = Field(None) - y: Optional[float] = Field(None) - r_g_b_a: Optional[float] = Field(None) - - -class ImageSeriesDataArray(Arraylike): - - frame: float = Field(...) - x: float = Field(...) - y: float = Field(...) - z: Optional[float] = Field(None) - - -class ImageSeriesDimensionArray(Arraylike): - - rank: int = Field(...) - - -class ImageSeriesExternalFileArray(Arraylike): - - num_files: str = Field(...) - - -class OpticalSeriesFieldOfViewArray(Arraylike): - - width_height: Optional[float] = Field(None) - width_height_depth: Optional[float] = Field(None) - - -class OpticalSeriesDataArray(Arraylike): - - frame: float = Field(...) - x: float = Field(...) - y: float = Field(...) - r_g_b: Optional[float] = Field(None) - - -class IndexSeriesDataArray(Arraylike): - - num_times: int = Field(...) - - -class ImageArray(Arraylike): - - x: float = Field(...) - y: float = Field(...) - r_g_b: Optional[float] = Field(None) - r_g_b_a: Optional[float] = Field(None) - - -class ImageReferencesArray(Arraylike): - - num_images: Image = Field(...) - - -class TimeSeriesData(ConfiguredBaseModel): - """ - Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file. - """ - conversion: Optional[float] = Field(None, description="""Scalar to multiply each element in data to convert it to the specified 'unit'. If the data are stored in acquisition system units or other units that require a conversion to be interpretable, multiply the data by 'conversion' to convert the data to the specified 'unit'. e.g. if the data acquisition system stores values in this object as signed 16-bit integers (int16 range -32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data acquisition system gain is 8000X, then the 'conversion' multiplier to get from raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9.""") - offset: Optional[float] = Field(None, description="""Scalar to add to the data after scaling by 'conversion' to finalize its coercion to the specified 'unit'. Two common examples of this include (a) data stored in an unsigned type that requires a shift after scaling to re-center the data, and (b) specialized recording devices that naturally cause a scalar offset with respect to the true units.""") - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data, stored in the specified by unit, e.g., the change in value of the least significant bit, or a larger number if signal noise is known to be present. If unknown, use -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - continuity: Optional[str] = Field(None, description="""Optionally describe the continuity of the data. Can be \"continuous\", \"instantaneous\", or \"step\". For example, a voltage trace would be \"continuous\", because samples are recorded from a continuous process. An array of lick times would be \"instantaneous\", because the data represents distinct moments in time. Times of image presentations would be \"step\" because the picture remains the same until the next timepoint. This field is optional, but is useful in providing information about the underlying data. It may inform the way this data is interpreted, the way it is visualized, and what analysis methods are applicable.""") - array: Optional[TimeSeriesDataArray] = Field(None) - - -class TimeSeriesDataArray(Arraylike): - - num_times: Any = Field(...) - num_DIM2: Optional[Any] = Field(None) - num_DIM3: Optional[Any] = Field(None) - num_DIM4: Optional[Any] = Field(None) - - -class TimeSeriesStartingTime(ConfiguredBaseModel): - """ - Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute. - """ - rate: Optional[float] = Field(None, description="""Sampling rate, in Hz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement for time, which is fixed to 'seconds'.""") - - -class TimeSeriesTimestamps(ConfiguredBaseModel): - """ - Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. - """ - interval: Optional[int] = Field(None, description="""Value is '1'""") - unit: Optional[str] = Field(None, description="""Unit of measurement for timestamps, which is fixed to 'seconds'.""") - array: Optional[TimeSeriesTimestampsArray] = Field(None) - - -class TimeSeriesTimestampsArray(Arraylike): - - num_times: float = Field(...) - - -class TimeSeriesControl(ConfiguredBaseModel): - """ - Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data. - """ - array: Optional[TimeSeriesControlArray] = Field(None) - - -class TimeSeriesControlArray(Arraylike): - - num_times: int = Field(...) - - -class TimeSeriesControlDescription(ConfiguredBaseModel): - """ - Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0. - """ - array: Optional[TimeSeriesControlDescriptionArray] = Field(None) - - -class TimeSeriesControlDescriptionArray(Arraylike): - - num_control_values: str = Field(...) - - -class TimeSeriesSync(ConfiguredBaseModel): - """ - Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes. - """ - None - - -class VectorDataArray(Arraylike): - - dim0: Any = Field(...) - dim1: Optional[Any] = Field(None) - dim2: Optional[Any] = Field(None) - dim3: Optional[Any] = Field(None) - - -class VectorIndexArray(Arraylike): - - num_rows: int = Field(...) - - -class ElementIdentifiersArray(Arraylike): - - num_elements: int = Field(...) - - -class DynamicTableRegionArray(Arraylike): - - num_rows: int = Field(...) - - -class DynamicTableIdArray(Arraylike): - - num_rows: int = Field(...) - - -class Data(ConfiguredBaseModel): - """ - An abstract data type for a dataset. - """ - None - - -class NWBData(Data): - """ - An abstract data type for a dataset. - """ - None - - -class Image(NWBData): - """ - An abstract data type for an image. Shape can be 2-D (x, y), or 3-D where the third dimension can have three or four elements, e.g. (x, y, (r, g, b)) or (x, y, (r, g, b, a)). - """ - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - array: Optional[ImageArray] = Field(None) - - -class GrayscaleImage(Image): - """ - A grayscale image. - """ - array: Optional[GrayscaleImageArray] = Field(None) - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - - -class RGBImage(Image): - """ - A color image. - """ - array: Optional[RGBImageArray] = Field(None) - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - - -class RGBAImage(Image): - """ - A color image with transparency. - """ - array: Optional[RGBAImageArray] = Field(None) - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - - -class ImageReferences(NWBData): - """ - Ordered dataset of references to Image objects. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class ImagesOrderOfImages(ImageReferences): - """ - Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class VectorData(Data): - """ - An n-dimensional dataset representing a column of a DynamicTable. If used without an accompanying VectorIndex, first dimension is along the rows of the DynamicTable and each step along the first dimension is a cell of the larger table. VectorData can also be used to represent a ragged array if paired with a VectorIndex. This allows for storing arrays of varying length in a single cell of the DynamicTable by indexing into this VectorData. The first vector is at VectorData[0:VectorIndex[0]]. The second vector is at VectorData[VectorIndex[0]:VectorIndex[1]], and so on. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class TimeSeriesReferenceVectorData(VectorData): - """ - Column storing references to a TimeSeries (rows). For each TimeSeries this VectorData column stores the start_index and count to indicate the range in time to be selected as well as an object reference to the TimeSeries. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class VectorIndex(VectorData): - """ - Used with VectorData to encode a ragged array. An array of indices into the first dimension of the target VectorData, and forming a map between the rows of a DynamicTable and the indices of the VectorData. The name of the VectorIndex is expected to be the name of the target VectorData object followed by \"_index\". - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ElementIdentifiers(Data): - """ - A list of unique identifiers for values within a dataset, e.g. rows of a DynamicTable. - """ - array: Optional[ElementIdentifiersArray] = Field(None) - - -class DynamicTableRegion(VectorData): - """ - DynamicTableRegion provides a link from one table to an index or region of another. The `table` attribute is a link to another `DynamicTable`, indicating which table is referenced, and the data is int(s) indicating the row(s) (0-indexed) of the target array. `DynamicTableRegion`s can be used to associate rows with repeated meta-data without data duplication. They can also be used to create hierarchical relationships between multiple `DynamicTable`s. `DynamicTableRegion` objects may be paired with a `VectorIndex` object to create ragged references, so a single cell of a `DynamicTable` can reference many rows of another `DynamicTable`. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DynamicTableId(ElementIdentifiers): - """ - Array of unique identifiers for the rows of this dynamic table. - """ - array: Optional[DynamicTableIdArray] = Field(None) - - -class Container(ConfiguredBaseModel): - """ - An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class NWBContainer(Container): - """ - An abstract data type for a generic container storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class NWBDataInterface(NWBContainer): - """ - An abstract data type for a generic container storing collections of data, as opposed to metadata. - """ - None - - -class TimeSeries(NWBDataInterface): - """ - General purpose time series. - """ - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - data: TimeSeriesData = Field(..., description="""Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class ImageSeries(TimeSeries): - """ - General image data that is common between acquisition and stimulus time series. Sometimes the image data is stored in the file in a raw format while other times it will be stored as a series of external image files in the host file system. The data field will either be binary data, if the data is stored in the NWB file, or empty, if the data is stored in an external image stack. [frame][x][y] or [frame][x][y][z]. - """ - data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class ImageMaskSeries(ImageSeries): - """ - An alpha mask that is applied to a presented visual stimulus. The 'data' array contains an array of mask values that are applied to the displayed image. Mask values are stored as RGBA. Mask can vary with time. The timestamps array indicates the starting time of a mask, and that mask pattern continues until it's explicitly changed. - """ - data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class OpticalSeries(ImageSeries): - """ - Image data that is presented or recorded. A stimulus template movie will be stored only as an image. When the image is presented as stimulus, additional data is required, such as field of view (e.g., how much of the visual field the image covers, or how what is the area of the target being imaged). If the OpticalSeries represents acquired imaging data, orientation is also important. - """ - distance: Optional[OpticalSeriesDistance] = Field(None, description="""Distance from camera/monitor to target/eye.""") - field_of_view: Optional[OpticalSeriesFieldOfView] = Field(None, description="""Width, height and depth of image, or imaged area, in meters.""") - data: OpticalSeriesData = Field(..., description="""Images presented to subject, either grayscale or RGB""") - orientation: Optional[OpticalSeriesOrientation] = Field(None, description="""Description of image relative to some reference frame (e.g., which way is up). Must also specify frame of reference.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class IndexSeries(TimeSeries): - """ - Stores indices to image frames stored in an ImageSeries. The purpose of the IndexSeries is to allow a static image stack to be stored in an Images object, and the images in the stack to be referenced out-of-order. This can be for the display of individual images, or of movie segments (as a movie is simply a series of images). The data field stores the index of the frame in the referenced Images object, and the timestamps array indicates when that image was displayed. - """ - data: IndexSeriesData = Field(..., description="""Index of the image (using zero-indexing) in the linked Images object.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class ProcessingModule(NWBContainer): - """ - A collection of processed data. - """ - description: Optional[str] = Field(None, description="""Description of this collection of processed data.""") - NWBDataInterface: Optional[List[NWBDataInterface]] = Field(default_factory=list, description="""Data objects stored in this collection.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tables stored in this collection.""") - - -class Images(NWBDataInterface): - """ - A collection of images with an optional way to specify the order of the images using the \"order_of_images\" dataset. An order must be specified if the images are referenced by index, e.g., from an IndexSeries. - """ - description: Optional[str] = Field(None, description="""Description of this collection of images.""") - Image: List[Image] = Field(default_factory=list, description="""Images stored in this collection.""") - order_of_images: Optional[ImagesOrderOfImages] = Field(None, description="""Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images.""") - - -class DynamicTable(Container): - """ - A group containing multiple datasets that are aligned on the first dimension (Currently, this requirement if left up to APIs to check and enforce). These datasets represent different columns in the table. Apart from a column that contains unique identifiers for each row, there are no other required datasets. Users are free to add any number of custom VectorData objects (columns) here. DynamicTable also supports ragged array columns, where each element can be of a different size. To add a ragged array column, use a VectorIndex type to index the corresponding VectorData type. See documentation for VectorData and VectorIndex for more details. Unlike a compound data type, which is analogous to storing an array-of-structs, a DynamicTable can be thought of as a struct-of-arrays. This provides an alternative structure to choose from when optimizing storage for anticipated access patterns. Additionally, this type provides a way of creating a table without having to define a compound type up front. Although this convenience may be attractive, users should think carefully about how data will be accessed. DynamicTable is more appropriate for column-centric access, whereas a dataset with a compound type would be more appropriate for row-centric access. Finally, data size should also be taken into account. For small tables, performance loss may be an acceptable trade-off for the flexibility of a DynamicTable. - """ - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class AlignedDynamicTable(DynamicTable): - """ - DynamicTable container that supports storing a collection of sub-tables. Each sub-table is a DynamicTable itself that is aligned with the main table by row index. I.e., all DynamicTables stored in this group MUST have the same number of rows. This type effectively defines a 2-level table in which the main data is stored in the main table implemented by this type and additional columns of the table are grouped into categories, with each category being represented by a separate DynamicTable stored within the group. - """ - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimpleMultiContainer(Container): - """ - A simple Container for holding onto multiple containers. - """ - Data: Optional[List[Data]] = Field(default_factory=list, description="""Data objects held within this SimpleMultiContainer.""") - Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") - - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -ImageSeriesData.update_forward_refs() -ImageSeriesDimension.update_forward_refs() -ImageSeriesExternalFile.update_forward_refs() -ImageSeriesFormat.update_forward_refs() -OpticalSeriesDistance.update_forward_refs() -OpticalSeriesFieldOfView.update_forward_refs() -OpticalSeriesData.update_forward_refs() -OpticalSeriesOrientation.update_forward_refs() -IndexSeriesData.update_forward_refs() -Arraylike.update_forward_refs() -GrayscaleImageArray.update_forward_refs() -RGBImageArray.update_forward_refs() -RGBAImageArray.update_forward_refs() -ImageSeriesDataArray.update_forward_refs() -ImageSeriesDimensionArray.update_forward_refs() -ImageSeriesExternalFileArray.update_forward_refs() -OpticalSeriesFieldOfViewArray.update_forward_refs() -OpticalSeriesDataArray.update_forward_refs() -IndexSeriesDataArray.update_forward_refs() -ImageArray.update_forward_refs() -ImageReferencesArray.update_forward_refs() -TimeSeriesData.update_forward_refs() -TimeSeriesDataArray.update_forward_refs() -TimeSeriesStartingTime.update_forward_refs() -TimeSeriesTimestamps.update_forward_refs() -TimeSeriesTimestampsArray.update_forward_refs() -TimeSeriesControl.update_forward_refs() -TimeSeriesControlArray.update_forward_refs() -TimeSeriesControlDescription.update_forward_refs() -TimeSeriesControlDescriptionArray.update_forward_refs() -TimeSeriesSync.update_forward_refs() -VectorDataArray.update_forward_refs() -VectorIndexArray.update_forward_refs() -ElementIdentifiersArray.update_forward_refs() -DynamicTableRegionArray.update_forward_refs() -DynamicTableIdArray.update_forward_refs() -Data.update_forward_refs() -NWBData.update_forward_refs() -Image.update_forward_refs() -GrayscaleImage.update_forward_refs() -RGBImage.update_forward_refs() -RGBAImage.update_forward_refs() -ImageReferences.update_forward_refs() -ImagesOrderOfImages.update_forward_refs() -VectorData.update_forward_refs() -TimeSeriesReferenceVectorData.update_forward_refs() -VectorIndex.update_forward_refs() -ElementIdentifiers.update_forward_refs() -DynamicTableRegion.update_forward_refs() -DynamicTableId.update_forward_refs() -Container.update_forward_refs() -NWBContainer.update_forward_refs() -NWBDataInterface.update_forward_refs() -TimeSeries.update_forward_refs() -ImageSeries.update_forward_refs() -ImageMaskSeries.update_forward_refs() -OpticalSeries.update_forward_refs() -IndexSeries.update_forward_refs() -ProcessingModule.update_forward_refs() -Images.update_forward_refs() -DynamicTable.update_forward_refs() -AlignedDynamicTable.update_forward_refs() -SimpleMultiContainer.update_forward_refs() diff --git a/nwb_linkml/models/core.nwb.misc.py b/nwb_linkml/models/core.nwb.misc.py deleted file mode 100644 index ef1f38f..0000000 --- a/nwb_linkml/models/core.nwb.misc.py +++ /dev/null @@ -1,831 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): - pass - - -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - -class AbstractFeatureSeriesData(ConfiguredBaseModel): - """ - Values of each feature at each time. - """ - unit: Optional[str] = Field(None, description="""Since there can be different units for different features, store the units in 'feature_units'. The default value for this attribute is \"see 'feature_units'\".""") - array: Optional[AbstractFeatureSeriesDataArray] = Field(None) - - -class AbstractFeatureSeriesFeatureUnits(ConfiguredBaseModel): - """ - Units of each feature. - """ - array: Optional[AbstractFeatureSeriesFeatureUnitsArray] = Field(None) - - -class AbstractFeatureSeriesFeatures(ConfiguredBaseModel): - """ - Description of the features represented in TimeSeries::data. - """ - array: Optional[AbstractFeatureSeriesFeaturesArray] = Field(None) - - -class AnnotationSeriesData(ConfiguredBaseModel): - """ - Annotations made during an experiment. - """ - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data. Annotations have no units, so the value is fixed to -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Annotations have no units, so the value is fixed to 'n/a'.""") - array: Optional[AnnotationSeriesDataArray] = Field(None) - - -class IntervalSeriesData(ConfiguredBaseModel): - """ - Use values >0 if interval started, <0 if interval ended. - """ - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data. Annotations have no units, so the value is fixed to -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Annotations have no units, so the value is fixed to 'n/a'.""") - array: Optional[IntervalSeriesDataArray] = Field(None) - - -class DecompositionSeriesData(ConfiguredBaseModel): - """ - Data decomposed into frequency bands. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion'.""") - array: Optional[DecompositionSeriesDataArray] = Field(None) - - -class DecompositionSeriesMetric(ConfiguredBaseModel): - """ - The metric used, e.g. phase, amplitude, power. - """ - None - - -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - -class AbstractFeatureSeriesDataArray(Arraylike): - - num_times: float = Field(...) - num_features: Optional[float] = Field(None) - - -class AbstractFeatureSeriesFeatureUnitsArray(Arraylike): - - num_features: str = Field(...) - - -class AbstractFeatureSeriesFeaturesArray(Arraylike): - - num_features: str = Field(...) - - -class AnnotationSeriesDataArray(Arraylike): - - num_times: str = Field(...) - - -class IntervalSeriesDataArray(Arraylike): - - num_times: int = Field(...) - - -class DecompositionSeriesDataArray(Arraylike): - - num_times: Optional[float] = Field(None) - num_channels: Optional[float] = Field(None) - num_bands: Optional[float] = Field(None) - - -class DecompositionSeriesBandsBandLimitsArray(Arraylike): - - num_bands: Optional[float] = Field(None) - low_high: Optional[float] = Field(None) - - -class DecompositionSeriesBandsBandMeanArray(Arraylike): - - num_bands: float = Field(...) - - -class DecompositionSeriesBandsBandStdevArray(Arraylike): - - num_bands: float = Field(...) - - -class UnitsObsIntervalsArray(Arraylike): - - num_intervals: Optional[float] = Field(None) - start|end: Optional[float] = Field(None) - - -class UnitsWaveformMeanArray(Arraylike): - - num_units: float = Field(...) - num_samples: float = Field(...) - num_electrodes: Optional[float] = Field(None) - - -class UnitsWaveformSdArray(Arraylike): - - num_units: float = Field(...) - num_samples: float = Field(...) - num_electrodes: Optional[float] = Field(None) - - -class UnitsWaveformsArray(Arraylike): - - num_waveforms: Optional[float] = Field(None) - num_samples: Optional[float] = Field(None) - - -class VectorDataArray(Arraylike): - - dim0: Any = Field(...) - dim1: Optional[Any] = Field(None) - dim2: Optional[Any] = Field(None) - dim3: Optional[Any] = Field(None) - - -class VectorIndexArray(Arraylike): - - num_rows: int = Field(...) - - -class ElementIdentifiersArray(Arraylike): - - num_elements: int = Field(...) - - -class DynamicTableRegionArray(Arraylike): - - num_rows: int = Field(...) - - -class DynamicTableIdArray(Arraylike): - - num_rows: int = Field(...) - - -class Data(ConfiguredBaseModel): - """ - An abstract data type for a dataset. - """ - None - - -class VectorData(Data): - """ - An n-dimensional dataset representing a column of a DynamicTable. If used without an accompanying VectorIndex, first dimension is along the rows of the DynamicTable and each step along the first dimension is a cell of the larger table. VectorData can also be used to represent a ragged array if paired with a VectorIndex. This allows for storing arrays of varying length in a single cell of the DynamicTable by indexing into this VectorData. The first vector is at VectorData[0:VectorIndex[0]]. The second vector is at VectorData[VectorIndex[0]:VectorIndex[1]], and so on. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class DecompositionSeriesBandsBandName(VectorData): - """ - Name of the band, e.g. theta. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class DecompositionSeriesBandsBandLimits(VectorData): - """ - Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center. - """ - array: Optional[DecompositionSeriesBandsBandLimitsArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class DecompositionSeriesBandsBandMean(VectorData): - """ - The mean Gaussian filters, in Hz. - """ - array: Optional[DecompositionSeriesBandsBandMeanArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class DecompositionSeriesBandsBandStdev(VectorData): - """ - The standard deviation of Gaussian filters, in Hz. - """ - array: Optional[DecompositionSeriesBandsBandStdevArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsSpikeTimes(VectorData): - """ - Spike times for each unit in seconds. - """ - resolution: Optional[float] = Field(None, description="""The smallest possible difference between two spike times. Usually 1 divided by the acquisition sampling rate from which spike times were extracted, but could be larger if the acquisition time series was downsampled or smaller if the acquisition time series was smoothed/interpolated and it is possible for the spike time to be between samples.""") - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class UnitsObsIntervals(VectorData): - """ - Observation intervals for each unit. - """ - array: Optional[UnitsObsIntervalsArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsElectrodeGroup(VectorData): - """ - Electrode group that each spike unit came from. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class UnitsWaveformMean(VectorData): - """ - Spike waveform mean for each spike unit. - """ - sampling_rate: Optional[float] = Field(None, description="""Sampling rate, in hertz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement. This value is fixed to 'volts'.""") - array: Optional[UnitsWaveformMeanArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsWaveformSd(VectorData): - """ - Spike waveform standard deviation for each spike unit. - """ - sampling_rate: Optional[float] = Field(None, description="""Sampling rate, in hertz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement. This value is fixed to 'volts'.""") - array: Optional[UnitsWaveformSdArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsWaveforms(VectorData): - """ - Individual waveforms for each spike on each electrode. This is a doubly indexed column. The 'waveforms_index' column indexes which waveforms in this column belong to the same spike event for a given unit, where each waveform was recorded from a different electrode. The 'waveforms_index_index' column indexes the 'waveforms_index' column to indicate which spike events belong to a given unit. For example, if the 'waveforms_index_index' column has values [2, 5, 6], then the first 2 elements of the 'waveforms_index' column correspond to the 2 spike events of the first unit, the next 3 elements of the 'waveforms_index' column correspond to the 3 spike events of the second unit, and the next 1 element of the 'waveforms_index' column corresponds to the 1 spike event of the third unit. If the 'waveforms_index' column has values [3, 6, 8, 10, 12, 13], then the first 3 elements of the 'waveforms' column contain the 3 spike waveforms that were recorded from 3 different electrodes for the first spike time of the first unit. See https://nwb-schema.readthedocs.io/en/stable/format_description.html#doubly-ragged-arrays for a graphical representation of this example. When there is only one electrode for each unit (i.e., each spike time is associated with a single waveform), then the 'waveforms_index' column will have values 1, 2, ..., N, where N is the number of spike events. The number of electrodes for each spike event should be the same within a given unit. The 'electrodes' column should be used to indicate which electrodes are associated with each unit, and the order of the waveforms within a given unit x spike event should be in the same order as the electrodes referenced in the 'electrodes' column of this table. The number of samples for each waveform must be the same. - """ - sampling_rate: Optional[float] = Field(None, description="""Sampling rate, in hertz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement. This value is fixed to 'volts'.""") - array: Optional[UnitsWaveformsArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class VectorIndex(VectorData): - """ - Used with VectorData to encode a ragged array. An array of indices into the first dimension of the target VectorData, and forming a map between the rows of a DynamicTable and the indices of the VectorData. The name of the VectorIndex is expected to be the name of the target VectorData object followed by \"_index\". - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsSpikeTimesIndex(VectorIndex): - """ - Index into the spike_times dataset. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsObsIntervalsIndex(VectorIndex): - """ - Index into the obs_intervals dataset. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsElectrodesIndex(VectorIndex): - """ - Index into electrodes. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsWaveformsIndex(VectorIndex): - """ - Index into the waveforms dataset. One value for every spike event. See 'waveforms' for more detail. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsWaveformsIndexIndex(VectorIndex): - """ - Index into the waveforms_index dataset. One value for every unit (row in the table). See 'waveforms' for more detail. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ElementIdentifiers(Data): - """ - A list of unique identifiers for values within a dataset, e.g. rows of a DynamicTable. - """ - array: Optional[ElementIdentifiersArray] = Field(None) - - -class DynamicTableRegion(VectorData): - """ - DynamicTableRegion provides a link from one table to an index or region of another. The `table` attribute is a link to another `DynamicTable`, indicating which table is referenced, and the data is int(s) indicating the row(s) (0-indexed) of the target array. `DynamicTableRegion`s can be used to associate rows with repeated meta-data without data duplication. They can also be used to create hierarchical relationships between multiple `DynamicTable`s. `DynamicTableRegion` objects may be paired with a `VectorIndex` object to create ragged references, so a single cell of a `DynamicTable` can reference many rows of another `DynamicTable`. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DecompositionSeriesSourceChannels(DynamicTableRegion): - """ - DynamicTableRegion pointer to the channels that this decomposition series was generated from. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class UnitsElectrodes(DynamicTableRegion): - """ - Electrode that each spike unit came from, specified using a DynamicTableRegion. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DynamicTableId(ElementIdentifiers): - """ - Array of unique identifiers for the rows of this dynamic table. - """ - array: Optional[DynamicTableIdArray] = Field(None) - - -class Container(ConfiguredBaseModel): - """ - An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class DynamicTable(Container): - """ - A group containing multiple datasets that are aligned on the first dimension (Currently, this requirement if left up to APIs to check and enforce). These datasets represent different columns in the table. Apart from a column that contains unique identifiers for each row, there are no other required datasets. Users are free to add any number of custom VectorData objects (columns) here. DynamicTable also supports ragged array columns, where each element can be of a different size. To add a ragged array column, use a VectorIndex type to index the corresponding VectorData type. See documentation for VectorData and VectorIndex for more details. Unlike a compound data type, which is analogous to storing an array-of-structs, a DynamicTable can be thought of as a struct-of-arrays. This provides an alternative structure to choose from when optimizing storage for anticipated access patterns. Additionally, this type provides a way of creating a table without having to define a compound type up front. Although this convenience may be attractive, users should think carefully about how data will be accessed. DynamicTable is more appropriate for column-centric access, whereas a dataset with a compound type would be more appropriate for row-centric access. Finally, data size should also be taken into account. For small tables, performance loss may be an acceptable trade-off for the flexibility of a DynamicTable. - """ - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class DecompositionSeriesBands(DynamicTable): - """ - Table for describing the bands that this series was generated from. There should be one row in this table for each band. - """ - band_name: DecompositionSeriesBandsBandName = Field(..., description="""Name of the band, e.g. theta.""") - band_limits: DecompositionSeriesBandsBandLimits = Field(..., description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""") - band_mean: DecompositionSeriesBandsBandMean = Field(..., description="""The mean Gaussian filters, in Hz.""") - band_stdev: DecompositionSeriesBandsBandStdev = Field(..., description="""The standard deviation of Gaussian filters, in Hz.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class Units(DynamicTable): - """ - Data about spiking units. Event times of observed units (e.g. cell, synapse, etc.) should be concatenated and stored in spike_times. - """ - spike_times_index: Optional[UnitsSpikeTimesIndex] = Field(None, description="""Index into the spike_times dataset.""") - spike_times: Optional[UnitsSpikeTimes] = Field(None, description="""Spike times for each unit in seconds.""") - obs_intervals_index: Optional[UnitsObsIntervalsIndex] = Field(None, description="""Index into the obs_intervals dataset.""") - obs_intervals: Optional[UnitsObsIntervals] = Field(None, description="""Observation intervals for each unit.""") - electrodes_index: Optional[UnitsElectrodesIndex] = Field(None, description="""Index into electrodes.""") - electrodes: Optional[UnitsElectrodes] = Field(None, description="""Electrode that each spike unit came from, specified using a DynamicTableRegion.""") - electrode_group: Optional[UnitsElectrodeGroup] = Field(None, description="""Electrode group that each spike unit came from.""") - waveform_mean: Optional[UnitsWaveformMean] = Field(None, description="""Spike waveform mean for each spike unit.""") - waveform_sd: Optional[UnitsWaveformSd] = Field(None, description="""Spike waveform standard deviation for each spike unit.""") - waveforms: Optional[UnitsWaveforms] = Field(None, description="""Individual waveforms for each spike on each electrode. This is a doubly indexed column. The 'waveforms_index' column indexes which waveforms in this column belong to the same spike event for a given unit, where each waveform was recorded from a different electrode. The 'waveforms_index_index' column indexes the 'waveforms_index' column to indicate which spike events belong to a given unit. For example, if the 'waveforms_index_index' column has values [2, 5, 6], then the first 2 elements of the 'waveforms_index' column correspond to the 2 spike events of the first unit, the next 3 elements of the 'waveforms_index' column correspond to the 3 spike events of the second unit, and the next 1 element of the 'waveforms_index' column corresponds to the 1 spike event of the third unit. If the 'waveforms_index' column has values [3, 6, 8, 10, 12, 13], then the first 3 elements of the 'waveforms' column contain the 3 spike waveforms that were recorded from 3 different electrodes for the first spike time of the first unit. See https://nwb-schema.readthedocs.io/en/stable/format_description.html#doubly-ragged-arrays for a graphical representation of this example. When there is only one electrode for each unit (i.e., each spike time is associated with a single waveform), then the 'waveforms_index' column will have values 1, 2, ..., N, where N is the number of spike events. The number of electrodes for each spike event should be the same within a given unit. The 'electrodes' column should be used to indicate which electrodes are associated with each unit, and the order of the waveforms within a given unit x spike event should be in the same order as the electrodes referenced in the 'electrodes' column of this table. The number of samples for each waveform must be the same.""") - waveforms_index: Optional[UnitsWaveformsIndex] = Field(None, description="""Index into the waveforms dataset. One value for every spike event. See 'waveforms' for more detail.""") - waveforms_index_index: Optional[UnitsWaveformsIndexIndex] = Field(None, description="""Index into the waveforms_index dataset. One value for every unit (row in the table). See 'waveforms' for more detail.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class AlignedDynamicTable(DynamicTable): - """ - DynamicTable container that supports storing a collection of sub-tables. Each sub-table is a DynamicTable itself that is aligned with the main table by row index. I.e., all DynamicTables stored in this group MUST have the same number of rows. This type effectively defines a 2-level table in which the main data is stored in the main table implemented by this type and additional columns of the table are grouped into categories, with each category being represented by a separate DynamicTable stored within the group. - """ - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimpleMultiContainer(Container): - """ - A simple Container for holding onto multiple containers. - """ - Data: Optional[List[Data]] = Field(default_factory=list, description="""Data objects held within this SimpleMultiContainer.""") - Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") - - -class NWBData(Data): - """ - An abstract data type for a dataset. - """ - None - - -class TimeSeriesReferenceVectorData(VectorData): - """ - Column storing references to a TimeSeries (rows). For each TimeSeries this VectorData column stores the start_index and count to indicate the range in time to be selected as well as an object reference to the TimeSeries. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class Image(NWBData): - """ - An abstract data type for an image. Shape can be 2-D (x, y), or 3-D where the third dimension can have three or four elements, e.g. (x, y, (r, g, b)) or (x, y, (r, g, b, a)). - """ - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - array: Optional[ImageArray] = Field(None) - - -class ImageArray(Arraylike): - - x: float = Field(...) - y: float = Field(...) - r_g_b: Optional[float] = Field(None) - r_g_b_a: Optional[float] = Field(None) - - -class ImageReferences(NWBData): - """ - Ordered dataset of references to Image objects. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class ImageReferencesArray(Arraylike): - - num_images: Image = Field(...) - - -class NWBContainer(Container): - """ - An abstract data type for a generic container storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class NWBDataInterface(NWBContainer): - """ - An abstract data type for a generic container storing collections of data, as opposed to metadata. - """ - None - - -class TimeSeries(NWBDataInterface): - """ - General purpose time series. - """ - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - data: TimeSeriesData = Field(..., description="""Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class AbstractFeatureSeries(TimeSeries): - """ - Abstract features, such as quantitative descriptions of sensory stimuli. The TimeSeries::data field is a 2D array, storing those features (e.g., for visual grating stimulus this might be orientation, spatial frequency and contrast). Null stimuli (eg, uniform gray) can be marked as being an independent feature (eg, 1.0 for gray, 0.0 for actual stimulus) or by storing NaNs for feature values, or through use of the TimeSeries::control fields. A set of features is considered to persist until the next set of features is defined. The final set of features stored should be the null set. This is useful when storing the raw stimulus is impractical. - """ - data: AbstractFeatureSeriesData = Field(..., description="""Values of each feature at each time.""") - feature_units: Optional[AbstractFeatureSeriesFeatureUnits] = Field(None, description="""Units of each feature.""") - features: AbstractFeatureSeriesFeatures = Field(..., description="""Description of the features represented in TimeSeries::data.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class AnnotationSeries(TimeSeries): - """ - Stores user annotations made during an experiment. The data[] field stores a text array, and timestamps are stored for each annotation (ie, interval=1). This is largely an alias to a standard TimeSeries storing a text array but that is identifiable as storing annotations in a machine-readable way. - """ - data: AnnotationSeriesData = Field(..., description="""Annotations made during an experiment.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class IntervalSeries(TimeSeries): - """ - Stores intervals of data. The timestamps field stores the beginning and end of intervals. The data field stores whether the interval just started (>0 value) or ended (<0 value). Different interval types can be represented in the same series by using multiple key values (eg, 1 for feature A, 2 for feature B, 3 for feature C, etc). The field data stores an 8-bit integer. This is largely an alias of a standard TimeSeries but that is identifiable as representing time intervals in a machine-readable way. - """ - data: IntervalSeriesData = Field(..., description="""Use values >0 if interval started, <0 if interval ended.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class DecompositionSeries(TimeSeries): - """ - Spectral analysis of a time series, e.g. of an LFP or a speech signal. - """ - data: DecompositionSeriesData = Field(..., description="""Data decomposed into frequency bands.""") - metric: DecompositionSeriesMetric = Field(..., description="""The metric used, e.g. phase, amplitude, power.""") - source_channels: Optional[DecompositionSeriesSourceChannels] = Field(None, description="""DynamicTableRegion pointer to the channels that this decomposition series was generated from.""") - bands: DecompositionSeriesBands = Field(..., description="""Table for describing the bands that this series was generated from. There should be one row in this table for each band.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class TimeSeriesData(ConfiguredBaseModel): - """ - Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file. - """ - conversion: Optional[float] = Field(None, description="""Scalar to multiply each element in data to convert it to the specified 'unit'. If the data are stored in acquisition system units or other units that require a conversion to be interpretable, multiply the data by 'conversion' to convert the data to the specified 'unit'. e.g. if the data acquisition system stores values in this object as signed 16-bit integers (int16 range -32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data acquisition system gain is 8000X, then the 'conversion' multiplier to get from raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9.""") - offset: Optional[float] = Field(None, description="""Scalar to add to the data after scaling by 'conversion' to finalize its coercion to the specified 'unit'. Two common examples of this include (a) data stored in an unsigned type that requires a shift after scaling to re-center the data, and (b) specialized recording devices that naturally cause a scalar offset with respect to the true units.""") - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data, stored in the specified by unit, e.g., the change in value of the least significant bit, or a larger number if signal noise is known to be present. If unknown, use -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - continuity: Optional[str] = Field(None, description="""Optionally describe the continuity of the data. Can be \"continuous\", \"instantaneous\", or \"step\". For example, a voltage trace would be \"continuous\", because samples are recorded from a continuous process. An array of lick times would be \"instantaneous\", because the data represents distinct moments in time. Times of image presentations would be \"step\" because the picture remains the same until the next timepoint. This field is optional, but is useful in providing information about the underlying data. It may inform the way this data is interpreted, the way it is visualized, and what analysis methods are applicable.""") - array: Optional[TimeSeriesDataArray] = Field(None) - - -class TimeSeriesDataArray(Arraylike): - - num_times: Any = Field(...) - num_DIM2: Optional[Any] = Field(None) - num_DIM3: Optional[Any] = Field(None) - num_DIM4: Optional[Any] = Field(None) - - -class TimeSeriesStartingTime(ConfiguredBaseModel): - """ - Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute. - """ - rate: Optional[float] = Field(None, description="""Sampling rate, in Hz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement for time, which is fixed to 'seconds'.""") - - -class TimeSeriesTimestamps(ConfiguredBaseModel): - """ - Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. - """ - interval: Optional[int] = Field(None, description="""Value is '1'""") - unit: Optional[str] = Field(None, description="""Unit of measurement for timestamps, which is fixed to 'seconds'.""") - array: Optional[TimeSeriesTimestampsArray] = Field(None) - - -class TimeSeriesTimestampsArray(Arraylike): - - num_times: float = Field(...) - - -class TimeSeriesControl(ConfiguredBaseModel): - """ - Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data. - """ - array: Optional[TimeSeriesControlArray] = Field(None) - - -class TimeSeriesControlArray(Arraylike): - - num_times: int = Field(...) - - -class TimeSeriesControlDescription(ConfiguredBaseModel): - """ - Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0. - """ - array: Optional[TimeSeriesControlDescriptionArray] = Field(None) - - -class TimeSeriesControlDescriptionArray(Arraylike): - - num_control_values: str = Field(...) - - -class TimeSeriesSync(ConfiguredBaseModel): - """ - Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes. - """ - None - - -class ProcessingModule(NWBContainer): - """ - A collection of processed data. - """ - description: Optional[str] = Field(None, description="""Description of this collection of processed data.""") - NWBDataInterface: Optional[List[NWBDataInterface]] = Field(default_factory=list, description="""Data objects stored in this collection.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tables stored in this collection.""") - - -class Images(NWBDataInterface): - """ - A collection of images with an optional way to specify the order of the images using the \"order_of_images\" dataset. An order must be specified if the images are referenced by index, e.g., from an IndexSeries. - """ - description: Optional[str] = Field(None, description="""Description of this collection of images.""") - Image: List[Image] = Field(default_factory=list, description="""Images stored in this collection.""") - order_of_images: Optional[ImagesOrderOfImages] = Field(None, description="""Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images.""") - - -class ImagesOrderOfImages(ImageReferences): - """ - Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images. - """ - array: Optional[ImageReferencesArray] = Field(None) - - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -AbstractFeatureSeriesData.update_forward_refs() -AbstractFeatureSeriesFeatureUnits.update_forward_refs() -AbstractFeatureSeriesFeatures.update_forward_refs() -AnnotationSeriesData.update_forward_refs() -IntervalSeriesData.update_forward_refs() -DecompositionSeriesData.update_forward_refs() -DecompositionSeriesMetric.update_forward_refs() -Arraylike.update_forward_refs() -AbstractFeatureSeriesDataArray.update_forward_refs() -AbstractFeatureSeriesFeatureUnitsArray.update_forward_refs() -AbstractFeatureSeriesFeaturesArray.update_forward_refs() -AnnotationSeriesDataArray.update_forward_refs() -IntervalSeriesDataArray.update_forward_refs() -DecompositionSeriesDataArray.update_forward_refs() -DecompositionSeriesBandsBandLimitsArray.update_forward_refs() -DecompositionSeriesBandsBandMeanArray.update_forward_refs() -DecompositionSeriesBandsBandStdevArray.update_forward_refs() -UnitsObsIntervalsArray.update_forward_refs() -UnitsWaveformMeanArray.update_forward_refs() -UnitsWaveformSdArray.update_forward_refs() -UnitsWaveformsArray.update_forward_refs() -VectorDataArray.update_forward_refs() -VectorIndexArray.update_forward_refs() -ElementIdentifiersArray.update_forward_refs() -DynamicTableRegionArray.update_forward_refs() -DynamicTableIdArray.update_forward_refs() -Data.update_forward_refs() -VectorData.update_forward_refs() -DecompositionSeriesBandsBandName.update_forward_refs() -DecompositionSeriesBandsBandLimits.update_forward_refs() -DecompositionSeriesBandsBandMean.update_forward_refs() -DecompositionSeriesBandsBandStdev.update_forward_refs() -UnitsSpikeTimes.update_forward_refs() -UnitsObsIntervals.update_forward_refs() -UnitsElectrodeGroup.update_forward_refs() -UnitsWaveformMean.update_forward_refs() -UnitsWaveformSd.update_forward_refs() -UnitsWaveforms.update_forward_refs() -VectorIndex.update_forward_refs() -UnitsSpikeTimesIndex.update_forward_refs() -UnitsObsIntervalsIndex.update_forward_refs() -UnitsElectrodesIndex.update_forward_refs() -UnitsWaveformsIndex.update_forward_refs() -UnitsWaveformsIndexIndex.update_forward_refs() -ElementIdentifiers.update_forward_refs() -DynamicTableRegion.update_forward_refs() -DecompositionSeriesSourceChannels.update_forward_refs() -UnitsElectrodes.update_forward_refs() -DynamicTableId.update_forward_refs() -Container.update_forward_refs() -DynamicTable.update_forward_refs() -DecompositionSeriesBands.update_forward_refs() -Units.update_forward_refs() -AlignedDynamicTable.update_forward_refs() -SimpleMultiContainer.update_forward_refs() -NWBData.update_forward_refs() -TimeSeriesReferenceVectorData.update_forward_refs() -Image.update_forward_refs() -ImageArray.update_forward_refs() -ImageReferences.update_forward_refs() -ImageReferencesArray.update_forward_refs() -NWBContainer.update_forward_refs() -NWBDataInterface.update_forward_refs() -TimeSeries.update_forward_refs() -AbstractFeatureSeries.update_forward_refs() -AnnotationSeries.update_forward_refs() -IntervalSeries.update_forward_refs() -DecompositionSeries.update_forward_refs() -TimeSeriesData.update_forward_refs() -TimeSeriesDataArray.update_forward_refs() -TimeSeriesStartingTime.update_forward_refs() -TimeSeriesTimestamps.update_forward_refs() -TimeSeriesTimestampsArray.update_forward_refs() -TimeSeriesControl.update_forward_refs() -TimeSeriesControlArray.update_forward_refs() -TimeSeriesControlDescription.update_forward_refs() -TimeSeriesControlDescriptionArray.update_forward_refs() -TimeSeriesSync.update_forward_refs() -ProcessingModule.update_forward_refs() -Images.update_forward_refs() -ImagesOrderOfImages.update_forward_refs() diff --git a/nwb_linkml/models/core.nwb.ogen.py b/nwb_linkml/models/core.nwb.ogen.py deleted file mode 100644 index 643e45f..0000000 --- a/nwb_linkml/models/core.nwb.ogen.py +++ /dev/null @@ -1,475 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): - pass - - -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - -class OptogeneticSeriesData(ConfiguredBaseModel): - """ - Applied power for optogenetic stimulus, in watts. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for data, which is fixed to 'watts'.""") - array: Optional[OptogeneticSeriesDataArray] = Field(None) - - -class OptogeneticStimulusSiteDescription(ConfiguredBaseModel): - """ - Description of stimulation site. - """ - None - - -class OptogeneticStimulusSiteExcitationLambda(ConfiguredBaseModel): - """ - Excitation wavelength, in nm. - """ - None - - -class OptogeneticStimulusSiteLocation(ConfiguredBaseModel): - """ - Location of the stimulation site. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible. - """ - None - - -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - -class OptogeneticSeriesDataArray(Arraylike): - - num_times: float = Field(...) - - -class ImageArray(Arraylike): - - x: float = Field(...) - y: float = Field(...) - r_g_b: Optional[float] = Field(None) - r_g_b_a: Optional[float] = Field(None) - - -class ImageReferencesArray(Arraylike): - - num_images: Image = Field(...) - - -class TimeSeriesData(ConfiguredBaseModel): - """ - Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file. - """ - conversion: Optional[float] = Field(None, description="""Scalar to multiply each element in data to convert it to the specified 'unit'. If the data are stored in acquisition system units or other units that require a conversion to be interpretable, multiply the data by 'conversion' to convert the data to the specified 'unit'. e.g. if the data acquisition system stores values in this object as signed 16-bit integers (int16 range -32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data acquisition system gain is 8000X, then the 'conversion' multiplier to get from raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9.""") - offset: Optional[float] = Field(None, description="""Scalar to add to the data after scaling by 'conversion' to finalize its coercion to the specified 'unit'. Two common examples of this include (a) data stored in an unsigned type that requires a shift after scaling to re-center the data, and (b) specialized recording devices that naturally cause a scalar offset with respect to the true units.""") - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data, stored in the specified by unit, e.g., the change in value of the least significant bit, or a larger number if signal noise is known to be present. If unknown, use -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - continuity: Optional[str] = Field(None, description="""Optionally describe the continuity of the data. Can be \"continuous\", \"instantaneous\", or \"step\". For example, a voltage trace would be \"continuous\", because samples are recorded from a continuous process. An array of lick times would be \"instantaneous\", because the data represents distinct moments in time. Times of image presentations would be \"step\" because the picture remains the same until the next timepoint. This field is optional, but is useful in providing information about the underlying data. It may inform the way this data is interpreted, the way it is visualized, and what analysis methods are applicable.""") - array: Optional[TimeSeriesDataArray] = Field(None) - - -class TimeSeriesDataArray(Arraylike): - - num_times: Any = Field(...) - num_DIM2: Optional[Any] = Field(None) - num_DIM3: Optional[Any] = Field(None) - num_DIM4: Optional[Any] = Field(None) - - -class TimeSeriesStartingTime(ConfiguredBaseModel): - """ - Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute. - """ - rate: Optional[float] = Field(None, description="""Sampling rate, in Hz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement for time, which is fixed to 'seconds'.""") - - -class TimeSeriesTimestamps(ConfiguredBaseModel): - """ - Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. - """ - interval: Optional[int] = Field(None, description="""Value is '1'""") - unit: Optional[str] = Field(None, description="""Unit of measurement for timestamps, which is fixed to 'seconds'.""") - array: Optional[TimeSeriesTimestampsArray] = Field(None) - - -class TimeSeriesTimestampsArray(Arraylike): - - num_times: float = Field(...) - - -class TimeSeriesControl(ConfiguredBaseModel): - """ - Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data. - """ - array: Optional[TimeSeriesControlArray] = Field(None) - - -class TimeSeriesControlArray(Arraylike): - - num_times: int = Field(...) - - -class TimeSeriesControlDescription(ConfiguredBaseModel): - """ - Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0. - """ - array: Optional[TimeSeriesControlDescriptionArray] = Field(None) - - -class TimeSeriesControlDescriptionArray(Arraylike): - - num_control_values: str = Field(...) - - -class TimeSeriesSync(ConfiguredBaseModel): - """ - Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes. - """ - None - - -class VectorDataArray(Arraylike): - - dim0: Any = Field(...) - dim1: Optional[Any] = Field(None) - dim2: Optional[Any] = Field(None) - dim3: Optional[Any] = Field(None) - - -class VectorIndexArray(Arraylike): - - num_rows: int = Field(...) - - -class ElementIdentifiersArray(Arraylike): - - num_elements: int = Field(...) - - -class DynamicTableRegionArray(Arraylike): - - num_rows: int = Field(...) - - -class DynamicTableIdArray(Arraylike): - - num_rows: int = Field(...) - - -class Data(ConfiguredBaseModel): - """ - An abstract data type for a dataset. - """ - None - - -class NWBData(Data): - """ - An abstract data type for a dataset. - """ - None - - -class Image(NWBData): - """ - An abstract data type for an image. Shape can be 2-D (x, y), or 3-D where the third dimension can have three or four elements, e.g. (x, y, (r, g, b)) or (x, y, (r, g, b, a)). - """ - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - array: Optional[ImageArray] = Field(None) - - -class ImageReferences(NWBData): - """ - Ordered dataset of references to Image objects. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class ImagesOrderOfImages(ImageReferences): - """ - Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class VectorData(Data): - """ - An n-dimensional dataset representing a column of a DynamicTable. If used without an accompanying VectorIndex, first dimension is along the rows of the DynamicTable and each step along the first dimension is a cell of the larger table. VectorData can also be used to represent a ragged array if paired with a VectorIndex. This allows for storing arrays of varying length in a single cell of the DynamicTable by indexing into this VectorData. The first vector is at VectorData[0:VectorIndex[0]]. The second vector is at VectorData[VectorIndex[0]:VectorIndex[1]], and so on. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class TimeSeriesReferenceVectorData(VectorData): - """ - Column storing references to a TimeSeries (rows). For each TimeSeries this VectorData column stores the start_index and count to indicate the range in time to be selected as well as an object reference to the TimeSeries. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class VectorIndex(VectorData): - """ - Used with VectorData to encode a ragged array. An array of indices into the first dimension of the target VectorData, and forming a map between the rows of a DynamicTable and the indices of the VectorData. The name of the VectorIndex is expected to be the name of the target VectorData object followed by \"_index\". - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ElementIdentifiers(Data): - """ - A list of unique identifiers for values within a dataset, e.g. rows of a DynamicTable. - """ - array: Optional[ElementIdentifiersArray] = Field(None) - - -class DynamicTableRegion(VectorData): - """ - DynamicTableRegion provides a link from one table to an index or region of another. The `table` attribute is a link to another `DynamicTable`, indicating which table is referenced, and the data is int(s) indicating the row(s) (0-indexed) of the target array. `DynamicTableRegion`s can be used to associate rows with repeated meta-data without data duplication. They can also be used to create hierarchical relationships between multiple `DynamicTable`s. `DynamicTableRegion` objects may be paired with a `VectorIndex` object to create ragged references, so a single cell of a `DynamicTable` can reference many rows of another `DynamicTable`. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DynamicTableId(ElementIdentifiers): - """ - Array of unique identifiers for the rows of this dynamic table. - """ - array: Optional[DynamicTableIdArray] = Field(None) - - -class Container(ConfiguredBaseModel): - """ - An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class NWBContainer(Container): - """ - An abstract data type for a generic container storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class OptogeneticStimulusSite(NWBContainer): - """ - A site of optogenetic stimulation. - """ - description: OptogeneticStimulusSiteDescription = Field(..., description="""Description of stimulation site.""") - excitation_lambda: OptogeneticStimulusSiteExcitationLambda = Field(..., description="""Excitation wavelength, in nm.""") - location: OptogeneticStimulusSiteLocation = Field(..., description="""Location of the stimulation site. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible.""") - - -class NWBDataInterface(NWBContainer): - """ - An abstract data type for a generic container storing collections of data, as opposed to metadata. - """ - None - - -class TimeSeries(NWBDataInterface): - """ - General purpose time series. - """ - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - data: TimeSeriesData = Field(..., description="""Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class OptogeneticSeries(TimeSeries): - """ - An optogenetic stimulus. - """ - data: OptogeneticSeriesData = Field(..., description="""Applied power for optogenetic stimulus, in watts.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class ProcessingModule(NWBContainer): - """ - A collection of processed data. - """ - description: Optional[str] = Field(None, description="""Description of this collection of processed data.""") - NWBDataInterface: Optional[List[NWBDataInterface]] = Field(default_factory=list, description="""Data objects stored in this collection.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tables stored in this collection.""") - - -class Images(NWBDataInterface): - """ - A collection of images with an optional way to specify the order of the images using the \"order_of_images\" dataset. An order must be specified if the images are referenced by index, e.g., from an IndexSeries. - """ - description: Optional[str] = Field(None, description="""Description of this collection of images.""") - Image: List[Image] = Field(default_factory=list, description="""Images stored in this collection.""") - order_of_images: Optional[ImagesOrderOfImages] = Field(None, description="""Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images.""") - - -class DynamicTable(Container): - """ - A group containing multiple datasets that are aligned on the first dimension (Currently, this requirement if left up to APIs to check and enforce). These datasets represent different columns in the table. Apart from a column that contains unique identifiers for each row, there are no other required datasets. Users are free to add any number of custom VectorData objects (columns) here. DynamicTable also supports ragged array columns, where each element can be of a different size. To add a ragged array column, use a VectorIndex type to index the corresponding VectorData type. See documentation for VectorData and VectorIndex for more details. Unlike a compound data type, which is analogous to storing an array-of-structs, a DynamicTable can be thought of as a struct-of-arrays. This provides an alternative structure to choose from when optimizing storage for anticipated access patterns. Additionally, this type provides a way of creating a table without having to define a compound type up front. Although this convenience may be attractive, users should think carefully about how data will be accessed. DynamicTable is more appropriate for column-centric access, whereas a dataset with a compound type would be more appropriate for row-centric access. Finally, data size should also be taken into account. For small tables, performance loss may be an acceptable trade-off for the flexibility of a DynamicTable. - """ - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class AlignedDynamicTable(DynamicTable): - """ - DynamicTable container that supports storing a collection of sub-tables. Each sub-table is a DynamicTable itself that is aligned with the main table by row index. I.e., all DynamicTables stored in this group MUST have the same number of rows. This type effectively defines a 2-level table in which the main data is stored in the main table implemented by this type and additional columns of the table are grouped into categories, with each category being represented by a separate DynamicTable stored within the group. - """ - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimpleMultiContainer(Container): - """ - A simple Container for holding onto multiple containers. - """ - Data: Optional[List[Data]] = Field(default_factory=list, description="""Data objects held within this SimpleMultiContainer.""") - Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") - - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -OptogeneticSeriesData.update_forward_refs() -OptogeneticStimulusSiteDescription.update_forward_refs() -OptogeneticStimulusSiteExcitationLambda.update_forward_refs() -OptogeneticStimulusSiteLocation.update_forward_refs() -Arraylike.update_forward_refs() -OptogeneticSeriesDataArray.update_forward_refs() -ImageArray.update_forward_refs() -ImageReferencesArray.update_forward_refs() -TimeSeriesData.update_forward_refs() -TimeSeriesDataArray.update_forward_refs() -TimeSeriesStartingTime.update_forward_refs() -TimeSeriesTimestamps.update_forward_refs() -TimeSeriesTimestampsArray.update_forward_refs() -TimeSeriesControl.update_forward_refs() -TimeSeriesControlArray.update_forward_refs() -TimeSeriesControlDescription.update_forward_refs() -TimeSeriesControlDescriptionArray.update_forward_refs() -TimeSeriesSync.update_forward_refs() -VectorDataArray.update_forward_refs() -VectorIndexArray.update_forward_refs() -ElementIdentifiersArray.update_forward_refs() -DynamicTableRegionArray.update_forward_refs() -DynamicTableIdArray.update_forward_refs() -Data.update_forward_refs() -NWBData.update_forward_refs() -Image.update_forward_refs() -ImageReferences.update_forward_refs() -ImagesOrderOfImages.update_forward_refs() -VectorData.update_forward_refs() -TimeSeriesReferenceVectorData.update_forward_refs() -VectorIndex.update_forward_refs() -ElementIdentifiers.update_forward_refs() -DynamicTableRegion.update_forward_refs() -DynamicTableId.update_forward_refs() -Container.update_forward_refs() -NWBContainer.update_forward_refs() -OptogeneticStimulusSite.update_forward_refs() -NWBDataInterface.update_forward_refs() -TimeSeries.update_forward_refs() -OptogeneticSeries.update_forward_refs() -ProcessingModule.update_forward_refs() -Images.update_forward_refs() -DynamicTable.update_forward_refs() -AlignedDynamicTable.update_forward_refs() -SimpleMultiContainer.update_forward_refs() diff --git a/nwb_linkml/models/core.nwb.ophys.py b/nwb_linkml/models/core.nwb.ophys.py deleted file mode 100644 index fba460c..0000000 --- a/nwb_linkml/models/core.nwb.ophys.py +++ /dev/null @@ -1,1053 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): - pass - - -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - -class TwoPhotonSeriesFieldOfView(ConfiguredBaseModel): - """ - Width, height and depth of image, or imaged area, in meters. - """ - array: Optional[TwoPhotonSeriesFieldOfViewArray] = Field(None) - - -class RoiResponseSeriesData(ConfiguredBaseModel): - """ - Signals from ROIs. - """ - array: Optional[RoiResponseSeriesDataArray] = Field(None) - - -class PlaneSegmentationReferenceImages(ConfiguredBaseModel): - """ - Image stacks that the segmentation masks apply to. - """ - ImageSeries: Optional[List[ImageSeries]] = Field(default_factory=list, description="""One or more image stacks that the masks apply to (can be one-element stack).""") - - -class ImagingPlaneDescription(ConfiguredBaseModel): - """ - Description of the imaging plane. - """ - None - - -class ImagingPlaneExcitationLambda(ConfiguredBaseModel): - """ - Excitation wavelength, in nm. - """ - None - - -class ImagingPlaneImagingRate(ConfiguredBaseModel): - """ - Rate that images are acquired, in Hz. If the corresponding TimeSeries is present, the rate should be stored there instead. - """ - None - - -class ImagingPlaneIndicator(ConfiguredBaseModel): - """ - Calcium indicator. - """ - None - - -class ImagingPlaneLocation(ConfiguredBaseModel): - """ - Location of the imaging plane. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible. - """ - None - - -class ImagingPlaneManifold(ConfiguredBaseModel): - """ - DEPRECATED Physical position of each pixel. 'xyz' represents the position of the pixel relative to the defined coordinate space. Deprecated in favor of origin_coords and grid_spacing. - """ - conversion: Optional[float] = Field(None, description="""Scalar to multiply each element in data to convert it to the specified 'unit'. If the data are stored in acquisition system units or other units that require a conversion to be interpretable, multiply the data by 'conversion' to convert the data to the specified 'unit'. e.g. if the data acquisition system stores values in this object as pixels from x = -500 to 499, y = -500 to 499 that correspond to a 2 m x 2 m range, then the 'conversion' multiplier to get from raw data acquisition pixel units to meters is 2/1000.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. The default value is 'meters'.""") - array: Optional[ImagingPlaneManifoldArray] = Field(None) - - -class ImagingPlaneOriginCoords(ConfiguredBaseModel): - """ - Physical location of the first element of the imaging plane (0, 0) for 2-D data or (0, 0, 0) for 3-D data. See also reference_frame for what the physical location is relative to (e.g., bregma). - """ - unit: Optional[str] = Field(None, description="""Measurement units for origin_coords. The default value is 'meters'.""") - array: Optional[ImagingPlaneOriginCoordsArray] = Field(None) - - -class ImagingPlaneGridSpacing(ConfiguredBaseModel): - """ - Space between pixels in (x, y) or voxels in (x, y, z) directions, in the specified unit. Assumes imaging plane is a regular grid. See also reference_frame to interpret the grid. - """ - unit: Optional[str] = Field(None, description="""Measurement units for grid_spacing. The default value is 'meters'.""") - array: Optional[ImagingPlaneGridSpacingArray] = Field(None) - - -class ImagingPlaneReferenceFrame(ConfiguredBaseModel): - """ - Describes reference frame of origin_coords and grid_spacing. For example, this can be a text description of the anatomical location and orientation of the grid defined by origin_coords and grid_spacing or the vectors needed to transform or rotate the grid to a common anatomical axis (e.g., AP/DV/ML). This field is necessary to interpret origin_coords and grid_spacing. If origin_coords and grid_spacing are not present, then this field is not required. For example, if the microscope takes 10 x 10 x 2 images, where the first value of the data matrix (index (0, 0, 0)) corresponds to (-1.2, -0.6, -2) mm relative to bregma, the spacing between pixels is 0.2 mm in x, 0.2 mm in y and 0.5 mm in z, and larger numbers in x means more anterior, larger numbers in y means more rightward, and larger numbers in z means more ventral, then enter the following -- origin_coords = (-1.2, -0.6, -2) grid_spacing = (0.2, 0.2, 0.5) reference_frame = \"Origin coordinates are relative to bregma. First dimension corresponds to anterior-posterior axis (larger index = more anterior). Second dimension corresponds to medial-lateral axis (larger index = more rightward). Third dimension corresponds to dorsal-ventral axis (larger index = more ventral).\" - """ - None - - -class OpticalChannelDescription(ConfiguredBaseModel): - """ - Description or other notes about the channel. - """ - None - - -class OpticalChannelEmissionLambda(ConfiguredBaseModel): - """ - Emission wavelength for channel, in nm. - """ - None - - -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - -class TwoPhotonSeriesFieldOfViewArray(Arraylike): - - width|height: Optional[float] = Field(None) - width|height|depth: Optional[float] = Field(None) - - -class RoiResponseSeriesDataArray(Arraylike): - - num_times: float = Field(...) - num_ROIs: Optional[float] = Field(None) - - -class PlaneSegmentationImageMaskArray(Arraylike): - - num_roi: Any = Field(...) - num_x: Any = Field(...) - num_y: Any = Field(...) - num_z: Optional[Any] = Field(None) - - -class ImagingPlaneManifoldArray(Arraylike): - - height: float = Field(...) - width: float = Field(...) - x_y_z: float = Field(...) - depth: Optional[float] = Field(None) - - -class ImagingPlaneOriginCoordsArray(Arraylike): - - x_y: Optional[float] = Field(None) - x_y_z: Optional[float] = Field(None) - - -class ImagingPlaneGridSpacingArray(Arraylike): - - x_y: Optional[float] = Field(None) - x_y_z: Optional[float] = Field(None) - - -class VectorDataArray(Arraylike): - - dim0: Any = Field(...) - dim1: Optional[Any] = Field(None) - dim2: Optional[Any] = Field(None) - dim3: Optional[Any] = Field(None) - - -class VectorIndexArray(Arraylike): - - num_rows: int = Field(...) - - -class ElementIdentifiersArray(Arraylike): - - num_elements: int = Field(...) - - -class DynamicTableRegionArray(Arraylike): - - num_rows: int = Field(...) - - -class DynamicTableIdArray(Arraylike): - - num_rows: int = Field(...) - - -class Data(ConfiguredBaseModel): - """ - An abstract data type for a dataset. - """ - None - - -class VectorData(Data): - """ - An n-dimensional dataset representing a column of a DynamicTable. If used without an accompanying VectorIndex, first dimension is along the rows of the DynamicTable and each step along the first dimension is a cell of the larger table. VectorData can also be used to represent a ragged array if paired with a VectorIndex. This allows for storing arrays of varying length in a single cell of the DynamicTable by indexing into this VectorData. The first vector is at VectorData[0:VectorIndex[0]]. The second vector is at VectorData[VectorIndex[0]:VectorIndex[1]], and so on. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class PlaneSegmentationImageMask(VectorData): - """ - ROI masks for each ROI. Each image mask is the size of the original imaging plane (or volume) and members of the ROI are finite non-zero. - """ - array: Optional[PlaneSegmentationImageMaskArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class PlaneSegmentationPixelMask(VectorData): - """ - Pixel masks for each ROI: a list of indices and weights for the ROI. Pixel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class PlaneSegmentationVoxelMask(VectorData): - """ - Voxel masks for each ROI: a list of indices and weights for the ROI. Voxel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class VectorIndex(VectorData): - """ - Used with VectorData to encode a ragged array. An array of indices into the first dimension of the target VectorData, and forming a map between the rows of a DynamicTable and the indices of the VectorData. The name of the VectorIndex is expected to be the name of the target VectorData object followed by \"_index\". - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class PlaneSegmentationPixelMaskIndex(VectorIndex): - """ - Index into pixel_mask. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class PlaneSegmentationVoxelMaskIndex(VectorIndex): - """ - Index into voxel_mask. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ElementIdentifiers(Data): - """ - A list of unique identifiers for values within a dataset, e.g. rows of a DynamicTable. - """ - array: Optional[ElementIdentifiersArray] = Field(None) - - -class DynamicTableRegion(VectorData): - """ - DynamicTableRegion provides a link from one table to an index or region of another. The `table` attribute is a link to another `DynamicTable`, indicating which table is referenced, and the data is int(s) indicating the row(s) (0-indexed) of the target array. `DynamicTableRegion`s can be used to associate rows with repeated meta-data without data duplication. They can also be used to create hierarchical relationships between multiple `DynamicTable`s. `DynamicTableRegion` objects may be paired with a `VectorIndex` object to create ragged references, so a single cell of a `DynamicTable` can reference many rows of another `DynamicTable`. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class RoiResponseSeriesRois(DynamicTableRegion): - """ - DynamicTableRegion referencing into an ROITable containing information on the ROIs stored in this timeseries. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DynamicTableId(ElementIdentifiers): - """ - Array of unique identifiers for the rows of this dynamic table. - """ - array: Optional[DynamicTableIdArray] = Field(None) - - -class Container(ConfiguredBaseModel): - """ - An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class DynamicTable(Container): - """ - A group containing multiple datasets that are aligned on the first dimension (Currently, this requirement if left up to APIs to check and enforce). These datasets represent different columns in the table. Apart from a column that contains unique identifiers for each row, there are no other required datasets. Users are free to add any number of custom VectorData objects (columns) here. DynamicTable also supports ragged array columns, where each element can be of a different size. To add a ragged array column, use a VectorIndex type to index the corresponding VectorData type. See documentation for VectorData and VectorIndex for more details. Unlike a compound data type, which is analogous to storing an array-of-structs, a DynamicTable can be thought of as a struct-of-arrays. This provides an alternative structure to choose from when optimizing storage for anticipated access patterns. Additionally, this type provides a way of creating a table without having to define a compound type up front. Although this convenience may be attractive, users should think carefully about how data will be accessed. DynamicTable is more appropriate for column-centric access, whereas a dataset with a compound type would be more appropriate for row-centric access. Finally, data size should also be taken into account. For small tables, performance loss may be an acceptable trade-off for the flexibility of a DynamicTable. - """ - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class PlaneSegmentation(DynamicTable): - """ - Results from image segmentation of a specific imaging plane. - """ - image_mask: Optional[PlaneSegmentationImageMask] = Field(None, description="""ROI masks for each ROI. Each image mask is the size of the original imaging plane (or volume) and members of the ROI are finite non-zero.""") - pixel_mask_index: Optional[PlaneSegmentationPixelMaskIndex] = Field(None, description="""Index into pixel_mask.""") - pixel_mask: Optional[PlaneSegmentationPixelMask] = Field(None, description="""Pixel masks for each ROI: a list of indices and weights for the ROI. Pixel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation""") - voxel_mask_index: Optional[PlaneSegmentationVoxelMaskIndex] = Field(None, description="""Index into voxel_mask.""") - voxel_mask: Optional[PlaneSegmentationVoxelMask] = Field(None, description="""Voxel masks for each ROI: a list of indices and weights for the ROI. Voxel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation""") - reference_images: PlaneSegmentationReferenceImages = Field(..., description="""Image stacks that the segmentation masks apply to.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class AlignedDynamicTable(DynamicTable): - """ - DynamicTable container that supports storing a collection of sub-tables. Each sub-table is a DynamicTable itself that is aligned with the main table by row index. I.e., all DynamicTables stored in this group MUST have the same number of rows. This type effectively defines a 2-level table in which the main data is stored in the main table implemented by this type and additional columns of the table are grouped into categories, with each category being represented by a separate DynamicTable stored within the group. - """ - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimpleMultiContainer(Container): - """ - A simple Container for holding onto multiple containers. - """ - Data: Optional[List[Data]] = Field(default_factory=list, description="""Data objects held within this SimpleMultiContainer.""") - Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") - - -class NWBData(Data): - """ - An abstract data type for a dataset. - """ - None - - -class TimeSeriesReferenceVectorData(VectorData): - """ - Column storing references to a TimeSeries (rows). For each TimeSeries this VectorData column stores the start_index and count to indicate the range in time to be selected as well as an object reference to the TimeSeries. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class Image(NWBData): - """ - An abstract data type for an image. Shape can be 2-D (x, y), or 3-D where the third dimension can have three or four elements, e.g. (x, y, (r, g, b)) or (x, y, (r, g, b, a)). - """ - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - array: Optional[ImageArray] = Field(None) - - -class ImageArray(Arraylike): - - x: float = Field(...) - y: float = Field(...) - r_g_b: Optional[float] = Field(None) - r_g_b_a: Optional[float] = Field(None) - - -class ImageReferences(NWBData): - """ - Ordered dataset of references to Image objects. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class ImageReferencesArray(Arraylike): - - num_images: Image = Field(...) - - -class NWBContainer(Container): - """ - An abstract data type for a generic container storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class ImagingPlane(NWBContainer): - """ - An imaging plane and its metadata. - """ - description: Optional[ImagingPlaneDescription] = Field(None, description="""Description of the imaging plane.""") - excitation_lambda: ImagingPlaneExcitationLambda = Field(..., description="""Excitation wavelength, in nm.""") - imaging_rate: Optional[ImagingPlaneImagingRate] = Field(None, description="""Rate that images are acquired, in Hz. If the corresponding TimeSeries is present, the rate should be stored there instead.""") - indicator: ImagingPlaneIndicator = Field(..., description="""Calcium indicator.""") - location: ImagingPlaneLocation = Field(..., description="""Location of the imaging plane. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible.""") - manifold: Optional[ImagingPlaneManifold] = Field(None, description="""DEPRECATED Physical position of each pixel. 'xyz' represents the position of the pixel relative to the defined coordinate space. Deprecated in favor of origin_coords and grid_spacing.""") - origin_coords: Optional[ImagingPlaneOriginCoords] = Field(None, description="""Physical location of the first element of the imaging plane (0, 0) for 2-D data or (0, 0, 0) for 3-D data. See also reference_frame for what the physical location is relative to (e.g., bregma).""") - grid_spacing: Optional[ImagingPlaneGridSpacing] = Field(None, description="""Space between pixels in (x, y) or voxels in (x, y, z) directions, in the specified unit. Assumes imaging plane is a regular grid. See also reference_frame to interpret the grid.""") - reference_frame: Optional[ImagingPlaneReferenceFrame] = Field(None, description="""Describes reference frame of origin_coords and grid_spacing. For example, this can be a text description of the anatomical location and orientation of the grid defined by origin_coords and grid_spacing or the vectors needed to transform or rotate the grid to a common anatomical axis (e.g., AP/DV/ML). This field is necessary to interpret origin_coords and grid_spacing. If origin_coords and grid_spacing are not present, then this field is not required. For example, if the microscope takes 10 x 10 x 2 images, where the first value of the data matrix (index (0, 0, 0)) corresponds to (-1.2, -0.6, -2) mm relative to bregma, the spacing between pixels is 0.2 mm in x, 0.2 mm in y and 0.5 mm in z, and larger numbers in x means more anterior, larger numbers in y means more rightward, and larger numbers in z means more ventral, then enter the following -- origin_coords = (-1.2, -0.6, -2) grid_spacing = (0.2, 0.2, 0.5) reference_frame = \"Origin coordinates are relative to bregma. First dimension corresponds to anterior-posterior axis (larger index = more anterior). Second dimension corresponds to medial-lateral axis (larger index = more rightward). Third dimension corresponds to dorsal-ventral axis (larger index = more ventral).\"""") - OpticalChannel: List[OpticalChannel] = Field(default_factory=list, description="""An optical channel used to record from an imaging plane.""") - - -class OpticalChannel(NWBContainer): - """ - An optical channel used to record from an imaging plane. - """ - description: OpticalChannelDescription = Field(..., description="""Description or other notes about the channel.""") - emission_lambda: OpticalChannelEmissionLambda = Field(..., description="""Emission wavelength for channel, in nm.""") - - -class NWBDataInterface(NWBContainer): - """ - An abstract data type for a generic container storing collections of data, as opposed to metadata. - """ - None - - -class DfOverF(NWBDataInterface): - """ - dF/F information about a region of interest (ROI). Storage hierarchy of dF/F should be the same as for segmentation (i.e., same names for ROIs and for image planes). - """ - RoiResponseSeries: List[RoiResponseSeries] = Field(default_factory=list, description="""RoiResponseSeries object(s) containing dF/F for a ROI.""") - - -class Fluorescence(NWBDataInterface): - """ - Fluorescence information about a region of interest (ROI). Storage hierarchy of fluorescence should be the same as for segmentation (ie, same names for ROIs and for image planes). - """ - RoiResponseSeries: List[RoiResponseSeries] = Field(default_factory=list, description="""RoiResponseSeries object(s) containing fluorescence data for a ROI.""") - - -class ImageSegmentation(NWBDataInterface): - """ - Stores pixels in an image that represent different regions of interest (ROIs) or masks. All segmentation for a given imaging plane is stored together, with storage for multiple imaging planes (masks) supported. Each ROI is stored in its own subgroup, with the ROI group containing both a 2D mask and a list of pixels that make up this mask. Segments can also be used for masking neuropil. If segmentation is allowed to change with time, a new imaging plane (or module) is required and ROI names should remain consistent between them. - """ - PlaneSegmentation: List[PlaneSegmentation] = Field(default_factory=list, description="""Results from image segmentation of a specific imaging plane.""") - - -class MotionCorrection(NWBDataInterface): - """ - An image stack where all frames are shifted (registered) to a common coordinate system, to account for movement and drift between frames. Note: each frame at each point in time is assumed to be 2-D (has only x & y dimensions). - """ - CorrectedImageStack: List[CorrectedImageStack] = Field(default_factory=list, description="""Reuslts from motion correction of an image stack.""") - - -class CorrectedImageStack(NWBDataInterface): - """ - Reuslts from motion correction of an image stack. - """ - corrected: CorrectedImageStackCorrected = Field(..., description="""Image stack with frames shifted to the common coordinates.""") - xy_translation: CorrectedImageStackXyTranslation = Field(..., description="""Stores the x,y delta necessary to align each frame to the common coordinates, for example, to align each frame to a reference image.""") - - -class TimeSeries(NWBDataInterface): - """ - General purpose time series. - """ - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - data: TimeSeriesData = Field(..., description="""Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class RoiResponseSeries(TimeSeries): - """ - ROI responses over an imaging plane. The first dimension represents time. The second dimension, if present, represents ROIs. - """ - data: RoiResponseSeriesData = Field(..., description="""Signals from ROIs.""") - rois: RoiResponseSeriesRois = Field(..., description="""DynamicTableRegion referencing into an ROITable containing information on the ROIs stored in this timeseries.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class CorrectedImageStackXyTranslation(TimeSeries): - """ - Stores the x,y delta necessary to align each frame to the common coordinates, for example, to align each frame to a reference image. - """ - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - data: TimeSeriesData = Field(..., description="""Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class TimeSeriesData(ConfiguredBaseModel): - """ - Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file. - """ - conversion: Optional[float] = Field(None, description="""Scalar to multiply each element in data to convert it to the specified 'unit'. If the data are stored in acquisition system units or other units that require a conversion to be interpretable, multiply the data by 'conversion' to convert the data to the specified 'unit'. e.g. if the data acquisition system stores values in this object as signed 16-bit integers (int16 range -32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data acquisition system gain is 8000X, then the 'conversion' multiplier to get from raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9.""") - offset: Optional[float] = Field(None, description="""Scalar to add to the data after scaling by 'conversion' to finalize its coercion to the specified 'unit'. Two common examples of this include (a) data stored in an unsigned type that requires a shift after scaling to re-center the data, and (b) specialized recording devices that naturally cause a scalar offset with respect to the true units.""") - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data, stored in the specified by unit, e.g., the change in value of the least significant bit, or a larger number if signal noise is known to be present. If unknown, use -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - continuity: Optional[str] = Field(None, description="""Optionally describe the continuity of the data. Can be \"continuous\", \"instantaneous\", or \"step\". For example, a voltage trace would be \"continuous\", because samples are recorded from a continuous process. An array of lick times would be \"instantaneous\", because the data represents distinct moments in time. Times of image presentations would be \"step\" because the picture remains the same until the next timepoint. This field is optional, but is useful in providing information about the underlying data. It may inform the way this data is interpreted, the way it is visualized, and what analysis methods are applicable.""") - array: Optional[TimeSeriesDataArray] = Field(None) - - -class TimeSeriesDataArray(Arraylike): - - num_times: Any = Field(...) - num_DIM2: Optional[Any] = Field(None) - num_DIM3: Optional[Any] = Field(None) - num_DIM4: Optional[Any] = Field(None) - - -class TimeSeriesStartingTime(ConfiguredBaseModel): - """ - Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute. - """ - rate: Optional[float] = Field(None, description="""Sampling rate, in Hz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement for time, which is fixed to 'seconds'.""") - - -class TimeSeriesTimestamps(ConfiguredBaseModel): - """ - Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. - """ - interval: Optional[int] = Field(None, description="""Value is '1'""") - unit: Optional[str] = Field(None, description="""Unit of measurement for timestamps, which is fixed to 'seconds'.""") - array: Optional[TimeSeriesTimestampsArray] = Field(None) - - -class TimeSeriesTimestampsArray(Arraylike): - - num_times: float = Field(...) - - -class TimeSeriesControl(ConfiguredBaseModel): - """ - Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data. - """ - array: Optional[TimeSeriesControlArray] = Field(None) - - -class TimeSeriesControlArray(Arraylike): - - num_times: int = Field(...) - - -class TimeSeriesControlDescription(ConfiguredBaseModel): - """ - Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0. - """ - array: Optional[TimeSeriesControlDescriptionArray] = Field(None) - - -class TimeSeriesControlDescriptionArray(Arraylike): - - num_control_values: str = Field(...) - - -class TimeSeriesSync(ConfiguredBaseModel): - """ - Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes. - """ - None - - -class ProcessingModule(NWBContainer): - """ - A collection of processed data. - """ - description: Optional[str] = Field(None, description="""Description of this collection of processed data.""") - NWBDataInterface: Optional[List[NWBDataInterface]] = Field(default_factory=list, description="""Data objects stored in this collection.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tables stored in this collection.""") - - -class Images(NWBDataInterface): - """ - A collection of images with an optional way to specify the order of the images using the \"order_of_images\" dataset. An order must be specified if the images are referenced by index, e.g., from an IndexSeries. - """ - description: Optional[str] = Field(None, description="""Description of this collection of images.""") - Image: List[Image] = Field(default_factory=list, description="""Images stored in this collection.""") - order_of_images: Optional[ImagesOrderOfImages] = Field(None, description="""Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images.""") - - -class ImagesOrderOfImages(ImageReferences): - """ - Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class GrayscaleImage(Image): - """ - A grayscale image. - """ - array: Optional[GrayscaleImageArray] = Field(None) - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - - -class GrayscaleImageArray(Arraylike): - - x: Optional[float] = Field(None) - y: Optional[float] = Field(None) - - -class RGBImage(Image): - """ - A color image. - """ - array: Optional[RGBImageArray] = Field(None) - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - - -class RGBImageArray(Arraylike): - - x: Optional[float] = Field(None) - y: Optional[float] = Field(None) - r_g_b: Optional[float] = Field(None) - - -class RGBAImage(Image): - """ - A color image with transparency. - """ - array: Optional[RGBAImageArray] = Field(None) - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - - -class RGBAImageArray(Arraylike): - - x: Optional[float] = Field(None) - y: Optional[float] = Field(None) - r_g_b_a: Optional[float] = Field(None) - - -class ImageSeries(TimeSeries): - """ - General image data that is common between acquisition and stimulus time series. Sometimes the image data is stored in the file in a raw format while other times it will be stored as a series of external image files in the host file system. The data field will either be binary data, if the data is stored in the NWB file, or empty, if the data is stored in an external image stack. [frame][x][y] or [frame][x][y][z]. - """ - data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class OnePhotonSeries(ImageSeries): - """ - Image stack recorded over time from 1-photon microscope. - """ - pmt_gain: Optional[float] = Field(None, description="""Photomultiplier gain.""") - scan_line_rate: Optional[float] = Field(None, description="""Lines imaged per second. This is also stored in /general/optophysiology but is kept here as it is useful information for analysis, and so good to be stored w/ the actual data.""") - exposure_time: Optional[float] = Field(None, description="""Exposure time of the sample; often the inverse of the frequency.""") - binning: Optional[int] = Field(None, description="""Amount of pixels combined into 'bins'; could be 1, 2, 4, 8, etc.""") - power: Optional[float] = Field(None, description="""Power of the excitation in mW, if known.""") - intensity: Optional[float] = Field(None, description="""Intensity of the excitation in mW/mm^2, if known.""") - data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class TwoPhotonSeries(ImageSeries): - """ - Image stack recorded over time from 2-photon microscope. - """ - pmt_gain: Optional[float] = Field(None, description="""Photomultiplier gain.""") - scan_line_rate: Optional[float] = Field(None, description="""Lines imaged per second. This is also stored in /general/optophysiology but is kept here as it is useful information for analysis, and so good to be stored w/ the actual data.""") - field_of_view: Optional[TwoPhotonSeriesFieldOfView] = Field(None, description="""Width, height and depth of image, or imaged area, in meters.""") - data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class CorrectedImageStackCorrected(ImageSeries): - """ - Image stack with frames shifted to the common coordinates. - """ - data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class ImageSeriesData(ConfiguredBaseModel): - """ - Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array. - """ - array: Optional[ImageSeriesDataArray] = Field(None) - - -class ImageSeriesDataArray(Arraylike): - - frame: float = Field(...) - x: float = Field(...) - y: float = Field(...) - z: Optional[float] = Field(None) - - -class ImageSeriesDimension(ConfiguredBaseModel): - """ - Number of pixels on x, y, (and z) axes. - """ - array: Optional[ImageSeriesDimensionArray] = Field(None) - - -class ImageSeriesDimensionArray(Arraylike): - - rank: int = Field(...) - - -class ImageSeriesExternalFile(ConfiguredBaseModel): - """ - Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file. - """ - starting_frame: Optional[int] = Field(None, description="""Each external image may contain one or more consecutive frames of the full ImageSeries. This attribute serves as an index to indicate which frames each file contains, to facilitate random access. The 'starting_frame' attribute, hence, contains a list of frame numbers within the full ImageSeries of the first frame of each file listed in the parent 'external_file' dataset. Zero-based indexing is used (hence, the first element will always be zero). For example, if the 'external_file' dataset has three paths to files and the first file has 5 frames, the second file has 10 frames, and the third file has 20 frames, then this attribute will have values [0, 5, 15]. If there is a single external file that holds all of the frames of the ImageSeries (and so there is a single element in the 'external_file' dataset), then this attribute should have value [0].""") - array: Optional[ImageSeriesExternalFileArray] = Field(None) - - -class ImageSeriesExternalFileArray(Arraylike): - - num_files: str = Field(...) - - -class ImageSeriesFormat(ConfiguredBaseModel): - """ - Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed. - """ - None - - -class ImageMaskSeries(ImageSeries): - """ - An alpha mask that is applied to a presented visual stimulus. The 'data' array contains an array of mask values that are applied to the displayed image. Mask values are stored as RGBA. Mask can vary with time. The timestamps array indicates the starting time of a mask, and that mask pattern continues until it's explicitly changed. - """ - data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class OpticalSeries(ImageSeries): - """ - Image data that is presented or recorded. A stimulus template movie will be stored only as an image. When the image is presented as stimulus, additional data is required, such as field of view (e.g., how much of the visual field the image covers, or how what is the area of the target being imaged). If the OpticalSeries represents acquired imaging data, orientation is also important. - """ - distance: Optional[OpticalSeriesDistance] = Field(None, description="""Distance from camera/monitor to target/eye.""") - field_of_view: Optional[OpticalSeriesFieldOfView] = Field(None, description="""Width, height and depth of image, or imaged area, in meters.""") - data: OpticalSeriesData = Field(..., description="""Images presented to subject, either grayscale or RGB""") - orientation: Optional[OpticalSeriesOrientation] = Field(None, description="""Description of image relative to some reference frame (e.g., which way is up). Must also specify frame of reference.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class OpticalSeriesDistance(ConfiguredBaseModel): - """ - Distance from camera/monitor to target/eye. - """ - None - - -class OpticalSeriesFieldOfView(ConfiguredBaseModel): - """ - Width, height and depth of image, or imaged area, in meters. - """ - array: Optional[OpticalSeriesFieldOfViewArray] = Field(None) - - -class OpticalSeriesFieldOfViewArray(Arraylike): - - width_height: Optional[float] = Field(None) - width_height_depth: Optional[float] = Field(None) - - -class OpticalSeriesData(ConfiguredBaseModel): - """ - Images presented to subject, either grayscale or RGB - """ - array: Optional[OpticalSeriesDataArray] = Field(None) - - -class OpticalSeriesDataArray(Arraylike): - - frame: float = Field(...) - x: float = Field(...) - y: float = Field(...) - r_g_b: Optional[float] = Field(None) - - -class OpticalSeriesOrientation(ConfiguredBaseModel): - """ - Description of image relative to some reference frame (e.g., which way is up). Must also specify frame of reference. - """ - None - - -class IndexSeries(TimeSeries): - """ - Stores indices to image frames stored in an ImageSeries. The purpose of the IndexSeries is to allow a static image stack to be stored in an Images object, and the images in the stack to be referenced out-of-order. This can be for the display of individual images, or of movie segments (as a movie is simply a series of images). The data field stores the index of the frame in the referenced Images object, and the timestamps array indicates when that image was displayed. - """ - data: IndexSeriesData = Field(..., description="""Index of the image (using zero-indexing) in the linked Images object.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class IndexSeriesData(ConfiguredBaseModel): - """ - Index of the image (using zero-indexing) in the linked Images object. - """ - conversion: Optional[float] = Field(None, description="""This field is unused by IndexSeries.""") - resolution: Optional[float] = Field(None, description="""This field is unused by IndexSeries.""") - offset: Optional[float] = Field(None, description="""This field is unused by IndexSeries.""") - unit: Optional[str] = Field(None, description="""This field is unused by IndexSeries and has the value N/A.""") - array: Optional[IndexSeriesDataArray] = Field(None) - - -class IndexSeriesDataArray(Arraylike): - - num_times: int = Field(...) - - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -TwoPhotonSeriesFieldOfView.update_forward_refs() -RoiResponseSeriesData.update_forward_refs() -PlaneSegmentationReferenceImages.update_forward_refs() -ImagingPlaneDescription.update_forward_refs() -ImagingPlaneExcitationLambda.update_forward_refs() -ImagingPlaneImagingRate.update_forward_refs() -ImagingPlaneIndicator.update_forward_refs() -ImagingPlaneLocation.update_forward_refs() -ImagingPlaneManifold.update_forward_refs() -ImagingPlaneOriginCoords.update_forward_refs() -ImagingPlaneGridSpacing.update_forward_refs() -ImagingPlaneReferenceFrame.update_forward_refs() -OpticalChannelDescription.update_forward_refs() -OpticalChannelEmissionLambda.update_forward_refs() -Arraylike.update_forward_refs() -TwoPhotonSeriesFieldOfViewArray.update_forward_refs() -RoiResponseSeriesDataArray.update_forward_refs() -PlaneSegmentationImageMaskArray.update_forward_refs() -ImagingPlaneManifoldArray.update_forward_refs() -ImagingPlaneOriginCoordsArray.update_forward_refs() -ImagingPlaneGridSpacingArray.update_forward_refs() -VectorDataArray.update_forward_refs() -VectorIndexArray.update_forward_refs() -ElementIdentifiersArray.update_forward_refs() -DynamicTableRegionArray.update_forward_refs() -DynamicTableIdArray.update_forward_refs() -Data.update_forward_refs() -VectorData.update_forward_refs() -PlaneSegmentationImageMask.update_forward_refs() -PlaneSegmentationPixelMask.update_forward_refs() -PlaneSegmentationVoxelMask.update_forward_refs() -VectorIndex.update_forward_refs() -PlaneSegmentationPixelMaskIndex.update_forward_refs() -PlaneSegmentationVoxelMaskIndex.update_forward_refs() -ElementIdentifiers.update_forward_refs() -DynamicTableRegion.update_forward_refs() -RoiResponseSeriesRois.update_forward_refs() -DynamicTableId.update_forward_refs() -Container.update_forward_refs() -DynamicTable.update_forward_refs() -PlaneSegmentation.update_forward_refs() -AlignedDynamicTable.update_forward_refs() -SimpleMultiContainer.update_forward_refs() -NWBData.update_forward_refs() -TimeSeriesReferenceVectorData.update_forward_refs() -Image.update_forward_refs() -ImageArray.update_forward_refs() -ImageReferences.update_forward_refs() -ImageReferencesArray.update_forward_refs() -NWBContainer.update_forward_refs() -ImagingPlane.update_forward_refs() -OpticalChannel.update_forward_refs() -NWBDataInterface.update_forward_refs() -DfOverF.update_forward_refs() -Fluorescence.update_forward_refs() -ImageSegmentation.update_forward_refs() -MotionCorrection.update_forward_refs() -CorrectedImageStack.update_forward_refs() -TimeSeries.update_forward_refs() -RoiResponseSeries.update_forward_refs() -CorrectedImageStackXyTranslation.update_forward_refs() -TimeSeriesData.update_forward_refs() -TimeSeriesDataArray.update_forward_refs() -TimeSeriesStartingTime.update_forward_refs() -TimeSeriesTimestamps.update_forward_refs() -TimeSeriesTimestampsArray.update_forward_refs() -TimeSeriesControl.update_forward_refs() -TimeSeriesControlArray.update_forward_refs() -TimeSeriesControlDescription.update_forward_refs() -TimeSeriesControlDescriptionArray.update_forward_refs() -TimeSeriesSync.update_forward_refs() -ProcessingModule.update_forward_refs() -Images.update_forward_refs() -ImagesOrderOfImages.update_forward_refs() -GrayscaleImage.update_forward_refs() -GrayscaleImageArray.update_forward_refs() -RGBImage.update_forward_refs() -RGBImageArray.update_forward_refs() -RGBAImage.update_forward_refs() -RGBAImageArray.update_forward_refs() -ImageSeries.update_forward_refs() -OnePhotonSeries.update_forward_refs() -TwoPhotonSeries.update_forward_refs() -CorrectedImageStackCorrected.update_forward_refs() -ImageSeriesData.update_forward_refs() -ImageSeriesDataArray.update_forward_refs() -ImageSeriesDimension.update_forward_refs() -ImageSeriesDimensionArray.update_forward_refs() -ImageSeriesExternalFile.update_forward_refs() -ImageSeriesExternalFileArray.update_forward_refs() -ImageSeriesFormat.update_forward_refs() -ImageMaskSeries.update_forward_refs() -OpticalSeries.update_forward_refs() -OpticalSeriesDistance.update_forward_refs() -OpticalSeriesFieldOfView.update_forward_refs() -OpticalSeriesFieldOfViewArray.update_forward_refs() -OpticalSeriesData.update_forward_refs() -OpticalSeriesDataArray.update_forward_refs() -OpticalSeriesOrientation.update_forward_refs() -IndexSeries.update_forward_refs() -IndexSeriesData.update_forward_refs() -IndexSeriesDataArray.update_forward_refs() diff --git a/nwb_linkml/models/core.nwb.retinotopy.py b/nwb_linkml/models/core.nwb.retinotopy.py deleted file mode 100644 index 1f5b205..0000000 --- a/nwb_linkml/models/core.nwb.retinotopy.py +++ /dev/null @@ -1,568 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): - pass - - -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - -class ImagingRetinotopyAxis1PhaseMap(ConfiguredBaseModel): - """ - Phase response to stimulus on the first measured axis. - """ - dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") - field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") - unit: Optional[str] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""") - array: Optional[ImagingRetinotopyAxis1PhaseMapArray] = Field(None) - - -class ImagingRetinotopyAxis1PowerMap(ConfiguredBaseModel): - """ - Power response on the first measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power. - """ - dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") - field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") - unit: Optional[str] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""") - array: Optional[ImagingRetinotopyAxis1PowerMapArray] = Field(None) - - -class ImagingRetinotopyAxis2PhaseMap(ConfiguredBaseModel): - """ - Phase response to stimulus on the second measured axis. - """ - dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") - field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") - unit: Optional[str] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""") - array: Optional[ImagingRetinotopyAxis2PhaseMapArray] = Field(None) - - -class ImagingRetinotopyAxis2PowerMap(ConfiguredBaseModel): - """ - Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power. - """ - dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") - field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") - unit: Optional[str] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""") - array: Optional[ImagingRetinotopyAxis2PowerMapArray] = Field(None) - - -class ImagingRetinotopyAxisDescriptions(ConfiguredBaseModel): - """ - Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta']. - """ - array: Optional[ImagingRetinotopyAxisDescriptionsArray] = Field(None) - - -class ImagingRetinotopyFocalDepthImage(ConfiguredBaseModel): - """ - Gray-scale image taken with same settings/parameters (e.g., focal depth, wavelength) as data collection. Array format: [rows][columns]. - """ - bits_per_pixel: Optional[int] = Field(None, description="""Number of bits used to represent each value. This is necessary to determine maximum (white) pixel value.""") - dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") - field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") - focal_depth: Optional[float] = Field(None, description="""Focal depth offset, in meters.""") - format: Optional[str] = Field(None, description="""Format of image. Right now only 'raw' is supported.""") - array: Optional[ImagingRetinotopyFocalDepthImageArray] = Field(None) - - -class ImagingRetinotopySignMap(ConfiguredBaseModel): - """ - Sine of the angle between the direction of the gradient in axis_1 and axis_2. - """ - dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") - field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") - array: Optional[ImagingRetinotopySignMapArray] = Field(None) - - -class ImagingRetinotopyVasculatureImage(ConfiguredBaseModel): - """ - Gray-scale anatomical image of cortical surface. Array structure: [rows][columns] - """ - bits_per_pixel: Optional[int] = Field(None, description="""Number of bits used to represent each value. This is necessary to determine maximum (white) pixel value""") - dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") - field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") - format: Optional[str] = Field(None, description="""Format of image. Right now only 'raw' is supported.""") - array: Optional[ImagingRetinotopyVasculatureImageArray] = Field(None) - - -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - -class ImagingRetinotopyAxis1PhaseMapArray(Arraylike): - - num_rows: Optional[float] = Field(None) - num_cols: Optional[float] = Field(None) - - -class ImagingRetinotopyAxis1PowerMapArray(Arraylike): - - num_rows: Optional[float] = Field(None) - num_cols: Optional[float] = Field(None) - - -class ImagingRetinotopyAxis2PhaseMapArray(Arraylike): - - num_rows: Optional[float] = Field(None) - num_cols: Optional[float] = Field(None) - - -class ImagingRetinotopyAxis2PowerMapArray(Arraylike): - - num_rows: Optional[float] = Field(None) - num_cols: Optional[float] = Field(None) - - -class ImagingRetinotopyAxisDescriptionsArray(Arraylike): - - axis_1_axis_2: str = Field(...) - - -class ImagingRetinotopyFocalDepthImageArray(Arraylike): - - num_rows: Optional[int] = Field(None) - num_cols: Optional[int] = Field(None) - - -class ImagingRetinotopySignMapArray(Arraylike): - - num_rows: Optional[float] = Field(None) - num_cols: Optional[float] = Field(None) - - -class ImagingRetinotopyVasculatureImageArray(Arraylike): - - num_rows: Optional[int] = Field(None) - num_cols: Optional[int] = Field(None) - - -class ImageArray(Arraylike): - - x: float = Field(...) - y: float = Field(...) - r_g_b: Optional[float] = Field(None) - r_g_b_a: Optional[float] = Field(None) - - -class ImageReferencesArray(Arraylike): - - num_images: Image = Field(...) - - -class TimeSeriesData(ConfiguredBaseModel): - """ - Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file. - """ - conversion: Optional[float] = Field(None, description="""Scalar to multiply each element in data to convert it to the specified 'unit'. If the data are stored in acquisition system units or other units that require a conversion to be interpretable, multiply the data by 'conversion' to convert the data to the specified 'unit'. e.g. if the data acquisition system stores values in this object as signed 16-bit integers (int16 range -32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data acquisition system gain is 8000X, then the 'conversion' multiplier to get from raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9.""") - offset: Optional[float] = Field(None, description="""Scalar to add to the data after scaling by 'conversion' to finalize its coercion to the specified 'unit'. Two common examples of this include (a) data stored in an unsigned type that requires a shift after scaling to re-center the data, and (b) specialized recording devices that naturally cause a scalar offset with respect to the true units.""") - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data, stored in the specified by unit, e.g., the change in value of the least significant bit, or a larger number if signal noise is known to be present. If unknown, use -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - continuity: Optional[str] = Field(None, description="""Optionally describe the continuity of the data. Can be \"continuous\", \"instantaneous\", or \"step\". For example, a voltage trace would be \"continuous\", because samples are recorded from a continuous process. An array of lick times would be \"instantaneous\", because the data represents distinct moments in time. Times of image presentations would be \"step\" because the picture remains the same until the next timepoint. This field is optional, but is useful in providing information about the underlying data. It may inform the way this data is interpreted, the way it is visualized, and what analysis methods are applicable.""") - array: Optional[TimeSeriesDataArray] = Field(None) - - -class TimeSeriesDataArray(Arraylike): - - num_times: Any = Field(...) - num_DIM2: Optional[Any] = Field(None) - num_DIM3: Optional[Any] = Field(None) - num_DIM4: Optional[Any] = Field(None) - - -class TimeSeriesStartingTime(ConfiguredBaseModel): - """ - Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute. - """ - rate: Optional[float] = Field(None, description="""Sampling rate, in Hz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement for time, which is fixed to 'seconds'.""") - - -class TimeSeriesTimestamps(ConfiguredBaseModel): - """ - Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. - """ - interval: Optional[int] = Field(None, description="""Value is '1'""") - unit: Optional[str] = Field(None, description="""Unit of measurement for timestamps, which is fixed to 'seconds'.""") - array: Optional[TimeSeriesTimestampsArray] = Field(None) - - -class TimeSeriesTimestampsArray(Arraylike): - - num_times: float = Field(...) - - -class TimeSeriesControl(ConfiguredBaseModel): - """ - Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data. - """ - array: Optional[TimeSeriesControlArray] = Field(None) - - -class TimeSeriesControlArray(Arraylike): - - num_times: int = Field(...) - - -class TimeSeriesControlDescription(ConfiguredBaseModel): - """ - Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0. - """ - array: Optional[TimeSeriesControlDescriptionArray] = Field(None) - - -class TimeSeriesControlDescriptionArray(Arraylike): - - num_control_values: str = Field(...) - - -class TimeSeriesSync(ConfiguredBaseModel): - """ - Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes. - """ - None - - -class VectorDataArray(Arraylike): - - dim0: Any = Field(...) - dim1: Optional[Any] = Field(None) - dim2: Optional[Any] = Field(None) - dim3: Optional[Any] = Field(None) - - -class VectorIndexArray(Arraylike): - - num_rows: int = Field(...) - - -class ElementIdentifiersArray(Arraylike): - - num_elements: int = Field(...) - - -class DynamicTableRegionArray(Arraylike): - - num_rows: int = Field(...) - - -class DynamicTableIdArray(Arraylike): - - num_rows: int = Field(...) - - -class Data(ConfiguredBaseModel): - """ - An abstract data type for a dataset. - """ - None - - -class NWBData(Data): - """ - An abstract data type for a dataset. - """ - None - - -class Image(NWBData): - """ - An abstract data type for an image. Shape can be 2-D (x, y), or 3-D where the third dimension can have three or four elements, e.g. (x, y, (r, g, b)) or (x, y, (r, g, b, a)). - """ - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - array: Optional[ImageArray] = Field(None) - - -class ImageReferences(NWBData): - """ - Ordered dataset of references to Image objects. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class ImagesOrderOfImages(ImageReferences): - """ - Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class VectorData(Data): - """ - An n-dimensional dataset representing a column of a DynamicTable. If used without an accompanying VectorIndex, first dimension is along the rows of the DynamicTable and each step along the first dimension is a cell of the larger table. VectorData can also be used to represent a ragged array if paired with a VectorIndex. This allows for storing arrays of varying length in a single cell of the DynamicTable by indexing into this VectorData. The first vector is at VectorData[0:VectorIndex[0]]. The second vector is at VectorData[VectorIndex[0]:VectorIndex[1]], and so on. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class TimeSeriesReferenceVectorData(VectorData): - """ - Column storing references to a TimeSeries (rows). For each TimeSeries this VectorData column stores the start_index and count to indicate the range in time to be selected as well as an object reference to the TimeSeries. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class VectorIndex(VectorData): - """ - Used with VectorData to encode a ragged array. An array of indices into the first dimension of the target VectorData, and forming a map between the rows of a DynamicTable and the indices of the VectorData. The name of the VectorIndex is expected to be the name of the target VectorData object followed by \"_index\". - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ElementIdentifiers(Data): - """ - A list of unique identifiers for values within a dataset, e.g. rows of a DynamicTable. - """ - array: Optional[ElementIdentifiersArray] = Field(None) - - -class DynamicTableRegion(VectorData): - """ - DynamicTableRegion provides a link from one table to an index or region of another. The `table` attribute is a link to another `DynamicTable`, indicating which table is referenced, and the data is int(s) indicating the row(s) (0-indexed) of the target array. `DynamicTableRegion`s can be used to associate rows with repeated meta-data without data duplication. They can also be used to create hierarchical relationships between multiple `DynamicTable`s. `DynamicTableRegion` objects may be paired with a `VectorIndex` object to create ragged references, so a single cell of a `DynamicTable` can reference many rows of another `DynamicTable`. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DynamicTableId(ElementIdentifiers): - """ - Array of unique identifiers for the rows of this dynamic table. - """ - array: Optional[DynamicTableIdArray] = Field(None) - - -class Container(ConfiguredBaseModel): - """ - An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class NWBContainer(Container): - """ - An abstract data type for a generic container storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class NWBDataInterface(NWBContainer): - """ - An abstract data type for a generic container storing collections of data, as opposed to metadata. - """ - None - - -class ImagingRetinotopy(NWBDataInterface): - """ - Intrinsic signal optical imaging or widefield imaging for measuring retinotopy. Stores orthogonal maps (e.g., altitude/azimuth; radius/theta) of responses to specific stimuli and a combined polarity map from which to identify visual areas. This group does not store the raw responses imaged during retinotopic mapping or the stimuli presented, but rather the resulting phase and power maps after applying a Fourier transform on the averaged responses. Note: for data consistency, all images and arrays are stored in the format [row][column] and [row, col], which equates to [y][x]. Field of view and dimension arrays may appear backward (i.e., y before x). - """ - axis_1_phase_map: ImagingRetinotopyAxis1PhaseMap = Field(..., description="""Phase response to stimulus on the first measured axis.""") - axis_1_power_map: Optional[ImagingRetinotopyAxis1PowerMap] = Field(None, description="""Power response on the first measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""") - axis_2_phase_map: ImagingRetinotopyAxis2PhaseMap = Field(..., description="""Phase response to stimulus on the second measured axis.""") - axis_2_power_map: Optional[ImagingRetinotopyAxis2PowerMap] = Field(None, description="""Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""") - axis_descriptions: ImagingRetinotopyAxisDescriptions = Field(..., description="""Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta'].""") - focal_depth_image: Optional[ImagingRetinotopyFocalDepthImage] = Field(None, description="""Gray-scale image taken with same settings/parameters (e.g., focal depth, wavelength) as data collection. Array format: [rows][columns].""") - sign_map: Optional[ImagingRetinotopySignMap] = Field(None, description="""Sine of the angle between the direction of the gradient in axis_1 and axis_2.""") - vasculature_image: ImagingRetinotopyVasculatureImage = Field(..., description="""Gray-scale anatomical image of cortical surface. Array structure: [rows][columns]""") - - -class TimeSeries(NWBDataInterface): - """ - General purpose time series. - """ - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - data: TimeSeriesData = Field(..., description="""Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class ProcessingModule(NWBContainer): - """ - A collection of processed data. - """ - description: Optional[str] = Field(None, description="""Description of this collection of processed data.""") - NWBDataInterface: Optional[List[NWBDataInterface]] = Field(default_factory=list, description="""Data objects stored in this collection.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tables stored in this collection.""") - - -class Images(NWBDataInterface): - """ - A collection of images with an optional way to specify the order of the images using the \"order_of_images\" dataset. An order must be specified if the images are referenced by index, e.g., from an IndexSeries. - """ - description: Optional[str] = Field(None, description="""Description of this collection of images.""") - Image: List[Image] = Field(default_factory=list, description="""Images stored in this collection.""") - order_of_images: Optional[ImagesOrderOfImages] = Field(None, description="""Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images.""") - - -class DynamicTable(Container): - """ - A group containing multiple datasets that are aligned on the first dimension (Currently, this requirement if left up to APIs to check and enforce). These datasets represent different columns in the table. Apart from a column that contains unique identifiers for each row, there are no other required datasets. Users are free to add any number of custom VectorData objects (columns) here. DynamicTable also supports ragged array columns, where each element can be of a different size. To add a ragged array column, use a VectorIndex type to index the corresponding VectorData type. See documentation for VectorData and VectorIndex for more details. Unlike a compound data type, which is analogous to storing an array-of-structs, a DynamicTable can be thought of as a struct-of-arrays. This provides an alternative structure to choose from when optimizing storage for anticipated access patterns. Additionally, this type provides a way of creating a table without having to define a compound type up front. Although this convenience may be attractive, users should think carefully about how data will be accessed. DynamicTable is more appropriate for column-centric access, whereas a dataset with a compound type would be more appropriate for row-centric access. Finally, data size should also be taken into account. For small tables, performance loss may be an acceptable trade-off for the flexibility of a DynamicTable. - """ - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class AlignedDynamicTable(DynamicTable): - """ - DynamicTable container that supports storing a collection of sub-tables. Each sub-table is a DynamicTable itself that is aligned with the main table by row index. I.e., all DynamicTables stored in this group MUST have the same number of rows. This type effectively defines a 2-level table in which the main data is stored in the main table implemented by this type and additional columns of the table are grouped into categories, with each category being represented by a separate DynamicTable stored within the group. - """ - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimpleMultiContainer(Container): - """ - A simple Container for holding onto multiple containers. - """ - Data: Optional[List[Data]] = Field(default_factory=list, description="""Data objects held within this SimpleMultiContainer.""") - Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") - - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -ImagingRetinotopyAxis1PhaseMap.update_forward_refs() -ImagingRetinotopyAxis1PowerMap.update_forward_refs() -ImagingRetinotopyAxis2PhaseMap.update_forward_refs() -ImagingRetinotopyAxis2PowerMap.update_forward_refs() -ImagingRetinotopyAxisDescriptions.update_forward_refs() -ImagingRetinotopyFocalDepthImage.update_forward_refs() -ImagingRetinotopySignMap.update_forward_refs() -ImagingRetinotopyVasculatureImage.update_forward_refs() -Arraylike.update_forward_refs() -ImagingRetinotopyAxis1PhaseMapArray.update_forward_refs() -ImagingRetinotopyAxis1PowerMapArray.update_forward_refs() -ImagingRetinotopyAxis2PhaseMapArray.update_forward_refs() -ImagingRetinotopyAxis2PowerMapArray.update_forward_refs() -ImagingRetinotopyAxisDescriptionsArray.update_forward_refs() -ImagingRetinotopyFocalDepthImageArray.update_forward_refs() -ImagingRetinotopySignMapArray.update_forward_refs() -ImagingRetinotopyVasculatureImageArray.update_forward_refs() -ImageArray.update_forward_refs() -ImageReferencesArray.update_forward_refs() -TimeSeriesData.update_forward_refs() -TimeSeriesDataArray.update_forward_refs() -TimeSeriesStartingTime.update_forward_refs() -TimeSeriesTimestamps.update_forward_refs() -TimeSeriesTimestampsArray.update_forward_refs() -TimeSeriesControl.update_forward_refs() -TimeSeriesControlArray.update_forward_refs() -TimeSeriesControlDescription.update_forward_refs() -TimeSeriesControlDescriptionArray.update_forward_refs() -TimeSeriesSync.update_forward_refs() -VectorDataArray.update_forward_refs() -VectorIndexArray.update_forward_refs() -ElementIdentifiersArray.update_forward_refs() -DynamicTableRegionArray.update_forward_refs() -DynamicTableIdArray.update_forward_refs() -Data.update_forward_refs() -NWBData.update_forward_refs() -Image.update_forward_refs() -ImageReferences.update_forward_refs() -ImagesOrderOfImages.update_forward_refs() -VectorData.update_forward_refs() -TimeSeriesReferenceVectorData.update_forward_refs() -VectorIndex.update_forward_refs() -ElementIdentifiers.update_forward_refs() -DynamicTableRegion.update_forward_refs() -DynamicTableId.update_forward_refs() -Container.update_forward_refs() -NWBContainer.update_forward_refs() -NWBDataInterface.update_forward_refs() -ImagingRetinotopy.update_forward_refs() -TimeSeries.update_forward_refs() -ProcessingModule.update_forward_refs() -Images.update_forward_refs() -DynamicTable.update_forward_refs() -AlignedDynamicTable.update_forward_refs() -SimpleMultiContainer.update_forward_refs() diff --git a/nwb_linkml/models/core.py b/nwb_linkml/models/core.py index 5378200..ac69d88 100644 --- a/nwb_linkml/models/core.py +++ b/nwb_linkml/models/core.py @@ -3,6 +3,7 @@ from datetime import datetime, date from enum import Enum from typing import List, Dict, Optional, Any, Union from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 import sys if sys.version_info >= (3, 8): from typing import Literal @@ -10,6 +11,7 @@ else: from typing_extensions import Literal + metamodel_version = "None" version = "2.6.0-alpha" @@ -26,3661 +28,6 @@ class ConfiguredBaseModel(WeakRefShimBaseModel, pass -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - -class ImagingRetinotopyAxis1PhaseMap(ConfiguredBaseModel): - """ - Phase response to stimulus on the first measured axis. - """ - dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") - field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") - unit: Optional[str] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""") - array: Optional[ImagingRetinotopyAxis1PhaseMapArray] = Field(None) - - -class ImagingRetinotopyAxis1PowerMap(ConfiguredBaseModel): - """ - Power response on the first measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power. - """ - dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") - field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") - unit: Optional[str] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""") - array: Optional[ImagingRetinotopyAxis1PowerMapArray] = Field(None) - - -class ImagingRetinotopyAxis2PhaseMap(ConfiguredBaseModel): - """ - Phase response to stimulus on the second measured axis. - """ - dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") - field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") - unit: Optional[str] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""") - array: Optional[ImagingRetinotopyAxis2PhaseMapArray] = Field(None) - - -class ImagingRetinotopyAxis2PowerMap(ConfiguredBaseModel): - """ - Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power. - """ - dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") - field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") - unit: Optional[str] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""") - array: Optional[ImagingRetinotopyAxis2PowerMapArray] = Field(None) - - -class ImagingRetinotopyAxisDescriptions(ConfiguredBaseModel): - """ - Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta']. - """ - array: Optional[ImagingRetinotopyAxisDescriptionsArray] = Field(None) - - -class ImagingRetinotopyFocalDepthImage(ConfiguredBaseModel): - """ - Gray-scale image taken with same settings/parameters (e.g., focal depth, wavelength) as data collection. Array format: [rows][columns]. - """ - bits_per_pixel: Optional[int] = Field(None, description="""Number of bits used to represent each value. This is necessary to determine maximum (white) pixel value.""") - dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") - field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") - focal_depth: Optional[float] = Field(None, description="""Focal depth offset, in meters.""") - format: Optional[str] = Field(None, description="""Format of image. Right now only 'raw' is supported.""") - array: Optional[ImagingRetinotopyFocalDepthImageArray] = Field(None) - - -class ImagingRetinotopySignMap(ConfiguredBaseModel): - """ - Sine of the angle between the direction of the gradient in axis_1 and axis_2. - """ - dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") - field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") - array: Optional[ImagingRetinotopySignMapArray] = Field(None) - - -class ImagingRetinotopyVasculatureImage(ConfiguredBaseModel): - """ - Gray-scale anatomical image of cortical surface. Array structure: [rows][columns] - """ - bits_per_pixel: Optional[int] = Field(None, description="""Number of bits used to represent each value. This is necessary to determine maximum (white) pixel value""") - dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") - field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") - format: Optional[str] = Field(None, description="""Format of image. Right now only 'raw' is supported.""") - array: Optional[ImagingRetinotopyVasculatureImageArray] = Field(None) - - -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - -class ImagingRetinotopyAxis1PhaseMapArray(Arraylike): - - num_rows: Optional[float] = Field(None) - num_cols: Optional[float] = Field(None) - - -class ImagingRetinotopyAxis1PowerMapArray(Arraylike): - - num_rows: Optional[float] = Field(None) - num_cols: Optional[float] = Field(None) - - -class ImagingRetinotopyAxis2PhaseMapArray(Arraylike): - - num_rows: Optional[float] = Field(None) - num_cols: Optional[float] = Field(None) - - -class ImagingRetinotopyAxis2PowerMapArray(Arraylike): - - num_rows: Optional[float] = Field(None) - num_cols: Optional[float] = Field(None) - - -class ImagingRetinotopyAxisDescriptionsArray(Arraylike): - - axis_1_axis_2: str = Field(...) - - -class ImagingRetinotopyFocalDepthImageArray(Arraylike): - - num_rows: Optional[int] = Field(None) - num_cols: Optional[int] = Field(None) - - -class ImagingRetinotopySignMapArray(Arraylike): - - num_rows: Optional[float] = Field(None) - num_cols: Optional[float] = Field(None) - - -class ImagingRetinotopyVasculatureImageArray(Arraylike): - - num_rows: Optional[int] = Field(None) - num_cols: Optional[int] = Field(None) - - -class ImageArray(Arraylike): - - x: float = Field(...) - y: float = Field(...) - r_g_b: Optional[float] = Field(None) - r_g_b_a: Optional[float] = Field(None) - - -class ImageReferencesArray(Arraylike): - - num_images: Image = Field(...) - - -class TimeSeriesData(ConfiguredBaseModel): - """ - Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file. - """ - conversion: Optional[float] = Field(None, description="""Scalar to multiply each element in data to convert it to the specified 'unit'. If the data are stored in acquisition system units or other units that require a conversion to be interpretable, multiply the data by 'conversion' to convert the data to the specified 'unit'. e.g. if the data acquisition system stores values in this object as signed 16-bit integers (int16 range -32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data acquisition system gain is 8000X, then the 'conversion' multiplier to get from raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9.""") - offset: Optional[float] = Field(None, description="""Scalar to add to the data after scaling by 'conversion' to finalize its coercion to the specified 'unit'. Two common examples of this include (a) data stored in an unsigned type that requires a shift after scaling to re-center the data, and (b) specialized recording devices that naturally cause a scalar offset with respect to the true units.""") - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data, stored in the specified by unit, e.g., the change in value of the least significant bit, or a larger number if signal noise is known to be present. If unknown, use -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - continuity: Optional[str] = Field(None, description="""Optionally describe the continuity of the data. Can be \"continuous\", \"instantaneous\", or \"step\". For example, a voltage trace would be \"continuous\", because samples are recorded from a continuous process. An array of lick times would be \"instantaneous\", because the data represents distinct moments in time. Times of image presentations would be \"step\" because the picture remains the same until the next timepoint. This field is optional, but is useful in providing information about the underlying data. It may inform the way this data is interpreted, the way it is visualized, and what analysis methods are applicable.""") - array: Optional[TimeSeriesDataArray] = Field(None) - - -class TimeSeriesDataArray(Arraylike): - - num_times: Any = Field(...) - num_DIM2: Optional[Any] = Field(None) - num_DIM3: Optional[Any] = Field(None) - num_DIM4: Optional[Any] = Field(None) - - -class TimeSeriesStartingTime(ConfiguredBaseModel): - """ - Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute. - """ - rate: Optional[float] = Field(None, description="""Sampling rate, in Hz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement for time, which is fixed to 'seconds'.""") - - -class TimeSeriesTimestamps(ConfiguredBaseModel): - """ - Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. - """ - interval: Optional[int] = Field(None, description="""Value is '1'""") - unit: Optional[str] = Field(None, description="""Unit of measurement for timestamps, which is fixed to 'seconds'.""") - array: Optional[TimeSeriesTimestampsArray] = Field(None) - - -class TimeSeriesTimestampsArray(Arraylike): - - num_times: float = Field(...) - - -class TimeSeriesControl(ConfiguredBaseModel): - """ - Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data. - """ - array: Optional[TimeSeriesControlArray] = Field(None) - - -class TimeSeriesControlArray(Arraylike): - - num_times: int = Field(...) - - -class TimeSeriesControlDescription(ConfiguredBaseModel): - """ - Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0. - """ - array: Optional[TimeSeriesControlDescriptionArray] = Field(None) - - -class TimeSeriesControlDescriptionArray(Arraylike): - - num_control_values: str = Field(...) - - -class TimeSeriesSync(ConfiguredBaseModel): - """ - Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes. - """ - None - - -class VectorDataArray(Arraylike): - - dim0: Any = Field(...) - dim1: Optional[Any] = Field(None) - dim2: Optional[Any] = Field(None) - dim3: Optional[Any] = Field(None) - - -class VectorIndexArray(Arraylike): - - num_rows: int = Field(...) - - -class ElementIdentifiersArray(Arraylike): - - num_elements: int = Field(...) - - -class DynamicTableRegionArray(Arraylike): - - num_rows: int = Field(...) - - -class DynamicTableIdArray(Arraylike): - - num_rows: int = Field(...) - - -class Data(ConfiguredBaseModel): - """ - An abstract data type for a dataset. - """ - None - - -class NWBData(Data): - """ - An abstract data type for a dataset. - """ - None - - -class Image(NWBData): - """ - An abstract data type for an image. Shape can be 2-D (x, y), or 3-D where the third dimension can have three or four elements, e.g. (x, y, (r, g, b)) or (x, y, (r, g, b, a)). - """ - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - array: Optional[ImageArray] = Field(None) - - -class ImageReferences(NWBData): - """ - Ordered dataset of references to Image objects. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class ImagesOrderOfImages(ImageReferences): - """ - Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images. - """ - array: Optional[ImageReferencesArray] = Field(None) - - -class VectorData(Data): - """ - An n-dimensional dataset representing a column of a DynamicTable. If used without an accompanying VectorIndex, first dimension is along the rows of the DynamicTable and each step along the first dimension is a cell of the larger table. VectorData can also be used to represent a ragged array if paired with a VectorIndex. This allows for storing arrays of varying length in a single cell of the DynamicTable by indexing into this VectorData. The first vector is at VectorData[0:VectorIndex[0]]. The second vector is at VectorData[VectorIndex[0]:VectorIndex[1]], and so on. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class TimeSeriesReferenceVectorData(VectorData): - """ - Column storing references to a TimeSeries (rows). For each TimeSeries this VectorData column stores the start_index and count to indicate the range in time to be selected as well as an object reference to the TimeSeries. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class VectorIndex(VectorData): - """ - Used with VectorData to encode a ragged array. An array of indices into the first dimension of the target VectorData, and forming a map between the rows of a DynamicTable and the indices of the VectorData. The name of the VectorIndex is expected to be the name of the target VectorData object followed by \"_index\". - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ElementIdentifiers(Data): - """ - A list of unique identifiers for values within a dataset, e.g. rows of a DynamicTable. - """ - array: Optional[ElementIdentifiersArray] = Field(None) - - -class DynamicTableRegion(VectorData): - """ - DynamicTableRegion provides a link from one table to an index or region of another. The `table` attribute is a link to another `DynamicTable`, indicating which table is referenced, and the data is int(s) indicating the row(s) (0-indexed) of the target array. `DynamicTableRegion`s can be used to associate rows with repeated meta-data without data duplication. They can also be used to create hierarchical relationships between multiple `DynamicTable`s. `DynamicTableRegion` objects may be paired with a `VectorIndex` object to create ragged references, so a single cell of a `DynamicTable` can reference many rows of another `DynamicTable`. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DynamicTableId(ElementIdentifiers): - """ - Array of unique identifiers for the rows of this dynamic table. - """ - array: Optional[DynamicTableIdArray] = Field(None) - - -class Container(ConfiguredBaseModel): - """ - An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class NWBContainer(Container): - """ - An abstract data type for a generic container storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class NWBDataInterface(NWBContainer): - """ - An abstract data type for a generic container storing collections of data, as opposed to metadata. - """ - None - - -class ImagingRetinotopy(NWBDataInterface): - """ - Intrinsic signal optical imaging or widefield imaging for measuring retinotopy. Stores orthogonal maps (e.g., altitude/azimuth; radius/theta) of responses to specific stimuli and a combined polarity map from which to identify visual areas. This group does not store the raw responses imaged during retinotopic mapping or the stimuli presented, but rather the resulting phase and power maps after applying a Fourier transform on the averaged responses. Note: for data consistency, all images and arrays are stored in the format [row][column] and [row, col], which equates to [y][x]. Field of view and dimension arrays may appear backward (i.e., y before x). - """ - axis_1_phase_map: ImagingRetinotopyAxis1PhaseMap = Field(..., description="""Phase response to stimulus on the first measured axis.""") - axis_1_power_map: Optional[ImagingRetinotopyAxis1PowerMap] = Field(None, description="""Power response on the first measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""") - axis_2_phase_map: ImagingRetinotopyAxis2PhaseMap = Field(..., description="""Phase response to stimulus on the second measured axis.""") - axis_2_power_map: Optional[ImagingRetinotopyAxis2PowerMap] = Field(None, description="""Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""") - axis_descriptions: ImagingRetinotopyAxisDescriptions = Field(..., description="""Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta'].""") - focal_depth_image: Optional[ImagingRetinotopyFocalDepthImage] = Field(None, description="""Gray-scale image taken with same settings/parameters (e.g., focal depth, wavelength) as data collection. Array format: [rows][columns].""") - sign_map: Optional[ImagingRetinotopySignMap] = Field(None, description="""Sine of the angle between the direction of the gradient in axis_1 and axis_2.""") - vasculature_image: ImagingRetinotopyVasculatureImage = Field(..., description="""Gray-scale anatomical image of cortical surface. Array structure: [rows][columns]""") - - -class TimeSeries(NWBDataInterface): - """ - General purpose time series. - """ - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - data: TimeSeriesData = Field(..., description="""Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class ProcessingModule(NWBContainer): - """ - A collection of processed data. - """ - description: Optional[str] = Field(None, description="""Description of this collection of processed data.""") - NWBDataInterface: Optional[List[NWBDataInterface]] = Field(default_factory=list, description="""Data objects stored in this collection.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tables stored in this collection.""") - - -class Images(NWBDataInterface): - """ - A collection of images with an optional way to specify the order of the images using the \"order_of_images\" dataset. An order must be specified if the images are referenced by index, e.g., from an IndexSeries. - """ - description: Optional[str] = Field(None, description="""Description of this collection of images.""") - Image: List[Image] = Field(default_factory=list, description="""Images stored in this collection.""") - order_of_images: Optional[ImagesOrderOfImages] = Field(None, description="""Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images.""") - - -class DynamicTable(Container): - """ - A group containing multiple datasets that are aligned on the first dimension (Currently, this requirement if left up to APIs to check and enforce). These datasets represent different columns in the table. Apart from a column that contains unique identifiers for each row, there are no other required datasets. Users are free to add any number of custom VectorData objects (columns) here. DynamicTable also supports ragged array columns, where each element can be of a different size. To add a ragged array column, use a VectorIndex type to index the corresponding VectorData type. See documentation for VectorData and VectorIndex for more details. Unlike a compound data type, which is analogous to storing an array-of-structs, a DynamicTable can be thought of as a struct-of-arrays. This provides an alternative structure to choose from when optimizing storage for anticipated access patterns. Additionally, this type provides a way of creating a table without having to define a compound type up front. Although this convenience may be attractive, users should think carefully about how data will be accessed. DynamicTable is more appropriate for column-centric access, whereas a dataset with a compound type would be more appropriate for row-centric access. Finally, data size should also be taken into account. For small tables, performance loss may be an acceptable trade-off for the flexibility of a DynamicTable. - """ - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class AlignedDynamicTable(DynamicTable): - """ - DynamicTable container that supports storing a collection of sub-tables. Each sub-table is a DynamicTable itself that is aligned with the main table by row index. I.e., all DynamicTables stored in this group MUST have the same number of rows. This type effectively defines a 2-level table in which the main data is stored in the main table implemented by this type and additional columns of the table are grouped into categories, with each category being represented by a separate DynamicTable stored within the group. - """ - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimpleMultiContainer(Container): - """ - A simple Container for holding onto multiple containers. - """ - Data: Optional[List[Data]] = Field(default_factory=list, description="""Data objects held within this SimpleMultiContainer.""") - Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") - - -class TwoPhotonSeriesFieldOfView(ConfiguredBaseModel): - """ - Width, height and depth of image, or imaged area, in meters. - """ - array: Optional[TwoPhotonSeriesFieldOfViewArray] = Field(None) - - -class TwoPhotonSeriesFieldOfViewArray(Arraylike): - - width|height: Optional[float] = Field(None) - width|height|depth: Optional[float] = Field(None) - - -class RoiResponseSeries(TimeSeries): - """ - ROI responses over an imaging plane. The first dimension represents time. The second dimension, if present, represents ROIs. - """ - data: RoiResponseSeriesData = Field(..., description="""Signals from ROIs.""") - rois: RoiResponseSeriesRois = Field(..., description="""DynamicTableRegion referencing into an ROITable containing information on the ROIs stored in this timeseries.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class RoiResponseSeriesData(ConfiguredBaseModel): - """ - Signals from ROIs. - """ - array: Optional[RoiResponseSeriesDataArray] = Field(None) - - -class RoiResponseSeriesDataArray(Arraylike): - - num_times: float = Field(...) - num_ROIs: Optional[float] = Field(None) - - -class RoiResponseSeriesRois(DynamicTableRegion): - """ - DynamicTableRegion referencing into an ROITable containing information on the ROIs stored in this timeseries. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DfOverF(NWBDataInterface): - """ - dF/F information about a region of interest (ROI). Storage hierarchy of dF/F should be the same as for segmentation (i.e., same names for ROIs and for image planes). - """ - RoiResponseSeries: List[RoiResponseSeries] = Field(default_factory=list, description="""RoiResponseSeries object(s) containing dF/F for a ROI.""") - - -class Fluorescence(NWBDataInterface): - """ - Fluorescence information about a region of interest (ROI). Storage hierarchy of fluorescence should be the same as for segmentation (ie, same names for ROIs and for image planes). - """ - RoiResponseSeries: List[RoiResponseSeries] = Field(default_factory=list, description="""RoiResponseSeries object(s) containing fluorescence data for a ROI.""") - - -class ImageSegmentation(NWBDataInterface): - """ - Stores pixels in an image that represent different regions of interest (ROIs) or masks. All segmentation for a given imaging plane is stored together, with storage for multiple imaging planes (masks) supported. Each ROI is stored in its own subgroup, with the ROI group containing both a 2D mask and a list of pixels that make up this mask. Segments can also be used for masking neuropil. If segmentation is allowed to change with time, a new imaging plane (or module) is required and ROI names should remain consistent between them. - """ - PlaneSegmentation: List[PlaneSegmentation] = Field(default_factory=list, description="""Results from image segmentation of a specific imaging plane.""") - - -class PlaneSegmentation(DynamicTable): - """ - Results from image segmentation of a specific imaging plane. - """ - image_mask: Optional[PlaneSegmentationImageMask] = Field(None, description="""ROI masks for each ROI. Each image mask is the size of the original imaging plane (or volume) and members of the ROI are finite non-zero.""") - pixel_mask_index: Optional[PlaneSegmentationPixelMaskIndex] = Field(None, description="""Index into pixel_mask.""") - pixel_mask: Optional[PlaneSegmentationPixelMask] = Field(None, description="""Pixel masks for each ROI: a list of indices and weights for the ROI. Pixel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation""") - voxel_mask_index: Optional[PlaneSegmentationVoxelMaskIndex] = Field(None, description="""Index into voxel_mask.""") - voxel_mask: Optional[PlaneSegmentationVoxelMask] = Field(None, description="""Voxel masks for each ROI: a list of indices and weights for the ROI. Voxel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation""") - reference_images: PlaneSegmentationReferenceImages = Field(..., description="""Image stacks that the segmentation masks apply to.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class PlaneSegmentationImageMask(VectorData): - """ - ROI masks for each ROI. Each image mask is the size of the original imaging plane (or volume) and members of the ROI are finite non-zero. - """ - array: Optional[PlaneSegmentationImageMaskArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class PlaneSegmentationImageMaskArray(Arraylike): - - num_roi: Any = Field(...) - num_x: Any = Field(...) - num_y: Any = Field(...) - num_z: Optional[Any] = Field(None) - - -class PlaneSegmentationPixelMaskIndex(VectorIndex): - """ - Index into pixel_mask. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class PlaneSegmentationPixelMask(VectorData): - """ - Pixel masks for each ROI: a list of indices and weights for the ROI. Pixel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class PlaneSegmentationVoxelMaskIndex(VectorIndex): - """ - Index into voxel_mask. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class PlaneSegmentationVoxelMask(VectorData): - """ - Voxel masks for each ROI: a list of indices and weights for the ROI. Voxel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class PlaneSegmentationReferenceImages(ConfiguredBaseModel): - """ - Image stacks that the segmentation masks apply to. - """ - ImageSeries: Optional[List[ImageSeries]] = Field(default_factory=list, description="""One or more image stacks that the masks apply to (can be one-element stack).""") - - -class ImagingPlane(NWBContainer): - """ - An imaging plane and its metadata. - """ - description: Optional[ImagingPlaneDescription] = Field(None, description="""Description of the imaging plane.""") - excitation_lambda: ImagingPlaneExcitationLambda = Field(..., description="""Excitation wavelength, in nm.""") - imaging_rate: Optional[ImagingPlaneImagingRate] = Field(None, description="""Rate that images are acquired, in Hz. If the corresponding TimeSeries is present, the rate should be stored there instead.""") - indicator: ImagingPlaneIndicator = Field(..., description="""Calcium indicator.""") - location: ImagingPlaneLocation = Field(..., description="""Location of the imaging plane. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible.""") - manifold: Optional[ImagingPlaneManifold] = Field(None, description="""DEPRECATED Physical position of each pixel. 'xyz' represents the position of the pixel relative to the defined coordinate space. Deprecated in favor of origin_coords and grid_spacing.""") - origin_coords: Optional[ImagingPlaneOriginCoords] = Field(None, description="""Physical location of the first element of the imaging plane (0, 0) for 2-D data or (0, 0, 0) for 3-D data. See also reference_frame for what the physical location is relative to (e.g., bregma).""") - grid_spacing: Optional[ImagingPlaneGridSpacing] = Field(None, description="""Space between pixels in (x, y) or voxels in (x, y, z) directions, in the specified unit. Assumes imaging plane is a regular grid. See also reference_frame to interpret the grid.""") - reference_frame: Optional[ImagingPlaneReferenceFrame] = Field(None, description="""Describes reference frame of origin_coords and grid_spacing. For example, this can be a text description of the anatomical location and orientation of the grid defined by origin_coords and grid_spacing or the vectors needed to transform or rotate the grid to a common anatomical axis (e.g., AP/DV/ML). This field is necessary to interpret origin_coords and grid_spacing. If origin_coords and grid_spacing are not present, then this field is not required. For example, if the microscope takes 10 x 10 x 2 images, where the first value of the data matrix (index (0, 0, 0)) corresponds to (-1.2, -0.6, -2) mm relative to bregma, the spacing between pixels is 0.2 mm in x, 0.2 mm in y and 0.5 mm in z, and larger numbers in x means more anterior, larger numbers in y means more rightward, and larger numbers in z means more ventral, then enter the following -- origin_coords = (-1.2, -0.6, -2) grid_spacing = (0.2, 0.2, 0.5) reference_frame = \"Origin coordinates are relative to bregma. First dimension corresponds to anterior-posterior axis (larger index = more anterior). Second dimension corresponds to medial-lateral axis (larger index = more rightward). Third dimension corresponds to dorsal-ventral axis (larger index = more ventral).\"""") - OpticalChannel: List[OpticalChannel] = Field(default_factory=list, description="""An optical channel used to record from an imaging plane.""") - - -class ImagingPlaneDescription(ConfiguredBaseModel): - """ - Description of the imaging plane. - """ - None - - -class ImagingPlaneExcitationLambda(ConfiguredBaseModel): - """ - Excitation wavelength, in nm. - """ - None - - -class ImagingPlaneImagingRate(ConfiguredBaseModel): - """ - Rate that images are acquired, in Hz. If the corresponding TimeSeries is present, the rate should be stored there instead. - """ - None - - -class ImagingPlaneIndicator(ConfiguredBaseModel): - """ - Calcium indicator. - """ - None - - -class ImagingPlaneLocation(ConfiguredBaseModel): - """ - Location of the imaging plane. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible. - """ - None - - -class ImagingPlaneManifold(ConfiguredBaseModel): - """ - DEPRECATED Physical position of each pixel. 'xyz' represents the position of the pixel relative to the defined coordinate space. Deprecated in favor of origin_coords and grid_spacing. - """ - conversion: Optional[float] = Field(None, description="""Scalar to multiply each element in data to convert it to the specified 'unit'. If the data are stored in acquisition system units or other units that require a conversion to be interpretable, multiply the data by 'conversion' to convert the data to the specified 'unit'. e.g. if the data acquisition system stores values in this object as pixels from x = -500 to 499, y = -500 to 499 that correspond to a 2 m x 2 m range, then the 'conversion' multiplier to get from raw data acquisition pixel units to meters is 2/1000.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. The default value is 'meters'.""") - array: Optional[ImagingPlaneManifoldArray] = Field(None) - - -class ImagingPlaneManifoldArray(Arraylike): - - height: float = Field(...) - width: float = Field(...) - x_y_z: float = Field(...) - depth: Optional[float] = Field(None) - - -class ImagingPlaneOriginCoords(ConfiguredBaseModel): - """ - Physical location of the first element of the imaging plane (0, 0) for 2-D data or (0, 0, 0) for 3-D data. See also reference_frame for what the physical location is relative to (e.g., bregma). - """ - unit: Optional[str] = Field(None, description="""Measurement units for origin_coords. The default value is 'meters'.""") - array: Optional[ImagingPlaneOriginCoordsArray] = Field(None) - - -class ImagingPlaneOriginCoordsArray(Arraylike): - - x_y: Optional[float] = Field(None) - x_y_z: Optional[float] = Field(None) - - -class ImagingPlaneGridSpacing(ConfiguredBaseModel): - """ - Space between pixels in (x, y) or voxels in (x, y, z) directions, in the specified unit. Assumes imaging plane is a regular grid. See also reference_frame to interpret the grid. - """ - unit: Optional[str] = Field(None, description="""Measurement units for grid_spacing. The default value is 'meters'.""") - array: Optional[ImagingPlaneGridSpacingArray] = Field(None) - - -class ImagingPlaneGridSpacingArray(Arraylike): - - x_y: Optional[float] = Field(None) - x_y_z: Optional[float] = Field(None) - - -class ImagingPlaneReferenceFrame(ConfiguredBaseModel): - """ - Describes reference frame of origin_coords and grid_spacing. For example, this can be a text description of the anatomical location and orientation of the grid defined by origin_coords and grid_spacing or the vectors needed to transform or rotate the grid to a common anatomical axis (e.g., AP/DV/ML). This field is necessary to interpret origin_coords and grid_spacing. If origin_coords and grid_spacing are not present, then this field is not required. For example, if the microscope takes 10 x 10 x 2 images, where the first value of the data matrix (index (0, 0, 0)) corresponds to (-1.2, -0.6, -2) mm relative to bregma, the spacing between pixels is 0.2 mm in x, 0.2 mm in y and 0.5 mm in z, and larger numbers in x means more anterior, larger numbers in y means more rightward, and larger numbers in z means more ventral, then enter the following -- origin_coords = (-1.2, -0.6, -2) grid_spacing = (0.2, 0.2, 0.5) reference_frame = \"Origin coordinates are relative to bregma. First dimension corresponds to anterior-posterior axis (larger index = more anterior). Second dimension corresponds to medial-lateral axis (larger index = more rightward). Third dimension corresponds to dorsal-ventral axis (larger index = more ventral).\" - """ - None - - -class OpticalChannel(NWBContainer): - """ - An optical channel used to record from an imaging plane. - """ - description: OpticalChannelDescription = Field(..., description="""Description or other notes about the channel.""") - emission_lambda: OpticalChannelEmissionLambda = Field(..., description="""Emission wavelength for channel, in nm.""") - - -class OpticalChannelDescription(ConfiguredBaseModel): - """ - Description or other notes about the channel. - """ - None - - -class OpticalChannelEmissionLambda(ConfiguredBaseModel): - """ - Emission wavelength for channel, in nm. - """ - None - - -class MotionCorrection(NWBDataInterface): - """ - An image stack where all frames are shifted (registered) to a common coordinate system, to account for movement and drift between frames. Note: each frame at each point in time is assumed to be 2-D (has only x & y dimensions). - """ - CorrectedImageStack: List[CorrectedImageStack] = Field(default_factory=list, description="""Reuslts from motion correction of an image stack.""") - - -class CorrectedImageStack(NWBDataInterface): - """ - Reuslts from motion correction of an image stack. - """ - corrected: CorrectedImageStackCorrected = Field(..., description="""Image stack with frames shifted to the common coordinates.""") - xy_translation: CorrectedImageStackXyTranslation = Field(..., description="""Stores the x,y delta necessary to align each frame to the common coordinates, for example, to align each frame to a reference image.""") - - -class CorrectedImageStackXyTranslation(TimeSeries): - """ - Stores the x,y delta necessary to align each frame to the common coordinates, for example, to align each frame to a reference image. - """ - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - data: TimeSeriesData = Field(..., description="""Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class GrayscaleImage(Image): - """ - A grayscale image. - """ - array: Optional[GrayscaleImageArray] = Field(None) - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - - -class GrayscaleImageArray(Arraylike): - - x: Optional[float] = Field(None) - y: Optional[float] = Field(None) - - -class RGBImage(Image): - """ - A color image. - """ - array: Optional[RGBImageArray] = Field(None) - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - - -class RGBImageArray(Arraylike): - - x: Optional[float] = Field(None) - y: Optional[float] = Field(None) - r_g_b: Optional[float] = Field(None) - - -class RGBAImage(Image): - """ - A color image with transparency. - """ - array: Optional[RGBAImageArray] = Field(None) - resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") - description: Optional[str] = Field(None, description="""Description of the image.""") - - -class RGBAImageArray(Arraylike): - - x: Optional[float] = Field(None) - y: Optional[float] = Field(None) - r_g_b_a: Optional[float] = Field(None) - - -class ImageSeries(TimeSeries): - """ - General image data that is common between acquisition and stimulus time series. Sometimes the image data is stored in the file in a raw format while other times it will be stored as a series of external image files in the host file system. The data field will either be binary data, if the data is stored in the NWB file, or empty, if the data is stored in an external image stack. [frame][x][y] or [frame][x][y][z]. - """ - data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class OnePhotonSeries(ImageSeries): - """ - Image stack recorded over time from 1-photon microscope. - """ - pmt_gain: Optional[float] = Field(None, description="""Photomultiplier gain.""") - scan_line_rate: Optional[float] = Field(None, description="""Lines imaged per second. This is also stored in /general/optophysiology but is kept here as it is useful information for analysis, and so good to be stored w/ the actual data.""") - exposure_time: Optional[float] = Field(None, description="""Exposure time of the sample; often the inverse of the frequency.""") - binning: Optional[int] = Field(None, description="""Amount of pixels combined into 'bins'; could be 1, 2, 4, 8, etc.""") - power: Optional[float] = Field(None, description="""Power of the excitation in mW, if known.""") - intensity: Optional[float] = Field(None, description="""Intensity of the excitation in mW/mm^2, if known.""") - data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class TwoPhotonSeries(ImageSeries): - """ - Image stack recorded over time from 2-photon microscope. - """ - pmt_gain: Optional[float] = Field(None, description="""Photomultiplier gain.""") - scan_line_rate: Optional[float] = Field(None, description="""Lines imaged per second. This is also stored in /general/optophysiology but is kept here as it is useful information for analysis, and so good to be stored w/ the actual data.""") - field_of_view: Optional[TwoPhotonSeriesFieldOfView] = Field(None, description="""Width, height and depth of image, or imaged area, in meters.""") - data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class CorrectedImageStackCorrected(ImageSeries): - """ - Image stack with frames shifted to the common coordinates. - """ - data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class ImageSeriesData(ConfiguredBaseModel): - """ - Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array. - """ - array: Optional[ImageSeriesDataArray] = Field(None) - - -class ImageSeriesDataArray(Arraylike): - - frame: float = Field(...) - x: float = Field(...) - y: float = Field(...) - z: Optional[float] = Field(None) - - -class ImageSeriesDimension(ConfiguredBaseModel): - """ - Number of pixels on x, y, (and z) axes. - """ - array: Optional[ImageSeriesDimensionArray] = Field(None) - - -class ImageSeriesDimensionArray(Arraylike): - - rank: int = Field(...) - - -class ImageSeriesExternalFile(ConfiguredBaseModel): - """ - Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file. - """ - starting_frame: Optional[int] = Field(None, description="""Each external image may contain one or more consecutive frames of the full ImageSeries. This attribute serves as an index to indicate which frames each file contains, to facilitate random access. The 'starting_frame' attribute, hence, contains a list of frame numbers within the full ImageSeries of the first frame of each file listed in the parent 'external_file' dataset. Zero-based indexing is used (hence, the first element will always be zero). For example, if the 'external_file' dataset has three paths to files and the first file has 5 frames, the second file has 10 frames, and the third file has 20 frames, then this attribute will have values [0, 5, 15]. If there is a single external file that holds all of the frames of the ImageSeries (and so there is a single element in the 'external_file' dataset), then this attribute should have value [0].""") - array: Optional[ImageSeriesExternalFileArray] = Field(None) - - -class ImageSeriesExternalFileArray(Arraylike): - - num_files: str = Field(...) - - -class ImageSeriesFormat(ConfiguredBaseModel): - """ - Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed. - """ - None - - -class ImageMaskSeries(ImageSeries): - """ - An alpha mask that is applied to a presented visual stimulus. The 'data' array contains an array of mask values that are applied to the displayed image. Mask values are stored as RGBA. Mask can vary with time. The timestamps array indicates the starting time of a mask, and that mask pattern continues until it's explicitly changed. - """ - data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class OpticalSeries(ImageSeries): - """ - Image data that is presented or recorded. A stimulus template movie will be stored only as an image. When the image is presented as stimulus, additional data is required, such as field of view (e.g., how much of the visual field the image covers, or how what is the area of the target being imaged). If the OpticalSeries represents acquired imaging data, orientation is also important. - """ - distance: Optional[OpticalSeriesDistance] = Field(None, description="""Distance from camera/monitor to target/eye.""") - field_of_view: Optional[OpticalSeriesFieldOfView] = Field(None, description="""Width, height and depth of image, or imaged area, in meters.""") - data: OpticalSeriesData = Field(..., description="""Images presented to subject, either grayscale or RGB""") - orientation: Optional[OpticalSeriesOrientation] = Field(None, description="""Description of image relative to some reference frame (e.g., which way is up). Must also specify frame of reference.""") - dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") - external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") - format: Optional[ImageSeriesFormat] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class OpticalSeriesDistance(ConfiguredBaseModel): - """ - Distance from camera/monitor to target/eye. - """ - None - - -class OpticalSeriesFieldOfView(ConfiguredBaseModel): - """ - Width, height and depth of image, or imaged area, in meters. - """ - array: Optional[OpticalSeriesFieldOfViewArray] = Field(None) - - -class OpticalSeriesFieldOfViewArray(Arraylike): - - width_height: Optional[float] = Field(None) - width_height_depth: Optional[float] = Field(None) - - -class OpticalSeriesData(ConfiguredBaseModel): - """ - Images presented to subject, either grayscale or RGB - """ - array: Optional[OpticalSeriesDataArray] = Field(None) - - -class OpticalSeriesDataArray(Arraylike): - - frame: float = Field(...) - x: float = Field(...) - y: float = Field(...) - r_g_b: Optional[float] = Field(None) - - -class OpticalSeriesOrientation(ConfiguredBaseModel): - """ - Description of image relative to some reference frame (e.g., which way is up). Must also specify frame of reference. - """ - None - - -class IndexSeries(TimeSeries): - """ - Stores indices to image frames stored in an ImageSeries. The purpose of the IndexSeries is to allow a static image stack to be stored in an Images object, and the images in the stack to be referenced out-of-order. This can be for the display of individual images, or of movie segments (as a movie is simply a series of images). The data field stores the index of the frame in the referenced Images object, and the timestamps array indicates when that image was displayed. - """ - data: IndexSeriesData = Field(..., description="""Index of the image (using zero-indexing) in the linked Images object.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class IndexSeriesData(ConfiguredBaseModel): - """ - Index of the image (using zero-indexing) in the linked Images object. - """ - conversion: Optional[float] = Field(None, description="""This field is unused by IndexSeries.""") - resolution: Optional[float] = Field(None, description="""This field is unused by IndexSeries.""") - offset: Optional[float] = Field(None, description="""This field is unused by IndexSeries.""") - unit: Optional[str] = Field(None, description="""This field is unused by IndexSeries and has the value N/A.""") - array: Optional[IndexSeriesDataArray] = Field(None) - - -class IndexSeriesDataArray(Arraylike): - - num_times: int = Field(...) - - -class OptogeneticSeries(TimeSeries): - """ - An optogenetic stimulus. - """ - data: OptogeneticSeriesData = Field(..., description="""Applied power for optogenetic stimulus, in watts.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class OptogeneticSeriesData(ConfiguredBaseModel): - """ - Applied power for optogenetic stimulus, in watts. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for data, which is fixed to 'watts'.""") - array: Optional[OptogeneticSeriesDataArray] = Field(None) - - -class OptogeneticSeriesDataArray(Arraylike): - - num_times: float = Field(...) - - -class OptogeneticStimulusSite(NWBContainer): - """ - A site of optogenetic stimulation. - """ - description: OptogeneticStimulusSiteDescription = Field(..., description="""Description of stimulation site.""") - excitation_lambda: OptogeneticStimulusSiteExcitationLambda = Field(..., description="""Excitation wavelength, in nm.""") - location: OptogeneticStimulusSiteLocation = Field(..., description="""Location of the stimulation site. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible.""") - - -class OptogeneticStimulusSiteDescription(ConfiguredBaseModel): - """ - Description of stimulation site. - """ - None - - -class OptogeneticStimulusSiteExcitationLambda(ConfiguredBaseModel): - """ - Excitation wavelength, in nm. - """ - None - - -class OptogeneticStimulusSiteLocation(ConfiguredBaseModel): - """ - Location of the stimulation site. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible. - """ - None - - -class PatchClampSeries(TimeSeries): - """ - An abstract base class for patch-clamp data - stimulus or response, current or voltage. - """ - stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") - sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") - data: PatchClampSeriesData = Field(..., description="""Recorded voltage or current.""") - gain: Optional[PatchClampSeriesGain] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class PatchClampSeriesData(ConfiguredBaseModel): - """ - Recorded voltage or current. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - array: Optional[PatchClampSeriesDataArray] = Field(None) - - -class PatchClampSeriesDataArray(Arraylike): - - num_times: float = Field(...) - - -class PatchClampSeriesGain(ConfiguredBaseModel): - """ - Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp). - """ - None - - -class CurrentClampSeries(PatchClampSeries): - """ - Voltage data from an intracellular current-clamp recording. A corresponding CurrentClampStimulusSeries (stored separately as a stimulus) is used to store the current injected. - """ - data: CurrentClampSeriesData = Field(..., description="""Recorded voltage.""") - bias_current: Optional[CurrentClampSeriesBiasCurrent] = Field(None, description="""Bias current, in amps.""") - bridge_balance: Optional[CurrentClampSeriesBridgeBalance] = Field(None, description="""Bridge balance, in ohms.""") - capacitance_compensation: Optional[CurrentClampSeriesCapacitanceCompensation] = Field(None, description="""Capacitance compensation, in farads.""") - stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") - sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") - gain: Optional[PatchClampSeriesGain] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class CurrentClampSeriesData(ConfiguredBaseModel): - """ - Recorded voltage. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'volts'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - - -class CurrentClampSeriesBiasCurrent(ConfiguredBaseModel): - """ - Bias current, in amps. - """ - None - - -class CurrentClampSeriesBridgeBalance(ConfiguredBaseModel): - """ - Bridge balance, in ohms. - """ - None - - -class CurrentClampSeriesCapacitanceCompensation(ConfiguredBaseModel): - """ - Capacitance compensation, in farads. - """ - None - - -class IZeroClampSeries(CurrentClampSeries): - """ - Voltage data from an intracellular recording when all current and amplifier settings are off (i.e., CurrentClampSeries fields will be zero). There is no CurrentClampStimulusSeries associated with an IZero series because the amplifier is disconnected and no stimulus can reach the cell. - """ - stimulus_description: Optional[str] = Field(None, description="""An IZeroClampSeries has no stimulus, so this attribute is automatically set to \"N/A\"""") - bias_current: IZeroClampSeriesBiasCurrent = Field(..., description="""Bias current, in amps, fixed to 0.0.""") - bridge_balance: IZeroClampSeriesBridgeBalance = Field(..., description="""Bridge balance, in ohms, fixed to 0.0.""") - capacitance_compensation: IZeroClampSeriesCapacitanceCompensation = Field(..., description="""Capacitance compensation, in farads, fixed to 0.0.""") - data: CurrentClampSeriesData = Field(..., description="""Recorded voltage.""") - sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") - gain: Optional[PatchClampSeriesGain] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class IZeroClampSeriesBiasCurrent(ConfiguredBaseModel): - """ - Bias current, in amps, fixed to 0.0. - """ - None - - -class IZeroClampSeriesBridgeBalance(ConfiguredBaseModel): - """ - Bridge balance, in ohms, fixed to 0.0. - """ - None - - -class IZeroClampSeriesCapacitanceCompensation(ConfiguredBaseModel): - """ - Capacitance compensation, in farads, fixed to 0.0. - """ - None - - -class CurrentClampStimulusSeries(PatchClampSeries): - """ - Stimulus current applied during current clamp recording. - """ - data: CurrentClampStimulusSeriesData = Field(..., description="""Stimulus current applied.""") - stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") - sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") - gain: Optional[PatchClampSeriesGain] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class CurrentClampStimulusSeriesData(ConfiguredBaseModel): - """ - Stimulus current applied. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'amperes'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - - -class VoltageClampSeries(PatchClampSeries): - """ - Current data from an intracellular voltage-clamp recording. A corresponding VoltageClampStimulusSeries (stored separately as a stimulus) is used to store the voltage injected. - """ - data: VoltageClampSeriesData = Field(..., description="""Recorded current.""") - capacitance_fast: Optional[VoltageClampSeriesCapacitanceFast] = Field(None, description="""Fast capacitance, in farads.""") - capacitance_slow: Optional[VoltageClampSeriesCapacitanceSlow] = Field(None, description="""Slow capacitance, in farads.""") - resistance_comp_bandwidth: Optional[VoltageClampSeriesResistanceCompBandwidth] = Field(None, description="""Resistance compensation bandwidth, in hertz.""") - resistance_comp_correction: Optional[VoltageClampSeriesResistanceCompCorrection] = Field(None, description="""Resistance compensation correction, in percent.""") - resistance_comp_prediction: Optional[VoltageClampSeriesResistanceCompPrediction] = Field(None, description="""Resistance compensation prediction, in percent.""") - whole_cell_capacitance_comp: Optional[VoltageClampSeriesWholeCellCapacitanceComp] = Field(None, description="""Whole cell capacitance compensation, in farads.""") - whole_cell_series_resistance_comp: Optional[VoltageClampSeriesWholeCellSeriesResistanceComp] = Field(None, description="""Whole cell series resistance compensation, in ohms.""") - stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") - sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") - gain: Optional[PatchClampSeriesGain] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class VoltageClampSeriesData(ConfiguredBaseModel): - """ - Recorded current. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'amperes'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - - -class VoltageClampSeriesCapacitanceFast(ConfiguredBaseModel): - """ - Fast capacitance, in farads. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for capacitance_fast, which is fixed to 'farads'.""") - - -class VoltageClampSeriesCapacitanceSlow(ConfiguredBaseModel): - """ - Slow capacitance, in farads. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for capacitance_fast, which is fixed to 'farads'.""") - - -class VoltageClampSeriesResistanceCompBandwidth(ConfiguredBaseModel): - """ - Resistance compensation bandwidth, in hertz. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for resistance_comp_bandwidth, which is fixed to 'hertz'.""") - - -class VoltageClampSeriesResistanceCompCorrection(ConfiguredBaseModel): - """ - Resistance compensation correction, in percent. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for resistance_comp_correction, which is fixed to 'percent'.""") - - -class VoltageClampSeriesResistanceCompPrediction(ConfiguredBaseModel): - """ - Resistance compensation prediction, in percent. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for resistance_comp_prediction, which is fixed to 'percent'.""") - - -class VoltageClampSeriesWholeCellCapacitanceComp(ConfiguredBaseModel): - """ - Whole cell capacitance compensation, in farads. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for whole_cell_capacitance_comp, which is fixed to 'farads'.""") - - -class VoltageClampSeriesWholeCellSeriesResistanceComp(ConfiguredBaseModel): - """ - Whole cell series resistance compensation, in ohms. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for whole_cell_series_resistance_comp, which is fixed to 'ohms'.""") - - -class VoltageClampStimulusSeries(PatchClampSeries): - """ - Stimulus voltage applied during a voltage clamp recording. - """ - data: VoltageClampStimulusSeriesData = Field(..., description="""Stimulus voltage applied.""") - stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") - sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") - gain: Optional[PatchClampSeriesGain] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class VoltageClampStimulusSeriesData(ConfiguredBaseModel): - """ - Stimulus voltage applied. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'volts'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - - -class IntracellularElectrode(NWBContainer): - """ - An intracellular electrode and its metadata. - """ - cell_id: Optional[IntracellularElectrodeCellId] = Field(None, description="""unique ID of the cell""") - description: IntracellularElectrodeDescription = Field(..., description="""Description of electrode (e.g., whole-cell, sharp, etc.).""") - filtering: Optional[IntracellularElectrodeFiltering] = Field(None, description="""Electrode specific filtering.""") - initial_access_resistance: Optional[IntracellularElectrodeInitialAccessResistance] = Field(None, description="""Initial access resistance.""") - location: Optional[IntracellularElectrodeLocation] = Field(None, description="""Location of the electrode. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible.""") - resistance: Optional[IntracellularElectrodeResistance] = Field(None, description="""Electrode resistance, in ohms.""") - seal: Optional[IntracellularElectrodeSeal] = Field(None, description="""Information about seal used for recording.""") - slice: Optional[IntracellularElectrodeSlice] = Field(None, description="""Information about slice used for recording.""") - - -class IntracellularElectrodeCellId(ConfiguredBaseModel): - """ - unique ID of the cell - """ - None - - -class IntracellularElectrodeDescription(ConfiguredBaseModel): - """ - Description of electrode (e.g., whole-cell, sharp, etc.). - """ - None - - -class IntracellularElectrodeFiltering(ConfiguredBaseModel): - """ - Electrode specific filtering. - """ - None - - -class IntracellularElectrodeInitialAccessResistance(ConfiguredBaseModel): - """ - Initial access resistance. - """ - None - - -class IntracellularElectrodeLocation(ConfiguredBaseModel): - """ - Location of the electrode. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible. - """ - None - - -class IntracellularElectrodeResistance(ConfiguredBaseModel): - """ - Electrode resistance, in ohms. - """ - None - - -class IntracellularElectrodeSeal(ConfiguredBaseModel): - """ - Information about seal used for recording. - """ - None - - -class IntracellularElectrodeSlice(ConfiguredBaseModel): - """ - Information about slice used for recording. - """ - None - - -class SweepTable(DynamicTable): - """ - [DEPRECATED] Table used to group different PatchClampSeries. SweepTable is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable tables. Additional SequentialRecordingsTable, RepetitionsTable, and ExperimentalConditions tables provide enhanced support for experiment metadata. - """ - sweep_number: SweepTableSweepNumber = Field(..., description="""Sweep number of the PatchClampSeries in that row.""") - series: SweepTableSeries = Field(..., description="""The PatchClampSeries with the sweep number in that row.""") - series_index: SweepTableSeriesIndex = Field(..., description="""Index for series.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SweepTableSweepNumber(VectorData): - """ - Sweep number of the PatchClampSeries in that row. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class SweepTableSeries(VectorData): - """ - The PatchClampSeries with the sweep number in that row. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class SweepTableSeriesIndex(VectorIndex): - """ - Index for series. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class IntracellularElectrodesTable(DynamicTable): - """ - Table for storing intracellular electrode related metadata. - """ - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - electrode: IntracellularElectrodesTableElectrode = Field(..., description="""Column for storing the reference to the intracellular electrode.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class IntracellularElectrodesTableElectrode(VectorData): - """ - Column for storing the reference to the intracellular electrode. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class IntracellularStimuliTable(DynamicTable): - """ - Table for storing intracellular stimulus related metadata. - """ - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - stimulus: IntracellularStimuliTableStimulus = Field(..., description="""Column storing the reference to the recorded stimulus for the recording (rows).""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class IntracellularStimuliTableStimulus(TimeSeriesReferenceVectorData): - """ - Column storing the reference to the recorded stimulus for the recording (rows). - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class IntracellularResponsesTable(DynamicTable): - """ - Table for storing intracellular response related metadata. - """ - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - response: IntracellularResponsesTableResponse = Field(..., description="""Column storing the reference to the recorded response for the recording (rows)""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class IntracellularResponsesTableResponse(TimeSeriesReferenceVectorData): - """ - Column storing the reference to the recorded response for the recording (rows) - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class IntracellularRecordingsTable(AlignedDynamicTable): - """ - A table to group together a stimulus and response from a single electrode and a single simultaneous recording. Each row in the table represents a single recording consisting typically of a stimulus and a corresponding response. In some cases, however, only a stimulus or a response is recorded as part of an experiment. In this case, both the stimulus and response will point to the same TimeSeries while the idx_start and count of the invalid column will be set to -1, thus, indicating that no values have been recorded for the stimulus or response, respectively. Note, a recording MUST contain at least a stimulus or a response. Typically the stimulus and response are PatchClampSeries. However, the use of AD/DA channels that are not associated to an electrode is also common in intracellular electrophysiology, in which case other TimeSeries may be used. - """ - description: Optional[str] = Field(None, description="""Description of the contents of this table. Inherited from AlignedDynamicTable and overwritten here to fix the value of the attribute.""") - electrodes: IntracellularRecordingsTableElectrodes = Field(..., description="""Table for storing intracellular electrode related metadata.""") - stimuli: IntracellularRecordingsTableStimuli = Field(..., description="""Table for storing intracellular stimulus related metadata.""") - responses: IntracellularRecordingsTableResponses = Field(..., description="""Table for storing intracellular response related metadata.""") - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class IntracellularRecordingsTableElectrodes(IntracellularElectrodesTable): - """ - Table for storing intracellular electrode related metadata. - """ - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - electrode: IntracellularElectrodesTableElectrode = Field(..., description="""Column for storing the reference to the intracellular electrode.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class IntracellularRecordingsTableStimuli(IntracellularStimuliTable): - """ - Table for storing intracellular stimulus related metadata. - """ - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - stimulus: IntracellularStimuliTableStimulus = Field(..., description="""Column storing the reference to the recorded stimulus for the recording (rows).""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class IntracellularRecordingsTableResponses(IntracellularResponsesTable): - """ - Table for storing intracellular response related metadata. - """ - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - response: IntracellularResponsesTableResponse = Field(..., description="""Column storing the reference to the recorded response for the recording (rows)""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimultaneousRecordingsTable(DynamicTable): - """ - A table for grouping different intracellular recordings from the IntracellularRecordingsTable table together that were recorded simultaneously from different electrodes. - """ - recordings: SimultaneousRecordingsTableRecordings = Field(..., description="""A reference to one or more rows in the IntracellularRecordingsTable table.""") - recordings_index: SimultaneousRecordingsTableRecordingsIndex = Field(..., description="""Index dataset for the recordings column.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimultaneousRecordingsTableRecordings(DynamicTableRegion): - """ - A reference to one or more rows in the IntracellularRecordingsTable table. - """ - table: Optional[IntracellularRecordingsTable] = Field(None, description="""Reference to the IntracellularRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class SimultaneousRecordingsTableRecordingsIndex(VectorIndex): - """ - Index dataset for the recordings column. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class SequentialRecordingsTable(DynamicTable): - """ - A table for grouping different sequential recordings from the SimultaneousRecordingsTable table together. This is typically used to group together sequential recordings where a sequence of stimuli of the same type with varying parameters have been presented in a sequence. - """ - simultaneous_recordings: SequentialRecordingsTableSimultaneousRecordings = Field(..., description="""A reference to one or more rows in the SimultaneousRecordingsTable table.""") - simultaneous_recordings_index: SequentialRecordingsTableSimultaneousRecordingsIndex = Field(..., description="""Index dataset for the simultaneous_recordings column.""") - stimulus_type: SequentialRecordingsTableStimulusType = Field(..., description="""The type of stimulus used for the sequential recording.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SequentialRecordingsTableSimultaneousRecordings(DynamicTableRegion): - """ - A reference to one or more rows in the SimultaneousRecordingsTable table. - """ - table: Optional[SimultaneousRecordingsTable] = Field(None, description="""Reference to the SimultaneousRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class SequentialRecordingsTableSimultaneousRecordingsIndex(VectorIndex): - """ - Index dataset for the simultaneous_recordings column. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class SequentialRecordingsTableStimulusType(VectorData): - """ - The type of stimulus used for the sequential recording. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class RepetitionsTable(DynamicTable): - """ - A table for grouping different sequential intracellular recordings together. With each SequentialRecording typically representing a particular type of stimulus, the RepetitionsTable table is typically used to group sets of stimuli applied in sequence. - """ - sequential_recordings: RepetitionsTableSequentialRecordings = Field(..., description="""A reference to one or more rows in the SequentialRecordingsTable table.""") - sequential_recordings_index: RepetitionsTableSequentialRecordingsIndex = Field(..., description="""Index dataset for the sequential_recordings column.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class RepetitionsTableSequentialRecordings(DynamicTableRegion): - """ - A reference to one or more rows in the SequentialRecordingsTable table. - """ - table: Optional[SequentialRecordingsTable] = Field(None, description="""Reference to the SequentialRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class RepetitionsTableSequentialRecordingsIndex(VectorIndex): - """ - Index dataset for the sequential_recordings column. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ExperimentalConditionsTable(DynamicTable): - """ - A table for grouping different intracellular recording repetitions together that belong to the same experimental condition. - """ - repetitions: ExperimentalConditionsTableRepetitions = Field(..., description="""A reference to one or more rows in the RepetitionsTable table.""") - repetitions_index: ExperimentalConditionsTableRepetitionsIndex = Field(..., description="""Index dataset for the repetitions column.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class ExperimentalConditionsTableRepetitions(DynamicTableRegion): - """ - A reference to one or more rows in the RepetitionsTable table. - """ - table: Optional[RepetitionsTable] = Field(None, description="""Reference to the RepetitionsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class ExperimentalConditionsTableRepetitionsIndex(VectorIndex): - """ - Index dataset for the repetitions column. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ElectricalSeries(TimeSeries): - """ - A time series of acquired voltage data from extracellular recordings. The data field is an int or float array storing data in volts. The first dimension should always represent time. The second dimension, if present, should represent channels. - """ - filtering: Optional[str] = Field(None, description="""Filtering applied to all channels of the data. For example, if this ElectricalSeries represents high-pass-filtered data (also known as AP Band), then this value could be \"High-pass 4-pole Bessel filter at 500 Hz\". If this ElectricalSeries represents low-pass-filtered LFP data and the type of filter is unknown, then this value could be \"Low-pass filter at 300 Hz\". If a non-standard filter type is used, provide as much detail about the filter properties as possible.""") - data: ElectricalSeriesData = Field(..., description="""Recorded voltage data.""") - electrodes: ElectricalSeriesElectrodes = Field(..., description="""DynamicTableRegion pointer to the electrodes that this time series was generated from.""") - channel_conversion: Optional[ElectricalSeriesChannelConversion] = Field(None, description="""Channel-specific conversion factor. Multiply the data in the 'data' dataset by these values along the channel axis (as indicated by axis attribute) AND by the global conversion factor in the 'conversion' attribute of 'data' to get the data values in Volts, i.e, data in Volts = data * data.conversion * channel_conversion. This approach allows for both global and per-channel data conversion factors needed to support the storage of electrical recordings as native values generated by data acquisition systems. If this dataset is not present, then there is no channel-specific conversion factor, i.e. it is 1 for all channels.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class ElectricalSeriesData(ConfiguredBaseModel): - """ - Recorded voltage data. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. This value is fixed to 'volts'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion', followed by 'channel_conversion' (if present), and then add 'offset'.""") - array: Optional[ElectricalSeriesDataArray] = Field(None) - - -class ElectricalSeriesDataArray(Arraylike): - - num_times: float = Field(...) - num_channels: Optional[float] = Field(None) - num_samples: Optional[float] = Field(None) - - -class ElectricalSeriesElectrodes(DynamicTableRegion): - """ - DynamicTableRegion pointer to the electrodes that this time series was generated from. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class ElectricalSeriesChannelConversion(ConfiguredBaseModel): - """ - Channel-specific conversion factor. Multiply the data in the 'data' dataset by these values along the channel axis (as indicated by axis attribute) AND by the global conversion factor in the 'conversion' attribute of 'data' to get the data values in Volts, i.e, data in Volts = data * data.conversion * channel_conversion. This approach allows for both global and per-channel data conversion factors needed to support the storage of electrical recordings as native values generated by data acquisition systems. If this dataset is not present, then there is no channel-specific conversion factor, i.e. it is 1 for all channels. - """ - axis: Optional[int] = Field(None, description="""The zero-indexed axis of the 'data' dataset that the channel-specific conversion factor corresponds to. This value is fixed to 1.""") - array: Optional[ElectricalSeriesChannelConversionArray] = Field(None) - - -class ElectricalSeriesChannelConversionArray(Arraylike): - - num_channels: float = Field(...) - - -class SpikeEventSeries(ElectricalSeries): - """ - Stores snapshots/snippets of recorded spike events (i.e., threshold crossings). This may also be raw data, as reported by ephys hardware. If so, the TimeSeries::description field should describe how events were detected. All SpikeEventSeries should reside in a module (under EventWaveform interface) even if the spikes were reported and stored by hardware. All events span the same recording channels and store snapshots of equal duration. TimeSeries::data array structure: [num events] [num channels] [num samples] (or [num events] [num samples] for single electrode). - """ - data: SpikeEventSeriesData = Field(..., description="""Spike waveforms.""") - timestamps: SpikeEventSeriesTimestamps = Field(..., description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. Timestamps are required for the events. Unlike for TimeSeries, timestamps are required for SpikeEventSeries and are thus re-specified here.""") - filtering: Optional[str] = Field(None, description="""Filtering applied to all channels of the data. For example, if this ElectricalSeries represents high-pass-filtered data (also known as AP Band), then this value could be \"High-pass 4-pole Bessel filter at 500 Hz\". If this ElectricalSeries represents low-pass-filtered LFP data and the type of filter is unknown, then this value could be \"Low-pass filter at 300 Hz\". If a non-standard filter type is used, provide as much detail about the filter properties as possible.""") - electrodes: ElectricalSeriesElectrodes = Field(..., description="""DynamicTableRegion pointer to the electrodes that this time series was generated from.""") - channel_conversion: Optional[ElectricalSeriesChannelConversion] = Field(None, description="""Channel-specific conversion factor. Multiply the data in the 'data' dataset by these values along the channel axis (as indicated by axis attribute) AND by the global conversion factor in the 'conversion' attribute of 'data' to get the data values in Volts, i.e, data in Volts = data * data.conversion * channel_conversion. This approach allows for both global and per-channel data conversion factors needed to support the storage of electrical recordings as native values generated by data acquisition systems. If this dataset is not present, then there is no channel-specific conversion factor, i.e. it is 1 for all channels.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class SpikeEventSeriesData(ConfiguredBaseModel): - """ - Spike waveforms. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for waveforms, which is fixed to 'volts'.""") - array: Optional[SpikeEventSeriesDataArray] = Field(None) - - -class SpikeEventSeriesDataArray(Arraylike): - - num_events: float = Field(...) - num_samples: float = Field(...) - num_channels: Optional[float] = Field(None) - - -class SpikeEventSeriesTimestamps(ConfiguredBaseModel): - """ - Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. Timestamps are required for the events. Unlike for TimeSeries, timestamps are required for SpikeEventSeries and are thus re-specified here. - """ - interval: Optional[int] = Field(None, description="""Value is '1'""") - unit: Optional[str] = Field(None, description="""Unit of measurement for timestamps, which is fixed to 'seconds'.""") - array: Optional[SpikeEventSeriesTimestampsArray] = Field(None) - - -class SpikeEventSeriesTimestampsArray(Arraylike): - - num_times: float = Field(...) - - -class FeatureExtraction(NWBDataInterface): - """ - Features, such as PC1 and PC2, that are extracted from signals stored in a SpikeEventSeries or other source. - """ - description: FeatureExtractionDescription = Field(..., description="""Description of features (eg, ''PC1'') for each of the extracted features.""") - features: FeatureExtractionFeatures = Field(..., description="""Multi-dimensional array of features extracted from each event.""") - times: FeatureExtractionTimes = Field(..., description="""Times of events that features correspond to (can be a link).""") - electrodes: FeatureExtractionElectrodes = Field(..., description="""DynamicTableRegion pointer to the electrodes that this time series was generated from.""") - - -class FeatureExtractionDescription(ConfiguredBaseModel): - """ - Description of features (eg, ''PC1'') for each of the extracted features. - """ - array: Optional[FeatureExtractionDescriptionArray] = Field(None) - - -class FeatureExtractionDescriptionArray(Arraylike): - - num_features: str = Field(...) - - -class FeatureExtractionFeatures(ConfiguredBaseModel): - """ - Multi-dimensional array of features extracted from each event. - """ - array: Optional[FeatureExtractionFeaturesArray] = Field(None) - - -class FeatureExtractionFeaturesArray(Arraylike): - - num_events: Optional[float] = Field(None) - num_channels: Optional[float] = Field(None) - num_features: Optional[float] = Field(None) - - -class FeatureExtractionTimes(ConfiguredBaseModel): - """ - Times of events that features correspond to (can be a link). - """ - array: Optional[FeatureExtractionTimesArray] = Field(None) - - -class FeatureExtractionTimesArray(Arraylike): - - num_events: float = Field(...) - - -class FeatureExtractionElectrodes(DynamicTableRegion): - """ - DynamicTableRegion pointer to the electrodes that this time series was generated from. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class EventDetection(NWBDataInterface): - """ - Detected spike events from voltage trace(s). - """ - detection_method: EventDetectionDetectionMethod = Field(..., description="""Description of how events were detected, such as voltage threshold, or dV/dT threshold, as well as relevant values.""") - source_idx: EventDetectionSourceIdx = Field(..., description="""Indices (zero-based) into source ElectricalSeries::data array corresponding to time of event. ''description'' should define what is meant by time of event (e.g., .25 ms before action potential peak, zero-crossing time, etc). The index points to each event from the raw data.""") - times: EventDetectionTimes = Field(..., description="""Timestamps of events, in seconds.""") - - -class EventDetectionDetectionMethod(ConfiguredBaseModel): - """ - Description of how events were detected, such as voltage threshold, or dV/dT threshold, as well as relevant values. - """ - None - - -class EventDetectionSourceIdx(ConfiguredBaseModel): - """ - Indices (zero-based) into source ElectricalSeries::data array corresponding to time of event. ''description'' should define what is meant by time of event (e.g., .25 ms before action potential peak, zero-crossing time, etc). The index points to each event from the raw data. - """ - array: Optional[EventDetectionSourceIdxArray] = Field(None) - - -class EventDetectionSourceIdxArray(Arraylike): - - num_events: int = Field(...) - - -class EventDetectionTimes(ConfiguredBaseModel): - """ - Timestamps of events, in seconds. - """ - unit: Optional[str] = Field(None, description="""Unit of measurement for event times, which is fixed to 'seconds'.""") - array: Optional[EventDetectionTimesArray] = Field(None) - - -class EventDetectionTimesArray(Arraylike): - - num_events: float = Field(...) - - -class EventWaveform(NWBDataInterface): - """ - Represents either the waveforms of detected events, as extracted from a raw data trace in /acquisition, or the event waveforms that were stored during experiment acquisition. - """ - SpikeEventSeries: Optional[List[SpikeEventSeries]] = Field(default_factory=list, description="""SpikeEventSeries object(s) containing detected spike event waveforms.""") - - -class FilteredEphys(NWBDataInterface): - """ - Electrophysiology data from one or more channels that has been subjected to filtering. Examples of filtered data include Theta and Gamma (LFP has its own interface). FilteredEphys modules publish an ElectricalSeries for each filtered channel or set of channels. The name of each ElectricalSeries is arbitrary but should be informative. The source of the filtered data, whether this is from analysis of another time series or as acquired by hardware, should be noted in each's TimeSeries::description field. There is no assumed 1::1 correspondence between filtered ephys signals and electrodes, as a single signal can apply to many nearby electrodes, and one electrode may have different filtered (e.g., theta and/or gamma) signals represented. Filter properties should be noted in the ElectricalSeries 'filtering' attribute. - """ - ElectricalSeries: List[ElectricalSeries] = Field(default_factory=list, description="""ElectricalSeries object(s) containing filtered electrophysiology data.""") - - -class LFP(NWBDataInterface): - """ - LFP data from one or more channels. The electrode map in each published ElectricalSeries will identify which channels are providing LFP data. Filter properties should be noted in the ElectricalSeries 'filtering' attribute. - """ - ElectricalSeries: List[ElectricalSeries] = Field(default_factory=list, description="""ElectricalSeries object(s) containing LFP data for one or more channels.""") - - -class ElectrodeGroup(NWBContainer): - """ - A physical grouping of electrodes, e.g. a shank of an array. - """ - description: Optional[str] = Field(None, description="""Description of this electrode group.""") - location: Optional[str] = Field(None, description="""Location of electrode group. Specify the area, layer, comments on estimation of area/layer, etc. Use standard atlas names for anatomical regions when possible.""") - position: Optional[ElectrodeGroupPosition] = Field(None, description="""stereotaxic or common framework coordinates""") - - -class ElectrodeGroupPosition(ConfiguredBaseModel): - """ - stereotaxic or common framework coordinates - """ - None - - -class ClusterWaveforms(NWBDataInterface): - """ - DEPRECATED The mean waveform shape, including standard deviation, of the different clusters. Ideally, the waveform analysis should be performed on data that is only high-pass filtered. This is a separate module because it is expected to require updating. For example, IMEC probes may require different storage requirements to store/display mean waveforms, requiring a new interface or an extension of this one. - """ - waveform_filtering: ClusterWaveformsWaveformFiltering = Field(..., description="""Filtering applied to data before generating mean/sd""") - waveform_mean: ClusterWaveformsWaveformMean = Field(..., description="""The mean waveform for each cluster, using the same indices for each wave as cluster numbers in the associated Clustering module (i.e, cluster 3 is in array slot [3]). Waveforms corresponding to gaps in cluster sequence should be empty (e.g., zero- filled)""") - waveform_sd: ClusterWaveformsWaveformSd = Field(..., description="""Stdev of waveforms for each cluster, using the same indices as in mean""") - - -class ClusterWaveformsWaveformFiltering(ConfiguredBaseModel): - """ - Filtering applied to data before generating mean/sd - """ - None - - -class ClusterWaveformsWaveformMean(ConfiguredBaseModel): - """ - The mean waveform for each cluster, using the same indices for each wave as cluster numbers in the associated Clustering module (i.e, cluster 3 is in array slot [3]). Waveforms corresponding to gaps in cluster sequence should be empty (e.g., zero- filled) - """ - array: Optional[ClusterWaveformsWaveformMeanArray] = Field(None) - - -class ClusterWaveformsWaveformMeanArray(Arraylike): - - num_clusters: Optional[float] = Field(None) - num_samples: Optional[float] = Field(None) - - -class ClusterWaveformsWaveformSd(ConfiguredBaseModel): - """ - Stdev of waveforms for each cluster, using the same indices as in mean - """ - array: Optional[ClusterWaveformsWaveformSdArray] = Field(None) - - -class ClusterWaveformsWaveformSdArray(Arraylike): - - num_clusters: Optional[float] = Field(None) - num_samples: Optional[float] = Field(None) - - -class Clustering(NWBDataInterface): - """ - DEPRECATED Clustered spike data, whether from automatic clustering tools (e.g., klustakwik) or as a result of manual sorting. - """ - description: ClusteringDescription = Field(..., description="""Description of clusters or clustering, (e.g. cluster 0 is noise, clusters curated using Klusters, etc)""") - num: ClusteringNum = Field(..., description="""Cluster number of each event""") - peak_over_rms: ClusteringPeakOverRms = Field(..., description="""Maximum ratio of waveform peak to RMS on any channel in the cluster (provides a basic clustering metric).""") - times: ClusteringTimes = Field(..., description="""Times of clustered events, in seconds. This may be a link to times field in associated FeatureExtraction module.""") - - -class ClusteringDescription(ConfiguredBaseModel): - """ - Description of clusters or clustering, (e.g. cluster 0 is noise, clusters curated using Klusters, etc) - """ - None - - -class ClusteringNum(ConfiguredBaseModel): - """ - Cluster number of each event - """ - array: Optional[ClusteringNumArray] = Field(None) - - -class ClusteringNumArray(Arraylike): - - num_events: int = Field(...) - - -class ClusteringPeakOverRms(ConfiguredBaseModel): - """ - Maximum ratio of waveform peak to RMS on any channel in the cluster (provides a basic clustering metric). - """ - array: Optional[ClusteringPeakOverRmsArray] = Field(None) - - -class ClusteringPeakOverRmsArray(Arraylike): - - num_clusters: float = Field(...) - - -class ClusteringTimes(ConfiguredBaseModel): - """ - Times of clustered events, in seconds. This may be a link to times field in associated FeatureExtraction module. - """ - array: Optional[ClusteringTimesArray] = Field(None) - - -class ClusteringTimesArray(Arraylike): - - num_events: float = Field(...) - - -class SpatialSeries(TimeSeries): - """ - Direction, e.g., of gaze or travel, or position. The TimeSeries::data field is a 2D array storing position or direction relative to some reference frame. Array structure: [num measurements] [num dimensions]. Each SpatialSeries has a text dataset reference_frame that indicates the zero-position, or the zero-axes for direction. For example, if representing gaze direction, 'straight-ahead' might be a specific pixel on the monitor, or some other point in space. For position data, the 0,0 point might be the top-left corner of an enclosure, as viewed from the tracking camera. The unit of data will indicate how to interpret SpatialSeries values. - """ - data: SpatialSeriesData = Field(..., description="""1-D or 2-D array storing position or direction relative to some reference frame.""") - reference_frame: Optional[SpatialSeriesReferenceFrame] = Field(None, description="""Description defining what exactly 'straight-ahead' means.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class SpatialSeriesData(ConfiguredBaseModel): - """ - 1-D or 2-D array storing position or direction relative to some reference frame. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. The default value is 'meters'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") - array: Optional[SpatialSeriesDataArray] = Field(None) - - -class SpatialSeriesDataArray(Arraylike): - - num_times: float = Field(...) - x: Optional[float] = Field(None) - xy: Optional[float] = Field(None) - xyz: Optional[float] = Field(None) - - -class SpatialSeriesReferenceFrame(ConfiguredBaseModel): - """ - Description defining what exactly 'straight-ahead' means. - """ - None - - -class BehavioralEpochs(NWBDataInterface): - """ - TimeSeries for storing behavioral epochs. The objective of this and the other two Behavioral interfaces (e.g. BehavioralEvents and BehavioralTimeSeries) is to provide generic hooks for software tools/scripts. This allows a tool/script to take the output one specific interface (e.g., UnitTimes) and plot that data relative to another data modality (e.g., behavioral events) without having to define all possible modalities in advance. Declaring one of these interfaces means that one or more TimeSeries of the specified type is published. These TimeSeries should reside in a group having the same name as the interface. For example, if a BehavioralTimeSeries interface is declared, the module will have one or more TimeSeries defined in the module sub-group 'BehavioralTimeSeries'. BehavioralEpochs should use IntervalSeries. BehavioralEvents is used for irregular events. BehavioralTimeSeries is for continuous data. - """ - IntervalSeries: Optional[List[IntervalSeries]] = Field(default_factory=list, description="""IntervalSeries object containing start and stop times of epochs.""") - - -class BehavioralEvents(NWBDataInterface): - """ - TimeSeries for storing behavioral events. See description of BehavioralEpochs for more details. - """ - TimeSeries: Optional[List[TimeSeries]] = Field(default_factory=list, description="""TimeSeries object containing behavioral events.""") - - -class BehavioralTimeSeries(NWBDataInterface): - """ - TimeSeries for storing Behavoioral time series data. See description of BehavioralEpochs for more details. - """ - TimeSeries: Optional[List[TimeSeries]] = Field(default_factory=list, description="""TimeSeries object containing continuous behavioral data.""") - - -class PupilTracking(NWBDataInterface): - """ - Eye-tracking data, representing pupil size. - """ - TimeSeries: List[TimeSeries] = Field(default_factory=list, description="""TimeSeries object containing time series data on pupil size.""") - - -class EyeTracking(NWBDataInterface): - """ - Eye-tracking data, representing direction of gaze. - """ - SpatialSeries: Optional[List[SpatialSeries]] = Field(default_factory=list, description="""SpatialSeries object containing data measuring direction of gaze.""") - - -class CompassDirection(NWBDataInterface): - """ - With a CompassDirection interface, a module publishes a SpatialSeries object representing a floating point value for theta. The SpatialSeries::reference_frame field should indicate what direction corresponds to 0 and which is the direction of rotation (this should be clockwise). The si_unit for the SpatialSeries should be radians or degrees. - """ - SpatialSeries: Optional[List[SpatialSeries]] = Field(default_factory=list, description="""SpatialSeries object containing direction of gaze travel.""") - - -class Position(NWBDataInterface): - """ - Position data, whether along the x, x/y or x/y/z axis. - """ - SpatialSeries: List[SpatialSeries] = Field(default_factory=list, description="""SpatialSeries object containing position data.""") - - -class AbstractFeatureSeries(TimeSeries): - """ - Abstract features, such as quantitative descriptions of sensory stimuli. The TimeSeries::data field is a 2D array, storing those features (e.g., for visual grating stimulus this might be orientation, spatial frequency and contrast). Null stimuli (eg, uniform gray) can be marked as being an independent feature (eg, 1.0 for gray, 0.0 for actual stimulus) or by storing NaNs for feature values, or through use of the TimeSeries::control fields. A set of features is considered to persist until the next set of features is defined. The final set of features stored should be the null set. This is useful when storing the raw stimulus is impractical. - """ - data: AbstractFeatureSeriesData = Field(..., description="""Values of each feature at each time.""") - feature_units: Optional[AbstractFeatureSeriesFeatureUnits] = Field(None, description="""Units of each feature.""") - features: AbstractFeatureSeriesFeatures = Field(..., description="""Description of the features represented in TimeSeries::data.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class AbstractFeatureSeriesData(ConfiguredBaseModel): - """ - Values of each feature at each time. - """ - unit: Optional[str] = Field(None, description="""Since there can be different units for different features, store the units in 'feature_units'. The default value for this attribute is \"see 'feature_units'\".""") - array: Optional[AbstractFeatureSeriesDataArray] = Field(None) - - -class AbstractFeatureSeriesDataArray(Arraylike): - - num_times: float = Field(...) - num_features: Optional[float] = Field(None) - - -class AbstractFeatureSeriesFeatureUnits(ConfiguredBaseModel): - """ - Units of each feature. - """ - array: Optional[AbstractFeatureSeriesFeatureUnitsArray] = Field(None) - - -class AbstractFeatureSeriesFeatureUnitsArray(Arraylike): - - num_features: str = Field(...) - - -class AbstractFeatureSeriesFeatures(ConfiguredBaseModel): - """ - Description of the features represented in TimeSeries::data. - """ - array: Optional[AbstractFeatureSeriesFeaturesArray] = Field(None) - - -class AbstractFeatureSeriesFeaturesArray(Arraylike): - - num_features: str = Field(...) - - -class AnnotationSeries(TimeSeries): - """ - Stores user annotations made during an experiment. The data[] field stores a text array, and timestamps are stored for each annotation (ie, interval=1). This is largely an alias to a standard TimeSeries storing a text array but that is identifiable as storing annotations in a machine-readable way. - """ - data: AnnotationSeriesData = Field(..., description="""Annotations made during an experiment.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class AnnotationSeriesData(ConfiguredBaseModel): - """ - Annotations made during an experiment. - """ - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data. Annotations have no units, so the value is fixed to -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Annotations have no units, so the value is fixed to 'n/a'.""") - array: Optional[AnnotationSeriesDataArray] = Field(None) - - -class AnnotationSeriesDataArray(Arraylike): - - num_times: str = Field(...) - - -class IntervalSeries(TimeSeries): - """ - Stores intervals of data. The timestamps field stores the beginning and end of intervals. The data field stores whether the interval just started (>0 value) or ended (<0 value). Different interval types can be represented in the same series by using multiple key values (eg, 1 for feature A, 2 for feature B, 3 for feature C, etc). The field data stores an 8-bit integer. This is largely an alias of a standard TimeSeries but that is identifiable as representing time intervals in a machine-readable way. - """ - data: IntervalSeriesData = Field(..., description="""Use values >0 if interval started, <0 if interval ended.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class IntervalSeriesData(ConfiguredBaseModel): - """ - Use values >0 if interval started, <0 if interval ended. - """ - resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data. Annotations have no units, so the value is fixed to -1.0.""") - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Annotations have no units, so the value is fixed to 'n/a'.""") - array: Optional[IntervalSeriesDataArray] = Field(None) - - -class IntervalSeriesDataArray(Arraylike): - - num_times: int = Field(...) - - -class DecompositionSeries(TimeSeries): - """ - Spectral analysis of a time series, e.g. of an LFP or a speech signal. - """ - data: DecompositionSeriesData = Field(..., description="""Data decomposed into frequency bands.""") - metric: DecompositionSeriesMetric = Field(..., description="""The metric used, e.g. phase, amplitude, power.""") - source_channels: Optional[DecompositionSeriesSourceChannels] = Field(None, description="""DynamicTableRegion pointer to the channels that this decomposition series was generated from.""") - bands: DecompositionSeriesBands = Field(..., description="""Table for describing the bands that this series was generated from. There should be one row in this table for each band.""") - description: Optional[str] = Field(None, description="""Description of the time series.""") - comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") - starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") - timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") - control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") - control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") - sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") - - -class DecompositionSeriesData(ConfiguredBaseModel): - """ - Data decomposed into frequency bands. - """ - unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion'.""") - array: Optional[DecompositionSeriesDataArray] = Field(None) - - -class DecompositionSeriesDataArray(Arraylike): - - num_times: Optional[float] = Field(None) - num_channels: Optional[float] = Field(None) - num_bands: Optional[float] = Field(None) - - -class DecompositionSeriesMetric(ConfiguredBaseModel): - """ - The metric used, e.g. phase, amplitude, power. - """ - None - - -class DecompositionSeriesSourceChannels(DynamicTableRegion): - """ - DynamicTableRegion pointer to the channels that this decomposition series was generated from. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DecompositionSeriesBands(DynamicTable): - """ - Table for describing the bands that this series was generated from. There should be one row in this table for each band. - """ - band_name: DecompositionSeriesBandsBandName = Field(..., description="""Name of the band, e.g. theta.""") - band_limits: DecompositionSeriesBandsBandLimits = Field(..., description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""") - band_mean: DecompositionSeriesBandsBandMean = Field(..., description="""The mean Gaussian filters, in Hz.""") - band_stdev: DecompositionSeriesBandsBandStdev = Field(..., description="""The standard deviation of Gaussian filters, in Hz.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class DecompositionSeriesBandsBandName(VectorData): - """ - Name of the band, e.g. theta. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class DecompositionSeriesBandsBandLimits(VectorData): - """ - Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center. - """ - array: Optional[DecompositionSeriesBandsBandLimitsArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class DecompositionSeriesBandsBandLimitsArray(Arraylike): - - num_bands: Optional[float] = Field(None) - low_high: Optional[float] = Field(None) - - -class DecompositionSeriesBandsBandMean(VectorData): - """ - The mean Gaussian filters, in Hz. - """ - array: Optional[DecompositionSeriesBandsBandMeanArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class DecompositionSeriesBandsBandMeanArray(Arraylike): - - num_bands: float = Field(...) - - -class DecompositionSeriesBandsBandStdev(VectorData): - """ - The standard deviation of Gaussian filters, in Hz. - """ - array: Optional[DecompositionSeriesBandsBandStdevArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class DecompositionSeriesBandsBandStdevArray(Arraylike): - - num_bands: float = Field(...) - - -class Units(DynamicTable): - """ - Data about spiking units. Event times of observed units (e.g. cell, synapse, etc.) should be concatenated and stored in spike_times. - """ - spike_times_index: Optional[UnitsSpikeTimesIndex] = Field(None, description="""Index into the spike_times dataset.""") - spike_times: Optional[UnitsSpikeTimes] = Field(None, description="""Spike times for each unit in seconds.""") - obs_intervals_index: Optional[UnitsObsIntervalsIndex] = Field(None, description="""Index into the obs_intervals dataset.""") - obs_intervals: Optional[UnitsObsIntervals] = Field(None, description="""Observation intervals for each unit.""") - electrodes_index: Optional[UnitsElectrodesIndex] = Field(None, description="""Index into electrodes.""") - electrodes: Optional[UnitsElectrodes] = Field(None, description="""Electrode that each spike unit came from, specified using a DynamicTableRegion.""") - electrode_group: Optional[UnitsElectrodeGroup] = Field(None, description="""Electrode group that each spike unit came from.""") - waveform_mean: Optional[UnitsWaveformMean] = Field(None, description="""Spike waveform mean for each spike unit.""") - waveform_sd: Optional[UnitsWaveformSd] = Field(None, description="""Spike waveform standard deviation for each spike unit.""") - waveforms: Optional[UnitsWaveforms] = Field(None, description="""Individual waveforms for each spike on each electrode. This is a doubly indexed column. The 'waveforms_index' column indexes which waveforms in this column belong to the same spike event for a given unit, where each waveform was recorded from a different electrode. The 'waveforms_index_index' column indexes the 'waveforms_index' column to indicate which spike events belong to a given unit. For example, if the 'waveforms_index_index' column has values [2, 5, 6], then the first 2 elements of the 'waveforms_index' column correspond to the 2 spike events of the first unit, the next 3 elements of the 'waveforms_index' column correspond to the 3 spike events of the second unit, and the next 1 element of the 'waveforms_index' column corresponds to the 1 spike event of the third unit. If the 'waveforms_index' column has values [3, 6, 8, 10, 12, 13], then the first 3 elements of the 'waveforms' column contain the 3 spike waveforms that were recorded from 3 different electrodes for the first spike time of the first unit. See https://nwb-schema.readthedocs.io/en/stable/format_description.html#doubly-ragged-arrays for a graphical representation of this example. When there is only one electrode for each unit (i.e., each spike time is associated with a single waveform), then the 'waveforms_index' column will have values 1, 2, ..., N, where N is the number of spike events. The number of electrodes for each spike event should be the same within a given unit. The 'electrodes' column should be used to indicate which electrodes are associated with each unit, and the order of the waveforms within a given unit x spike event should be in the same order as the electrodes referenced in the 'electrodes' column of this table. The number of samples for each waveform must be the same.""") - waveforms_index: Optional[UnitsWaveformsIndex] = Field(None, description="""Index into the waveforms dataset. One value for every spike event. See 'waveforms' for more detail.""") - waveforms_index_index: Optional[UnitsWaveformsIndexIndex] = Field(None, description="""Index into the waveforms_index dataset. One value for every unit (row in the table). See 'waveforms' for more detail.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class UnitsSpikeTimesIndex(VectorIndex): - """ - Index into the spike_times dataset. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsSpikeTimes(VectorData): - """ - Spike times for each unit in seconds. - """ - resolution: Optional[float] = Field(None, description="""The smallest possible difference between two spike times. Usually 1 divided by the acquisition sampling rate from which spike times were extracted, but could be larger if the acquisition time series was downsampled or smaller if the acquisition time series was smoothed/interpolated and it is possible for the spike time to be between samples.""") - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class UnitsObsIntervalsIndex(VectorIndex): - """ - Index into the obs_intervals dataset. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsObsIntervals(VectorData): - """ - Observation intervals for each unit. - """ - array: Optional[UnitsObsIntervalsArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsObsIntervalsArray(Arraylike): - - num_intervals: Optional[float] = Field(None) - start|end: Optional[float] = Field(None) - - -class UnitsElectrodesIndex(VectorIndex): - """ - Index into electrodes. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsElectrodes(DynamicTableRegion): - """ - Electrode that each spike unit came from, specified using a DynamicTableRegion. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class UnitsElectrodeGroup(VectorData): - """ - Electrode group that each spike unit came from. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class UnitsWaveformMean(VectorData): - """ - Spike waveform mean for each spike unit. - """ - sampling_rate: Optional[float] = Field(None, description="""Sampling rate, in hertz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement. This value is fixed to 'volts'.""") - array: Optional[UnitsWaveformMeanArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsWaveformMeanArray(Arraylike): - - num_units: float = Field(...) - num_samples: float = Field(...) - num_electrodes: Optional[float] = Field(None) - - -class UnitsWaveformSd(VectorData): - """ - Spike waveform standard deviation for each spike unit. - """ - sampling_rate: Optional[float] = Field(None, description="""Sampling rate, in hertz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement. This value is fixed to 'volts'.""") - array: Optional[UnitsWaveformSdArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsWaveformSdArray(Arraylike): - - num_units: float = Field(...) - num_samples: float = Field(...) - num_electrodes: Optional[float] = Field(None) - - -class UnitsWaveforms(VectorData): - """ - Individual waveforms for each spike on each electrode. This is a doubly indexed column. The 'waveforms_index' column indexes which waveforms in this column belong to the same spike event for a given unit, where each waveform was recorded from a different electrode. The 'waveforms_index_index' column indexes the 'waveforms_index' column to indicate which spike events belong to a given unit. For example, if the 'waveforms_index_index' column has values [2, 5, 6], then the first 2 elements of the 'waveforms_index' column correspond to the 2 spike events of the first unit, the next 3 elements of the 'waveforms_index' column correspond to the 3 spike events of the second unit, and the next 1 element of the 'waveforms_index' column corresponds to the 1 spike event of the third unit. If the 'waveforms_index' column has values [3, 6, 8, 10, 12, 13], then the first 3 elements of the 'waveforms' column contain the 3 spike waveforms that were recorded from 3 different electrodes for the first spike time of the first unit. See https://nwb-schema.readthedocs.io/en/stable/format_description.html#doubly-ragged-arrays for a graphical representation of this example. When there is only one electrode for each unit (i.e., each spike time is associated with a single waveform), then the 'waveforms_index' column will have values 1, 2, ..., N, where N is the number of spike events. The number of electrodes for each spike event should be the same within a given unit. The 'electrodes' column should be used to indicate which electrodes are associated with each unit, and the order of the waveforms within a given unit x spike event should be in the same order as the electrodes referenced in the 'electrodes' column of this table. The number of samples for each waveform must be the same. - """ - sampling_rate: Optional[float] = Field(None, description="""Sampling rate, in hertz.""") - unit: Optional[str] = Field(None, description="""Unit of measurement. This value is fixed to 'volts'.""") - array: Optional[UnitsWaveformsArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsWaveformsArray(Arraylike): - - num_waveforms: Optional[float] = Field(None) - num_samples: Optional[float] = Field(None) - - -class UnitsWaveformsIndex(VectorIndex): - """ - Index into the waveforms dataset. One value for every spike event. See 'waveforms' for more detail. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class UnitsWaveformsIndexIndex(VectorIndex): - """ - Index into the waveforms_index dataset. One value for every unit (row in the table). See 'waveforms' for more detail. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ScratchData(NWBData): - """ - Any one-off datasets - """ - notes: Optional[str] = Field(None, description="""Any notes the user has about the dataset being stored""") - - -class NWBFile(NWBContainer): - """ - An NWB file storing cellular-based neurophysiology data from a single experimental session. - """ - nwb_version: Optional[str] = Field(None, description="""File version string. Use semantic versioning, e.g. 1.2.1. This will be the name of the format with trailing major, minor and patch numbers.""") - file_create_date: NWBFileFileCreateDate = Field(..., description="""A record of the date the file was created and of subsequent modifications. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted strings: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in \"Z\" with no timezone offset. Date accuracy is up to milliseconds. The file can be created after the experiment was run, so this may differ from the experiment start time. Each modification to the nwb file adds a new entry to the array.""") - identifier: NWBFileIdentifier = Field(..., description="""A unique text identifier for the file. For example, concatenated lab name, file creation date/time and experimentalist, or a hash of these and/or other values. The goal is that the string should be unique to all other files.""") - session_description: NWBFileSessionDescription = Field(..., description="""A description of the experimental session and data in the file.""") - session_start_time: NWBFileSessionStartTime = Field(..., description="""Date and time of the experiment/session start. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted string: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in \"Z\" with no timezone offset. Date accuracy is up to milliseconds.""") - timestamps_reference_time: NWBFileTimestampsReferenceTime = Field(..., description="""Date and time corresponding to time zero of all timestamps. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted string: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in \"Z\" with no timezone offset. Date accuracy is up to milliseconds. All times stored in the file use this time as reference (i.e., time zero).""") - acquisition: NWBFileAcquisition = Field(..., description="""Data streams recorded from the system, including ephys, ophys, tracking, etc. This group should be read-only after the experiment is completed and timestamps are corrected to a common timebase. The data stored here may be links to raw data stored in external NWB files. This will allow keeping bulky raw data out of the file while preserving the option of keeping some/all in the file. Acquired data includes tracking and experimental data streams (i.e., everything measured from the system). If bulky data is stored in the /acquisition group, the data can exist in a separate NWB file that is linked to by the file being used for processing and analysis.""") - analysis: NWBFileAnalysis = Field(..., description="""Lab-specific and custom scientific analysis of data. There is no defined format for the content of this group - the format is up to the individual user/lab. To facilitate sharing analysis data between labs, the contents here should be stored in standard types (e.g., neurodata_types) and appropriately documented. The file can store lab-specific and custom data analysis without restriction on its form or schema, reducing data formatting restrictions on end users. Such data should be placed in the analysis group. The analysis data should be documented so that it could be shared with other labs.""") - scratch: Optional[NWBFileScratch] = Field(None, description="""A place to store one-off analysis results. Data placed here is not intended for sharing. By placing data here, users acknowledge that there is no guarantee that their data meets any standard.""") - processing: NWBFileProcessing = Field(..., description="""The home for ProcessingModules. These modules perform intermediate analysis of data that is necessary to perform before scientific analysis. Examples include spike clustering, extracting position from tracking data, stitching together image slices. ProcessingModules can be large and express many data sets from relatively complex analysis (e.g., spike detection and clustering) or small, representing extraction of position information from tracking video, or even binary lick/no-lick decisions. Common software tools (e.g., klustakwik, MClust) are expected to read/write data here. 'Processing' refers to intermediate analysis of the acquired data to make it more amenable to scientific analysis.""") - stimulus: NWBFileStimulus = Field(..., description="""Data pushed into the system (eg, video stimulus, sound, voltage, etc) and secondary representations of that data (eg, measurements of something used as a stimulus). This group should be made read-only after experiment complete and timestamps are corrected to common timebase. Stores both presented stimuli and stimulus templates, the latter in case the same stimulus is presented multiple times, or is pulled from an external stimulus library. Stimuli are here defined as any signal that is pushed into the system as part of the experiment (eg, sound, video, voltage, etc). Many different experiments can use the same stimuli, and stimuli can be re-used during an experiment. The stimulus group is organized so that one version of template stimuli can be stored and these be used multiple times. These templates can exist in the present file or can be linked to a remote library file.""") - general: NWBFileGeneral = Field(..., description="""Experimental metadata, including protocol, notes and description of hardware device(s). The metadata stored in this section should be used to describe the experiment. Metadata necessary for interpreting the data is stored with the data. General experimental metadata, including animal strain, experimental protocols, experimenter, devices, etc, are stored under 'general'. Core metadata (e.g., that required to interpret data fields) is stored with the data itself, and implicitly defined by the file specification (e.g., time is in seconds). The strategy used here for storing non-core metadata is to use free-form text fields, such as would appear in sentences or paragraphs from a Methods section. Metadata fields are text to enable them to be more general, for example to represent ranges instead of numerical values. Machine-readable metadata is stored as attributes to these free-form datasets. All entries in the below table are to be included when data is present. Unused groups (e.g., intracellular_ephys in an optophysiology experiment) should not be created unless there is data to store within them.""") - intervals: Optional[NWBFileIntervals] = Field(None, description="""Experimental intervals, whether that be logically distinct sub-experiments having a particular scientific goal, trials (see trials subgroup) during an experiment, or epochs (see epochs subgroup) deriving from analysis of data.""") - units: Optional[NWBFileUnits] = Field(None, description="""Data about sorted spike units.""") - - -class NWBFileFileCreateDate(ConfiguredBaseModel): - """ - A record of the date the file was created and of subsequent modifications. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted strings: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in \"Z\" with no timezone offset. Date accuracy is up to milliseconds. The file can be created after the experiment was run, so this may differ from the experiment start time. Each modification to the nwb file adds a new entry to the array. - """ - array: Optional[NWBFileFileCreateDateArray] = Field(None) - - -class NWBFileFileCreateDateArray(Arraylike): - - num_modifications: date = Field(...) - - -class NWBFileIdentifier(ConfiguredBaseModel): - """ - A unique text identifier for the file. For example, concatenated lab name, file creation date/time and experimentalist, or a hash of these and/or other values. The goal is that the string should be unique to all other files. - """ - None - - -class NWBFileSessionDescription(ConfiguredBaseModel): - """ - A description of the experimental session and data in the file. - """ - None - - -class NWBFileSessionStartTime(ConfiguredBaseModel): - """ - Date and time of the experiment/session start. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted string: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in \"Z\" with no timezone offset. Date accuracy is up to milliseconds. - """ - None - - -class NWBFileTimestampsReferenceTime(ConfiguredBaseModel): - """ - Date and time corresponding to time zero of all timestamps. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted string: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in \"Z\" with no timezone offset. Date accuracy is up to milliseconds. All times stored in the file use this time as reference (i.e., time zero). - """ - None - - -class NWBFileAcquisition(ConfiguredBaseModel): - """ - Data streams recorded from the system, including ephys, ophys, tracking, etc. This group should be read-only after the experiment is completed and timestamps are corrected to a common timebase. The data stored here may be links to raw data stored in external NWB files. This will allow keeping bulky raw data out of the file while preserving the option of keeping some/all in the file. Acquired data includes tracking and experimental data streams (i.e., everything measured from the system). If bulky data is stored in the /acquisition group, the data can exist in a separate NWB file that is linked to by the file being used for processing and analysis. - """ - NWBDataInterface: Optional[List[NWBDataInterface]] = Field(default_factory=list, description="""Acquired, raw data.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tabular data that is relevant to acquisition""") - - -class NWBFileAnalysis(ConfiguredBaseModel): - """ - Lab-specific and custom scientific analysis of data. There is no defined format for the content of this group - the format is up to the individual user/lab. To facilitate sharing analysis data between labs, the contents here should be stored in standard types (e.g., neurodata_types) and appropriately documented. The file can store lab-specific and custom data analysis without restriction on its form or schema, reducing data formatting restrictions on end users. Such data should be placed in the analysis group. The analysis data should be documented so that it could be shared with other labs. - """ - NWBContainer: Optional[List[NWBContainer]] = Field(default_factory=list, description="""Custom analysis results.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tabular data that is relevant to data stored in analysis""") - - -class NWBFileScratch(ConfiguredBaseModel): - """ - A place to store one-off analysis results. Data placed here is not intended for sharing. By placing data here, users acknowledge that there is no guarantee that their data meets any standard. - """ - ScratchData: Optional[List[ScratchData]] = Field(default_factory=list, description="""Any one-off datasets""") - NWBContainer: Optional[List[NWBContainer]] = Field(default_factory=list, description="""Any one-off containers""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Any one-off tables""") - - -class NWBFileProcessing(ConfiguredBaseModel): - """ - The home for ProcessingModules. These modules perform intermediate analysis of data that is necessary to perform before scientific analysis. Examples include spike clustering, extracting position from tracking data, stitching together image slices. ProcessingModules can be large and express many data sets from relatively complex analysis (e.g., spike detection and clustering) or small, representing extraction of position information from tracking video, or even binary lick/no-lick decisions. Common software tools (e.g., klustakwik, MClust) are expected to read/write data here. 'Processing' refers to intermediate analysis of the acquired data to make it more amenable to scientific analysis. - """ - ProcessingModule: Optional[List[ProcessingModule]] = Field(default_factory=list, description="""Intermediate analysis of acquired data.""") - - -class NWBFileStimulus(ConfiguredBaseModel): - """ - Data pushed into the system (eg, video stimulus, sound, voltage, etc) and secondary representations of that data (eg, measurements of something used as a stimulus). This group should be made read-only after experiment complete and timestamps are corrected to common timebase. Stores both presented stimuli and stimulus templates, the latter in case the same stimulus is presented multiple times, or is pulled from an external stimulus library. Stimuli are here defined as any signal that is pushed into the system as part of the experiment (eg, sound, video, voltage, etc). Many different experiments can use the same stimuli, and stimuli can be re-used during an experiment. The stimulus group is organized so that one version of template stimuli can be stored and these be used multiple times. These templates can exist in the present file or can be linked to a remote library file. - """ - presentation: NWBFileStimulusPresentation = Field(..., description="""Stimuli presented during the experiment.""") - templates: NWBFileStimulusTemplates = Field(..., description="""Template stimuli. Timestamps in templates are based on stimulus design and are relative to the beginning of the stimulus. When templates are used, the stimulus instances must convert presentation times to the experiment`s time reference frame.""") - - -class NWBFileStimulusPresentation(ConfiguredBaseModel): - """ - Stimuli presented during the experiment. - """ - TimeSeries: Optional[List[TimeSeries]] = Field(default_factory=list, description="""TimeSeries objects containing data of presented stimuli.""") - - -class NWBFileStimulusTemplates(ConfiguredBaseModel): - """ - Template stimuli. Timestamps in templates are based on stimulus design and are relative to the beginning of the stimulus. When templates are used, the stimulus instances must convert presentation times to the experiment`s time reference frame. - """ - TimeSeries: Optional[List[TimeSeries]] = Field(default_factory=list, description="""TimeSeries objects containing template data of presented stimuli.""") - Images: Optional[List[Images]] = Field(default_factory=list, description="""Images objects containing images of presented stimuli.""") - - -class NWBFileGeneral(ConfiguredBaseModel): - """ - Experimental metadata, including protocol, notes and description of hardware device(s). The metadata stored in this section should be used to describe the experiment. Metadata necessary for interpreting the data is stored with the data. General experimental metadata, including animal strain, experimental protocols, experimenter, devices, etc, are stored under 'general'. Core metadata (e.g., that required to interpret data fields) is stored with the data itself, and implicitly defined by the file specification (e.g., time is in seconds). The strategy used here for storing non-core metadata is to use free-form text fields, such as would appear in sentences or paragraphs from a Methods section. Metadata fields are text to enable them to be more general, for example to represent ranges instead of numerical values. Machine-readable metadata is stored as attributes to these free-form datasets. All entries in the below table are to be included when data is present. Unused groups (e.g., intracellular_ephys in an optophysiology experiment) should not be created unless there is data to store within them. - """ - data_collection: Optional[NWBFileGeneralDataCollection] = Field(None, description="""Notes about data collection and analysis.""") - experiment_description: Optional[NWBFileGeneralExperimentDescription] = Field(None, description="""General description of the experiment.""") - experimenter: Optional[NWBFileGeneralExperimenter] = Field(None, description="""Name of person(s) who performed the experiment. Can also specify roles of different people involved.""") - institution: Optional[NWBFileGeneralInstitution] = Field(None, description="""Institution(s) where experiment was performed.""") - keywords: Optional[NWBFileGeneralKeywords] = Field(None, description="""Terms to search over.""") - lab: Optional[NWBFileGeneralLab] = Field(None, description="""Laboratory where experiment was performed.""") - notes: Optional[NWBFileGeneralNotes] = Field(None, description="""Notes about the experiment.""") - pharmacology: Optional[NWBFileGeneralPharmacology] = Field(None, description="""Description of drugs used, including how and when they were administered. Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc.""") - protocol: Optional[NWBFileGeneralProtocol] = Field(None, description="""Experimental protocol, if applicable. e.g., include IACUC protocol number.""") - related_publications: Optional[NWBFileGeneralRelatedPublications] = Field(None, description="""Publication information. PMID, DOI, URL, etc.""") - session_id: Optional[NWBFileGeneralSessionId] = Field(None, description="""Lab-specific ID for the session.""") - slices: Optional[NWBFileGeneralSlices] = Field(None, description="""Description of slices, including information about preparation thickness, orientation, temperature, and bath solution.""") - source_script: Optional[NWBFileGeneralSourceScript] = Field(None, description="""Script file or link to public source code used to create this NWB file.""") - stimulus: Optional[NWBFileGeneralStimulus] = Field(None, description="""Notes about stimuli, such as how and where they were presented.""") - surgery: Optional[NWBFileGeneralSurgery] = Field(None, description="""Narrative description about surgery/surgeries, including date(s) and who performed surgery.""") - virus: Optional[NWBFileGeneralVirus] = Field(None, description="""Information about virus(es) used in experiments, including virus ID, source, date made, injection location, volume, etc.""") - LabMetaData: Optional[List[LabMetaData]] = Field(default_factory=list, description="""Place-holder than can be extended so that lab-specific meta-data can be placed in /general.""") - devices: Optional[NWBFileGeneralDevices] = Field(None, description="""Description of hardware devices used during experiment, e.g., monitors, ADC boards, microscopes, etc.""") - subject: Optional[NWBFileGeneralSubject] = Field(None, description="""Information about the animal or person from which the data was measured.""") - extracellular_ephys: Optional[NWBFileGeneralExtracellularEphys] = Field(None, description="""Metadata related to extracellular electrophysiology.""") - intracellular_ephys: Optional[NWBFileGeneralIntracellularEphys] = Field(None, description="""Metadata related to intracellular electrophysiology.""") - optogenetics: Optional[NWBFileGeneralOptogenetics] = Field(None, description="""Metadata describing optogenetic stimuluation.""") - optophysiology: Optional[NWBFileGeneralOptophysiology] = Field(None, description="""Metadata related to optophysiology.""") - - -class NWBFileGeneralDataCollection(ConfiguredBaseModel): - """ - Notes about data collection and analysis. - """ - None - - -class NWBFileGeneralExperimentDescription(ConfiguredBaseModel): - """ - General description of the experiment. - """ - None - - -class NWBFileGeneralExperimenter(ConfiguredBaseModel): - """ - Name of person(s) who performed the experiment. Can also specify roles of different people involved. - """ - array: Optional[NWBFileGeneralExperimenterArray] = Field(None) - - -class NWBFileGeneralExperimenterArray(Arraylike): - - num_experimenters: str = Field(...) - - -class NWBFileGeneralInstitution(ConfiguredBaseModel): - """ - Institution(s) where experiment was performed. - """ - None - - -class NWBFileGeneralKeywords(ConfiguredBaseModel): - """ - Terms to search over. - """ - array: Optional[NWBFileGeneralKeywordsArray] = Field(None) - - -class NWBFileGeneralKeywordsArray(Arraylike): - - num_keywords: str = Field(...) - - -class NWBFileGeneralLab(ConfiguredBaseModel): - """ - Laboratory where experiment was performed. - """ - None - - -class NWBFileGeneralNotes(ConfiguredBaseModel): - """ - Notes about the experiment. - """ - None - - -class NWBFileGeneralPharmacology(ConfiguredBaseModel): - """ - Description of drugs used, including how and when they were administered. Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc. - """ - None - - -class NWBFileGeneralProtocol(ConfiguredBaseModel): - """ - Experimental protocol, if applicable. e.g., include IACUC protocol number. - """ - None - - -class NWBFileGeneralRelatedPublications(ConfiguredBaseModel): - """ - Publication information. PMID, DOI, URL, etc. - """ - array: Optional[NWBFileGeneralRelatedPublicationsArray] = Field(None) - - -class NWBFileGeneralRelatedPublicationsArray(Arraylike): - - num_publications: str = Field(...) - - -class NWBFileGeneralSessionId(ConfiguredBaseModel): - """ - Lab-specific ID for the session. - """ - None - - -class NWBFileGeneralSlices(ConfiguredBaseModel): - """ - Description of slices, including information about preparation thickness, orientation, temperature, and bath solution. - """ - None - - -class NWBFileGeneralSourceScript(ConfiguredBaseModel): - """ - Script file or link to public source code used to create this NWB file. - """ - file_name: Optional[str] = Field(None, description="""Name of script file.""") - - -class NWBFileGeneralStimulus(ConfiguredBaseModel): - """ - Notes about stimuli, such as how and where they were presented. - """ - None - - -class NWBFileGeneralSurgery(ConfiguredBaseModel): - """ - Narrative description about surgery/surgeries, including date(s) and who performed surgery. - """ - None - - -class NWBFileGeneralVirus(ConfiguredBaseModel): - """ - Information about virus(es) used in experiments, including virus ID, source, date made, injection location, volume, etc. - """ - None - - -class NWBFileGeneralDevices(ConfiguredBaseModel): - """ - Description of hardware devices used during experiment, e.g., monitors, ADC boards, microscopes, etc. - """ - Device: Optional[List[Device]] = Field(default_factory=list, description="""Data acquisition devices.""") - - -class NWBFileGeneralExtracellularEphys(ConfiguredBaseModel): - """ - Metadata related to extracellular electrophysiology. - """ - ElectrodeGroup: Optional[List[ElectrodeGroup]] = Field(default_factory=list, description="""Physical group of electrodes.""") - electrodes: Optional[NWBFileGeneralExtracellularEphysElectrodes] = Field(None, description="""A table of all electrodes (i.e. channels) used for recording.""") - - -class NWBFileGeneralExtracellularEphysElectrodes(DynamicTable): - """ - A table of all electrodes (i.e. channels) used for recording. - """ - x: Optional[NWBFileGeneralExtracellularEphysElectrodesX] = Field(None, description="""x coordinate of the channel location in the brain (+x is posterior).""") - y: Optional[NWBFileGeneralExtracellularEphysElectrodesY] = Field(None, description="""y coordinate of the channel location in the brain (+y is inferior).""") - z: Optional[NWBFileGeneralExtracellularEphysElectrodesZ] = Field(None, description="""z coordinate of the channel location in the brain (+z is right).""") - imp: Optional[NWBFileGeneralExtracellularEphysElectrodesImp] = Field(None, description="""Impedance of the channel, in ohms.""") - location: NWBFileGeneralExtracellularEphysElectrodesLocation = Field(..., description="""Location of the electrode (channel). Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible.""") - filtering: Optional[NWBFileGeneralExtracellularEphysElectrodesFiltering] = Field(None, description="""Description of hardware filtering, including the filter name and frequency cutoffs.""") - group: NWBFileGeneralExtracellularEphysElectrodesGroup = Field(..., description="""Reference to the ElectrodeGroup this electrode is a part of.""") - group_name: NWBFileGeneralExtracellularEphysElectrodesGroupName = Field(..., description="""Name of the ElectrodeGroup this electrode is a part of.""") - rel_x: Optional[NWBFileGeneralExtracellularEphysElectrodesRelX] = Field(None, description="""x coordinate in electrode group""") - rel_y: Optional[NWBFileGeneralExtracellularEphysElectrodesRelY] = Field(None, description="""y coordinate in electrode group""") - rel_z: Optional[NWBFileGeneralExtracellularEphysElectrodesRelZ] = Field(None, description="""z coordinate in electrode group""") - reference: Optional[NWBFileGeneralExtracellularEphysElectrodesReference] = Field(None, description="""Description of the reference electrode and/or reference scheme used for this electrode, e.g., \"stainless steel skull screw\" or \"online common average referencing\".""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileGeneralExtracellularEphysElectrodesX(VectorData): - """ - x coordinate of the channel location in the brain (+x is posterior). - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesY(VectorData): - """ - y coordinate of the channel location in the brain (+y is inferior). - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesZ(VectorData): - """ - z coordinate of the channel location in the brain (+z is right). - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesImp(VectorData): - """ - Impedance of the channel, in ohms. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesLocation(VectorData): - """ - Location of the electrode (channel). Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesFiltering(VectorData): - """ - Description of hardware filtering, including the filter name and frequency cutoffs. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesGroup(VectorData): - """ - Reference to the ElectrodeGroup this electrode is a part of. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesGroupName(VectorData): - """ - Name of the ElectrodeGroup this electrode is a part of. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesRelX(VectorData): - """ - x coordinate in electrode group - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesRelY(VectorData): - """ - y coordinate in electrode group - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesRelZ(VectorData): - """ - z coordinate in electrode group - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralExtracellularEphysElectrodesReference(VectorData): - """ - Description of the reference electrode and/or reference scheme used for this electrode, e.g., \"stainless steel skull screw\" or \"online common average referencing\". - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class NWBFileGeneralIntracellularEphys(ConfiguredBaseModel): - """ - Metadata related to intracellular electrophysiology. - """ - filtering: Optional[NWBFileGeneralIntracellularEphysFiltering] = Field(None, description="""[DEPRECATED] Use IntracellularElectrode.filtering instead. Description of filtering used. Includes filtering type and parameters, frequency fall-off, etc. If this changes between TimeSeries, filter description should be stored as a text attribute for each TimeSeries.""") - IntracellularElectrode: Optional[List[IntracellularElectrode]] = Field(default_factory=list, description="""An intracellular electrode.""") - sweep_table: Optional[NWBFileGeneralIntracellularEphysSweepTable] = Field(None, description="""[DEPRECATED] Table used to group different PatchClampSeries. SweepTable is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable tables. Additional SequentialRecordingsTable, RepetitionsTable and ExperimentalConditions tables provide enhanced support for experiment metadata.""") - intracellular_recordings: Optional[NWBFileGeneralIntracellularEphysIntracellularRecordings] = Field(None, description="""A table to group together a stimulus and response from a single electrode and a single simultaneous recording. Each row in the table represents a single recording consisting typically of a stimulus and a corresponding response. In some cases, however, only a stimulus or a response are recorded as as part of an experiment. In this case both, the stimulus and response will point to the same TimeSeries while the idx_start and count of the invalid column will be set to -1, thus, indicating that no values have been recorded for the stimulus or response, respectively. Note, a recording MUST contain at least a stimulus or a response. Typically the stimulus and response are PatchClampSeries. However, the use of AD/DA channels that are not associated to an electrode is also common in intracellular electrophysiology, in which case other TimeSeries may be used.""") - simultaneous_recordings: Optional[NWBFileGeneralIntracellularEphysSimultaneousRecordings] = Field(None, description="""A table for grouping different intracellular recordings from the IntracellularRecordingsTable table together that were recorded simultaneously from different electrodes""") - sequential_recordings: Optional[NWBFileGeneralIntracellularEphysSequentialRecordings] = Field(None, description="""A table for grouping different sequential recordings from the SimultaneousRecordingsTable table together. This is typically used to group together sequential recordings where the a sequence of stimuli of the same type with varying parameters have been presented in a sequence.""") - repetitions: Optional[NWBFileGeneralIntracellularEphysRepetitions] = Field(None, description="""A table for grouping different sequential intracellular recordings together. With each SequentialRecording typically representing a particular type of stimulus, the RepetitionsTable table is typically used to group sets of stimuli applied in sequence.""") - experimental_conditions: Optional[NWBFileGeneralIntracellularEphysExperimentalConditions] = Field(None, description="""A table for grouping different intracellular recording repetitions together that belong to the same experimental experimental_conditions.""") - - -class NWBFileGeneralIntracellularEphysFiltering(ConfiguredBaseModel): - """ - [DEPRECATED] Use IntracellularElectrode.filtering instead. Description of filtering used. Includes filtering type and parameters, frequency fall-off, etc. If this changes between TimeSeries, filter description should be stored as a text attribute for each TimeSeries. - """ - None - - -class NWBFileGeneralIntracellularEphysSweepTable(SweepTable): - """ - [DEPRECATED] Table used to group different PatchClampSeries. SweepTable is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable tables. Additional SequentialRecordingsTable, RepetitionsTable and ExperimentalConditions tables provide enhanced support for experiment metadata. - """ - sweep_number: SweepTableSweepNumber = Field(..., description="""Sweep number of the PatchClampSeries in that row.""") - series: SweepTableSeries = Field(..., description="""The PatchClampSeries with the sweep number in that row.""") - series_index: SweepTableSeriesIndex = Field(..., description="""Index for series.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileGeneralIntracellularEphysIntracellularRecordings(IntracellularRecordingsTable): - """ - A table to group together a stimulus and response from a single electrode and a single simultaneous recording. Each row in the table represents a single recording consisting typically of a stimulus and a corresponding response. In some cases, however, only a stimulus or a response are recorded as as part of an experiment. In this case both, the stimulus and response will point to the same TimeSeries while the idx_start and count of the invalid column will be set to -1, thus, indicating that no values have been recorded for the stimulus or response, respectively. Note, a recording MUST contain at least a stimulus or a response. Typically the stimulus and response are PatchClampSeries. However, the use of AD/DA channels that are not associated to an electrode is also common in intracellular electrophysiology, in which case other TimeSeries may be used. - """ - description: Optional[str] = Field(None, description="""Description of the contents of this table. Inherited from AlignedDynamicTable and overwritten here to fix the value of the attribute.""") - electrodes: IntracellularRecordingsTableElectrodes = Field(..., description="""Table for storing intracellular electrode related metadata.""") - stimuli: IntracellularRecordingsTableStimuli = Field(..., description="""Table for storing intracellular stimulus related metadata.""") - responses: IntracellularRecordingsTableResponses = Field(..., description="""Table for storing intracellular response related metadata.""") - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileGeneralIntracellularEphysSimultaneousRecordings(SimultaneousRecordingsTable): - """ - A table for grouping different intracellular recordings from the IntracellularRecordingsTable table together that were recorded simultaneously from different electrodes - """ - recordings: SimultaneousRecordingsTableRecordings = Field(..., description="""A reference to one or more rows in the IntracellularRecordingsTable table.""") - recordings_index: SimultaneousRecordingsTableRecordingsIndex = Field(..., description="""Index dataset for the recordings column.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileGeneralIntracellularEphysSequentialRecordings(SequentialRecordingsTable): - """ - A table for grouping different sequential recordings from the SimultaneousRecordingsTable table together. This is typically used to group together sequential recordings where the a sequence of stimuli of the same type with varying parameters have been presented in a sequence. - """ - simultaneous_recordings: SequentialRecordingsTableSimultaneousRecordings = Field(..., description="""A reference to one or more rows in the SimultaneousRecordingsTable table.""") - simultaneous_recordings_index: SequentialRecordingsTableSimultaneousRecordingsIndex = Field(..., description="""Index dataset for the simultaneous_recordings column.""") - stimulus_type: SequentialRecordingsTableStimulusType = Field(..., description="""The type of stimulus used for the sequential recording.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileGeneralIntracellularEphysRepetitions(RepetitionsTable): - """ - A table for grouping different sequential intracellular recordings together. With each SequentialRecording typically representing a particular type of stimulus, the RepetitionsTable table is typically used to group sets of stimuli applied in sequence. - """ - sequential_recordings: RepetitionsTableSequentialRecordings = Field(..., description="""A reference to one or more rows in the SequentialRecordingsTable table.""") - sequential_recordings_index: RepetitionsTableSequentialRecordingsIndex = Field(..., description="""Index dataset for the sequential_recordings column.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileGeneralIntracellularEphysExperimentalConditions(ExperimentalConditionsTable): - """ - A table for grouping different intracellular recording repetitions together that belong to the same experimental experimental_conditions. - """ - repetitions: ExperimentalConditionsTableRepetitions = Field(..., description="""A reference to one or more rows in the RepetitionsTable table.""") - repetitions_index: ExperimentalConditionsTableRepetitionsIndex = Field(..., description="""Index dataset for the repetitions column.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileGeneralOptogenetics(ConfiguredBaseModel): - """ - Metadata describing optogenetic stimuluation. - """ - OptogeneticStimulusSite: Optional[List[OptogeneticStimulusSite]] = Field(default_factory=list, description="""An optogenetic stimulation site.""") - - -class NWBFileGeneralOptophysiology(ConfiguredBaseModel): - """ - Metadata related to optophysiology. - """ - ImagingPlane: Optional[List[ImagingPlane]] = Field(default_factory=list, description="""An imaging plane.""") - - -class NWBFileIntervals(ConfiguredBaseModel): - """ - Experimental intervals, whether that be logically distinct sub-experiments having a particular scientific goal, trials (see trials subgroup) during an experiment, or epochs (see epochs subgroup) deriving from analysis of data. - """ - epochs: Optional[NWBFileIntervalsEpochs] = Field(None, description="""Divisions in time marking experimental stages or sub-divisions of a single recording session.""") - trials: Optional[NWBFileIntervalsTrials] = Field(None, description="""Repeated experimental events that have a logical grouping.""") - invalid_times: Optional[NWBFileIntervalsInvalidTimes] = Field(None, description="""Time intervals that should be removed from analysis.""") - TimeIntervals: Optional[List[TimeIntervals]] = Field(default_factory=list, description="""Optional additional table(s) for describing other experimental time intervals.""") - - -class NWBFileUnits(Units): - """ - Data about sorted spike units. - """ - spike_times_index: Optional[UnitsSpikeTimesIndex] = Field(None, description="""Index into the spike_times dataset.""") - spike_times: Optional[UnitsSpikeTimes] = Field(None, description="""Spike times for each unit in seconds.""") - obs_intervals_index: Optional[UnitsObsIntervalsIndex] = Field(None, description="""Index into the obs_intervals dataset.""") - obs_intervals: Optional[UnitsObsIntervals] = Field(None, description="""Observation intervals for each unit.""") - electrodes_index: Optional[UnitsElectrodesIndex] = Field(None, description="""Index into electrodes.""") - electrodes: Optional[UnitsElectrodes] = Field(None, description="""Electrode that each spike unit came from, specified using a DynamicTableRegion.""") - electrode_group: Optional[UnitsElectrodeGroup] = Field(None, description="""Electrode group that each spike unit came from.""") - waveform_mean: Optional[UnitsWaveformMean] = Field(None, description="""Spike waveform mean for each spike unit.""") - waveform_sd: Optional[UnitsWaveformSd] = Field(None, description="""Spike waveform standard deviation for each spike unit.""") - waveforms: Optional[UnitsWaveforms] = Field(None, description="""Individual waveforms for each spike on each electrode. This is a doubly indexed column. The 'waveforms_index' column indexes which waveforms in this column belong to the same spike event for a given unit, where each waveform was recorded from a different electrode. The 'waveforms_index_index' column indexes the 'waveforms_index' column to indicate which spike events belong to a given unit. For example, if the 'waveforms_index_index' column has values [2, 5, 6], then the first 2 elements of the 'waveforms_index' column correspond to the 2 spike events of the first unit, the next 3 elements of the 'waveforms_index' column correspond to the 3 spike events of the second unit, and the next 1 element of the 'waveforms_index' column corresponds to the 1 spike event of the third unit. If the 'waveforms_index' column has values [3, 6, 8, 10, 12, 13], then the first 3 elements of the 'waveforms' column contain the 3 spike waveforms that were recorded from 3 different electrodes for the first spike time of the first unit. See https://nwb-schema.readthedocs.io/en/stable/format_description.html#doubly-ragged-arrays for a graphical representation of this example. When there is only one electrode for each unit (i.e., each spike time is associated with a single waveform), then the 'waveforms_index' column will have values 1, 2, ..., N, where N is the number of spike events. The number of electrodes for each spike event should be the same within a given unit. The 'electrodes' column should be used to indicate which electrodes are associated with each unit, and the order of the waveforms within a given unit x spike event should be in the same order as the electrodes referenced in the 'electrodes' column of this table. The number of samples for each waveform must be the same.""") - waveforms_index: Optional[UnitsWaveformsIndex] = Field(None, description="""Index into the waveforms dataset. One value for every spike event. See 'waveforms' for more detail.""") - waveforms_index_index: Optional[UnitsWaveformsIndexIndex] = Field(None, description="""Index into the waveforms_index dataset. One value for every unit (row in the table). See 'waveforms' for more detail.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class LabMetaData(NWBContainer): - """ - Lab-specific meta-data. - """ - None - - -class Subject(NWBContainer): - """ - Information about the animal or person from which the data was measured. - """ - age: Optional[SubjectAge] = Field(None, description="""Age of subject. Can be supplied instead of 'date_of_birth'.""") - date_of_birth: Optional[SubjectDateOfBirth] = Field(None, description="""Date of birth of subject. Can be supplied instead of 'age'.""") - description: Optional[SubjectDescription] = Field(None, description="""Description of subject and where subject came from (e.g., breeder, if animal).""") - genotype: Optional[SubjectGenotype] = Field(None, description="""Genetic strain. If absent, assume Wild Type (WT).""") - sex: Optional[SubjectSex] = Field(None, description="""Gender of subject.""") - species: Optional[SubjectSpecies] = Field(None, description="""Species of subject.""") - strain: Optional[SubjectStrain] = Field(None, description="""Strain of subject.""") - subject_id: Optional[SubjectSubjectId] = Field(None, description="""ID of animal/person used/participating in experiment (lab convention).""") - weight: Optional[SubjectWeight] = Field(None, description="""Weight at time of experiment, at time of surgery and at other important times.""") - - -class NWBFileGeneralSubject(Subject): - """ - Information about the animal or person from which the data was measured. - """ - age: Optional[SubjectAge] = Field(None, description="""Age of subject. Can be supplied instead of 'date_of_birth'.""") - date_of_birth: Optional[SubjectDateOfBirth] = Field(None, description="""Date of birth of subject. Can be supplied instead of 'age'.""") - description: Optional[SubjectDescription] = Field(None, description="""Description of subject and where subject came from (e.g., breeder, if animal).""") - genotype: Optional[SubjectGenotype] = Field(None, description="""Genetic strain. If absent, assume Wild Type (WT).""") - sex: Optional[SubjectSex] = Field(None, description="""Gender of subject.""") - species: Optional[SubjectSpecies] = Field(None, description="""Species of subject.""") - strain: Optional[SubjectStrain] = Field(None, description="""Strain of subject.""") - subject_id: Optional[SubjectSubjectId] = Field(None, description="""ID of animal/person used/participating in experiment (lab convention).""") - weight: Optional[SubjectWeight] = Field(None, description="""Weight at time of experiment, at time of surgery and at other important times.""") - - -class SubjectAge(ConfiguredBaseModel): - """ - Age of subject. Can be supplied instead of 'date_of_birth'. - """ - reference: Optional[str] = Field(None, description="""Age is with reference to this event. Can be 'birth' or 'gestational'. If reference is omitted, 'birth' is implied.""") - - -class SubjectDateOfBirth(ConfiguredBaseModel): - """ - Date of birth of subject. Can be supplied instead of 'age'. - """ - None - - -class SubjectDescription(ConfiguredBaseModel): - """ - Description of subject and where subject came from (e.g., breeder, if animal). - """ - None - - -class SubjectGenotype(ConfiguredBaseModel): - """ - Genetic strain. If absent, assume Wild Type (WT). - """ - None - - -class SubjectSex(ConfiguredBaseModel): - """ - Gender of subject. - """ - None - - -class SubjectSpecies(ConfiguredBaseModel): - """ - Species of subject. - """ - None - - -class SubjectStrain(ConfiguredBaseModel): - """ - Strain of subject. - """ - None - - -class SubjectSubjectId(ConfiguredBaseModel): - """ - ID of animal/person used/participating in experiment (lab convention). - """ - None - - -class SubjectWeight(ConfiguredBaseModel): - """ - Weight at time of experiment, at time of surgery and at other important times. - """ - None - - -class TimeIntervals(DynamicTable): - """ - A container for aggregating epoch data and the TimeSeries that each epoch applies to. - """ - start_time: TimeIntervalsStartTime = Field(..., description="""Start time of epoch, in seconds.""") - stop_time: TimeIntervalsStopTime = Field(..., description="""Stop time of epoch, in seconds.""") - tags: Optional[TimeIntervalsTags] = Field(None, description="""User-defined tags that identify or categorize events.""") - tags_index: Optional[TimeIntervalsTagsIndex] = Field(None, description="""Index for tags.""") - timeseries: Optional[TimeIntervalsTimeseries] = Field(None, description="""An index into a TimeSeries object.""") - timeseries_index: Optional[TimeIntervalsTimeseriesIndex] = Field(None, description="""Index for timeseries.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileIntervalsEpochs(TimeIntervals): - """ - Divisions in time marking experimental stages or sub-divisions of a single recording session. - """ - start_time: TimeIntervalsStartTime = Field(..., description="""Start time of epoch, in seconds.""") - stop_time: TimeIntervalsStopTime = Field(..., description="""Stop time of epoch, in seconds.""") - tags: Optional[TimeIntervalsTags] = Field(None, description="""User-defined tags that identify or categorize events.""") - tags_index: Optional[TimeIntervalsTagsIndex] = Field(None, description="""Index for tags.""") - timeseries: Optional[TimeIntervalsTimeseries] = Field(None, description="""An index into a TimeSeries object.""") - timeseries_index: Optional[TimeIntervalsTimeseriesIndex] = Field(None, description="""Index for timeseries.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileIntervalsTrials(TimeIntervals): - """ - Repeated experimental events that have a logical grouping. - """ - start_time: TimeIntervalsStartTime = Field(..., description="""Start time of epoch, in seconds.""") - stop_time: TimeIntervalsStopTime = Field(..., description="""Stop time of epoch, in seconds.""") - tags: Optional[TimeIntervalsTags] = Field(None, description="""User-defined tags that identify or categorize events.""") - tags_index: Optional[TimeIntervalsTagsIndex] = Field(None, description="""Index for tags.""") - timeseries: Optional[TimeIntervalsTimeseries] = Field(None, description="""An index into a TimeSeries object.""") - timeseries_index: Optional[TimeIntervalsTimeseriesIndex] = Field(None, description="""Index for timeseries.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class NWBFileIntervalsInvalidTimes(TimeIntervals): - """ - Time intervals that should be removed from analysis. - """ - start_time: TimeIntervalsStartTime = Field(..., description="""Start time of epoch, in seconds.""") - stop_time: TimeIntervalsStopTime = Field(..., description="""Stop time of epoch, in seconds.""") - tags: Optional[TimeIntervalsTags] = Field(None, description="""User-defined tags that identify or categorize events.""") - tags_index: Optional[TimeIntervalsTagsIndex] = Field(None, description="""Index for tags.""") - timeseries: Optional[TimeIntervalsTimeseries] = Field(None, description="""An index into a TimeSeries object.""") - timeseries_index: Optional[TimeIntervalsTimeseriesIndex] = Field(None, description="""Index for timeseries.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class TimeIntervalsStartTime(VectorData): - """ - Start time of epoch, in seconds. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class TimeIntervalsStopTime(VectorData): - """ - Stop time of epoch, in seconds. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class TimeIntervalsTags(VectorData): - """ - User-defined tags that identify or categorize events. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class TimeIntervalsTagsIndex(VectorIndex): - """ - Index for tags. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class TimeIntervalsTimeseries(TimeSeriesReferenceVectorData): - """ - An index into a TimeSeries object. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class TimeIntervalsTimeseriesIndex(VectorIndex): - """ - Index for timeseries. - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class Device(NWBContainer): - """ - Metadata about a data acquisition device, e.g., recording system, electrode, microscope. - """ - description: Optional[str] = Field(None, description="""Description of the device (e.g., model, firmware version, processing software version, etc.) as free-form text.""") - manufacturer: Optional[str] = Field(None, description="""The name of the manufacturer of the device.""") - - # Update forward refs # see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -ImagingRetinotopyAxis1PhaseMap.update_forward_refs() -ImagingRetinotopyAxis1PowerMap.update_forward_refs() -ImagingRetinotopyAxis2PhaseMap.update_forward_refs() -ImagingRetinotopyAxis2PowerMap.update_forward_refs() -ImagingRetinotopyAxisDescriptions.update_forward_refs() -ImagingRetinotopyFocalDepthImage.update_forward_refs() -ImagingRetinotopySignMap.update_forward_refs() -ImagingRetinotopyVasculatureImage.update_forward_refs() -Arraylike.update_forward_refs() -ImagingRetinotopyAxis1PhaseMapArray.update_forward_refs() -ImagingRetinotopyAxis1PowerMapArray.update_forward_refs() -ImagingRetinotopyAxis2PhaseMapArray.update_forward_refs() -ImagingRetinotopyAxis2PowerMapArray.update_forward_refs() -ImagingRetinotopyAxisDescriptionsArray.update_forward_refs() -ImagingRetinotopyFocalDepthImageArray.update_forward_refs() -ImagingRetinotopySignMapArray.update_forward_refs() -ImagingRetinotopyVasculatureImageArray.update_forward_refs() -ImageArray.update_forward_refs() -ImageReferencesArray.update_forward_refs() -TimeSeriesData.update_forward_refs() -TimeSeriesDataArray.update_forward_refs() -TimeSeriesStartingTime.update_forward_refs() -TimeSeriesTimestamps.update_forward_refs() -TimeSeriesTimestampsArray.update_forward_refs() -TimeSeriesControl.update_forward_refs() -TimeSeriesControlArray.update_forward_refs() -TimeSeriesControlDescription.update_forward_refs() -TimeSeriesControlDescriptionArray.update_forward_refs() -TimeSeriesSync.update_forward_refs() -VectorDataArray.update_forward_refs() -VectorIndexArray.update_forward_refs() -ElementIdentifiersArray.update_forward_refs() -DynamicTableRegionArray.update_forward_refs() -DynamicTableIdArray.update_forward_refs() -Data.update_forward_refs() -NWBData.update_forward_refs() -Image.update_forward_refs() -ImageReferences.update_forward_refs() -ImagesOrderOfImages.update_forward_refs() -VectorData.update_forward_refs() -TimeSeriesReferenceVectorData.update_forward_refs() -VectorIndex.update_forward_refs() -ElementIdentifiers.update_forward_refs() -DynamicTableRegion.update_forward_refs() -DynamicTableId.update_forward_refs() -Container.update_forward_refs() -NWBContainer.update_forward_refs() -NWBDataInterface.update_forward_refs() -ImagingRetinotopy.update_forward_refs() -TimeSeries.update_forward_refs() -ProcessingModule.update_forward_refs() -Images.update_forward_refs() -DynamicTable.update_forward_refs() -AlignedDynamicTable.update_forward_refs() -SimpleMultiContainer.update_forward_refs() -TwoPhotonSeriesFieldOfView.update_forward_refs() -TwoPhotonSeriesFieldOfViewArray.update_forward_refs() -RoiResponseSeries.update_forward_refs() -RoiResponseSeriesData.update_forward_refs() -RoiResponseSeriesDataArray.update_forward_refs() -RoiResponseSeriesRois.update_forward_refs() -DfOverF.update_forward_refs() -Fluorescence.update_forward_refs() -ImageSegmentation.update_forward_refs() -PlaneSegmentation.update_forward_refs() -PlaneSegmentationImageMask.update_forward_refs() -PlaneSegmentationImageMaskArray.update_forward_refs() -PlaneSegmentationPixelMaskIndex.update_forward_refs() -PlaneSegmentationPixelMask.update_forward_refs() -PlaneSegmentationVoxelMaskIndex.update_forward_refs() -PlaneSegmentationVoxelMask.update_forward_refs() -PlaneSegmentationReferenceImages.update_forward_refs() -ImagingPlane.update_forward_refs() -ImagingPlaneDescription.update_forward_refs() -ImagingPlaneExcitationLambda.update_forward_refs() -ImagingPlaneImagingRate.update_forward_refs() -ImagingPlaneIndicator.update_forward_refs() -ImagingPlaneLocation.update_forward_refs() -ImagingPlaneManifold.update_forward_refs() -ImagingPlaneManifoldArray.update_forward_refs() -ImagingPlaneOriginCoords.update_forward_refs() -ImagingPlaneOriginCoordsArray.update_forward_refs() -ImagingPlaneGridSpacing.update_forward_refs() -ImagingPlaneGridSpacingArray.update_forward_refs() -ImagingPlaneReferenceFrame.update_forward_refs() -OpticalChannel.update_forward_refs() -OpticalChannelDescription.update_forward_refs() -OpticalChannelEmissionLambda.update_forward_refs() -MotionCorrection.update_forward_refs() -CorrectedImageStack.update_forward_refs() -CorrectedImageStackXyTranslation.update_forward_refs() -GrayscaleImage.update_forward_refs() -GrayscaleImageArray.update_forward_refs() -RGBImage.update_forward_refs() -RGBImageArray.update_forward_refs() -RGBAImage.update_forward_refs() -RGBAImageArray.update_forward_refs() -ImageSeries.update_forward_refs() -OnePhotonSeries.update_forward_refs() -TwoPhotonSeries.update_forward_refs() -CorrectedImageStackCorrected.update_forward_refs() -ImageSeriesData.update_forward_refs() -ImageSeriesDataArray.update_forward_refs() -ImageSeriesDimension.update_forward_refs() -ImageSeriesDimensionArray.update_forward_refs() -ImageSeriesExternalFile.update_forward_refs() -ImageSeriesExternalFileArray.update_forward_refs() -ImageSeriesFormat.update_forward_refs() -ImageMaskSeries.update_forward_refs() -OpticalSeries.update_forward_refs() -OpticalSeriesDistance.update_forward_refs() -OpticalSeriesFieldOfView.update_forward_refs() -OpticalSeriesFieldOfViewArray.update_forward_refs() -OpticalSeriesData.update_forward_refs() -OpticalSeriesDataArray.update_forward_refs() -OpticalSeriesOrientation.update_forward_refs() -IndexSeries.update_forward_refs() -IndexSeriesData.update_forward_refs() -IndexSeriesDataArray.update_forward_refs() -OptogeneticSeries.update_forward_refs() -OptogeneticSeriesData.update_forward_refs() -OptogeneticSeriesDataArray.update_forward_refs() -OptogeneticStimulusSite.update_forward_refs() -OptogeneticStimulusSiteDescription.update_forward_refs() -OptogeneticStimulusSiteExcitationLambda.update_forward_refs() -OptogeneticStimulusSiteLocation.update_forward_refs() -PatchClampSeries.update_forward_refs() -PatchClampSeriesData.update_forward_refs() -PatchClampSeriesDataArray.update_forward_refs() -PatchClampSeriesGain.update_forward_refs() -CurrentClampSeries.update_forward_refs() -CurrentClampSeriesData.update_forward_refs() -CurrentClampSeriesBiasCurrent.update_forward_refs() -CurrentClampSeriesBridgeBalance.update_forward_refs() -CurrentClampSeriesCapacitanceCompensation.update_forward_refs() -IZeroClampSeries.update_forward_refs() -IZeroClampSeriesBiasCurrent.update_forward_refs() -IZeroClampSeriesBridgeBalance.update_forward_refs() -IZeroClampSeriesCapacitanceCompensation.update_forward_refs() -CurrentClampStimulusSeries.update_forward_refs() -CurrentClampStimulusSeriesData.update_forward_refs() -VoltageClampSeries.update_forward_refs() -VoltageClampSeriesData.update_forward_refs() -VoltageClampSeriesCapacitanceFast.update_forward_refs() -VoltageClampSeriesCapacitanceSlow.update_forward_refs() -VoltageClampSeriesResistanceCompBandwidth.update_forward_refs() -VoltageClampSeriesResistanceCompCorrection.update_forward_refs() -VoltageClampSeriesResistanceCompPrediction.update_forward_refs() -VoltageClampSeriesWholeCellCapacitanceComp.update_forward_refs() -VoltageClampSeriesWholeCellSeriesResistanceComp.update_forward_refs() -VoltageClampStimulusSeries.update_forward_refs() -VoltageClampStimulusSeriesData.update_forward_refs() -IntracellularElectrode.update_forward_refs() -IntracellularElectrodeCellId.update_forward_refs() -IntracellularElectrodeDescription.update_forward_refs() -IntracellularElectrodeFiltering.update_forward_refs() -IntracellularElectrodeInitialAccessResistance.update_forward_refs() -IntracellularElectrodeLocation.update_forward_refs() -IntracellularElectrodeResistance.update_forward_refs() -IntracellularElectrodeSeal.update_forward_refs() -IntracellularElectrodeSlice.update_forward_refs() -SweepTable.update_forward_refs() -SweepTableSweepNumber.update_forward_refs() -SweepTableSeries.update_forward_refs() -SweepTableSeriesIndex.update_forward_refs() -IntracellularElectrodesTable.update_forward_refs() -IntracellularElectrodesTableElectrode.update_forward_refs() -IntracellularStimuliTable.update_forward_refs() -IntracellularStimuliTableStimulus.update_forward_refs() -IntracellularResponsesTable.update_forward_refs() -IntracellularResponsesTableResponse.update_forward_refs() -IntracellularRecordingsTable.update_forward_refs() -IntracellularRecordingsTableElectrodes.update_forward_refs() -IntracellularRecordingsTableStimuli.update_forward_refs() -IntracellularRecordingsTableResponses.update_forward_refs() -SimultaneousRecordingsTable.update_forward_refs() -SimultaneousRecordingsTableRecordings.update_forward_refs() -SimultaneousRecordingsTableRecordingsIndex.update_forward_refs() -SequentialRecordingsTable.update_forward_refs() -SequentialRecordingsTableSimultaneousRecordings.update_forward_refs() -SequentialRecordingsTableSimultaneousRecordingsIndex.update_forward_refs() -SequentialRecordingsTableStimulusType.update_forward_refs() -RepetitionsTable.update_forward_refs() -RepetitionsTableSequentialRecordings.update_forward_refs() -RepetitionsTableSequentialRecordingsIndex.update_forward_refs() -ExperimentalConditionsTable.update_forward_refs() -ExperimentalConditionsTableRepetitions.update_forward_refs() -ExperimentalConditionsTableRepetitionsIndex.update_forward_refs() -ElectricalSeries.update_forward_refs() -ElectricalSeriesData.update_forward_refs() -ElectricalSeriesDataArray.update_forward_refs() -ElectricalSeriesElectrodes.update_forward_refs() -ElectricalSeriesChannelConversion.update_forward_refs() -ElectricalSeriesChannelConversionArray.update_forward_refs() -SpikeEventSeries.update_forward_refs() -SpikeEventSeriesData.update_forward_refs() -SpikeEventSeriesDataArray.update_forward_refs() -SpikeEventSeriesTimestamps.update_forward_refs() -SpikeEventSeriesTimestampsArray.update_forward_refs() -FeatureExtraction.update_forward_refs() -FeatureExtractionDescription.update_forward_refs() -FeatureExtractionDescriptionArray.update_forward_refs() -FeatureExtractionFeatures.update_forward_refs() -FeatureExtractionFeaturesArray.update_forward_refs() -FeatureExtractionTimes.update_forward_refs() -FeatureExtractionTimesArray.update_forward_refs() -FeatureExtractionElectrodes.update_forward_refs() -EventDetection.update_forward_refs() -EventDetectionDetectionMethod.update_forward_refs() -EventDetectionSourceIdx.update_forward_refs() -EventDetectionSourceIdxArray.update_forward_refs() -EventDetectionTimes.update_forward_refs() -EventDetectionTimesArray.update_forward_refs() -EventWaveform.update_forward_refs() -FilteredEphys.update_forward_refs() -LFP.update_forward_refs() -ElectrodeGroup.update_forward_refs() -ElectrodeGroupPosition.update_forward_refs() -ClusterWaveforms.update_forward_refs() -ClusterWaveformsWaveformFiltering.update_forward_refs() -ClusterWaveformsWaveformMean.update_forward_refs() -ClusterWaveformsWaveformMeanArray.update_forward_refs() -ClusterWaveformsWaveformSd.update_forward_refs() -ClusterWaveformsWaveformSdArray.update_forward_refs() -Clustering.update_forward_refs() -ClusteringDescription.update_forward_refs() -ClusteringNum.update_forward_refs() -ClusteringNumArray.update_forward_refs() -ClusteringPeakOverRms.update_forward_refs() -ClusteringPeakOverRmsArray.update_forward_refs() -ClusteringTimes.update_forward_refs() -ClusteringTimesArray.update_forward_refs() -SpatialSeries.update_forward_refs() -SpatialSeriesData.update_forward_refs() -SpatialSeriesDataArray.update_forward_refs() -SpatialSeriesReferenceFrame.update_forward_refs() -BehavioralEpochs.update_forward_refs() -BehavioralEvents.update_forward_refs() -BehavioralTimeSeries.update_forward_refs() -PupilTracking.update_forward_refs() -EyeTracking.update_forward_refs() -CompassDirection.update_forward_refs() -Position.update_forward_refs() -AbstractFeatureSeries.update_forward_refs() -AbstractFeatureSeriesData.update_forward_refs() -AbstractFeatureSeriesDataArray.update_forward_refs() -AbstractFeatureSeriesFeatureUnits.update_forward_refs() -AbstractFeatureSeriesFeatureUnitsArray.update_forward_refs() -AbstractFeatureSeriesFeatures.update_forward_refs() -AbstractFeatureSeriesFeaturesArray.update_forward_refs() -AnnotationSeries.update_forward_refs() -AnnotationSeriesData.update_forward_refs() -AnnotationSeriesDataArray.update_forward_refs() -IntervalSeries.update_forward_refs() -IntervalSeriesData.update_forward_refs() -IntervalSeriesDataArray.update_forward_refs() -DecompositionSeries.update_forward_refs() -DecompositionSeriesData.update_forward_refs() -DecompositionSeriesDataArray.update_forward_refs() -DecompositionSeriesMetric.update_forward_refs() -DecompositionSeriesSourceChannels.update_forward_refs() -DecompositionSeriesBands.update_forward_refs() -DecompositionSeriesBandsBandName.update_forward_refs() -DecompositionSeriesBandsBandLimits.update_forward_refs() -DecompositionSeriesBandsBandLimitsArray.update_forward_refs() -DecompositionSeriesBandsBandMean.update_forward_refs() -DecompositionSeriesBandsBandMeanArray.update_forward_refs() -DecompositionSeriesBandsBandStdev.update_forward_refs() -DecompositionSeriesBandsBandStdevArray.update_forward_refs() -Units.update_forward_refs() -UnitsSpikeTimesIndex.update_forward_refs() -UnitsSpikeTimes.update_forward_refs() -UnitsObsIntervalsIndex.update_forward_refs() -UnitsObsIntervals.update_forward_refs() -UnitsObsIntervalsArray.update_forward_refs() -UnitsElectrodesIndex.update_forward_refs() -UnitsElectrodes.update_forward_refs() -UnitsElectrodeGroup.update_forward_refs() -UnitsWaveformMean.update_forward_refs() -UnitsWaveformMeanArray.update_forward_refs() -UnitsWaveformSd.update_forward_refs() -UnitsWaveformSdArray.update_forward_refs() -UnitsWaveforms.update_forward_refs() -UnitsWaveformsArray.update_forward_refs() -UnitsWaveformsIndex.update_forward_refs() -UnitsWaveformsIndexIndex.update_forward_refs() -ScratchData.update_forward_refs() -NWBFile.update_forward_refs() -NWBFileFileCreateDate.update_forward_refs() -NWBFileFileCreateDateArray.update_forward_refs() -NWBFileIdentifier.update_forward_refs() -NWBFileSessionDescription.update_forward_refs() -NWBFileSessionStartTime.update_forward_refs() -NWBFileTimestampsReferenceTime.update_forward_refs() -NWBFileAcquisition.update_forward_refs() -NWBFileAnalysis.update_forward_refs() -NWBFileScratch.update_forward_refs() -NWBFileProcessing.update_forward_refs() -NWBFileStimulus.update_forward_refs() -NWBFileStimulusPresentation.update_forward_refs() -NWBFileStimulusTemplates.update_forward_refs() -NWBFileGeneral.update_forward_refs() -NWBFileGeneralDataCollection.update_forward_refs() -NWBFileGeneralExperimentDescription.update_forward_refs() -NWBFileGeneralExperimenter.update_forward_refs() -NWBFileGeneralExperimenterArray.update_forward_refs() -NWBFileGeneralInstitution.update_forward_refs() -NWBFileGeneralKeywords.update_forward_refs() -NWBFileGeneralKeywordsArray.update_forward_refs() -NWBFileGeneralLab.update_forward_refs() -NWBFileGeneralNotes.update_forward_refs() -NWBFileGeneralPharmacology.update_forward_refs() -NWBFileGeneralProtocol.update_forward_refs() -NWBFileGeneralRelatedPublications.update_forward_refs() -NWBFileGeneralRelatedPublicationsArray.update_forward_refs() -NWBFileGeneralSessionId.update_forward_refs() -NWBFileGeneralSlices.update_forward_refs() -NWBFileGeneralSourceScript.update_forward_refs() -NWBFileGeneralStimulus.update_forward_refs() -NWBFileGeneralSurgery.update_forward_refs() -NWBFileGeneralVirus.update_forward_refs() -NWBFileGeneralDevices.update_forward_refs() -NWBFileGeneralExtracellularEphys.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodes.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesX.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesY.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesZ.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesImp.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesLocation.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesFiltering.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesGroup.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesGroupName.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesRelX.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesRelY.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesRelZ.update_forward_refs() -NWBFileGeneralExtracellularEphysElectrodesReference.update_forward_refs() -NWBFileGeneralIntracellularEphys.update_forward_refs() -NWBFileGeneralIntracellularEphysFiltering.update_forward_refs() -NWBFileGeneralIntracellularEphysSweepTable.update_forward_refs() -NWBFileGeneralIntracellularEphysIntracellularRecordings.update_forward_refs() -NWBFileGeneralIntracellularEphysSimultaneousRecordings.update_forward_refs() -NWBFileGeneralIntracellularEphysSequentialRecordings.update_forward_refs() -NWBFileGeneralIntracellularEphysRepetitions.update_forward_refs() -NWBFileGeneralIntracellularEphysExperimentalConditions.update_forward_refs() -NWBFileGeneralOptogenetics.update_forward_refs() -NWBFileGeneralOptophysiology.update_forward_refs() -NWBFileIntervals.update_forward_refs() -NWBFileUnits.update_forward_refs() -LabMetaData.update_forward_refs() -Subject.update_forward_refs() -NWBFileGeneralSubject.update_forward_refs() -SubjectAge.update_forward_refs() -SubjectDateOfBirth.update_forward_refs() -SubjectDescription.update_forward_refs() -SubjectGenotype.update_forward_refs() -SubjectSex.update_forward_refs() -SubjectSpecies.update_forward_refs() -SubjectStrain.update_forward_refs() -SubjectSubjectId.update_forward_refs() -SubjectWeight.update_forward_refs() -TimeIntervals.update_forward_refs() -NWBFileIntervalsEpochs.update_forward_refs() -NWBFileIntervalsTrials.update_forward_refs() -NWBFileIntervalsInvalidTimes.update_forward_refs() -TimeIntervalsStartTime.update_forward_refs() -TimeIntervalsStopTime.update_forward_refs() -TimeIntervalsTags.update_forward_refs() -TimeIntervalsTagsIndex.update_forward_refs() -TimeIntervalsTimeseries.update_forward_refs() -TimeIntervalsTimeseriesIndex.update_forward_refs() -Device.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_base.py b/nwb_linkml/models/core_nwb_base.py new file mode 100644 index 0000000..16451d9 --- /dev/null +++ b/nwb_linkml/models/core_nwb_base.py @@ -0,0 +1,141 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .core_nwb_base_include import ( + TimeSeriesSync, + TimeSeriesControlDescription, + # ImageReferencesArray, + ImageArray, + TimeSeriesControl, + TimeSeriesData, + # ImagesOrderOfImages, + TimeSeriesTimestamps, + TimeSeriesStartingTime +) + +from .hdmf_common_base import ( + Container, + Data +) + +# from .hdmf_common_table import ( +# DynamicTable, +# VectorData +# ) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class NWBData(Data): + """ + An abstract data type for a dataset. + """ + None + + +# class TimeSeriesReferenceVectorData(VectorData): +# """ +# Column storing references to a TimeSeries (rows). For each TimeSeries this VectorData column stores the start_index and count to indicate the range in time to be selected as well as an object reference to the TimeSeries. +# """ +# description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") +# array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], Any]] = Field(None) +# + +class Image(NWBData): + """ + An abstract data type for an image. Shape can be 2-D (x, y), or 3-D where the third dimension can have three or four elements, e.g. (x, y, (r, g, b)) or (x, y, (r, g, b, a)). + """ + resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") + description: Optional[str] = Field(None, description="""Description of the image.""") + array: Optional[NDArray[Shape["* x, * y, 3 r_g_b, 4 r_g_b_a"], Number]] = Field(None) + + +# class ImageReferences(NWBData): +# """ +# Ordered dataset of references to Image objects. +# """ +# array: Optional[List[Image] | Image] = Field(None) +# + +class NWBContainer(Container): + """ + An abstract data type for a generic container storing collections of data and metadata. Base type for all data and metadata containers. + """ + None + + +class NWBDataInterface(NWBContainer): + """ + An abstract data type for a generic container storing collections of data, as opposed to metadata. + """ + None + + +class TimeSeries(NWBDataInterface): + """ + General purpose time series. + """ + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + data: TimeSeriesData = Field(..., description="""Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + +# class ProcessingModule(NWBContainer): +# """ +# A collection of processed data. +# """ +# description: Optional[str] = Field(None, description="""Description of this collection of processed data.""") +# NWBDataInterface: Optional[List[NWBDataInterface]] = Field(default_factory=list, description="""Data objects stored in this collection.""") +# DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tables stored in this collection.""") +# + +# class Images(NWBDataInterface): +# """ +# A collection of images with an optional way to specify the order of the images using the \"order_of_images\" dataset. An order must be specified if the images are referenced by index, e.g., from an IndexSeries. +# """ +# description: Optional[str] = Field(None, description="""Description of this collection of images.""") +# Image: List[Image] = Field(default_factory=list, description="""Images stored in this collection.""") +# order_of_images: Optional[ImagesOrderOfImages] = Field(None, description="""Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images.""") +# + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +NWBData.update_forward_refs() +# TimeSeriesReferenceVectorData.update_forward_refs() +Image.update_forward_refs() +# ImageReferences.update_forward_refs() +NWBContainer.update_forward_refs() +NWBDataInterface.update_forward_refs() +TimeSeries.update_forward_refs() +# ProcessingModule.update_forward_refs() +# Images.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_base_include.py b/nwb_linkml/models/core_nwb_base_include.py new file mode 100644 index 0000000..1468540 --- /dev/null +++ b/nwb_linkml/models/core_nwb_base_include.py @@ -0,0 +1,130 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .nwb_language import ( + Arraylike +) + +# from .core_nwb_base import ( +# ImageReferences, +# Image +# ) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class ImageArray(Arraylike): + + x: float = Field(...) + y: float = Field(...) + r_g_b: Optional[float] = Field(None) + r_g_b_a: Optional[float] = Field(None) + + +# class ImageReferencesArray(Arraylike): +# +# num_images: Image = Field(...) + + +class TimeSeriesData(ConfiguredBaseModel): + """ + Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file. + """ + conversion: Optional[float] = Field(None, description="""Scalar to multiply each element in data to convert it to the specified 'unit'. If the data are stored in acquisition system units or other units that require a conversion to be interpretable, multiply the data by 'conversion' to convert the data to the specified 'unit'. e.g. if the data acquisition system stores values in this object as signed 16-bit integers (int16 range -32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data acquisition system gain is 8000X, then the 'conversion' multiplier to get from raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9.""") + offset: Optional[float] = Field(None, description="""Scalar to add to the data after scaling by 'conversion' to finalize its coercion to the specified 'unit'. Two common examples of this include (a) data stored in an unsigned type that requires a shift after scaling to re-center the data, and (b) specialized recording devices that naturally cause a scalar offset with respect to the true units.""") + resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data, stored in the specified by unit, e.g., the change in value of the least significant bit, or a larger number if signal noise is known to be present. If unknown, use -1.0.""") + unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") + continuity: Optional[str] = Field(None, description="""Optionally describe the continuity of the data. Can be \"continuous\", \"instantaneous\", or \"step\". For example, a voltage trace would be \"continuous\", because samples are recorded from a continuous process. An array of lick times would be \"instantaneous\", because the data represents distinct moments in time. Times of image presentations would be \"step\" because the picture remains the same until the next timepoint. This field is optional, but is useful in providing information about the underlying data. It may inform the way this data is interpreted, the way it is visualized, and what analysis methods are applicable.""") + array: Optional[NDArray[Shape["* num_times, ..."], Number]] = Field(None) + + +class TimeSeriesDataArray(Arraylike): + + num_times: Any = Field(...) + num_DIM2: Optional[Any] = Field(None) + num_DIM3: Optional[Any] = Field(None) + num_DIM4: Optional[Any] = Field(None) + + +class TimeSeriesStartingTime(ConfiguredBaseModel): + """ + Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute. + """ + rate: Optional[float] = Field(None, description="""Sampling rate, in Hz.""") + unit: Optional[str] = Field(None, description="""Unit of measurement for time, which is fixed to 'seconds'.""") + + +class TimeSeriesTimestamps(ConfiguredBaseModel): + """ + Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. + """ + interval: Optional[int] = Field(None, description="""Value is '1'""") + unit: Optional[str] = Field(None, description="""Unit of measurement for timestamps, which is fixed to 'seconds'.""") + timestamps: Optional[List[float]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + + +class TimeSeriesControl(ConfiguredBaseModel): + """ + Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data. + """ + control: Optional[List[int]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + + +class TimeSeriesControlDescription(ConfiguredBaseModel): + """ + Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0. + """ + control_description: Optional[List[str]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + + +class TimeSeriesSync(ConfiguredBaseModel): + """ + Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes. + """ + None + + +# class ImagesOrderOfImages(ImageReferences): +# """ +# Ordered dataset of references to Image objects stored in the parent group. Each Image object in the Images group should be stored once and only once, so the dataset should have the same length as the number of images. +# """ +# array: Optional[List[Image] | Image] = Field(None) + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +ImageArray.update_forward_refs() +# ImageReferencesArray.update_forward_refs() +TimeSeriesData.update_forward_refs() +TimeSeriesDataArray.update_forward_refs() +TimeSeriesStartingTime.update_forward_refs() +TimeSeriesTimestamps.update_forward_refs() +TimeSeriesControl.update_forward_refs() +TimeSeriesControlDescription.update_forward_refs() +TimeSeriesSync.update_forward_refs() +# ImagesOrderOfImages.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_behavior.py b/nwb_linkml/models/core_nwb_behavior.py new file mode 100644 index 0000000..f6bb62e --- /dev/null +++ b/nwb_linkml/models/core_nwb_behavior.py @@ -0,0 +1,118 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .core_nwb_behavior_include import ( + SpatialSeriesData +) + +from .core_nwb_base import ( + TimeSeries, + NWBDataInterface +) + +from .core_nwb_misc import ( + IntervalSeries +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class SpatialSeries(TimeSeries): + """ + Direction, e.g., of gaze or travel, or position. The TimeSeries::data field is a 2D array storing position or direction relative to some reference frame. Array structure: [num measurements] [num dimensions]. Each SpatialSeries has a text dataset reference_frame that indicates the zero-position, or the zero-axes for direction. For example, if representing gaze direction, 'straight-ahead' might be a specific pixel on the monitor, or some other point in space. For position data, the 0,0 point might be the top-left corner of an enclosure, as viewed from the tracking camera. The unit of data will indicate how to interpret SpatialSeries values. + """ + data: SpatialSeriesData = Field(..., description="""1-D or 2-D array storing position or direction relative to some reference frame.""") + reference_frame: Optional[str] = Field(None, description="""Description defining what exactly 'straight-ahead' means.""") + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + +class BehavioralEpochs(NWBDataInterface): + """ + TimeSeries for storing behavioral epochs. The objective of this and the other two Behavioral interfaces (e.g. BehavioralEvents and BehavioralTimeSeries) is to provide generic hooks for software tools/scripts. This allows a tool/script to take the output one specific interface (e.g., UnitTimes) and plot that data relative to another data modality (e.g., behavioral events) without having to define all possible modalities in advance. Declaring one of these interfaces means that one or more TimeSeries of the specified type is published. These TimeSeries should reside in a group having the same name as the interface. For example, if a BehavioralTimeSeries interface is declared, the module will have one or more TimeSeries defined in the module sub-group 'BehavioralTimeSeries'. BehavioralEpochs should use IntervalSeries. BehavioralEvents is used for irregular events. BehavioralTimeSeries is for continuous data. + """ + IntervalSeries: Optional[List[IntervalSeries]] = Field(default_factory=list, description="""IntervalSeries object containing start and stop times of epochs.""") + + +class BehavioralEvents(NWBDataInterface): + """ + TimeSeries for storing behavioral events. See description of BehavioralEpochs for more details. + """ + TimeSeries: Optional[List[TimeSeries]] = Field(default_factory=list, description="""TimeSeries object containing behavioral events.""") + + +class BehavioralTimeSeries(NWBDataInterface): + """ + TimeSeries for storing Behavoioral time series data. See description of BehavioralEpochs for more details. + """ + TimeSeries: Optional[List[TimeSeries]] = Field(default_factory=list, description="""TimeSeries object containing continuous behavioral data.""") + + +class PupilTracking(NWBDataInterface): + """ + Eye-tracking data, representing pupil size. + """ + TimeSeries: List[TimeSeries] = Field(default_factory=list, description="""TimeSeries object containing time series data on pupil size.""") + + +class EyeTracking(NWBDataInterface): + """ + Eye-tracking data, representing direction of gaze. + """ + SpatialSeries: Optional[List[SpatialSeries]] = Field(default_factory=list, description="""SpatialSeries object containing data measuring direction of gaze.""") + + +class CompassDirection(NWBDataInterface): + """ + With a CompassDirection interface, a module publishes a SpatialSeries object representing a floating point value for theta. The SpatialSeries::reference_frame field should indicate what direction corresponds to 0 and which is the direction of rotation (this should be clockwise). The si_unit for the SpatialSeries should be radians or degrees. + """ + SpatialSeries: Optional[List[SpatialSeries]] = Field(default_factory=list, description="""SpatialSeries object containing direction of gaze travel.""") + + +class Position(NWBDataInterface): + """ + Position data, whether along the x, x/y or x/y/z axis. + """ + SpatialSeries: List[SpatialSeries] = Field(default_factory=list, description="""SpatialSeries object containing position data.""") + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +SpatialSeries.update_forward_refs() +BehavioralEpochs.update_forward_refs() +BehavioralEvents.update_forward_refs() +BehavioralTimeSeries.update_forward_refs() +PupilTracking.update_forward_refs() +EyeTracking.update_forward_refs() +CompassDirection.update_forward_refs() +Position.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_behavior_include.py b/nwb_linkml/models/core_nwb_behavior_include.py new file mode 100644 index 0000000..a16bee4 --- /dev/null +++ b/nwb_linkml/models/core_nwb_behavior_include.py @@ -0,0 +1,55 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .nwb_language import ( + Arraylike +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class SpatialSeriesData(ConfiguredBaseModel): + """ + 1-D or 2-D array storing position or direction relative to some reference frame. + """ + unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. The default value is 'meters'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") + array: Optional[NDArray[Shape["* num_times, 1 x, 2 x_y, 3 x_y_z"], Number]] = Field(None) + + +class SpatialSeriesDataArray(Arraylike): + + num_times: float = Field(...) + x: Optional[float] = Field(None) + xy: Optional[float] = Field(None) + xyz: Optional[float] = Field(None) + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +SpatialSeriesData.update_forward_refs() +SpatialSeriesDataArray.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_device.py b/nwb_linkml/models/core_nwb_device.py new file mode 100644 index 0000000..5e3e7f6 --- /dev/null +++ b/nwb_linkml/models/core_nwb_device.py @@ -0,0 +1,46 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .core_nwb_base import ( + NWBContainer +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class Device(NWBContainer): + """ + Metadata about a data acquisition device, e.g., recording system, electrode, microscope. + """ + description: Optional[str] = Field(None, description="""Description of the device (e.g., model, firmware version, processing software version, etc.) as free-form text.""") + manufacturer: Optional[str] = Field(None, description="""The name of the manufacturer of the device.""") + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +Device.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_device_include.py b/nwb_linkml/models/core_nwb_device_include.py new file mode 100644 index 0000000..c923ad6 --- /dev/null +++ b/nwb_linkml/models/core_nwb_device_include.py @@ -0,0 +1,33 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ diff --git a/nwb_linkml/models/core_nwb_ecephys.py b/nwb_linkml/models/core_nwb_ecephys.py new file mode 100644 index 0000000..28323c9 --- /dev/null +++ b/nwb_linkml/models/core_nwb_ecephys.py @@ -0,0 +1,170 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .core_nwb_ecephys_include import ( + ClusteringPeakOverRms, + FeatureExtractionDescription, + FeatureExtractionFeatures, + EventDetectionSourceIdx, + ClusteringTimes, + SpikeEventSeriesTimestamps, + EventDetectionTimes, + ClusterWaveformsWaveformMean, + SpikeEventSeriesData, + FeatureExtractionTimes, + ClusteringNum, + ElectricalSeriesChannelConversion, + ClusterWaveformsWaveformSd, + ElectricalSeriesData, + ElectricalSeriesElectrodes, + FeatureExtractionElectrodes +) + +from .core_nwb_base import ( + TimeSeries, + NWBContainer, + NWBDataInterface +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class ElectricalSeries(TimeSeries): + """ + A time series of acquired voltage data from extracellular recordings. The data field is an int or float array storing data in volts. The first dimension should always represent time. The second dimension, if present, should represent channels. + """ + filtering: Optional[str] = Field(None, description="""Filtering applied to all channels of the data. For example, if this ElectricalSeries represents high-pass-filtered data (also known as AP Band), then this value could be \"High-pass 4-pole Bessel filter at 500 Hz\". If this ElectricalSeries represents low-pass-filtered LFP data and the type of filter is unknown, then this value could be \"Low-pass filter at 300 Hz\". If a non-standard filter type is used, provide as much detail about the filter properties as possible.""") + data: ElectricalSeriesData = Field(..., description="""Recorded voltage data.""") + electrodes: ElectricalSeriesElectrodes = Field(..., description="""DynamicTableRegion pointer to the electrodes that this time series was generated from.""") + channel_conversion: Optional[ElectricalSeriesChannelConversion] = Field(None, description="""Channel-specific conversion factor. Multiply the data in the 'data' dataset by these values along the channel axis (as indicated by axis attribute) AND by the global conversion factor in the 'conversion' attribute of 'data' to get the data values in Volts, i.e, data in Volts = data * data.conversion * channel_conversion. This approach allows for both global and per-channel data conversion factors needed to support the storage of electrical recordings as native values generated by data acquisition systems. If this dataset is not present, then there is no channel-specific conversion factor, i.e. it is 1 for all channels.""") + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + +class SpikeEventSeries(ElectricalSeries): + """ + Stores snapshots/snippets of recorded spike events (i.e., threshold crossings). This may also be raw data, as reported by ephys hardware. If so, the TimeSeries::description field should describe how events were detected. All SpikeEventSeries should reside in a module (under EventWaveform interface) even if the spikes were reported and stored by hardware. All events span the same recording channels and store snapshots of equal duration. TimeSeries::data array structure: [num events] [num channels] [num samples] (or [num events] [num samples] for single electrode). + """ + data: SpikeEventSeriesData = Field(..., description="""Spike waveforms.""") + timestamps: SpikeEventSeriesTimestamps = Field(..., description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. Timestamps are required for the events. Unlike for TimeSeries, timestamps are required for SpikeEventSeries and are thus re-specified here.""") + filtering: Optional[str] = Field(None, description="""Filtering applied to all channels of the data. For example, if this ElectricalSeries represents high-pass-filtered data (also known as AP Band), then this value could be \"High-pass 4-pole Bessel filter at 500 Hz\". If this ElectricalSeries represents low-pass-filtered LFP data and the type of filter is unknown, then this value could be \"Low-pass filter at 300 Hz\". If a non-standard filter type is used, provide as much detail about the filter properties as possible.""") + electrodes: ElectricalSeriesElectrodes = Field(..., description="""DynamicTableRegion pointer to the electrodes that this time series was generated from.""") + channel_conversion: Optional[ElectricalSeriesChannelConversion] = Field(None, description="""Channel-specific conversion factor. Multiply the data in the 'data' dataset by these values along the channel axis (as indicated by axis attribute) AND by the global conversion factor in the 'conversion' attribute of 'data' to get the data values in Volts, i.e, data in Volts = data * data.conversion * channel_conversion. This approach allows for both global and per-channel data conversion factors needed to support the storage of electrical recordings as native values generated by data acquisition systems. If this dataset is not present, then there is no channel-specific conversion factor, i.e. it is 1 for all channels.""") + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + +class FeatureExtraction(NWBDataInterface): + """ + Features, such as PC1 and PC2, that are extracted from signals stored in a SpikeEventSeries or other source. + """ + description: FeatureExtractionDescription = Field(..., description="""Description of features (eg, ''PC1'') for each of the extracted features.""") + features: FeatureExtractionFeatures = Field(..., description="""Multi-dimensional array of features extracted from each event.""") + times: FeatureExtractionTimes = Field(..., description="""Times of events that features correspond to (can be a link).""") + electrodes: FeatureExtractionElectrodes = Field(..., description="""DynamicTableRegion pointer to the electrodes that this time series was generated from.""") + + +class EventDetection(NWBDataInterface): + """ + Detected spike events from voltage trace(s). + """ + detection_method: str = Field(..., description="""Description of how events were detected, such as voltage threshold, or dV/dT threshold, as well as relevant values.""") + source_idx: EventDetectionSourceIdx = Field(..., description="""Indices (zero-based) into source ElectricalSeries::data array corresponding to time of event. ''description'' should define what is meant by time of event (e.g., .25 ms before action potential peak, zero-crossing time, etc). The index points to each event from the raw data.""") + times: EventDetectionTimes = Field(..., description="""Timestamps of events, in seconds.""") + + +class EventWaveform(NWBDataInterface): + """ + Represents either the waveforms of detected events, as extracted from a raw data trace in /acquisition, or the event waveforms that were stored during experiment acquisition. + """ + SpikeEventSeries: Optional[List[SpikeEventSeries]] = Field(default_factory=list, description="""SpikeEventSeries object(s) containing detected spike event waveforms.""") + + +class FilteredEphys(NWBDataInterface): + """ + Electrophysiology data from one or more channels that has been subjected to filtering. Examples of filtered data include Theta and Gamma (LFP has its own interface). FilteredEphys modules publish an ElectricalSeries for each filtered channel or set of channels. The name of each ElectricalSeries is arbitrary but should be informative. The source of the filtered data, whether this is from analysis of another time series or as acquired by hardware, should be noted in each's TimeSeries::description field. There is no assumed 1::1 correspondence between filtered ephys signals and electrodes, as a single signal can apply to many nearby electrodes, and one electrode may have different filtered (e.g., theta and/or gamma) signals represented. Filter properties should be noted in the ElectricalSeries 'filtering' attribute. + """ + ElectricalSeries: List[ElectricalSeries] = Field(default_factory=list, description="""ElectricalSeries object(s) containing filtered electrophysiology data.""") + + +class LFP(NWBDataInterface): + """ + LFP data from one or more channels. The electrode map in each published ElectricalSeries will identify which channels are providing LFP data. Filter properties should be noted in the ElectricalSeries 'filtering' attribute. + """ + ElectricalSeries: List[ElectricalSeries] = Field(default_factory=list, description="""ElectricalSeries object(s) containing LFP data for one or more channels.""") + + +class ElectrodeGroup(NWBContainer): + """ + A physical grouping of electrodes, e.g. a shank of an array. + """ + description: Optional[str] = Field(None, description="""Description of this electrode group.""") + location: Optional[str] = Field(None, description="""Location of electrode group. Specify the area, layer, comments on estimation of area/layer, etc. Use standard atlas names for anatomical regions when possible.""") + position: Optional[Any] = Field(None, description="""stereotaxic or common framework coordinates""") + + +class ClusterWaveforms(NWBDataInterface): + """ + DEPRECATED The mean waveform shape, including standard deviation, of the different clusters. Ideally, the waveform analysis should be performed on data that is only high-pass filtered. This is a separate module because it is expected to require updating. For example, IMEC probes may require different storage requirements to store/display mean waveforms, requiring a new interface or an extension of this one. + """ + waveform_filtering: str = Field(..., description="""Filtering applied to data before generating mean/sd""") + waveform_mean: ClusterWaveformsWaveformMean = Field(..., description="""The mean waveform for each cluster, using the same indices for each wave as cluster numbers in the associated Clustering module (i.e, cluster 3 is in array slot [3]). Waveforms corresponding to gaps in cluster sequence should be empty (e.g., zero- filled)""") + waveform_sd: ClusterWaveformsWaveformSd = Field(..., description="""Stdev of waveforms for each cluster, using the same indices as in mean""") + + +class Clustering(NWBDataInterface): + """ + DEPRECATED Clustered spike data, whether from automatic clustering tools (e.g., klustakwik) or as a result of manual sorting. + """ + description: str = Field(..., description="""Description of clusters or clustering, (e.g. cluster 0 is noise, clusters curated using Klusters, etc)""") + num: ClusteringNum = Field(..., description="""Cluster number of each event""") + peak_over_rms: ClusteringPeakOverRms = Field(..., description="""Maximum ratio of waveform peak to RMS on any channel in the cluster (provides a basic clustering metric).""") + times: ClusteringTimes = Field(..., description="""Times of clustered events, in seconds. This may be a link to times field in associated FeatureExtraction module.""") + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +ElectricalSeries.update_forward_refs() +SpikeEventSeries.update_forward_refs() +FeatureExtraction.update_forward_refs() +EventDetection.update_forward_refs() +EventWaveform.update_forward_refs() +FilteredEphys.update_forward_refs() +LFP.update_forward_refs() +ElectrodeGroup.update_forward_refs() +ClusterWaveforms.update_forward_refs() +Clustering.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_ecephys_include.py b/nwb_linkml/models/core_nwb_ecephys_include.py new file mode 100644 index 0000000..b36e7ff --- /dev/null +++ b/nwb_linkml/models/core_nwb_ecephys_include.py @@ -0,0 +1,217 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .hdmf_common_table import ( + DynamicTableRegion +) + +from .nwb_language import ( + Arraylike +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class ElectricalSeriesData(ConfiguredBaseModel): + """ + Recorded voltage data. + """ + unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. This value is fixed to 'volts'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion', followed by 'channel_conversion' (if present), and then add 'offset'.""") + array: Optional[NDArray[Shape["* num_times, * num_channels, * num_samples"], Number]] = Field(None) + + +class ElectricalSeriesDataArray(Arraylike): + + num_times: float = Field(...) + num_channels: Optional[float] = Field(None) + num_samples: Optional[float] = Field(None) + + +class ElectricalSeriesElectrodes(DynamicTableRegion): + """ + DynamicTableRegion pointer to the electrodes that this time series was generated from. + """ + table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") + description: Optional[str] = Field(None, description="""Description of what this table region points to.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class ElectricalSeriesChannelConversion(ConfiguredBaseModel): + """ + Channel-specific conversion factor. Multiply the data in the 'data' dataset by these values along the channel axis (as indicated by axis attribute) AND by the global conversion factor in the 'conversion' attribute of 'data' to get the data values in Volts, i.e, data in Volts = data * data.conversion * channel_conversion. This approach allows for both global and per-channel data conversion factors needed to support the storage of electrical recordings as native values generated by data acquisition systems. If this dataset is not present, then there is no channel-specific conversion factor, i.e. it is 1 for all channels. + """ + axis: Optional[int] = Field(None, description="""The zero-indexed axis of the 'data' dataset that the channel-specific conversion factor corresponds to. This value is fixed to 1.""") + channel_conversion: Optional[List[float]] = Field(default_factory=list, description="""Channel-specific conversion factor. Multiply the data in the 'data' dataset by these values along the channel axis (as indicated by axis attribute) AND by the global conversion factor in the 'conversion' attribute of 'data' to get the data values in Volts, i.e, data in Volts = data * data.conversion * channel_conversion. This approach allows for both global and per-channel data conversion factors needed to support the storage of electrical recordings as native values generated by data acquisition systems. If this dataset is not present, then there is no channel-specific conversion factor, i.e. it is 1 for all channels.""") + + +class SpikeEventSeriesData(ConfiguredBaseModel): + """ + Spike waveforms. + """ + unit: Optional[str] = Field(None, description="""Unit of measurement for waveforms, which is fixed to 'volts'.""") + array: Optional[NDArray[Shape["* num_events, * num_samples, * num_channels"], Number]] = Field(None) + + +class SpikeEventSeriesDataArray(Arraylike): + + num_events: float = Field(...) + num_samples: float = Field(...) + num_channels: Optional[float] = Field(None) + + +class SpikeEventSeriesTimestamps(ConfiguredBaseModel): + """ + Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. Timestamps are required for the events. Unlike for TimeSeries, timestamps are required for SpikeEventSeries and are thus re-specified here. + """ + interval: Optional[int] = Field(None, description="""Value is '1'""") + unit: Optional[str] = Field(None, description="""Unit of measurement for timestamps, which is fixed to 'seconds'.""") + timestamps: List[float] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. Timestamps are required for the events. Unlike for TimeSeries, timestamps are required for SpikeEventSeries and are thus re-specified here.""") + + +class FeatureExtractionDescription(ConfiguredBaseModel): + """ + Description of features (eg, ''PC1'') for each of the extracted features. + """ + description: List[str] = Field(default_factory=list, description="""Description of features (eg, ''PC1'') for each of the extracted features.""") + + +class FeatureExtractionFeatures(ConfiguredBaseModel): + """ + Multi-dimensional array of features extracted from each event. + """ + array: Optional[NDArray[Shape["* num_events, * num_channels, * num_features"], Float32]] = Field(None) + + +class FeatureExtractionFeaturesArray(Arraylike): + + num_events: Optional[float] = Field(None) + num_channels: Optional[float] = Field(None) + num_features: Optional[float] = Field(None) + + +class FeatureExtractionTimes(ConfiguredBaseModel): + """ + Times of events that features correspond to (can be a link). + """ + times: List[float] = Field(default_factory=list, description="""Times of events that features correspond to (can be a link).""") + + +class FeatureExtractionElectrodes(DynamicTableRegion): + """ + DynamicTableRegion pointer to the electrodes that this time series was generated from. + """ + table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") + description: Optional[str] = Field(None, description="""Description of what this table region points to.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class EventDetectionSourceIdx(ConfiguredBaseModel): + """ + Indices (zero-based) into source ElectricalSeries::data array corresponding to time of event. ''description'' should define what is meant by time of event (e.g., .25 ms before action potential peak, zero-crossing time, etc). The index points to each event from the raw data. + """ + source_idx: List[int] = Field(default_factory=list, description="""Indices (zero-based) into source ElectricalSeries::data array corresponding to time of event. ''description'' should define what is meant by time of event (e.g., .25 ms before action potential peak, zero-crossing time, etc). The index points to each event from the raw data.""") + + +class EventDetectionTimes(ConfiguredBaseModel): + """ + Timestamps of events, in seconds. + """ + unit: Optional[str] = Field(None, description="""Unit of measurement for event times, which is fixed to 'seconds'.""") + times: List[float] = Field(default_factory=list, description="""Timestamps of events, in seconds.""") + + +class ClusterWaveformsWaveformMean(ConfiguredBaseModel): + """ + The mean waveform for each cluster, using the same indices for each wave as cluster numbers in the associated Clustering module (i.e, cluster 3 is in array slot [3]). Waveforms corresponding to gaps in cluster sequence should be empty (e.g., zero- filled) + """ + array: Optional[NDArray[Shape["* num_clusters, * num_samples"], Float32]] = Field(None) + + +class ClusterWaveformsWaveformMeanArray(Arraylike): + + num_clusters: Optional[float] = Field(None) + num_samples: Optional[float] = Field(None) + + +class ClusterWaveformsWaveformSd(ConfiguredBaseModel): + """ + Stdev of waveforms for each cluster, using the same indices as in mean + """ + array: Optional[NDArray[Shape["* num_clusters, * num_samples"], Float32]] = Field(None) + + +class ClusterWaveformsWaveformSdArray(Arraylike): + + num_clusters: Optional[float] = Field(None) + num_samples: Optional[float] = Field(None) + + +class ClusteringNum(ConfiguredBaseModel): + """ + Cluster number of each event + """ + num: List[int] = Field(default_factory=list, description="""Cluster number of each event""") + + +class ClusteringPeakOverRms(ConfiguredBaseModel): + """ + Maximum ratio of waveform peak to RMS on any channel in the cluster (provides a basic clustering metric). + """ + peak_over_rms: List[float] = Field(default_factory=list, description="""Maximum ratio of waveform peak to RMS on any channel in the cluster (provides a basic clustering metric).""") + + +class ClusteringTimes(ConfiguredBaseModel): + """ + Times of clustered events, in seconds. This may be a link to times field in associated FeatureExtraction module. + """ + times: List[float] = Field(default_factory=list, description="""Times of clustered events, in seconds. This may be a link to times field in associated FeatureExtraction module.""") + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +ElectricalSeriesData.update_forward_refs() +ElectricalSeriesDataArray.update_forward_refs() +ElectricalSeriesElectrodes.update_forward_refs() +ElectricalSeriesChannelConversion.update_forward_refs() +SpikeEventSeriesData.update_forward_refs() +SpikeEventSeriesDataArray.update_forward_refs() +SpikeEventSeriesTimestamps.update_forward_refs() +FeatureExtractionDescription.update_forward_refs() +FeatureExtractionFeatures.update_forward_refs() +FeatureExtractionFeaturesArray.update_forward_refs() +FeatureExtractionTimes.update_forward_refs() +FeatureExtractionElectrodes.update_forward_refs() +EventDetectionSourceIdx.update_forward_refs() +EventDetectionTimes.update_forward_refs() +ClusterWaveformsWaveformMean.update_forward_refs() +ClusterWaveformsWaveformMeanArray.update_forward_refs() +ClusterWaveformsWaveformSd.update_forward_refs() +ClusterWaveformsWaveformSdArray.update_forward_refs() +ClusteringNum.update_forward_refs() +ClusteringPeakOverRms.update_forward_refs() +ClusteringTimes.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_epoch.py b/nwb_linkml/models/core_nwb_epoch.py new file mode 100644 index 0000000..9834eaf --- /dev/null +++ b/nwb_linkml/models/core_nwb_epoch.py @@ -0,0 +1,60 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .core_nwb_epoch_include import ( + TimeIntervalsTimeseriesIndex, + TimeIntervalsTagsIndex, + TimeIntervalsTimeseries +) + +from .hdmf_common_table import ( + DynamicTable +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class TimeIntervals(DynamicTable): + """ + A container for aggregating epoch data and the TimeSeries that each epoch applies to. + """ + start_time: Optional[List[float]] = Field(default_factory=list, description="""Start time of epoch, in seconds.""") + stop_time: Optional[List[float]] = Field(default_factory=list, description="""Stop time of epoch, in seconds.""") + tags: Optional[List[str]] = Field(default_factory=list, description="""User-defined tags that identify or categorize events.""") + tags_index: Optional[TimeIntervalsTagsIndex] = Field(None, description="""Index for tags.""") + timeseries: Optional[TimeIntervalsTimeseries] = Field(None, description="""An index into a TimeSeries object.""") + timeseries_index: Optional[TimeIntervalsTimeseriesIndex] = Field(None, description="""Index for timeseries.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +TimeIntervals.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_epoch_include.py b/nwb_linkml/models/core_nwb_epoch_include.py new file mode 100644 index 0000000..170f9de --- /dev/null +++ b/nwb_linkml/models/core_nwb_epoch_include.py @@ -0,0 +1,70 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .core_nwb_base import ( + TimeSeriesReferenceVectorData +) + +from .hdmf_common_table import ( + VectorIndex +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class TimeIntervalsTagsIndex(VectorIndex): + """ + Index for tags. + """ + target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class TimeIntervalsTimeseries(TimeSeriesReferenceVectorData): + """ + An index into a TimeSeries object. + """ + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class TimeIntervalsTimeseriesIndex(VectorIndex): + """ + Index for timeseries. + """ + target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +TimeIntervalsTagsIndex.update_forward_refs() +TimeIntervalsTimeseries.update_forward_refs() +TimeIntervalsTimeseriesIndex.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_file.py b/nwb_linkml/models/core_nwb_file.py new file mode 100644 index 0000000..6001fb9 --- /dev/null +++ b/nwb_linkml/models/core_nwb_file.py @@ -0,0 +1,104 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .core_nwb_file_include import ( + NWBFileScratch, + NWBFileGeneral, + NWBFileIntervals, + NWBFileFileCreateDate, + NWBFileUnits, + SubjectAge, + NWBFileStimulus, + NWBFileAcquisition, + NWBFileProcessing, + NWBFileAnalysis +) + +from .core_nwb_base import ( + NWBContainer, + NWBData +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class ScratchData(NWBData): + """ + Any one-off datasets + """ + notes: Optional[str] = Field(None, description="""Any notes the user has about the dataset being stored""") + + +class NWBFile(NWBContainer): + """ + An NWB file storing cellular-based neurophysiology data from a single experimental session. + """ + nwb_version: Optional[str] = Field(None, description="""File version string. Use semantic versioning, e.g. 1.2.1. This will be the name of the format with trailing major, minor and patch numbers.""") + file_create_date: NWBFileFileCreateDate = Field(..., description="""A record of the date the file was created and of subsequent modifications. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted strings: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in \"Z\" with no timezone offset. Date accuracy is up to milliseconds. The file can be created after the experiment was run, so this may differ from the experiment start time. Each modification to the nwb file adds a new entry to the array.""") + identifier: str = Field(..., description="""A unique text identifier for the file. For example, concatenated lab name, file creation date/time and experimentalist, or a hash of these and/or other values. The goal is that the string should be unique to all other files.""") + session_description: str = Field(..., description="""A description of the experimental session and data in the file.""") + session_start_time: date = Field(..., description="""Date and time of the experiment/session start. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted string: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in \"Z\" with no timezone offset. Date accuracy is up to milliseconds.""") + timestamps_reference_time: date = Field(..., description="""Date and time corresponding to time zero of all timestamps. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted string: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in \"Z\" with no timezone offset. Date accuracy is up to milliseconds. All times stored in the file use this time as reference (i.e., time zero).""") + acquisition: NWBFileAcquisition = Field(..., description="""Data streams recorded from the system, including ephys, ophys, tracking, etc. This group should be read-only after the experiment is completed and timestamps are corrected to a common timebase. The data stored here may be links to raw data stored in external NWB files. This will allow keeping bulky raw data out of the file while preserving the option of keeping some/all in the file. Acquired data includes tracking and experimental data streams (i.e., everything measured from the system). If bulky data is stored in the /acquisition group, the data can exist in a separate NWB file that is linked to by the file being used for processing and analysis.""") + analysis: NWBFileAnalysis = Field(..., description="""Lab-specific and custom scientific analysis of data. There is no defined format for the content of this group - the format is up to the individual user/lab. To facilitate sharing analysis data between labs, the contents here should be stored in standard types (e.g., neurodata_types) and appropriately documented. The file can store lab-specific and custom data analysis without restriction on its form or schema, reducing data formatting restrictions on end users. Such data should be placed in the analysis group. The analysis data should be documented so that it could be shared with other labs.""") + scratch: Optional[NWBFileScratch] = Field(None, description="""A place to store one-off analysis results. Data placed here is not intended for sharing. By placing data here, users acknowledge that there is no guarantee that their data meets any standard.""") + processing: NWBFileProcessing = Field(..., description="""The home for ProcessingModules. These modules perform intermediate analysis of data that is necessary to perform before scientific analysis. Examples include spike clustering, extracting position from tracking data, stitching together image slices. ProcessingModules can be large and express many data sets from relatively complex analysis (e.g., spike detection and clustering) or small, representing extraction of position information from tracking video, or even binary lick/no-lick decisions. Common software tools (e.g., klustakwik, MClust) are expected to read/write data here. 'Processing' refers to intermediate analysis of the acquired data to make it more amenable to scientific analysis.""") + stimulus: NWBFileStimulus = Field(..., description="""Data pushed into the system (eg, video stimulus, sound, voltage, etc) and secondary representations of that data (eg, measurements of something used as a stimulus). This group should be made read-only after experiment complete and timestamps are corrected to common timebase. Stores both presented stimuli and stimulus templates, the latter in case the same stimulus is presented multiple times, or is pulled from an external stimulus library. Stimuli are here defined as any signal that is pushed into the system as part of the experiment (eg, sound, video, voltage, etc). Many different experiments can use the same stimuli, and stimuli can be re-used during an experiment. The stimulus group is organized so that one version of template stimuli can be stored and these be used multiple times. These templates can exist in the present file or can be linked to a remote library file.""") + general: NWBFileGeneral = Field(..., description="""Experimental metadata, including protocol, notes and description of hardware device(s). The metadata stored in this section should be used to describe the experiment. Metadata necessary for interpreting the data is stored with the data. General experimental metadata, including animal strain, experimental protocols, experimenter, devices, etc, are stored under 'general'. Core metadata (e.g., that required to interpret data fields) is stored with the data itself, and implicitly defined by the file specification (e.g., time is in seconds). The strategy used here for storing non-core metadata is to use free-form text fields, such as would appear in sentences or paragraphs from a Methods section. Metadata fields are text to enable them to be more general, for example to represent ranges instead of numerical values. Machine-readable metadata is stored as attributes to these free-form datasets. All entries in the below table are to be included when data is present. Unused groups (e.g., intracellular_ephys in an optophysiology experiment) should not be created unless there is data to store within them.""") + intervals: Optional[NWBFileIntervals] = Field(None, description="""Experimental intervals, whether that be logically distinct sub-experiments having a particular scientific goal, trials (see trials subgroup) during an experiment, or epochs (see epochs subgroup) deriving from analysis of data.""") + units: Optional[NWBFileUnits] = Field(None, description="""Data about sorted spike units.""") + + +class LabMetaData(NWBContainer): + """ + Lab-specific meta-data. + """ + None + + +class Subject(NWBContainer): + """ + Information about the animal or person from which the data was measured. + """ + age: Optional[SubjectAge] = Field(None, description="""Age of subject. Can be supplied instead of 'date_of_birth'.""") + date_of_birth: Optional[date] = Field(None, description="""Date of birth of subject. Can be supplied instead of 'age'.""") + description: Optional[str] = Field(None, description="""Description of subject and where subject came from (e.g., breeder, if animal).""") + genotype: Optional[str] = Field(None, description="""Genetic strain. If absent, assume Wild Type (WT).""") + sex: Optional[str] = Field(None, description="""Gender of subject.""") + species: Optional[str] = Field(None, description="""Species of subject.""") + strain: Optional[str] = Field(None, description="""Strain of subject.""") + subject_id: Optional[str] = Field(None, description="""ID of animal/person used/participating in experiment (lab convention).""") + weight: Optional[str] = Field(None, description="""Weight at time of experiment, at time of surgery and at other important times.""") + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +ScratchData.update_forward_refs() +NWBFile.update_forward_refs() +LabMetaData.update_forward_refs() +Subject.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_file_include.py b/nwb_linkml/models/core_nwb_file_include.py new file mode 100644 index 0000000..7590095 --- /dev/null +++ b/nwb_linkml/models/core_nwb_file_include.py @@ -0,0 +1,480 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .core_nwb_file import ( + LabMetaData, + ScratchData, + Subject +) + +from .core_nwb_misc import ( + Units +) + +from .core_nwb_base import ( + TimeSeries, + Images, + NWBContainer, + NWBDataInterface, + ProcessingModule +) + +from .core_nwb_icephys import ( + RepetitionsTable, + ExperimentalConditionsTable, + IntracellularElectrode, + SimultaneousRecordingsTable, + SweepTable, + SequentialRecordingsTable, + IntracellularRecordingsTable +) + +from .core_nwb_epoch import ( + TimeIntervals +) + +from .core_nwb_ogen import ( + OptogeneticStimulusSite +) + +from .core_nwb_device import ( + Device +) + +from .core_nwb_ecephys import ( + ElectrodeGroup +) + +from .hdmf_common_table import ( + DynamicTable +) + +from .core_nwb_ophys import ( + ImagingPlane +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class NWBFileFileCreateDate(ConfiguredBaseModel): + """ + A record of the date the file was created and of subsequent modifications. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted strings: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in \"Z\" with no timezone offset. Date accuracy is up to milliseconds. The file can be created after the experiment was run, so this may differ from the experiment start time. Each modification to the nwb file adds a new entry to the array. + """ + file_create_date: List[date] = Field(default_factory=list, description="""A record of the date the file was created and of subsequent modifications. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted strings: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in \"Z\" with no timezone offset. Date accuracy is up to milliseconds. The file can be created after the experiment was run, so this may differ from the experiment start time. Each modification to the nwb file adds a new entry to the array.""") + + +class NWBFileAcquisition(ConfiguredBaseModel): + """ + Data streams recorded from the system, including ephys, ophys, tracking, etc. This group should be read-only after the experiment is completed and timestamps are corrected to a common timebase. The data stored here may be links to raw data stored in external NWB files. This will allow keeping bulky raw data out of the file while preserving the option of keeping some/all in the file. Acquired data includes tracking and experimental data streams (i.e., everything measured from the system). If bulky data is stored in the /acquisition group, the data can exist in a separate NWB file that is linked to by the file being used for processing and analysis. + """ + NWBDataInterface: Optional[List[NWBDataInterface]] = Field(default_factory=list, description="""Acquired, raw data.""") + DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tabular data that is relevant to acquisition""") + + +class NWBFileAnalysis(ConfiguredBaseModel): + """ + Lab-specific and custom scientific analysis of data. There is no defined format for the content of this group - the format is up to the individual user/lab. To facilitate sharing analysis data between labs, the contents here should be stored in standard types (e.g., neurodata_types) and appropriately documented. The file can store lab-specific and custom data analysis without restriction on its form or schema, reducing data formatting restrictions on end users. Such data should be placed in the analysis group. The analysis data should be documented so that it could be shared with other labs. + """ + NWBContainer: Optional[List[NWBContainer]] = Field(default_factory=list, description="""Custom analysis results.""") + DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Tabular data that is relevant to data stored in analysis""") + + +class NWBFileScratch(ConfiguredBaseModel): + """ + A place to store one-off analysis results. Data placed here is not intended for sharing. By placing data here, users acknowledge that there is no guarantee that their data meets any standard. + """ + ScratchData: Optional[List[ScratchData]] = Field(default_factory=list, description="""Any one-off datasets""") + NWBContainer: Optional[List[NWBContainer]] = Field(default_factory=list, description="""Any one-off containers""") + DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""Any one-off tables""") + + +class NWBFileProcessing(ConfiguredBaseModel): + """ + The home for ProcessingModules. These modules perform intermediate analysis of data that is necessary to perform before scientific analysis. Examples include spike clustering, extracting position from tracking data, stitching together image slices. ProcessingModules can be large and express many data sets from relatively complex analysis (e.g., spike detection and clustering) or small, representing extraction of position information from tracking video, or even binary lick/no-lick decisions. Common software tools (e.g., klustakwik, MClust) are expected to read/write data here. 'Processing' refers to intermediate analysis of the acquired data to make it more amenable to scientific analysis. + """ + ProcessingModule: Optional[List[ProcessingModule]] = Field(default_factory=list, description="""Intermediate analysis of acquired data.""") + + +class NWBFileStimulus(ConfiguredBaseModel): + """ + Data pushed into the system (eg, video stimulus, sound, voltage, etc) and secondary representations of that data (eg, measurements of something used as a stimulus). This group should be made read-only after experiment complete and timestamps are corrected to common timebase. Stores both presented stimuli and stimulus templates, the latter in case the same stimulus is presented multiple times, or is pulled from an external stimulus library. Stimuli are here defined as any signal that is pushed into the system as part of the experiment (eg, sound, video, voltage, etc). Many different experiments can use the same stimuli, and stimuli can be re-used during an experiment. The stimulus group is organized so that one version of template stimuli can be stored and these be used multiple times. These templates can exist in the present file or can be linked to a remote library file. + """ + presentation: NWBFileStimulusPresentation = Field(..., description="""Stimuli presented during the experiment.""") + templates: NWBFileStimulusTemplates = Field(..., description="""Template stimuli. Timestamps in templates are based on stimulus design and are relative to the beginning of the stimulus. When templates are used, the stimulus instances must convert presentation times to the experiment`s time reference frame.""") + + +class NWBFileStimulusPresentation(ConfiguredBaseModel): + """ + Stimuli presented during the experiment. + """ + TimeSeries: Optional[List[TimeSeries]] = Field(default_factory=list, description="""TimeSeries objects containing data of presented stimuli.""") + + +class NWBFileStimulusTemplates(ConfiguredBaseModel): + """ + Template stimuli. Timestamps in templates are based on stimulus design and are relative to the beginning of the stimulus. When templates are used, the stimulus instances must convert presentation times to the experiment`s time reference frame. + """ + TimeSeries: Optional[List[TimeSeries]] = Field(default_factory=list, description="""TimeSeries objects containing template data of presented stimuli.""") + Images: Optional[List[Images]] = Field(default_factory=list, description="""Images objects containing images of presented stimuli.""") + + +class NWBFileGeneral(ConfiguredBaseModel): + """ + Experimental metadata, including protocol, notes and description of hardware device(s). The metadata stored in this section should be used to describe the experiment. Metadata necessary for interpreting the data is stored with the data. General experimental metadata, including animal strain, experimental protocols, experimenter, devices, etc, are stored under 'general'. Core metadata (e.g., that required to interpret data fields) is stored with the data itself, and implicitly defined by the file specification (e.g., time is in seconds). The strategy used here for storing non-core metadata is to use free-form text fields, such as would appear in sentences or paragraphs from a Methods section. Metadata fields are text to enable them to be more general, for example to represent ranges instead of numerical values. Machine-readable metadata is stored as attributes to these free-form datasets. All entries in the below table are to be included when data is present. Unused groups (e.g., intracellular_ephys in an optophysiology experiment) should not be created unless there is data to store within them. + """ + data_collection: Optional[str] = Field(None, description="""Notes about data collection and analysis.""") + experiment_description: Optional[str] = Field(None, description="""General description of the experiment.""") + experimenter: Optional[NWBFileGeneralExperimenter] = Field(None, description="""Name of person(s) who performed the experiment. Can also specify roles of different people involved.""") + institution: Optional[str] = Field(None, description="""Institution(s) where experiment was performed.""") + keywords: Optional[NWBFileGeneralKeywords] = Field(None, description="""Terms to search over.""") + lab: Optional[str] = Field(None, description="""Laboratory where experiment was performed.""") + notes: Optional[str] = Field(None, description="""Notes about the experiment.""") + pharmacology: Optional[str] = Field(None, description="""Description of drugs used, including how and when they were administered. Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc.""") + protocol: Optional[str] = Field(None, description="""Experimental protocol, if applicable. e.g., include IACUC protocol number.""") + related_publications: Optional[NWBFileGeneralRelatedPublications] = Field(None, description="""Publication information. PMID, DOI, URL, etc.""") + session_id: Optional[str] = Field(None, description="""Lab-specific ID for the session.""") + slices: Optional[str] = Field(None, description="""Description of slices, including information about preparation thickness, orientation, temperature, and bath solution.""") + source_script: Optional[NWBFileGeneralSourceScript] = Field(None, description="""Script file or link to public source code used to create this NWB file.""") + stimulus: Optional[str] = Field(None, description="""Notes about stimuli, such as how and where they were presented.""") + surgery: Optional[str] = Field(None, description="""Narrative description about surgery/surgeries, including date(s) and who performed surgery.""") + virus: Optional[str] = Field(None, description="""Information about virus(es) used in experiments, including virus ID, source, date made, injection location, volume, etc.""") + LabMetaData: Optional[List[LabMetaData]] = Field(default_factory=list, description="""Place-holder than can be extended so that lab-specific meta-data can be placed in /general.""") + devices: Optional[NWBFileGeneralDevices] = Field(None, description="""Description of hardware devices used during experiment, e.g., monitors, ADC boards, microscopes, etc.""") + subject: Optional[NWBFileGeneralSubject] = Field(None, description="""Information about the animal or person from which the data was measured.""") + extracellular_ephys: Optional[NWBFileGeneralExtracellularEphys] = Field(None, description="""Metadata related to extracellular electrophysiology.""") + intracellular_ephys: Optional[NWBFileGeneralIntracellularEphys] = Field(None, description="""Metadata related to intracellular electrophysiology.""") + optogenetics: Optional[NWBFileGeneralOptogenetics] = Field(None, description="""Metadata describing optogenetic stimuluation.""") + optophysiology: Optional[NWBFileGeneralOptophysiology] = Field(None, description="""Metadata related to optophysiology.""") + + +class NWBFileGeneralExperimenter(ConfiguredBaseModel): + """ + Name of person(s) who performed the experiment. Can also specify roles of different people involved. + """ + experimenter: Optional[List[str]] = Field(default_factory=list, description="""Name of person(s) who performed the experiment. Can also specify roles of different people involved.""") + + +class NWBFileGeneralKeywords(ConfiguredBaseModel): + """ + Terms to search over. + """ + keywords: Optional[List[str]] = Field(default_factory=list, description="""Terms to search over.""") + + +class NWBFileGeneralRelatedPublications(ConfiguredBaseModel): + """ + Publication information. PMID, DOI, URL, etc. + """ + related_publications: Optional[List[str]] = Field(default_factory=list, description="""Publication information. PMID, DOI, URL, etc.""") + + +class NWBFileGeneralSourceScript(ConfiguredBaseModel): + """ + Script file or link to public source code used to create this NWB file. + """ + file_name: Optional[str] = Field(None, description="""Name of script file.""") + + +class NWBFileGeneralDevices(ConfiguredBaseModel): + """ + Description of hardware devices used during experiment, e.g., monitors, ADC boards, microscopes, etc. + """ + Device: Optional[List[Device]] = Field(default_factory=list, description="""Data acquisition devices.""") + + +class NWBFileGeneralSubject(Subject): + """ + Information about the animal or person from which the data was measured. + """ + age: Optional[SubjectAge] = Field(None, description="""Age of subject. Can be supplied instead of 'date_of_birth'.""") + date_of_birth: Optional[date] = Field(None, description="""Date of birth of subject. Can be supplied instead of 'age'.""") + description: Optional[str] = Field(None, description="""Description of subject and where subject came from (e.g., breeder, if animal).""") + genotype: Optional[str] = Field(None, description="""Genetic strain. If absent, assume Wild Type (WT).""") + sex: Optional[str] = Field(None, description="""Gender of subject.""") + species: Optional[str] = Field(None, description="""Species of subject.""") + strain: Optional[str] = Field(None, description="""Strain of subject.""") + subject_id: Optional[str] = Field(None, description="""ID of animal/person used/participating in experiment (lab convention).""") + weight: Optional[str] = Field(None, description="""Weight at time of experiment, at time of surgery and at other important times.""") + + +class NWBFileGeneralExtracellularEphys(ConfiguredBaseModel): + """ + Metadata related to extracellular electrophysiology. + """ + ElectrodeGroup: Optional[List[ElectrodeGroup]] = Field(default_factory=list, description="""Physical group of electrodes.""") + electrodes: Optional[NWBFileGeneralExtracellularEphysElectrodes] = Field(None, description="""A table of all electrodes (i.e. channels) used for recording.""") + + +class NWBFileGeneralExtracellularEphysElectrodes(DynamicTable): + """ + A table of all electrodes (i.e. channels) used for recording. + """ + x: Optional[List[float]] = Field(default_factory=list, description="""x coordinate of the channel location in the brain (+x is posterior).""") + y: Optional[List[float]] = Field(default_factory=list, description="""y coordinate of the channel location in the brain (+y is inferior).""") + z: Optional[List[float]] = Field(default_factory=list, description="""z coordinate of the channel location in the brain (+z is right).""") + imp: Optional[List[float]] = Field(default_factory=list, description="""Impedance of the channel, in ohms.""") + location: Optional[List[str]] = Field(default_factory=list, description="""Location of the electrode (channel). Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible.""") + filtering: Optional[List[str]] = Field(default_factory=list, description="""Description of hardware filtering, including the filter name and frequency cutoffs.""") + group: Optional[List[ElectrodeGroup]] = Field(default_factory=list, description="""Reference to the ElectrodeGroup this electrode is a part of.""") + group_name: Optional[List[str]] = Field(default_factory=list, description="""Name of the ElectrodeGroup this electrode is a part of.""") + rel_x: Optional[List[float]] = Field(default_factory=list, description="""x coordinate in electrode group""") + rel_y: Optional[List[float]] = Field(default_factory=list, description="""y coordinate in electrode group""") + rel_z: Optional[List[float]] = Field(default_factory=list, description="""z coordinate in electrode group""") + reference: Optional[List[str]] = Field(default_factory=list, description="""Description of the reference electrode and/or reference scheme used for this electrode, e.g., \"stainless steel skull screw\" or \"online common average referencing\".""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class NWBFileGeneralIntracellularEphys(ConfiguredBaseModel): + """ + Metadata related to intracellular electrophysiology. + """ + filtering: Optional[str] = Field(None, description="""[DEPRECATED] Use IntracellularElectrode.filtering instead. Description of filtering used. Includes filtering type and parameters, frequency fall-off, etc. If this changes between TimeSeries, filter description should be stored as a text attribute for each TimeSeries.""") + IntracellularElectrode: Optional[List[IntracellularElectrode]] = Field(default_factory=list, description="""An intracellular electrode.""") + sweep_table: Optional[NWBFileGeneralIntracellularEphysSweepTable] = Field(None, description="""[DEPRECATED] Table used to group different PatchClampSeries. SweepTable is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable tables. Additional SequentialRecordingsTable, RepetitionsTable and ExperimentalConditions tables provide enhanced support for experiment metadata.""") + intracellular_recordings: Optional[NWBFileGeneralIntracellularEphysIntracellularRecordings] = Field(None, description="""A table to group together a stimulus and response from a single electrode and a single simultaneous recording. Each row in the table represents a single recording consisting typically of a stimulus and a corresponding response. In some cases, however, only a stimulus or a response are recorded as as part of an experiment. In this case both, the stimulus and response will point to the same TimeSeries while the idx_start and count of the invalid column will be set to -1, thus, indicating that no values have been recorded for the stimulus or response, respectively. Note, a recording MUST contain at least a stimulus or a response. Typically the stimulus and response are PatchClampSeries. However, the use of AD/DA channels that are not associated to an electrode is also common in intracellular electrophysiology, in which case other TimeSeries may be used.""") + simultaneous_recordings: Optional[NWBFileGeneralIntracellularEphysSimultaneousRecordings] = Field(None, description="""A table for grouping different intracellular recordings from the IntracellularRecordingsTable table together that were recorded simultaneously from different electrodes""") + sequential_recordings: Optional[NWBFileGeneralIntracellularEphysSequentialRecordings] = Field(None, description="""A table for grouping different sequential recordings from the SimultaneousRecordingsTable table together. This is typically used to group together sequential recordings where the a sequence of stimuli of the same type with varying parameters have been presented in a sequence.""") + repetitions: Optional[NWBFileGeneralIntracellularEphysRepetitions] = Field(None, description="""A table for grouping different sequential intracellular recordings together. With each SequentialRecording typically representing a particular type of stimulus, the RepetitionsTable table is typically used to group sets of stimuli applied in sequence.""") + experimental_conditions: Optional[NWBFileGeneralIntracellularEphysExperimentalConditions] = Field(None, description="""A table for grouping different intracellular recording repetitions together that belong to the same experimental experimental_conditions.""") + + +class NWBFileGeneralIntracellularEphysSweepTable(SweepTable): + """ + [DEPRECATED] Table used to group different PatchClampSeries. SweepTable is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable tables. Additional SequentialRecordingsTable, RepetitionsTable and ExperimentalConditions tables provide enhanced support for experiment metadata. + """ + sweep_number: Optional[List[int]] = Field(default_factory=list, description="""Sweep number of the PatchClampSeries in that row.""") + series: Optional[List[PatchClampSeries]] = Field(default_factory=list, description="""The PatchClampSeries with the sweep number in that row.""") + series_index: SweepTableSeriesIndex = Field(..., description="""Index for series.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class NWBFileGeneralIntracellularEphysIntracellularRecordings(IntracellularRecordingsTable): + """ + A table to group together a stimulus and response from a single electrode and a single simultaneous recording. Each row in the table represents a single recording consisting typically of a stimulus and a corresponding response. In some cases, however, only a stimulus or a response are recorded as as part of an experiment. In this case both, the stimulus and response will point to the same TimeSeries while the idx_start and count of the invalid column will be set to -1, thus, indicating that no values have been recorded for the stimulus or response, respectively. Note, a recording MUST contain at least a stimulus or a response. Typically the stimulus and response are PatchClampSeries. However, the use of AD/DA channels that are not associated to an electrode is also common in intracellular electrophysiology, in which case other TimeSeries may be used. + """ + description: Optional[str] = Field(None, description="""Description of the contents of this table. Inherited from AlignedDynamicTable and overwritten here to fix the value of the attribute.""") + electrodes: IntracellularRecordingsTableElectrodes = Field(..., description="""Table for storing intracellular electrode related metadata.""") + stimuli: IntracellularRecordingsTableStimuli = Field(..., description="""Table for storing intracellular stimulus related metadata.""") + responses: IntracellularRecordingsTableResponses = Field(..., description="""Table for storing intracellular response related metadata.""") + categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") + DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class NWBFileGeneralIntracellularEphysSimultaneousRecordings(SimultaneousRecordingsTable): + """ + A table for grouping different intracellular recordings from the IntracellularRecordingsTable table together that were recorded simultaneously from different electrodes + """ + recordings: SimultaneousRecordingsTableRecordings = Field(..., description="""A reference to one or more rows in the IntracellularRecordingsTable table.""") + recordings_index: SimultaneousRecordingsTableRecordingsIndex = Field(..., description="""Index dataset for the recordings column.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class NWBFileGeneralIntracellularEphysSequentialRecordings(SequentialRecordingsTable): + """ + A table for grouping different sequential recordings from the SimultaneousRecordingsTable table together. This is typically used to group together sequential recordings where the a sequence of stimuli of the same type with varying parameters have been presented in a sequence. + """ + simultaneous_recordings: SequentialRecordingsTableSimultaneousRecordings = Field(..., description="""A reference to one or more rows in the SimultaneousRecordingsTable table.""") + simultaneous_recordings_index: SequentialRecordingsTableSimultaneousRecordingsIndex = Field(..., description="""Index dataset for the simultaneous_recordings column.""") + stimulus_type: Optional[List[str]] = Field(default_factory=list, description="""The type of stimulus used for the sequential recording.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class NWBFileGeneralIntracellularEphysRepetitions(RepetitionsTable): + """ + A table for grouping different sequential intracellular recordings together. With each SequentialRecording typically representing a particular type of stimulus, the RepetitionsTable table is typically used to group sets of stimuli applied in sequence. + """ + sequential_recordings: RepetitionsTableSequentialRecordings = Field(..., description="""A reference to one or more rows in the SequentialRecordingsTable table.""") + sequential_recordings_index: RepetitionsTableSequentialRecordingsIndex = Field(..., description="""Index dataset for the sequential_recordings column.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class NWBFileGeneralIntracellularEphysExperimentalConditions(ExperimentalConditionsTable): + """ + A table for grouping different intracellular recording repetitions together that belong to the same experimental experimental_conditions. + """ + repetitions: ExperimentalConditionsTableRepetitions = Field(..., description="""A reference to one or more rows in the RepetitionsTable table.""") + repetitions_index: ExperimentalConditionsTableRepetitionsIndex = Field(..., description="""Index dataset for the repetitions column.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class NWBFileGeneralOptogenetics(ConfiguredBaseModel): + """ + Metadata describing optogenetic stimuluation. + """ + OptogeneticStimulusSite: Optional[List[OptogeneticStimulusSite]] = Field(default_factory=list, description="""An optogenetic stimulation site.""") + + +class NWBFileGeneralOptophysiology(ConfiguredBaseModel): + """ + Metadata related to optophysiology. + """ + ImagingPlane: Optional[List[ImagingPlane]] = Field(default_factory=list, description="""An imaging plane.""") + + +class NWBFileIntervals(ConfiguredBaseModel): + """ + Experimental intervals, whether that be logically distinct sub-experiments having a particular scientific goal, trials (see trials subgroup) during an experiment, or epochs (see epochs subgroup) deriving from analysis of data. + """ + epochs: Optional[NWBFileIntervalsEpochs] = Field(None, description="""Divisions in time marking experimental stages or sub-divisions of a single recording session.""") + trials: Optional[NWBFileIntervalsTrials] = Field(None, description="""Repeated experimental events that have a logical grouping.""") + invalid_times: Optional[NWBFileIntervalsInvalidTimes] = Field(None, description="""Time intervals that should be removed from analysis.""") + TimeIntervals: Optional[List[TimeIntervals]] = Field(default_factory=list, description="""Optional additional table(s) for describing other experimental time intervals.""") + + +class NWBFileIntervalsEpochs(TimeIntervals): + """ + Divisions in time marking experimental stages or sub-divisions of a single recording session. + """ + start_time: Optional[List[float]] = Field(default_factory=list, description="""Start time of epoch, in seconds.""") + stop_time: Optional[List[float]] = Field(default_factory=list, description="""Stop time of epoch, in seconds.""") + tags: Optional[List[str]] = Field(default_factory=list, description="""User-defined tags that identify or categorize events.""") + tags_index: Optional[TimeIntervalsTagsIndex] = Field(None, description="""Index for tags.""") + timeseries: Optional[TimeIntervalsTimeseries] = Field(None, description="""An index into a TimeSeries object.""") + timeseries_index: Optional[TimeIntervalsTimeseriesIndex] = Field(None, description="""Index for timeseries.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class NWBFileIntervalsTrials(TimeIntervals): + """ + Repeated experimental events that have a logical grouping. + """ + start_time: Optional[List[float]] = Field(default_factory=list, description="""Start time of epoch, in seconds.""") + stop_time: Optional[List[float]] = Field(default_factory=list, description="""Stop time of epoch, in seconds.""") + tags: Optional[List[str]] = Field(default_factory=list, description="""User-defined tags that identify or categorize events.""") + tags_index: Optional[TimeIntervalsTagsIndex] = Field(None, description="""Index for tags.""") + timeseries: Optional[TimeIntervalsTimeseries] = Field(None, description="""An index into a TimeSeries object.""") + timeseries_index: Optional[TimeIntervalsTimeseriesIndex] = Field(None, description="""Index for timeseries.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class NWBFileIntervalsInvalidTimes(TimeIntervals): + """ + Time intervals that should be removed from analysis. + """ + start_time: Optional[List[float]] = Field(default_factory=list, description="""Start time of epoch, in seconds.""") + stop_time: Optional[List[float]] = Field(default_factory=list, description="""Stop time of epoch, in seconds.""") + tags: Optional[List[str]] = Field(default_factory=list, description="""User-defined tags that identify or categorize events.""") + tags_index: Optional[TimeIntervalsTagsIndex] = Field(None, description="""Index for tags.""") + timeseries: Optional[TimeIntervalsTimeseries] = Field(None, description="""An index into a TimeSeries object.""") + timeseries_index: Optional[TimeIntervalsTimeseriesIndex] = Field(None, description="""Index for timeseries.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class NWBFileUnits(Units): + """ + Data about sorted spike units. + """ + spike_times_index: Optional[UnitsSpikeTimesIndex] = Field(None, description="""Index into the spike_times dataset.""") + spike_times: Optional[UnitsSpikeTimes] = Field(None, description="""Spike times for each unit in seconds.""") + obs_intervals_index: Optional[UnitsObsIntervalsIndex] = Field(None, description="""Index into the obs_intervals dataset.""") + obs_intervals: Optional[UnitsObsIntervals] = Field(None, description="""Observation intervals for each unit.""") + electrodes_index: Optional[UnitsElectrodesIndex] = Field(None, description="""Index into electrodes.""") + electrodes: Optional[UnitsElectrodes] = Field(None, description="""Electrode that each spike unit came from, specified using a DynamicTableRegion.""") + electrode_group: Optional[List[ElectrodeGroup]] = Field(default_factory=list, description="""Electrode group that each spike unit came from.""") + waveform_mean: Optional[UnitsWaveformMean] = Field(None, description="""Spike waveform mean for each spike unit.""") + waveform_sd: Optional[UnitsWaveformSd] = Field(None, description="""Spike waveform standard deviation for each spike unit.""") + waveforms: Optional[UnitsWaveforms] = Field(None, description="""Individual waveforms for each spike on each electrode. This is a doubly indexed column. The 'waveforms_index' column indexes which waveforms in this column belong to the same spike event for a given unit, where each waveform was recorded from a different electrode. The 'waveforms_index_index' column indexes the 'waveforms_index' column to indicate which spike events belong to a given unit. For example, if the 'waveforms_index_index' column has values [2, 5, 6], then the first 2 elements of the 'waveforms_index' column correspond to the 2 spike events of the first unit, the next 3 elements of the 'waveforms_index' column correspond to the 3 spike events of the second unit, and the next 1 element of the 'waveforms_index' column corresponds to the 1 spike event of the third unit. If the 'waveforms_index' column has values [3, 6, 8, 10, 12, 13], then the first 3 elements of the 'waveforms' column contain the 3 spike waveforms that were recorded from 3 different electrodes for the first spike time of the first unit. See https://nwb-schema.readthedocs.io/en/stable/format_description.html#doubly-ragged-arrays for a graphical representation of this example. When there is only one electrode for each unit (i.e., each spike time is associated with a single waveform), then the 'waveforms_index' column will have values 1, 2, ..., N, where N is the number of spike events. The number of electrodes for each spike event should be the same within a given unit. The 'electrodes' column should be used to indicate which electrodes are associated with each unit, and the order of the waveforms within a given unit x spike event should be in the same order as the electrodes referenced in the 'electrodes' column of this table. The number of samples for each waveform must be the same.""") + waveforms_index: Optional[UnitsWaveformsIndex] = Field(None, description="""Index into the waveforms dataset. One value for every spike event. See 'waveforms' for more detail.""") + waveforms_index_index: Optional[UnitsWaveformsIndexIndex] = Field(None, description="""Index into the waveforms_index dataset. One value for every unit (row in the table). See 'waveforms' for more detail.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class SubjectAge(ConfiguredBaseModel): + """ + Age of subject. Can be supplied instead of 'date_of_birth'. + """ + reference: Optional[str] = Field(None, description="""Age is with reference to this event. Can be 'birth' or 'gestational'. If reference is omitted, 'birth' is implied.""") + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +NWBFileFileCreateDate.update_forward_refs() +NWBFileAcquisition.update_forward_refs() +NWBFileAnalysis.update_forward_refs() +NWBFileScratch.update_forward_refs() +NWBFileProcessing.update_forward_refs() +NWBFileStimulus.update_forward_refs() +NWBFileStimulusPresentation.update_forward_refs() +NWBFileStimulusTemplates.update_forward_refs() +NWBFileGeneral.update_forward_refs() +NWBFileGeneralExperimenter.update_forward_refs() +NWBFileGeneralKeywords.update_forward_refs() +NWBFileGeneralRelatedPublications.update_forward_refs() +NWBFileGeneralSourceScript.update_forward_refs() +NWBFileGeneralDevices.update_forward_refs() +NWBFileGeneralSubject.update_forward_refs() +NWBFileGeneralExtracellularEphys.update_forward_refs() +NWBFileGeneralExtracellularEphysElectrodes.update_forward_refs() +NWBFileGeneralIntracellularEphys.update_forward_refs() +NWBFileGeneralIntracellularEphysSweepTable.update_forward_refs() +NWBFileGeneralIntracellularEphysIntracellularRecordings.update_forward_refs() +NWBFileGeneralIntracellularEphysSimultaneousRecordings.update_forward_refs() +NWBFileGeneralIntracellularEphysSequentialRecordings.update_forward_refs() +NWBFileGeneralIntracellularEphysRepetitions.update_forward_refs() +NWBFileGeneralIntracellularEphysExperimentalConditions.update_forward_refs() +NWBFileGeneralOptogenetics.update_forward_refs() +NWBFileGeneralOptophysiology.update_forward_refs() +NWBFileIntervals.update_forward_refs() +NWBFileIntervalsEpochs.update_forward_refs() +NWBFileIntervalsTrials.update_forward_refs() +NWBFileIntervalsInvalidTimes.update_forward_refs() +NWBFileUnits.update_forward_refs() +SubjectAge.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_icephys.py b/nwb_linkml/models/core_nwb_icephys.py new file mode 100644 index 0000000..d48d914 --- /dev/null +++ b/nwb_linkml/models/core_nwb_icephys.py @@ -0,0 +1,327 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .core_nwb_icephys_include import ( + IntracellularRecordingsTableResponses, + VoltageClampSeriesResistanceCompBandwidth, + RepetitionsTableSequentialRecordingsIndex, + ExperimentalConditionsTableRepetitionsIndex, + SequentialRecordingsTableSimultaneousRecordingsIndex, + IntracellularResponsesTableResponse, + VoltageClampSeriesWholeCellCapacitanceComp, + CurrentClampStimulusSeriesData, + IntracellularRecordingsTableElectrodes, + RepetitionsTableSequentialRecordings, + VoltageClampSeriesCapacitanceSlow, + IntracellularStimuliTableStimulus, + VoltageClampSeriesWholeCellSeriesResistanceComp, + VoltageClampSeriesData, + ExperimentalConditionsTableRepetitions, + PatchClampSeriesData, + VoltageClampSeriesResistanceCompPrediction, + IntracellularRecordingsTableStimuli, + CurrentClampSeriesData, + SimultaneousRecordingsTableRecordingsIndex, + SequentialRecordingsTableSimultaneousRecordings, + VoltageClampStimulusSeriesData, + VoltageClampSeriesResistanceCompCorrection, + SweepTableSeriesIndex, + VoltageClampSeriesCapacitanceFast, + SimultaneousRecordingsTableRecordings +) + +from .core_nwb_base import ( + TimeSeries, + NWBContainer, + DynamicTable +) + +from .hdmf_common_table import ( + AlignedDynamicTable +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class PatchClampSeries(TimeSeries): + """ + An abstract base class for patch-clamp data - stimulus or response, current or voltage. + """ + stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") + sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") + data: PatchClampSeriesData = Field(..., description="""Recorded voltage or current.""") + gain: Optional[float] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + +class CurrentClampSeries(PatchClampSeries): + """ + Voltage data from an intracellular current-clamp recording. A corresponding CurrentClampStimulusSeries (stored separately as a stimulus) is used to store the current injected. + """ + data: CurrentClampSeriesData = Field(..., description="""Recorded voltage.""") + bias_current: Optional[float] = Field(None, description="""Bias current, in amps.""") + bridge_balance: Optional[float] = Field(None, description="""Bridge balance, in ohms.""") + capacitance_compensation: Optional[float] = Field(None, description="""Capacitance compensation, in farads.""") + stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") + sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") + gain: Optional[float] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + +class IZeroClampSeries(CurrentClampSeries): + """ + Voltage data from an intracellular recording when all current and amplifier settings are off (i.e., CurrentClampSeries fields will be zero). There is no CurrentClampStimulusSeries associated with an IZero series because the amplifier is disconnected and no stimulus can reach the cell. + """ + stimulus_description: Optional[str] = Field(None, description="""An IZeroClampSeries has no stimulus, so this attribute is automatically set to \"N/A\"""") + bias_current: float = Field(..., description="""Bias current, in amps, fixed to 0.0.""") + bridge_balance: float = Field(..., description="""Bridge balance, in ohms, fixed to 0.0.""") + capacitance_compensation: float = Field(..., description="""Capacitance compensation, in farads, fixed to 0.0.""") + data: CurrentClampSeriesData = Field(..., description="""Recorded voltage.""") + sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") + gain: Optional[float] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + +class CurrentClampStimulusSeries(PatchClampSeries): + """ + Stimulus current applied during current clamp recording. + """ + data: CurrentClampStimulusSeriesData = Field(..., description="""Stimulus current applied.""") + stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") + sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") + gain: Optional[float] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + +class VoltageClampSeries(PatchClampSeries): + """ + Current data from an intracellular voltage-clamp recording. A corresponding VoltageClampStimulusSeries (stored separately as a stimulus) is used to store the voltage injected. + """ + data: VoltageClampSeriesData = Field(..., description="""Recorded current.""") + capacitance_fast: Optional[VoltageClampSeriesCapacitanceFast] = Field(None, description="""Fast capacitance, in farads.""") + capacitance_slow: Optional[VoltageClampSeriesCapacitanceSlow] = Field(None, description="""Slow capacitance, in farads.""") + resistance_comp_bandwidth: Optional[VoltageClampSeriesResistanceCompBandwidth] = Field(None, description="""Resistance compensation bandwidth, in hertz.""") + resistance_comp_correction: Optional[VoltageClampSeriesResistanceCompCorrection] = Field(None, description="""Resistance compensation correction, in percent.""") + resistance_comp_prediction: Optional[VoltageClampSeriesResistanceCompPrediction] = Field(None, description="""Resistance compensation prediction, in percent.""") + whole_cell_capacitance_comp: Optional[VoltageClampSeriesWholeCellCapacitanceComp] = Field(None, description="""Whole cell capacitance compensation, in farads.""") + whole_cell_series_resistance_comp: Optional[VoltageClampSeriesWholeCellSeriesResistanceComp] = Field(None, description="""Whole cell series resistance compensation, in ohms.""") + stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") + sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") + gain: Optional[float] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + +class VoltageClampStimulusSeries(PatchClampSeries): + """ + Stimulus voltage applied during a voltage clamp recording. + """ + data: VoltageClampStimulusSeriesData = Field(..., description="""Stimulus voltage applied.""") + stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""") + sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""") + gain: Optional[float] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""") + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + +class IntracellularElectrode(NWBContainer): + """ + An intracellular electrode and its metadata. + """ + cell_id: Optional[str] = Field(None, description="""unique ID of the cell""") + description: str = Field(..., description="""Description of electrode (e.g., whole-cell, sharp, etc.).""") + filtering: Optional[str] = Field(None, description="""Electrode specific filtering.""") + initial_access_resistance: Optional[str] = Field(None, description="""Initial access resistance.""") + location: Optional[str] = Field(None, description="""Location of the electrode. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible.""") + resistance: Optional[str] = Field(None, description="""Electrode resistance, in ohms.""") + seal: Optional[str] = Field(None, description="""Information about seal used for recording.""") + slice: Optional[str] = Field(None, description="""Information about slice used for recording.""") + + +class SweepTable(DynamicTable): + """ + [DEPRECATED] Table used to group different PatchClampSeries. SweepTable is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable tables. Additional SequentialRecordingsTable, RepetitionsTable, and ExperimentalConditions tables provide enhanced support for experiment metadata. + """ + sweep_number: Optional[List[int]] = Field(default_factory=list, description="""Sweep number of the PatchClampSeries in that row.""") + series: Optional[List[PatchClampSeries]] = Field(default_factory=list, description="""The PatchClampSeries with the sweep number in that row.""") + series_index: SweepTableSeriesIndex = Field(..., description="""Index for series.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class IntracellularElectrodesTable(DynamicTable): + """ + Table for storing intracellular electrode related metadata. + """ + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + electrode: Optional[List[IntracellularElectrode]] = Field(default_factory=list, description="""Column for storing the reference to the intracellular electrode.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class IntracellularStimuliTable(DynamicTable): + """ + Table for storing intracellular stimulus related metadata. + """ + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + stimulus: IntracellularStimuliTableStimulus = Field(..., description="""Column storing the reference to the recorded stimulus for the recording (rows).""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class IntracellularResponsesTable(DynamicTable): + """ + Table for storing intracellular response related metadata. + """ + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + response: IntracellularResponsesTableResponse = Field(..., description="""Column storing the reference to the recorded response for the recording (rows)""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class IntracellularRecordingsTable(AlignedDynamicTable): + """ + A table to group together a stimulus and response from a single electrode and a single simultaneous recording. Each row in the table represents a single recording consisting typically of a stimulus and a corresponding response. In some cases, however, only a stimulus or a response is recorded as part of an experiment. In this case, both the stimulus and response will point to the same TimeSeries while the idx_start and count of the invalid column will be set to -1, thus, indicating that no values have been recorded for the stimulus or response, respectively. Note, a recording MUST contain at least a stimulus or a response. Typically the stimulus and response are PatchClampSeries. However, the use of AD/DA channels that are not associated to an electrode is also common in intracellular electrophysiology, in which case other TimeSeries may be used. + """ + description: Optional[str] = Field(None, description="""Description of the contents of this table. Inherited from AlignedDynamicTable and overwritten here to fix the value of the attribute.""") + electrodes: IntracellularRecordingsTableElectrodes = Field(..., description="""Table for storing intracellular electrode related metadata.""") + stimuli: IntracellularRecordingsTableStimuli = Field(..., description="""Table for storing intracellular stimulus related metadata.""") + responses: IntracellularRecordingsTableResponses = Field(..., description="""Table for storing intracellular response related metadata.""") + categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") + DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class SimultaneousRecordingsTable(DynamicTable): + """ + A table for grouping different intracellular recordings from the IntracellularRecordingsTable table together that were recorded simultaneously from different electrodes. + """ + recordings: SimultaneousRecordingsTableRecordings = Field(..., description="""A reference to one or more rows in the IntracellularRecordingsTable table.""") + recordings_index: SimultaneousRecordingsTableRecordingsIndex = Field(..., description="""Index dataset for the recordings column.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class SequentialRecordingsTable(DynamicTable): + """ + A table for grouping different sequential recordings from the SimultaneousRecordingsTable table together. This is typically used to group together sequential recordings where a sequence of stimuli of the same type with varying parameters have been presented in a sequence. + """ + simultaneous_recordings: SequentialRecordingsTableSimultaneousRecordings = Field(..., description="""A reference to one or more rows in the SimultaneousRecordingsTable table.""") + simultaneous_recordings_index: SequentialRecordingsTableSimultaneousRecordingsIndex = Field(..., description="""Index dataset for the simultaneous_recordings column.""") + stimulus_type: Optional[List[str]] = Field(default_factory=list, description="""The type of stimulus used for the sequential recording.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class RepetitionsTable(DynamicTable): + """ + A table for grouping different sequential intracellular recordings together. With each SequentialRecording typically representing a particular type of stimulus, the RepetitionsTable table is typically used to group sets of stimuli applied in sequence. + """ + sequential_recordings: RepetitionsTableSequentialRecordings = Field(..., description="""A reference to one or more rows in the SequentialRecordingsTable table.""") + sequential_recordings_index: RepetitionsTableSequentialRecordingsIndex = Field(..., description="""Index dataset for the sequential_recordings column.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class ExperimentalConditionsTable(DynamicTable): + """ + A table for grouping different intracellular recording repetitions together that belong to the same experimental condition. + """ + repetitions: ExperimentalConditionsTableRepetitions = Field(..., description="""A reference to one or more rows in the RepetitionsTable table.""") + repetitions_index: ExperimentalConditionsTableRepetitionsIndex = Field(..., description="""Index dataset for the repetitions column.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +PatchClampSeries.update_forward_refs() +CurrentClampSeries.update_forward_refs() +IZeroClampSeries.update_forward_refs() +CurrentClampStimulusSeries.update_forward_refs() +VoltageClampSeries.update_forward_refs() +VoltageClampStimulusSeries.update_forward_refs() +IntracellularElectrode.update_forward_refs() +SweepTable.update_forward_refs() +IntracellularElectrodesTable.update_forward_refs() +IntracellularStimuliTable.update_forward_refs() +IntracellularResponsesTable.update_forward_refs() +IntracellularRecordingsTable.update_forward_refs() +SimultaneousRecordingsTable.update_forward_refs() +SequentialRecordingsTable.update_forward_refs() +RepetitionsTable.update_forward_refs() +ExperimentalConditionsTable.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_icephys_include.py b/nwb_linkml/models/core_nwb_icephys_include.py new file mode 100644 index 0000000..a014c3c --- /dev/null +++ b/nwb_linkml/models/core_nwb_icephys_include.py @@ -0,0 +1,293 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .hdmf_common_table import ( + DynamicTableRegion, + VectorIndex +) + +from .core_nwb_base import ( + TimeSeriesReferenceVectorData +) + +from .core_nwb_icephys import ( + SimultaneousRecordingsTable, + IntracellularElectrodesTable, + IntracellularResponsesTable, + SequentialRecordingsTable, + IntracellularRecordingsTable, + IntracellularStimuliTable, + RepetitionsTable +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class PatchClampSeriesData(ConfiguredBaseModel): + """ + Recorded voltage or current. + """ + unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") + data: List[float] = Field(default_factory=list, description="""Recorded voltage or current.""") + + +class CurrentClampSeriesData(ConfiguredBaseModel): + """ + Recorded voltage. + """ + unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'volts'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") + + +class CurrentClampStimulusSeriesData(ConfiguredBaseModel): + """ + Stimulus current applied. + """ + unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'amperes'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") + + +class VoltageClampSeriesData(ConfiguredBaseModel): + """ + Recorded current. + """ + unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'amperes'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") + + +class VoltageClampSeriesCapacitanceFast(ConfiguredBaseModel): + """ + Fast capacitance, in farads. + """ + unit: Optional[str] = Field(None, description="""Unit of measurement for capacitance_fast, which is fixed to 'farads'.""") + + +class VoltageClampSeriesCapacitanceSlow(ConfiguredBaseModel): + """ + Slow capacitance, in farads. + """ + unit: Optional[str] = Field(None, description="""Unit of measurement for capacitance_fast, which is fixed to 'farads'.""") + + +class VoltageClampSeriesResistanceCompBandwidth(ConfiguredBaseModel): + """ + Resistance compensation bandwidth, in hertz. + """ + unit: Optional[str] = Field(None, description="""Unit of measurement for resistance_comp_bandwidth, which is fixed to 'hertz'.""") + + +class VoltageClampSeriesResistanceCompCorrection(ConfiguredBaseModel): + """ + Resistance compensation correction, in percent. + """ + unit: Optional[str] = Field(None, description="""Unit of measurement for resistance_comp_correction, which is fixed to 'percent'.""") + + +class VoltageClampSeriesResistanceCompPrediction(ConfiguredBaseModel): + """ + Resistance compensation prediction, in percent. + """ + unit: Optional[str] = Field(None, description="""Unit of measurement for resistance_comp_prediction, which is fixed to 'percent'.""") + + +class VoltageClampSeriesWholeCellCapacitanceComp(ConfiguredBaseModel): + """ + Whole cell capacitance compensation, in farads. + """ + unit: Optional[str] = Field(None, description="""Unit of measurement for whole_cell_capacitance_comp, which is fixed to 'farads'.""") + + +class VoltageClampSeriesWholeCellSeriesResistanceComp(ConfiguredBaseModel): + """ + Whole cell series resistance compensation, in ohms. + """ + unit: Optional[str] = Field(None, description="""Unit of measurement for whole_cell_series_resistance_comp, which is fixed to 'ohms'.""") + + +class VoltageClampStimulusSeriesData(ConfiguredBaseModel): + """ + Stimulus voltage applied. + """ + unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'volts'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""") + + +class SweepTableSeriesIndex(VectorIndex): + """ + Index for series. + """ + target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class IntracellularStimuliTableStimulus(TimeSeriesReferenceVectorData): + """ + Column storing the reference to the recorded stimulus for the recording (rows). + """ + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class IntracellularResponsesTableResponse(TimeSeriesReferenceVectorData): + """ + Column storing the reference to the recorded response for the recording (rows) + """ + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class IntracellularRecordingsTableElectrodes(IntracellularElectrodesTable): + """ + Table for storing intracellular electrode related metadata. + """ + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + electrode: Optional[List[IntracellularElectrode]] = Field(default_factory=list, description="""Column for storing the reference to the intracellular electrode.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class IntracellularRecordingsTableStimuli(IntracellularStimuliTable): + """ + Table for storing intracellular stimulus related metadata. + """ + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + stimulus: IntracellularStimuliTableStimulus = Field(..., description="""Column storing the reference to the recorded stimulus for the recording (rows).""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class IntracellularRecordingsTableResponses(IntracellularResponsesTable): + """ + Table for storing intracellular response related metadata. + """ + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + response: IntracellularResponsesTableResponse = Field(..., description="""Column storing the reference to the recorded response for the recording (rows)""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class SimultaneousRecordingsTableRecordings(DynamicTableRegion): + """ + A reference to one or more rows in the IntracellularRecordingsTable table. + """ + table: Optional[IntracellularRecordingsTable] = Field(None, description="""Reference to the IntracellularRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""") + description: Optional[str] = Field(None, description="""Description of what this table region points to.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class SimultaneousRecordingsTableRecordingsIndex(VectorIndex): + """ + Index dataset for the recordings column. + """ + target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class SequentialRecordingsTableSimultaneousRecordings(DynamicTableRegion): + """ + A reference to one or more rows in the SimultaneousRecordingsTable table. + """ + table: Optional[SimultaneousRecordingsTable] = Field(None, description="""Reference to the SimultaneousRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""") + description: Optional[str] = Field(None, description="""Description of what this table region points to.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class SequentialRecordingsTableSimultaneousRecordingsIndex(VectorIndex): + """ + Index dataset for the simultaneous_recordings column. + """ + target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class RepetitionsTableSequentialRecordings(DynamicTableRegion): + """ + A reference to one or more rows in the SequentialRecordingsTable table. + """ + table: Optional[SequentialRecordingsTable] = Field(None, description="""Reference to the SequentialRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""") + description: Optional[str] = Field(None, description="""Description of what this table region points to.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class RepetitionsTableSequentialRecordingsIndex(VectorIndex): + """ + Index dataset for the sequential_recordings column. + """ + target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class ExperimentalConditionsTableRepetitions(DynamicTableRegion): + """ + A reference to one or more rows in the RepetitionsTable table. + """ + table: Optional[RepetitionsTable] = Field(None, description="""Reference to the RepetitionsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""") + description: Optional[str] = Field(None, description="""Description of what this table region points to.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class ExperimentalConditionsTableRepetitionsIndex(VectorIndex): + """ + Index dataset for the repetitions column. + """ + target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +PatchClampSeriesData.update_forward_refs() +CurrentClampSeriesData.update_forward_refs() +CurrentClampStimulusSeriesData.update_forward_refs() +VoltageClampSeriesData.update_forward_refs() +VoltageClampSeriesCapacitanceFast.update_forward_refs() +VoltageClampSeriesCapacitanceSlow.update_forward_refs() +VoltageClampSeriesResistanceCompBandwidth.update_forward_refs() +VoltageClampSeriesResistanceCompCorrection.update_forward_refs() +VoltageClampSeriesResistanceCompPrediction.update_forward_refs() +VoltageClampSeriesWholeCellCapacitanceComp.update_forward_refs() +VoltageClampSeriesWholeCellSeriesResistanceComp.update_forward_refs() +VoltageClampStimulusSeriesData.update_forward_refs() +SweepTableSeriesIndex.update_forward_refs() +IntracellularStimuliTableStimulus.update_forward_refs() +IntracellularResponsesTableResponse.update_forward_refs() +IntracellularRecordingsTableElectrodes.update_forward_refs() +IntracellularRecordingsTableStimuli.update_forward_refs() +IntracellularRecordingsTableResponses.update_forward_refs() +SimultaneousRecordingsTableRecordings.update_forward_refs() +SimultaneousRecordingsTableRecordingsIndex.update_forward_refs() +SequentialRecordingsTableSimultaneousRecordings.update_forward_refs() +SequentialRecordingsTableSimultaneousRecordingsIndex.update_forward_refs() +RepetitionsTableSequentialRecordings.update_forward_refs() +RepetitionsTableSequentialRecordingsIndex.update_forward_refs() +ExperimentalConditionsTableRepetitions.update_forward_refs() +ExperimentalConditionsTableRepetitionsIndex.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_image.py b/nwb_linkml/models/core_nwb_image.py new file mode 100644 index 0000000..7c9c9f4 --- /dev/null +++ b/nwb_linkml/models/core_nwb_image.py @@ -0,0 +1,152 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +# from .core_nwb_image_include import ( +# ImageSeriesData, +# OpticalSeriesFieldOfView, +# RGBAImageArray, +# IndexSeriesData, +# ImageSeriesDimension, +# OpticalSeriesData, +# ImageSeriesExternalFile, +# GrayscaleImageArray, +# RGBImageArray +# ) + +from .core_nwb_base import ( + Image, + TimeSeries +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class GrayscaleImage(ConfiguredBaseModel): + """ + A grayscale image. + """ + array: Optional[NDArray[Shape["* x, * y"], Number]] = Field(None) + resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") + description: Optional[str] = Field(None, description="""Description of the image.""") + + +class RGBImage(Image): + """ + A color image. + """ + array: Optional[NDArray[Shape["* x, * y, 3 r_g_b"], Number]] = Field(None) + resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") + description: Optional[str] = Field(None, description="""Description of the image.""") + + +class RGBAImage(Image): + """ + A color image with transparency. + """ + array: Optional[NDArray[Shape["* x, * y, 4 r_g_b_a"], Number]] = Field(None) + resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""") + description: Optional[str] = Field(None, description="""Description of the image.""") + +# +# class ImageSeries(TimeSeries): +# """ +# General image data that is common between acquisition and stimulus time series. Sometimes the image data is stored in the file in a raw format while other times it will be stored as a series of external image files in the host file system. The data field will either be binary data, if the data is stored in the NWB file, or empty, if the data is stored in an external image stack. [frame][x][y] or [frame][x][y][z]. +# """ +# data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") +# dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") +# external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") +# format: Optional[str] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") +# description: Optional[str] = Field(None, description="""Description of the time series.""") +# comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") +# starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") +# timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") +# control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") +# control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") +# sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") +# +# +# class ImageMaskSeries(ImageSeries): +# """ +# An alpha mask that is applied to a presented visual stimulus. The 'data' array contains an array of mask values that are applied to the displayed image. Mask values are stored as RGBA. Mask can vary with time. The timestamps array indicates the starting time of a mask, and that mask pattern continues until it's explicitly changed. +# """ +# data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") +# dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") +# external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") +# format: Optional[str] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") +# description: Optional[str] = Field(None, description="""Description of the time series.""") +# comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") +# starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") +# timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") +# control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") +# control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") +# sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") +# +# +# class OpticalSeries(ImageSeries): +# """ +# Image data that is presented or recorded. A stimulus template movie will be stored only as an image. When the image is presented as stimulus, additional data is required, such as field of view (e.g., how much of the visual field the image covers, or how what is the area of the target being imaged). If the OpticalSeries represents acquired imaging data, orientation is also important. +# """ +# distance: Optional[float] = Field(None, description="""Distance from camera/monitor to target/eye.""") +# field_of_view: Optional[OpticalSeriesFieldOfView] = Field(None, description="""Width, height and depth of image, or imaged area, in meters.""") +# data: OpticalSeriesData = Field(..., description="""Images presented to subject, either grayscale or RGB""") +# orientation: Optional[str] = Field(None, description="""Description of image relative to some reference frame (e.g., which way is up). Must also specify frame of reference.""") +# dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") +# external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") +# format: Optional[str] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") +# description: Optional[str] = Field(None, description="""Description of the time series.""") +# comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") +# starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") +# timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") +# control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") +# control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") +# sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") +# +# +# class IndexSeries(TimeSeries): +# """ +# Stores indices to image frames stored in an ImageSeries. The purpose of the IndexSeries is to allow a static image stack to be stored in an Images object, and the images in the stack to be referenced out-of-order. This can be for the display of individual images, or of movie segments (as a movie is simply a series of images). The data field stores the index of the frame in the referenced Images object, and the timestamps array indicates when that image was displayed. +# """ +# data: IndexSeriesData = Field(..., description="""Index of the image (using zero-indexing) in the linked Images object.""") +# description: Optional[str] = Field(None, description="""Description of the time series.""") +# comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") +# starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") +# timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") +# control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") +# control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") +# sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") +# +# +# +# # Update forward refs +# # see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +# GrayscaleImage.update_forward_refs() +# RGBImage.update_forward_refs() +# RGBAImage.update_forward_refs() +# ImageSeries.update_forward_refs() +# ImageMaskSeries.update_forward_refs() +# OpticalSeries.update_forward_refs() +# IndexSeries.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_image_include.py b/nwb_linkml/models/core_nwb_image_include.py new file mode 100644 index 0000000..bc3a474 --- /dev/null +++ b/nwb_linkml/models/core_nwb_image_include.py @@ -0,0 +1,138 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .nwb_language import ( + Arraylike +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class GrayscaleImageArray(Arraylike): + + x: Optional[float] = Field(None) + y: Optional[float] = Field(None) + + +class RGBImageArray(Arraylike): + + x: Optional[float] = Field(None) + y: Optional[float] = Field(None) + r_g_b: Optional[float] = Field(None) + + +class RGBAImageArray(Arraylike): + + x: Optional[float] = Field(None) + y: Optional[float] = Field(None) + r_g_b_a: Optional[float] = Field(None) + + +class ImageSeriesData(ConfiguredBaseModel): + """ + Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array. + """ + array: Optional[NDArray[Shape["* frame, * x, * y, * z"], Number]] = Field(None) + + +class ImageSeriesDataArray(Arraylike): + + frame: float = Field(...) + x: float = Field(...) + y: float = Field(...) + z: Optional[float] = Field(None) + + +class ImageSeriesDimension(ConfiguredBaseModel): + """ + Number of pixels on x, y, (and z) axes. + """ + dimension: Optional[List[int]] = Field(default_factory=list, description="""Number of pixels on x, y, (and z) axes.""") + + +class ImageSeriesExternalFile(ConfiguredBaseModel): + """ + Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file. + """ + starting_frame: Optional[int] = Field(None, description="""Each external image may contain one or more consecutive frames of the full ImageSeries. This attribute serves as an index to indicate which frames each file contains, to facilitate random access. The 'starting_frame' attribute, hence, contains a list of frame numbers within the full ImageSeries of the first frame of each file listed in the parent 'external_file' dataset. Zero-based indexing is used (hence, the first element will always be zero). For example, if the 'external_file' dataset has three paths to files and the first file has 5 frames, the second file has 10 frames, and the third file has 20 frames, then this attribute will have values [0, 5, 15]. If there is a single external file that holds all of the frames of the ImageSeries (and so there is a single element in the 'external_file' dataset), then this attribute should have value [0].""") + external_file: Optional[List[str]] = Field(default_factory=list, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") + + +class OpticalSeriesFieldOfView(ConfiguredBaseModel): + """ + Width, height and depth of image, or imaged area, in meters. + """ + array: Optional[NDArray[Shape["2 width_height, 3 width_height_depth"], Float32]] = Field(None) + + +class OpticalSeriesFieldOfViewArray(Arraylike): + + width_height: Optional[float] = Field(None) + width_height_depth: Optional[float] = Field(None) + + +class OpticalSeriesData(ConfiguredBaseModel): + """ + Images presented to subject, either grayscale or RGB + """ + array: Optional[NDArray[Shape["* frame, * x, * y, 3 r_g_b"], Number]] = Field(None) + + +class OpticalSeriesDataArray(Arraylike): + + frame: float = Field(...) + x: float = Field(...) + y: float = Field(...) + r_g_b: Optional[float] = Field(None) + + +class IndexSeriesData(ConfiguredBaseModel): + """ + Index of the image (using zero-indexing) in the linked Images object. + """ + conversion: Optional[float] = Field(None, description="""This field is unused by IndexSeries.""") + resolution: Optional[float] = Field(None, description="""This field is unused by IndexSeries.""") + offset: Optional[float] = Field(None, description="""This field is unused by IndexSeries.""") + unit: Optional[str] = Field(None, description="""This field is unused by IndexSeries and has the value N/A.""") + data: List[int] = Field(default_factory=list, description="""Index of the image (using zero-indexing) in the linked Images object.""") + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +GrayscaleImageArray.update_forward_refs() +RGBImageArray.update_forward_refs() +RGBAImageArray.update_forward_refs() +ImageSeriesData.update_forward_refs() +ImageSeriesDataArray.update_forward_refs() +ImageSeriesDimension.update_forward_refs() +ImageSeriesExternalFile.update_forward_refs() +OpticalSeriesFieldOfView.update_forward_refs() +OpticalSeriesFieldOfViewArray.update_forward_refs() +OpticalSeriesData.update_forward_refs() +OpticalSeriesDataArray.update_forward_refs() +IndexSeriesData.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_misc.py b/nwb_linkml/models/core_nwb_misc.py new file mode 100644 index 0000000..741df45 --- /dev/null +++ b/nwb_linkml/models/core_nwb_misc.py @@ -0,0 +1,155 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .core_nwb_misc_include import ( + AbstractFeatureSeriesFeatures, + UnitsElectrodesIndex, + UnitsObsIntervalsIndex, + DecompositionSeriesData, + UnitsSpikeTimes, + UnitsWaveformMean, + UnitsWaveformsIndexIndex, + UnitsWaveforms, + UnitsWaveformsIndex, + AnnotationSeriesData, + UnitsObsIntervals, + AbstractFeatureSeriesFeatureUnits, + DecompositionSeriesBands, + UnitsWaveformSd, + UnitsElectrodes, + IntervalSeriesData, + DecompositionSeriesSourceChannels, + AbstractFeatureSeriesData, + UnitsSpikeTimesIndex +) + +from .core_nwb_base import ( + TimeSeries +) + +from .core_nwb_ecephys import ( + ElectrodeGroup +) + +from .hdmf_common_table import ( + DynamicTable +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class AbstractFeatureSeries(TimeSeries): + """ + Abstract features, such as quantitative descriptions of sensory stimuli. The TimeSeries::data field is a 2D array, storing those features (e.g., for visual grating stimulus this might be orientation, spatial frequency and contrast). Null stimuli (eg, uniform gray) can be marked as being an independent feature (eg, 1.0 for gray, 0.0 for actual stimulus) or by storing NaNs for feature values, or through use of the TimeSeries::control fields. A set of features is considered to persist until the next set of features is defined. The final set of features stored should be the null set. This is useful when storing the raw stimulus is impractical. + """ + data: AbstractFeatureSeriesData = Field(..., description="""Values of each feature at each time.""") + feature_units: Optional[AbstractFeatureSeriesFeatureUnits] = Field(None, description="""Units of each feature.""") + features: AbstractFeatureSeriesFeatures = Field(..., description="""Description of the features represented in TimeSeries::data.""") + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + +class AnnotationSeries(TimeSeries): + """ + Stores user annotations made during an experiment. The data[] field stores a text array, and timestamps are stored for each annotation (ie, interval=1). This is largely an alias to a standard TimeSeries storing a text array but that is identifiable as storing annotations in a machine-readable way. + """ + data: AnnotationSeriesData = Field(..., description="""Annotations made during an experiment.""") + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + +class IntervalSeries(TimeSeries): + """ + Stores intervals of data. The timestamps field stores the beginning and end of intervals. The data field stores whether the interval just started (>0 value) or ended (<0 value). Different interval types can be represented in the same series by using multiple key values (eg, 1 for feature A, 2 for feature B, 3 for feature C, etc). The field data stores an 8-bit integer. This is largely an alias of a standard TimeSeries but that is identifiable as representing time intervals in a machine-readable way. + """ + data: IntervalSeriesData = Field(..., description="""Use values >0 if interval started, <0 if interval ended.""") + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + +class DecompositionSeries(TimeSeries): + """ + Spectral analysis of a time series, e.g. of an LFP or a speech signal. + """ + data: DecompositionSeriesData = Field(..., description="""Data decomposed into frequency bands.""") + metric: str = Field(..., description="""The metric used, e.g. phase, amplitude, power.""") + source_channels: Optional[DecompositionSeriesSourceChannels] = Field(None, description="""DynamicTableRegion pointer to the channels that this decomposition series was generated from.""") + bands: DecompositionSeriesBands = Field(..., description="""Table for describing the bands that this series was generated from. There should be one row in this table for each band.""") + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + +class Units(DynamicTable): + """ + Data about spiking units. Event times of observed units (e.g. cell, synapse, etc.) should be concatenated and stored in spike_times. + """ + spike_times_index: Optional[UnitsSpikeTimesIndex] = Field(None, description="""Index into the spike_times dataset.""") + spike_times: Optional[UnitsSpikeTimes] = Field(None, description="""Spike times for each unit in seconds.""") + obs_intervals_index: Optional[UnitsObsIntervalsIndex] = Field(None, description="""Index into the obs_intervals dataset.""") + obs_intervals: Optional[UnitsObsIntervals] = Field(None, description="""Observation intervals for each unit.""") + electrodes_index: Optional[UnitsElectrodesIndex] = Field(None, description="""Index into electrodes.""") + electrodes: Optional[UnitsElectrodes] = Field(None, description="""Electrode that each spike unit came from, specified using a DynamicTableRegion.""") + electrode_group: Optional[List[ElectrodeGroup]] = Field(default_factory=list, description="""Electrode group that each spike unit came from.""") + waveform_mean: Optional[UnitsWaveformMean] = Field(None, description="""Spike waveform mean for each spike unit.""") + waveform_sd: Optional[UnitsWaveformSd] = Field(None, description="""Spike waveform standard deviation for each spike unit.""") + waveforms: Optional[UnitsWaveforms] = Field(None, description="""Individual waveforms for each spike on each electrode. This is a doubly indexed column. The 'waveforms_index' column indexes which waveforms in this column belong to the same spike event for a given unit, where each waveform was recorded from a different electrode. The 'waveforms_index_index' column indexes the 'waveforms_index' column to indicate which spike events belong to a given unit. For example, if the 'waveforms_index_index' column has values [2, 5, 6], then the first 2 elements of the 'waveforms_index' column correspond to the 2 spike events of the first unit, the next 3 elements of the 'waveforms_index' column correspond to the 3 spike events of the second unit, and the next 1 element of the 'waveforms_index' column corresponds to the 1 spike event of the third unit. If the 'waveforms_index' column has values [3, 6, 8, 10, 12, 13], then the first 3 elements of the 'waveforms' column contain the 3 spike waveforms that were recorded from 3 different electrodes for the first spike time of the first unit. See https://nwb-schema.readthedocs.io/en/stable/format_description.html#doubly-ragged-arrays for a graphical representation of this example. When there is only one electrode for each unit (i.e., each spike time is associated with a single waveform), then the 'waveforms_index' column will have values 1, 2, ..., N, where N is the number of spike events. The number of electrodes for each spike event should be the same within a given unit. The 'electrodes' column should be used to indicate which electrodes are associated with each unit, and the order of the waveforms within a given unit x spike event should be in the same order as the electrodes referenced in the 'electrodes' column of this table. The number of samples for each waveform must be the same.""") + waveforms_index: Optional[UnitsWaveformsIndex] = Field(None, description="""Index into the waveforms dataset. One value for every spike event. See 'waveforms' for more detail.""") + waveforms_index_index: Optional[UnitsWaveformsIndexIndex] = Field(None, description="""Index into the waveforms_index dataset. One value for every unit (row in the table). See 'waveforms' for more detail.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +AbstractFeatureSeries.update_forward_refs() +AnnotationSeries.update_forward_refs() +IntervalSeries.update_forward_refs() +DecompositionSeries.update_forward_refs() +Units.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_misc_include.py b/nwb_linkml/models/core_nwb_misc_include.py new file mode 100644 index 0000000..33e78f7 --- /dev/null +++ b/nwb_linkml/models/core_nwb_misc_include.py @@ -0,0 +1,277 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .hdmf_common_table import ( + DynamicTableRegion, + DynamicTable, + VectorIndex, + VectorData +) + +from .nwb_language import ( + Arraylike +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class AbstractFeatureSeriesData(ConfiguredBaseModel): + """ + Values of each feature at each time. + """ + unit: Optional[str] = Field(None, description="""Since there can be different units for different features, store the units in 'feature_units'. The default value for this attribute is \"see 'feature_units'\".""") + array: Optional[NDArray[Shape["* num_times, * num_features"], Number]] = Field(None) + + +class AbstractFeatureSeriesDataArray(Arraylike): + + num_times: float = Field(...) + num_features: Optional[float] = Field(None) + + +class AbstractFeatureSeriesFeatureUnits(ConfiguredBaseModel): + """ + Units of each feature. + """ + feature_units: Optional[List[str]] = Field(default_factory=list, description="""Units of each feature.""") + + +class AbstractFeatureSeriesFeatures(ConfiguredBaseModel): + """ + Description of the features represented in TimeSeries::data. + """ + features: List[str] = Field(default_factory=list, description="""Description of the features represented in TimeSeries::data.""") + + +class AnnotationSeriesData(ConfiguredBaseModel): + """ + Annotations made during an experiment. + """ + resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data. Annotations have no units, so the value is fixed to -1.0.""") + unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Annotations have no units, so the value is fixed to 'n/a'.""") + data: List[str] = Field(default_factory=list, description="""Annotations made during an experiment.""") + + +class IntervalSeriesData(ConfiguredBaseModel): + """ + Use values >0 if interval started, <0 if interval ended. + """ + resolution: Optional[float] = Field(None, description="""Smallest meaningful difference between values in data. Annotations have no units, so the value is fixed to -1.0.""") + unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Annotations have no units, so the value is fixed to 'n/a'.""") + data: List[int] = Field(default_factory=list, description="""Use values >0 if interval started, <0 if interval ended.""") + + +class DecompositionSeriesData(ConfiguredBaseModel): + """ + Data decomposed into frequency bands. + """ + unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion'.""") + array: Optional[NDArray[Shape["* num_times, * num_channels, * num_bands"], Number]] = Field(None) + + +class DecompositionSeriesDataArray(Arraylike): + + num_times: Optional[float] = Field(None) + num_channels: Optional[float] = Field(None) + num_bands: Optional[float] = Field(None) + + +class DecompositionSeriesSourceChannels(DynamicTableRegion): + """ + DynamicTableRegion pointer to the channels that this decomposition series was generated from. + """ + table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") + description: Optional[str] = Field(None, description="""Description of what this table region points to.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class DecompositionSeriesBands(DynamicTable): + """ + Table for describing the bands that this series was generated from. There should be one row in this table for each band. + """ + band_name: Optional[List[str]] = Field(default_factory=list, description="""Name of the band, e.g. theta.""") + band_limits: DecompositionSeriesBandsBandLimits = Field(..., description="""Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center.""") + band_mean: DecompositionSeriesBandsBandMean = Field(..., description="""The mean Gaussian filters, in Hz.""") + band_stdev: DecompositionSeriesBandsBandStdev = Field(..., description="""The standard deviation of Gaussian filters, in Hz.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class DecompositionSeriesBandsBandLimits(VectorData): + """ + Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center. + """ + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class DecompositionSeriesBandsBandMean(VectorData): + """ + The mean Gaussian filters, in Hz. + """ + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class DecompositionSeriesBandsBandStdev(VectorData): + """ + The standard deviation of Gaussian filters, in Hz. + """ + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class UnitsSpikeTimesIndex(VectorIndex): + """ + Index into the spike_times dataset. + """ + target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class UnitsSpikeTimes(VectorData): + """ + Spike times for each unit in seconds. + """ + resolution: Optional[float] = Field(None, description="""The smallest possible difference between two spike times. Usually 1 divided by the acquisition sampling rate from which spike times were extracted, but could be larger if the acquisition time series was downsampled or smaller if the acquisition time series was smoothed/interpolated and it is possible for the spike time to be between samples.""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class UnitsObsIntervalsIndex(VectorIndex): + """ + Index into the obs_intervals dataset. + """ + target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class UnitsObsIntervals(VectorData): + """ + Observation intervals for each unit. + """ + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class UnitsElectrodesIndex(VectorIndex): + """ + Index into electrodes. + """ + target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class UnitsElectrodes(DynamicTableRegion): + """ + Electrode that each spike unit came from, specified using a DynamicTableRegion. + """ + table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") + description: Optional[str] = Field(None, description="""Description of what this table region points to.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class UnitsWaveformMean(VectorData): + """ + Spike waveform mean for each spike unit. + """ + sampling_rate: Optional[float] = Field(None, description="""Sampling rate, in hertz.""") + unit: Optional[str] = Field(None, description="""Unit of measurement. This value is fixed to 'volts'.""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class UnitsWaveformSd(VectorData): + """ + Spike waveform standard deviation for each spike unit. + """ + sampling_rate: Optional[float] = Field(None, description="""Sampling rate, in hertz.""") + unit: Optional[str] = Field(None, description="""Unit of measurement. This value is fixed to 'volts'.""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class UnitsWaveforms(VectorData): + """ + Individual waveforms for each spike on each electrode. This is a doubly indexed column. The 'waveforms_index' column indexes which waveforms in this column belong to the same spike event for a given unit, where each waveform was recorded from a different electrode. The 'waveforms_index_index' column indexes the 'waveforms_index' column to indicate which spike events belong to a given unit. For example, if the 'waveforms_index_index' column has values [2, 5, 6], then the first 2 elements of the 'waveforms_index' column correspond to the 2 spike events of the first unit, the next 3 elements of the 'waveforms_index' column correspond to the 3 spike events of the second unit, and the next 1 element of the 'waveforms_index' column corresponds to the 1 spike event of the third unit. If the 'waveforms_index' column has values [3, 6, 8, 10, 12, 13], then the first 3 elements of the 'waveforms' column contain the 3 spike waveforms that were recorded from 3 different electrodes for the first spike time of the first unit. See https://nwb-schema.readthedocs.io/en/stable/format_description.html#doubly-ragged-arrays for a graphical representation of this example. When there is only one electrode for each unit (i.e., each spike time is associated with a single waveform), then the 'waveforms_index' column will have values 1, 2, ..., N, where N is the number of spike events. The number of electrodes for each spike event should be the same within a given unit. The 'electrodes' column should be used to indicate which electrodes are associated with each unit, and the order of the waveforms within a given unit x spike event should be in the same order as the electrodes referenced in the 'electrodes' column of this table. The number of samples for each waveform must be the same. + """ + sampling_rate: Optional[float] = Field(None, description="""Sampling rate, in hertz.""") + unit: Optional[str] = Field(None, description="""Unit of measurement. This value is fixed to 'volts'.""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class UnitsWaveformsIndex(VectorIndex): + """ + Index into the waveforms dataset. One value for every spike event. See 'waveforms' for more detail. + """ + target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class UnitsWaveformsIndexIndex(VectorIndex): + """ + Index into the waveforms_index dataset. One value for every unit (row in the table). See 'waveforms' for more detail. + """ + target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +AbstractFeatureSeriesData.update_forward_refs() +AbstractFeatureSeriesDataArray.update_forward_refs() +AbstractFeatureSeriesFeatureUnits.update_forward_refs() +AbstractFeatureSeriesFeatures.update_forward_refs() +AnnotationSeriesData.update_forward_refs() +IntervalSeriesData.update_forward_refs() +DecompositionSeriesData.update_forward_refs() +DecompositionSeriesDataArray.update_forward_refs() +DecompositionSeriesSourceChannels.update_forward_refs() +DecompositionSeriesBands.update_forward_refs() +DecompositionSeriesBandsBandLimits.update_forward_refs() +DecompositionSeriesBandsBandMean.update_forward_refs() +DecompositionSeriesBandsBandStdev.update_forward_refs() +UnitsSpikeTimesIndex.update_forward_refs() +UnitsSpikeTimes.update_forward_refs() +UnitsObsIntervalsIndex.update_forward_refs() +UnitsObsIntervals.update_forward_refs() +UnitsElectrodesIndex.update_forward_refs() +UnitsElectrodes.update_forward_refs() +UnitsWaveformMean.update_forward_refs() +UnitsWaveformSd.update_forward_refs() +UnitsWaveforms.update_forward_refs() +UnitsWaveformsIndex.update_forward_refs() +UnitsWaveformsIndexIndex.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_ogen.py b/nwb_linkml/models/core_nwb_ogen.py new file mode 100644 index 0000000..704882d --- /dev/null +++ b/nwb_linkml/models/core_nwb_ogen.py @@ -0,0 +1,67 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .core_nwb_base import ( + NWBContainer, + TimeSeries +) + +from .core_nwb_ogen_include import ( + OptogeneticSeriesData +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class OptogeneticSeries(TimeSeries): + """ + An optogenetic stimulus. + """ + data: OptogeneticSeriesData = Field(..., description="""Applied power for optogenetic stimulus, in watts.""") + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + +class OptogeneticStimulusSite(NWBContainer): + """ + A site of optogenetic stimulation. + """ + description: str = Field(..., description="""Description of stimulation site.""") + excitation_lambda: float = Field(..., description="""Excitation wavelength, in nm.""") + location: str = Field(..., description="""Location of the stimulation site. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible.""") + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +OptogeneticSeries.update_forward_refs() +OptogeneticStimulusSite.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_ogen_include.py b/nwb_linkml/models/core_nwb_ogen_include.py new file mode 100644 index 0000000..357dc55 --- /dev/null +++ b/nwb_linkml/models/core_nwb_ogen_include.py @@ -0,0 +1,42 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class OptogeneticSeriesData(ConfiguredBaseModel): + """ + Applied power for optogenetic stimulus, in watts. + """ + unit: Optional[str] = Field(None, description="""Unit of measurement for data, which is fixed to 'watts'.""") + data: List[float] = Field(default_factory=list, description="""Applied power for optogenetic stimulus, in watts.""") + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +OptogeneticSeriesData.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_ophys.py b/nwb_linkml/models/core_nwb_ophys.py new file mode 100644 index 0000000..909acc2 --- /dev/null +++ b/nwb_linkml/models/core_nwb_ophys.py @@ -0,0 +1,207 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .core_nwb_ophys_include import ( + CorrectedImageStackXyTranslation, + PlaneSegmentationVoxelMaskIndex, + ImagingPlaneOriginCoords, + TwoPhotonSeriesFieldOfView, + RoiResponseSeriesRois, + CorrectedImageStackCorrected, + ImagingPlaneManifold, + PlaneSegmentationImageMask, + PlaneSegmentationReferenceImages, + ImagingPlaneGridSpacing, + RoiResponseSeriesData, + PlaneSegmentationPixelMaskIndex +) + +from .core_nwb_base import ( + TimeSeries, + NWBContainer, + NWBDataInterface +) + +from .hdmf_common_table import ( + DynamicTable +) + +from .core_nwb_image import ( + ImageSeries +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class OnePhotonSeries(ImageSeries): + """ + Image stack recorded over time from 1-photon microscope. + """ + pmt_gain: Optional[float] = Field(None, description="""Photomultiplier gain.""") + scan_line_rate: Optional[float] = Field(None, description="""Lines imaged per second. This is also stored in /general/optophysiology but is kept here as it is useful information for analysis, and so good to be stored w/ the actual data.""") + exposure_time: Optional[float] = Field(None, description="""Exposure time of the sample; often the inverse of the frequency.""") + binning: Optional[int] = Field(None, description="""Amount of pixels combined into 'bins'; could be 1, 2, 4, 8, etc.""") + power: Optional[float] = Field(None, description="""Power of the excitation in mW, if known.""") + intensity: Optional[float] = Field(None, description="""Intensity of the excitation in mW/mm^2, if known.""") + data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") + dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") + external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") + format: Optional[str] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + +class TwoPhotonSeries(ImageSeries): + """ + Image stack recorded over time from 2-photon microscope. + """ + pmt_gain: Optional[float] = Field(None, description="""Photomultiplier gain.""") + scan_line_rate: Optional[float] = Field(None, description="""Lines imaged per second. This is also stored in /general/optophysiology but is kept here as it is useful information for analysis, and so good to be stored w/ the actual data.""") + field_of_view: Optional[TwoPhotonSeriesFieldOfView] = Field(None, description="""Width, height and depth of image, or imaged area, in meters.""") + data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") + dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") + external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") + format: Optional[str] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + +class RoiResponseSeries(TimeSeries): + """ + ROI responses over an imaging plane. The first dimension represents time. The second dimension, if present, represents ROIs. + """ + data: RoiResponseSeriesData = Field(..., description="""Signals from ROIs.""") + rois: RoiResponseSeriesRois = Field(..., description="""DynamicTableRegion referencing into an ROITable containing information on the ROIs stored in this timeseries.""") + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + +class DfOverF(NWBDataInterface): + """ + dF/F information about a region of interest (ROI). Storage hierarchy of dF/F should be the same as for segmentation (i.e., same names for ROIs and for image planes). + """ + RoiResponseSeries: List[RoiResponseSeries] = Field(default_factory=list, description="""RoiResponseSeries object(s) containing dF/F for a ROI.""") + + +class Fluorescence(NWBDataInterface): + """ + Fluorescence information about a region of interest (ROI). Storage hierarchy of fluorescence should be the same as for segmentation (ie, same names for ROIs and for image planes). + """ + RoiResponseSeries: List[RoiResponseSeries] = Field(default_factory=list, description="""RoiResponseSeries object(s) containing fluorescence data for a ROI.""") + + +class ImageSegmentation(NWBDataInterface): + """ + Stores pixels in an image that represent different regions of interest (ROIs) or masks. All segmentation for a given imaging plane is stored together, with storage for multiple imaging planes (masks) supported. Each ROI is stored in its own subgroup, with the ROI group containing both a 2D mask and a list of pixels that make up this mask. Segments can also be used for masking neuropil. If segmentation is allowed to change with time, a new imaging plane (or module) is required and ROI names should remain consistent between them. + """ + PlaneSegmentation: List[PlaneSegmentation] = Field(default_factory=list, description="""Results from image segmentation of a specific imaging plane.""") + + +class PlaneSegmentation(DynamicTable): + """ + Results from image segmentation of a specific imaging plane. + """ + image_mask: Optional[PlaneSegmentationImageMask] = Field(None, description="""ROI masks for each ROI. Each image mask is the size of the original imaging plane (or volume) and members of the ROI are finite non-zero.""") + pixel_mask_index: Optional[PlaneSegmentationPixelMaskIndex] = Field(None, description="""Index into pixel_mask.""") + pixel_mask: Optional[List[Any]] = Field(default_factory=list, description="""Pixel masks for each ROI: a list of indices and weights for the ROI. Pixel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation""") + voxel_mask_index: Optional[PlaneSegmentationVoxelMaskIndex] = Field(None, description="""Index into voxel_mask.""") + voxel_mask: Optional[List[Any]] = Field(default_factory=list, description="""Voxel masks for each ROI: a list of indices and weights for the ROI. Voxel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation""") + reference_images: PlaneSegmentationReferenceImages = Field(..., description="""Image stacks that the segmentation masks apply to.""") + colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") + description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") + id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") + VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") + + +class ImagingPlane(NWBContainer): + """ + An imaging plane and its metadata. + """ + description: Optional[str] = Field(None, description="""Description of the imaging plane.""") + excitation_lambda: float = Field(..., description="""Excitation wavelength, in nm.""") + imaging_rate: Optional[float] = Field(None, description="""Rate that images are acquired, in Hz. If the corresponding TimeSeries is present, the rate should be stored there instead.""") + indicator: str = Field(..., description="""Calcium indicator.""") + location: str = Field(..., description="""Location of the imaging plane. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible.""") + manifold: Optional[ImagingPlaneManifold] = Field(None, description="""DEPRECATED Physical position of each pixel. 'xyz' represents the position of the pixel relative to the defined coordinate space. Deprecated in favor of origin_coords and grid_spacing.""") + origin_coords: Optional[ImagingPlaneOriginCoords] = Field(None, description="""Physical location of the first element of the imaging plane (0, 0) for 2-D data or (0, 0, 0) for 3-D data. See also reference_frame for what the physical location is relative to (e.g., bregma).""") + grid_spacing: Optional[ImagingPlaneGridSpacing] = Field(None, description="""Space between pixels in (x, y) or voxels in (x, y, z) directions, in the specified unit. Assumes imaging plane is a regular grid. See also reference_frame to interpret the grid.""") + reference_frame: Optional[str] = Field(None, description="""Describes reference frame of origin_coords and grid_spacing. For example, this can be a text description of the anatomical location and orientation of the grid defined by origin_coords and grid_spacing or the vectors needed to transform or rotate the grid to a common anatomical axis (e.g., AP/DV/ML). This field is necessary to interpret origin_coords and grid_spacing. If origin_coords and grid_spacing are not present, then this field is not required. For example, if the microscope takes 10 x 10 x 2 images, where the first value of the data matrix (index (0, 0, 0)) corresponds to (-1.2, -0.6, -2) mm relative to bregma, the spacing between pixels is 0.2 mm in x, 0.2 mm in y and 0.5 mm in z, and larger numbers in x means more anterior, larger numbers in y means more rightward, and larger numbers in z means more ventral, then enter the following -- origin_coords = (-1.2, -0.6, -2) grid_spacing = (0.2, 0.2, 0.5) reference_frame = \"Origin coordinates are relative to bregma. First dimension corresponds to anterior-posterior axis (larger index = more anterior). Second dimension corresponds to medial-lateral axis (larger index = more rightward). Third dimension corresponds to dorsal-ventral axis (larger index = more ventral).\"""") + OpticalChannel: List[OpticalChannel] = Field(default_factory=list, description="""An optical channel used to record from an imaging plane.""") + + +class OpticalChannel(NWBContainer): + """ + An optical channel used to record from an imaging plane. + """ + description: str = Field(..., description="""Description or other notes about the channel.""") + emission_lambda: float = Field(..., description="""Emission wavelength for channel, in nm.""") + + +class MotionCorrection(NWBDataInterface): + """ + An image stack where all frames are shifted (registered) to a common coordinate system, to account for movement and drift between frames. Note: each frame at each point in time is assumed to be 2-D (has only x & y dimensions). + """ + CorrectedImageStack: List[CorrectedImageStack] = Field(default_factory=list, description="""Reuslts from motion correction of an image stack.""") + + +class CorrectedImageStack(NWBDataInterface): + """ + Reuslts from motion correction of an image stack. + """ + corrected: CorrectedImageStackCorrected = Field(..., description="""Image stack with frames shifted to the common coordinates.""") + xy_translation: CorrectedImageStackXyTranslation = Field(..., description="""Stores the x,y delta necessary to align each frame to the common coordinates, for example, to align each frame to a reference image.""") + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +OnePhotonSeries.update_forward_refs() +TwoPhotonSeries.update_forward_refs() +RoiResponseSeries.update_forward_refs() +DfOverF.update_forward_refs() +Fluorescence.update_forward_refs() +ImageSegmentation.update_forward_refs() +PlaneSegmentation.update_forward_refs() +ImagingPlane.update_forward_refs() +OpticalChannel.update_forward_refs() +MotionCorrection.update_forward_refs() +CorrectedImageStack.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_ophys_include.py b/nwb_linkml/models/core_nwb_ophys_include.py new file mode 100644 index 0000000..5947ced --- /dev/null +++ b/nwb_linkml/models/core_nwb_ophys_include.py @@ -0,0 +1,212 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .hdmf_common_table import ( + DynamicTableRegion, + VectorIndex, + VectorData +) + +from .core_nwb_image import ( + ImageSeries +) + +from .nwb_language import ( + Arraylike +) + +from .core_nwb_base import ( + TimeSeries +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class TwoPhotonSeriesFieldOfView(ConfiguredBaseModel): + """ + Width, height and depth of image, or imaged area, in meters. + """ + array: Optional[NDArray[Shape["2 width|height, 3 width|height|depth"], Float32]] = Field(None) + + +class TwoPhotonSeriesFieldOfViewArray(Arraylike): + + width|height: Optional[float] = Field(None) + width|height|depth: Optional[float] = Field(None) + + +class RoiResponseSeriesData(ConfiguredBaseModel): + """ + Signals from ROIs. + """ + array: Optional[NDArray[Shape["* num_times, * num_ROIs"], Number]] = Field(None) + + +class RoiResponseSeriesDataArray(Arraylike): + + num_times: float = Field(...) + num_ROIs: Optional[float] = Field(None) + + +class RoiResponseSeriesRois(DynamicTableRegion): + """ + DynamicTableRegion referencing into an ROITable containing information on the ROIs stored in this timeseries. + """ + table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") + description: Optional[str] = Field(None, description="""Description of what this table region points to.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class PlaneSegmentationImageMask(VectorData): + """ + ROI masks for each ROI. Each image mask is the size of the original imaging plane (or volume) and members of the ROI are finite non-zero. + """ + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class PlaneSegmentationPixelMaskIndex(VectorIndex): + """ + Index into pixel_mask. + """ + target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class PlaneSegmentationVoxelMaskIndex(VectorIndex): + """ + Index into voxel_mask. + """ + target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + +class PlaneSegmentationReferenceImages(ConfiguredBaseModel): + """ + Image stacks that the segmentation masks apply to. + """ + ImageSeries: Optional[List[ImageSeries]] = Field(default_factory=list, description="""One or more image stacks that the masks apply to (can be one-element stack).""") + + +class ImagingPlaneManifold(ConfiguredBaseModel): + """ + DEPRECATED Physical position of each pixel. 'xyz' represents the position of the pixel relative to the defined coordinate space. Deprecated in favor of origin_coords and grid_spacing. + """ + conversion: Optional[float] = Field(None, description="""Scalar to multiply each element in data to convert it to the specified 'unit'. If the data are stored in acquisition system units or other units that require a conversion to be interpretable, multiply the data by 'conversion' to convert the data to the specified 'unit'. e.g. if the data acquisition system stores values in this object as pixels from x = -500 to 499, y = -500 to 499 that correspond to a 2 m x 2 m range, then the 'conversion' multiplier to get from raw data acquisition pixel units to meters is 2/1000.""") + unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. The default value is 'meters'.""") + array: Optional[NDArray[Shape["* height, * width, 3 x_y_z, * depth"], Float32]] = Field(None) + + +class ImagingPlaneManifoldArray(Arraylike): + + height: float = Field(...) + width: float = Field(...) + x_y_z: float = Field(...) + depth: Optional[float] = Field(None) + + +class ImagingPlaneOriginCoords(ConfiguredBaseModel): + """ + Physical location of the first element of the imaging plane (0, 0) for 2-D data or (0, 0, 0) for 3-D data. See also reference_frame for what the physical location is relative to (e.g., bregma). + """ + unit: Optional[str] = Field(None, description="""Measurement units for origin_coords. The default value is 'meters'.""") + array: Optional[NDArray[Shape["2 x_y, 3 x_y_z"], Float32]] = Field(None) + + +class ImagingPlaneOriginCoordsArray(Arraylike): + + x_y: Optional[float] = Field(None) + x_y_z: Optional[float] = Field(None) + + +class ImagingPlaneGridSpacing(ConfiguredBaseModel): + """ + Space between pixels in (x, y) or voxels in (x, y, z) directions, in the specified unit. Assumes imaging plane is a regular grid. See also reference_frame to interpret the grid. + """ + unit: Optional[str] = Field(None, description="""Measurement units for grid_spacing. The default value is 'meters'.""") + array: Optional[NDArray[Shape["2 x_y, 3 x_y_z"], Float32]] = Field(None) + + +class ImagingPlaneGridSpacingArray(Arraylike): + + x_y: Optional[float] = Field(None) + x_y_z: Optional[float] = Field(None) + + +class CorrectedImageStackCorrected(ImageSeries): + """ + Image stack with frames shifted to the common coordinates. + """ + data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""") + dimension: Optional[ImageSeriesDimension] = Field(None, description="""Number of pixels on x, y, (and z) axes.""") + external_file: Optional[ImageSeriesExternalFile] = Field(None, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""") + format: Optional[str] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""") + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + +class CorrectedImageStackXyTranslation(TimeSeries): + """ + Stores the x,y delta necessary to align each frame to the common coordinates, for example, to align each frame to a reference image. + """ + description: Optional[str] = Field(None, description="""Description of the time series.""") + comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""") + data: TimeSeriesData = Field(..., description="""Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file.""") + starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""") + timestamps: Optional[TimeSeriesTimestamps] = Field(None, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""") + control: Optional[TimeSeriesControl] = Field(None, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""") + control_description: Optional[TimeSeriesControlDescription] = Field(None, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""") + sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""") + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +TwoPhotonSeriesFieldOfView.update_forward_refs() +TwoPhotonSeriesFieldOfViewArray.update_forward_refs() +RoiResponseSeriesData.update_forward_refs() +RoiResponseSeriesDataArray.update_forward_refs() +RoiResponseSeriesRois.update_forward_refs() +PlaneSegmentationImageMask.update_forward_refs() +PlaneSegmentationPixelMaskIndex.update_forward_refs() +PlaneSegmentationVoxelMaskIndex.update_forward_refs() +PlaneSegmentationReferenceImages.update_forward_refs() +ImagingPlaneManifold.update_forward_refs() +ImagingPlaneManifoldArray.update_forward_refs() +ImagingPlaneOriginCoords.update_forward_refs() +ImagingPlaneOriginCoordsArray.update_forward_refs() +ImagingPlaneGridSpacing.update_forward_refs() +ImagingPlaneGridSpacingArray.update_forward_refs() +CorrectedImageStackCorrected.update_forward_refs() +CorrectedImageStackXyTranslation.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_retinotopy.py b/nwb_linkml/models/core_nwb_retinotopy.py new file mode 100644 index 0000000..feffd83 --- /dev/null +++ b/nwb_linkml/models/core_nwb_retinotopy.py @@ -0,0 +1,63 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .core_nwb_retinotopy_include import ( + ImagingRetinotopyAxisDescriptions, + ImagingRetinotopyFocalDepthImage, + ImagingRetinotopyAxis2PowerMap, + ImagingRetinotopyVasculatureImage, + ImagingRetinotopyAxis2PhaseMap, + ImagingRetinotopyAxis1PhaseMap, + ImagingRetinotopyAxis1PowerMap, + ImagingRetinotopySignMap +) + +from .core_nwb_base import ( + NWBDataInterface +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class ImagingRetinotopy(NWBDataInterface): + """ + Intrinsic signal optical imaging or widefield imaging for measuring retinotopy. Stores orthogonal maps (e.g., altitude/azimuth; radius/theta) of responses to specific stimuli and a combined polarity map from which to identify visual areas. This group does not store the raw responses imaged during retinotopic mapping or the stimuli presented, but rather the resulting phase and power maps after applying a Fourier transform on the averaged responses. Note: for data consistency, all images and arrays are stored in the format [row][column] and [row, col], which equates to [y][x]. Field of view and dimension arrays may appear backward (i.e., y before x). + """ + axis_1_phase_map: ImagingRetinotopyAxis1PhaseMap = Field(..., description="""Phase response to stimulus on the first measured axis.""") + axis_1_power_map: Optional[ImagingRetinotopyAxis1PowerMap] = Field(None, description="""Power response on the first measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""") + axis_2_phase_map: ImagingRetinotopyAxis2PhaseMap = Field(..., description="""Phase response to stimulus on the second measured axis.""") + axis_2_power_map: Optional[ImagingRetinotopyAxis2PowerMap] = Field(None, description="""Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.""") + axis_descriptions: ImagingRetinotopyAxisDescriptions = Field(..., description="""Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta'].""") + focal_depth_image: Optional[ImagingRetinotopyFocalDepthImage] = Field(None, description="""Gray-scale image taken with same settings/parameters (e.g., focal depth, wavelength) as data collection. Array format: [rows][columns].""") + sign_map: Optional[ImagingRetinotopySignMap] = Field(None, description="""Sine of the angle between the direction of the gradient in axis_1 and axis_2.""") + vasculature_image: ImagingRetinotopyVasculatureImage = Field(..., description="""Gray-scale anatomical image of cortical surface. Array structure: [rows][columns]""") + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +ImagingRetinotopy.update_forward_refs() diff --git a/nwb_linkml/models/core_nwb_retinotopy_include.py b/nwb_linkml/models/core_nwb_retinotopy_include.py new file mode 100644 index 0000000..136213e --- /dev/null +++ b/nwb_linkml/models/core_nwb_retinotopy_include.py @@ -0,0 +1,173 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .nwb_language import ( + Arraylike +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class ImagingRetinotopyAxis1PhaseMap(ConfiguredBaseModel): + """ + Phase response to stimulus on the first measured axis. + """ + dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") + field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") + unit: Optional[str] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""") + array: Optional[NDArray[Shape["* num_rows, * num_cols"], Float32]] = Field(None) + + +class ImagingRetinotopyAxis1PhaseMapArray(Arraylike): + + num_rows: Optional[float] = Field(None) + num_cols: Optional[float] = Field(None) + + +class ImagingRetinotopyAxis1PowerMap(ConfiguredBaseModel): + """ + Power response on the first measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power. + """ + dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") + field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") + unit: Optional[str] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""") + array: Optional[NDArray[Shape["* num_rows, * num_cols"], Float32]] = Field(None) + + +class ImagingRetinotopyAxis1PowerMapArray(Arraylike): + + num_rows: Optional[float] = Field(None) + num_cols: Optional[float] = Field(None) + + +class ImagingRetinotopyAxis2PhaseMap(ConfiguredBaseModel): + """ + Phase response to stimulus on the second measured axis. + """ + dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") + field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") + unit: Optional[str] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""") + array: Optional[NDArray[Shape["* num_rows, * num_cols"], Float32]] = Field(None) + + +class ImagingRetinotopyAxis2PhaseMapArray(Arraylike): + + num_rows: Optional[float] = Field(None) + num_cols: Optional[float] = Field(None) + + +class ImagingRetinotopyAxis2PowerMap(ConfiguredBaseModel): + """ + Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power. + """ + dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") + field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") + unit: Optional[str] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""") + array: Optional[NDArray[Shape["* num_rows, * num_cols"], Float32]] = Field(None) + + +class ImagingRetinotopyAxis2PowerMapArray(Arraylike): + + num_rows: Optional[float] = Field(None) + num_cols: Optional[float] = Field(None) + + +class ImagingRetinotopyAxisDescriptions(ConfiguredBaseModel): + """ + Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta']. + """ + axis_descriptions: List[str] = Field(default_factory=list, description="""Two-element array describing the contents of the two response axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta'].""") + + +class ImagingRetinotopyFocalDepthImage(ConfiguredBaseModel): + """ + Gray-scale image taken with same settings/parameters (e.g., focal depth, wavelength) as data collection. Array format: [rows][columns]. + """ + bits_per_pixel: Optional[int] = Field(None, description="""Number of bits used to represent each value. This is necessary to determine maximum (white) pixel value.""") + dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") + field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") + focal_depth: Optional[float] = Field(None, description="""Focal depth offset, in meters.""") + format: Optional[str] = Field(None, description="""Format of image. Right now only 'raw' is supported.""") + array: Optional[NDArray[Shape["* num_rows, * num_cols"], UInt16]] = Field(None) + + +class ImagingRetinotopyFocalDepthImageArray(Arraylike): + + num_rows: Optional[int] = Field(None) + num_cols: Optional[int] = Field(None) + + +class ImagingRetinotopySignMap(ConfiguredBaseModel): + """ + Sine of the angle between the direction of the gradient in axis_1 and axis_2. + """ + dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") + field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") + array: Optional[NDArray[Shape["* num_rows, * num_cols"], Float32]] = Field(None) + + +class ImagingRetinotopySignMapArray(Arraylike): + + num_rows: Optional[float] = Field(None) + num_cols: Optional[float] = Field(None) + + +class ImagingRetinotopyVasculatureImage(ConfiguredBaseModel): + """ + Gray-scale anatomical image of cortical surface. Array structure: [rows][columns] + """ + bits_per_pixel: Optional[int] = Field(None, description="""Number of bits used to represent each value. This is necessary to determine maximum (white) pixel value""") + dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""") + field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""") + format: Optional[str] = Field(None, description="""Format of image. Right now only 'raw' is supported.""") + array: Optional[NDArray[Shape["* num_rows, * num_cols"], UInt16]] = Field(None) + + +class ImagingRetinotopyVasculatureImageArray(Arraylike): + + num_rows: Optional[int] = Field(None) + num_cols: Optional[int] = Field(None) + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +ImagingRetinotopyAxis1PhaseMap.update_forward_refs() +ImagingRetinotopyAxis1PhaseMapArray.update_forward_refs() +ImagingRetinotopyAxis1PowerMap.update_forward_refs() +ImagingRetinotopyAxis1PowerMapArray.update_forward_refs() +ImagingRetinotopyAxis2PhaseMap.update_forward_refs() +ImagingRetinotopyAxis2PhaseMapArray.update_forward_refs() +ImagingRetinotopyAxis2PowerMap.update_forward_refs() +ImagingRetinotopyAxis2PowerMapArray.update_forward_refs() +ImagingRetinotopyAxisDescriptions.update_forward_refs() +ImagingRetinotopyFocalDepthImage.update_forward_refs() +ImagingRetinotopyFocalDepthImageArray.update_forward_refs() +ImagingRetinotopySignMap.update_forward_refs() +ImagingRetinotopySignMapArray.update_forward_refs() +ImagingRetinotopyVasculatureImage.update_forward_refs() +ImagingRetinotopyVasculatureImageArray.update_forward_refs() diff --git a/nwb_linkml/models/hdmf-common.py b/nwb_linkml/models/hdmf-common.py deleted file mode 100644 index 3c3df0b..0000000 --- a/nwb_linkml/models/hdmf-common.py +++ /dev/null @@ -1,272 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "1.8.0" - -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): - pass - - -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - -class CSRMatrixIndices(ConfiguredBaseModel): - """ - The column indices. - """ - array: Optional[CSRMatrixIndicesArray] = Field(None) - - -class CSRMatrixIndptr(ConfiguredBaseModel): - """ - The row index pointer. - """ - array: Optional[CSRMatrixIndptrArray] = Field(None) - - -class CSRMatrixData(ConfiguredBaseModel): - """ - The non-zero values in the matrix. - """ - array: Optional[CSRMatrixDataArray] = Field(None) - - -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - -class CSRMatrixIndicesArray(Arraylike): - - number_of_non_zero_values: int = Field(...) - - -class CSRMatrixIndptrArray(Arraylike): - - number_of_rows_in_the_matrix_+_1: int = Field(...) - - -class CSRMatrixDataArray(Arraylike): - - number_of_non_zero_values: Any = Field(...) - - -class Data(ConfiguredBaseModel): - """ - An abstract data type for a dataset. - """ - None - - -class Container(ConfiguredBaseModel): - """ - An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class CSRMatrix(Container): - """ - A compressed sparse row matrix. Data are stored in the standard CSR format, where column indices for row i are stored in indices[indptr[i]:indptr[i+1]] and their corresponding values are stored in data[indptr[i]:indptr[i+1]]. - """ - shape: Optional[int] = Field(None, description="""The shape (number of rows, number of columns) of this sparse matrix.""") - indices: CSRMatrixIndices = Field(..., description="""The column indices.""") - indptr: CSRMatrixIndptr = Field(..., description="""The row index pointer.""") - data: CSRMatrixData = Field(..., description="""The non-zero values in the matrix.""") - - -class SimpleMultiContainer(Container): - """ - A simple Container for holding onto multiple containers. - """ - Data: Optional[List[Data]] = Field(default_factory=list, description="""Data objects held within this SimpleMultiContainer.""") - Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") - - -class VectorData(Data): - """ - An n-dimensional dataset representing a column of a DynamicTable. If used without an accompanying VectorIndex, first dimension is along the rows of the DynamicTable and each step along the first dimension is a cell of the larger table. VectorData can also be used to represent a ragged array if paired with a VectorIndex. This allows for storing arrays of varying length in a single cell of the DynamicTable by indexing into this VectorData. The first vector is at VectorData[0:VectorIndex[0]]. The second vector is at VectorData[VectorIndex[0]:VectorIndex[1]], and so on. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class VectorDataArray(Arraylike): - - dim0: Any = Field(...) - dim1: Optional[Any] = Field(None) - dim2: Optional[Any] = Field(None) - dim3: Optional[Any] = Field(None) - - -class VectorIndex(VectorData): - """ - Used with VectorData to encode a ragged array. An array of indices into the first dimension of the target VectorData, and forming a map between the rows of a DynamicTable and the indices of the VectorData. The name of the VectorIndex is expected to be the name of the target VectorData object followed by \"_index\". - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class VectorIndexArray(Arraylike): - - num_rows: int = Field(...) - - -class ElementIdentifiers(Data): - """ - A list of unique identifiers for values within a dataset, e.g. rows of a DynamicTable. - """ - array: Optional[ElementIdentifiersArray] = Field(None) - - -class ElementIdentifiersArray(Arraylike): - - num_elements: int = Field(...) - - -class DynamicTableRegion(VectorData): - """ - DynamicTableRegion provides a link from one table to an index or region of another. The `table` attribute is a link to another `DynamicTable`, indicating which table is referenced, and the data is int(s) indicating the row(s) (0-indexed) of the target array. `DynamicTableRegion`s can be used to associate rows with repeated meta-data without data duplication. They can also be used to create hierarchical relationships between multiple `DynamicTable`s. `DynamicTableRegion` objects may be paired with a `VectorIndex` object to create ragged references, so a single cell of a `DynamicTable` can reference many rows of another `DynamicTable`. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DynamicTableRegionArray(Arraylike): - - num_rows: int = Field(...) - - -class DynamicTable(Container): - """ - A group containing multiple datasets that are aligned on the first dimension (Currently, this requirement if left up to APIs to check and enforce). These datasets represent different columns in the table. Apart from a column that contains unique identifiers for each row, there are no other required datasets. Users are free to add any number of custom VectorData objects (columns) here. DynamicTable also supports ragged array columns, where each element can be of a different size. To add a ragged array column, use a VectorIndex type to index the corresponding VectorData type. See documentation for VectorData and VectorIndex for more details. Unlike a compound data type, which is analogous to storing an array-of-structs, a DynamicTable can be thought of as a struct-of-arrays. This provides an alternative structure to choose from when optimizing storage for anticipated access patterns. Additionally, this type provides a way of creating a table without having to define a compound type up front. Although this convenience may be attractive, users should think carefully about how data will be accessed. DynamicTable is more appropriate for column-centric access, whereas a dataset with a compound type would be more appropriate for row-centric access. Finally, data size should also be taken into account. For small tables, performance loss may be an acceptable trade-off for the flexibility of a DynamicTable. - """ - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class DynamicTableId(ElementIdentifiers): - """ - Array of unique identifiers for the rows of this dynamic table. - """ - array: Optional[DynamicTableIdArray] = Field(None) - - -class DynamicTableIdArray(Arraylike): - - num_rows: int = Field(...) - - -class AlignedDynamicTable(DynamicTable): - """ - DynamicTable container that supports storing a collection of sub-tables. Each sub-table is a DynamicTable itself that is aligned with the main table by row index. I.e., all DynamicTables stored in this group MUST have the same number of rows. This type effectively defines a 2-level table in which the main data is stored in the main table implemented by this type and additional columns of the table are grouped into categories, with each category being represented by a separate DynamicTable stored within the group. - """ - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -CSRMatrixIndices.update_forward_refs() -CSRMatrixIndptr.update_forward_refs() -CSRMatrixData.update_forward_refs() -Arraylike.update_forward_refs() -CSRMatrixIndicesArray.update_forward_refs() -CSRMatrixIndptrArray.update_forward_refs() -CSRMatrixDataArray.update_forward_refs() -Data.update_forward_refs() -Container.update_forward_refs() -CSRMatrix.update_forward_refs() -SimpleMultiContainer.update_forward_refs() -VectorData.update_forward_refs() -VectorDataArray.update_forward_refs() -VectorIndex.update_forward_refs() -VectorIndexArray.update_forward_refs() -ElementIdentifiers.update_forward_refs() -ElementIdentifiersArray.update_forward_refs() -DynamicTableRegion.update_forward_refs() -DynamicTableRegionArray.update_forward_refs() -DynamicTable.update_forward_refs() -DynamicTableId.update_forward_refs() -DynamicTableIdArray.update_forward_refs() -AlignedDynamicTable.update_forward_refs() diff --git a/nwb_linkml/models/hdmf-common.sparse.py b/nwb_linkml/models/hdmf-common.sparse.py deleted file mode 100644 index 5b46b17..0000000 --- a/nwb_linkml/models/hdmf-common.sparse.py +++ /dev/null @@ -1,170 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): - pass - - -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - -class CSRMatrixIndices(ConfiguredBaseModel): - """ - The column indices. - """ - array: Optional[CSRMatrixIndicesArray] = Field(None) - - -class CSRMatrixIndptr(ConfiguredBaseModel): - """ - The row index pointer. - """ - array: Optional[CSRMatrixIndptrArray] = Field(None) - - -class CSRMatrixData(ConfiguredBaseModel): - """ - The non-zero values in the matrix. - """ - array: Optional[CSRMatrixDataArray] = Field(None) - - -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - -class CSRMatrixIndicesArray(Arraylike): - - number_of_non_zero_values: int = Field(...) - - -class CSRMatrixIndptrArray(Arraylike): - - number_of_rows_in_the_matrix_+_1: int = Field(...) - - -class CSRMatrixDataArray(Arraylike): - - number_of_non_zero_values: Any = Field(...) - - -class Data(ConfiguredBaseModel): - """ - An abstract data type for a dataset. - """ - None - - -class Container(ConfiguredBaseModel): - """ - An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class CSRMatrix(Container): - """ - A compressed sparse row matrix. Data are stored in the standard CSR format, where column indices for row i are stored in indices[indptr[i]:indptr[i+1]] and their corresponding values are stored in data[indptr[i]:indptr[i+1]]. - """ - shape: Optional[int] = Field(None, description="""The shape (number of rows, number of columns) of this sparse matrix.""") - indices: CSRMatrixIndices = Field(..., description="""The column indices.""") - indptr: CSRMatrixIndptr = Field(..., description="""The row index pointer.""") - data: CSRMatrixData = Field(..., description="""The non-zero values in the matrix.""") - - -class SimpleMultiContainer(Container): - """ - A simple Container for holding onto multiple containers. - """ - Data: Optional[List[Data]] = Field(default_factory=list, description="""Data objects held within this SimpleMultiContainer.""") - Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") - - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -CSRMatrixIndices.update_forward_refs() -CSRMatrixIndptr.update_forward_refs() -CSRMatrixData.update_forward_refs() -Arraylike.update_forward_refs() -CSRMatrixIndicesArray.update_forward_refs() -CSRMatrixIndptrArray.update_forward_refs() -CSRMatrixDataArray.update_forward_refs() -Data.update_forward_refs() -Container.update_forward_refs() -CSRMatrix.update_forward_refs() -SimpleMultiContainer.update_forward_refs() diff --git a/nwb_linkml/models/hdmf-common.table.py b/nwb_linkml/models/hdmf-common.table.py deleted file mode 100644 index f4ffcf9..0000000 --- a/nwb_linkml/models/hdmf-common.table.py +++ /dev/null @@ -1,219 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): - pass - - -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - -class VectorDataArray(Arraylike): - - dim0: Any = Field(...) - dim1: Optional[Any] = Field(None) - dim2: Optional[Any] = Field(None) - dim3: Optional[Any] = Field(None) - - -class VectorIndexArray(Arraylike): - - num_rows: int = Field(...) - - -class ElementIdentifiersArray(Arraylike): - - num_elements: int = Field(...) - - -class DynamicTableRegionArray(Arraylike): - - num_rows: int = Field(...) - - -class DynamicTableIdArray(Arraylike): - - num_rows: int = Field(...) - - -class Data(ConfiguredBaseModel): - """ - An abstract data type for a dataset. - """ - None - - -class VectorData(Data): - """ - An n-dimensional dataset representing a column of a DynamicTable. If used without an accompanying VectorIndex, first dimension is along the rows of the DynamicTable and each step along the first dimension is a cell of the larger table. VectorData can also be used to represent a ragged array if paired with a VectorIndex. This allows for storing arrays of varying length in a single cell of the DynamicTable by indexing into this VectorData. The first vector is at VectorData[0:VectorIndex[0]]. The second vector is at VectorData[VectorIndex[0]:VectorIndex[1]], and so on. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class VectorIndex(VectorData): - """ - Used with VectorData to encode a ragged array. An array of indices into the first dimension of the target VectorData, and forming a map between the rows of a DynamicTable and the indices of the VectorData. The name of the VectorIndex is expected to be the name of the target VectorData object followed by \"_index\". - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ElementIdentifiers(Data): - """ - A list of unique identifiers for values within a dataset, e.g. rows of a DynamicTable. - """ - array: Optional[ElementIdentifiersArray] = Field(None) - - -class DynamicTableRegion(VectorData): - """ - DynamicTableRegion provides a link from one table to an index or region of another. The `table` attribute is a link to another `DynamicTable`, indicating which table is referenced, and the data is int(s) indicating the row(s) (0-indexed) of the target array. `DynamicTableRegion`s can be used to associate rows with repeated meta-data without data duplication. They can also be used to create hierarchical relationships between multiple `DynamicTable`s. `DynamicTableRegion` objects may be paired with a `VectorIndex` object to create ragged references, so a single cell of a `DynamicTable` can reference many rows of another `DynamicTable`. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DynamicTableId(ElementIdentifiers): - """ - Array of unique identifiers for the rows of this dynamic table. - """ - array: Optional[DynamicTableIdArray] = Field(None) - - -class Container(ConfiguredBaseModel): - """ - An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class DynamicTable(Container): - """ - A group containing multiple datasets that are aligned on the first dimension (Currently, this requirement if left up to APIs to check and enforce). These datasets represent different columns in the table. Apart from a column that contains unique identifiers for each row, there are no other required datasets. Users are free to add any number of custom VectorData objects (columns) here. DynamicTable also supports ragged array columns, where each element can be of a different size. To add a ragged array column, use a VectorIndex type to index the corresponding VectorData type. See documentation for VectorData and VectorIndex for more details. Unlike a compound data type, which is analogous to storing an array-of-structs, a DynamicTable can be thought of as a struct-of-arrays. This provides an alternative structure to choose from when optimizing storage for anticipated access patterns. Additionally, this type provides a way of creating a table without having to define a compound type up front. Although this convenience may be attractive, users should think carefully about how data will be accessed. DynamicTable is more appropriate for column-centric access, whereas a dataset with a compound type would be more appropriate for row-centric access. Finally, data size should also be taken into account. For small tables, performance loss may be an acceptable trade-off for the flexibility of a DynamicTable. - """ - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class AlignedDynamicTable(DynamicTable): - """ - DynamicTable container that supports storing a collection of sub-tables. Each sub-table is a DynamicTable itself that is aligned with the main table by row index. I.e., all DynamicTables stored in this group MUST have the same number of rows. This type effectively defines a 2-level table in which the main data is stored in the main table implemented by this type and additional columns of the table are grouped into categories, with each category being represented by a separate DynamicTable stored within the group. - """ - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimpleMultiContainer(Container): - """ - A simple Container for holding onto multiple containers. - """ - Data: Optional[List[Data]] = Field(default_factory=list, description="""Data objects held within this SimpleMultiContainer.""") - Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") - - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -Arraylike.update_forward_refs() -VectorDataArray.update_forward_refs() -VectorIndexArray.update_forward_refs() -ElementIdentifiersArray.update_forward_refs() -DynamicTableRegionArray.update_forward_refs() -DynamicTableIdArray.update_forward_refs() -Data.update_forward_refs() -VectorData.update_forward_refs() -VectorIndex.update_forward_refs() -ElementIdentifiers.update_forward_refs() -DynamicTableRegion.update_forward_refs() -DynamicTableId.update_forward_refs() -Container.update_forward_refs() -DynamicTable.update_forward_refs() -AlignedDynamicTable.update_forward_refs() -SimpleMultiContainer.update_forward_refs() diff --git a/nwb_linkml/models/hdmf-experimental.experimental.py b/nwb_linkml/models/hdmf-experimental.experimental.py deleted file mode 100644 index 87172e3..0000000 --- a/nwb_linkml/models/hdmf-experimental.experimental.py +++ /dev/null @@ -1,229 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): - pass - - -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - -class VectorDataArray(Arraylike): - - dim0: Any = Field(...) - dim1: Optional[Any] = Field(None) - dim2: Optional[Any] = Field(None) - dim3: Optional[Any] = Field(None) - - -class VectorIndexArray(Arraylike): - - num_rows: int = Field(...) - - -class ElementIdentifiersArray(Arraylike): - - num_elements: int = Field(...) - - -class DynamicTableRegionArray(Arraylike): - - num_rows: int = Field(...) - - -class DynamicTableIdArray(Arraylike): - - num_rows: int = Field(...) - - -class Data(ConfiguredBaseModel): - """ - An abstract data type for a dataset. - """ - None - - -class VectorData(Data): - """ - An n-dimensional dataset representing a column of a DynamicTable. If used without an accompanying VectorIndex, first dimension is along the rows of the DynamicTable and each step along the first dimension is a cell of the larger table. VectorData can also be used to represent a ragged array if paired with a VectorIndex. This allows for storing arrays of varying length in a single cell of the DynamicTable by indexing into this VectorData. The first vector is at VectorData[0:VectorIndex[0]]. The second vector is at VectorData[VectorIndex[0]:VectorIndex[1]], and so on. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class EnumData(VectorData): - """ - Data that come from a fixed set of values. A data value of i corresponds to the i-th value in the VectorData referenced by the 'elements' attribute. - """ - elements: Optional[VectorData] = Field(None, description="""Reference to the VectorData object that contains the enumerable elements""") - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class VectorIndex(VectorData): - """ - Used with VectorData to encode a ragged array. An array of indices into the first dimension of the target VectorData, and forming a map between the rows of a DynamicTable and the indices of the VectorData. The name of the VectorIndex is expected to be the name of the target VectorData object followed by \"_index\". - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class ElementIdentifiers(Data): - """ - A list of unique identifiers for values within a dataset, e.g. rows of a DynamicTable. - """ - array: Optional[ElementIdentifiersArray] = Field(None) - - -class DynamicTableRegion(VectorData): - """ - DynamicTableRegion provides a link from one table to an index or region of another. The `table` attribute is a link to another `DynamicTable`, indicating which table is referenced, and the data is int(s) indicating the row(s) (0-indexed) of the target array. `DynamicTableRegion`s can be used to associate rows with repeated meta-data without data duplication. They can also be used to create hierarchical relationships between multiple `DynamicTable`s. `DynamicTableRegion` objects may be paired with a `VectorIndex` object to create ragged references, so a single cell of a `DynamicTable` can reference many rows of another `DynamicTable`. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DynamicTableId(ElementIdentifiers): - """ - Array of unique identifiers for the rows of this dynamic table. - """ - array: Optional[DynamicTableIdArray] = Field(None) - - -class Container(ConfiguredBaseModel): - """ - An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class DynamicTable(Container): - """ - A group containing multiple datasets that are aligned on the first dimension (Currently, this requirement if left up to APIs to check and enforce). These datasets represent different columns in the table. Apart from a column that contains unique identifiers for each row, there are no other required datasets. Users are free to add any number of custom VectorData objects (columns) here. DynamicTable also supports ragged array columns, where each element can be of a different size. To add a ragged array column, use a VectorIndex type to index the corresponding VectorData type. See documentation for VectorData and VectorIndex for more details. Unlike a compound data type, which is analogous to storing an array-of-structs, a DynamicTable can be thought of as a struct-of-arrays. This provides an alternative structure to choose from when optimizing storage for anticipated access patterns. Additionally, this type provides a way of creating a table without having to define a compound type up front. Although this convenience may be attractive, users should think carefully about how data will be accessed. DynamicTable is more appropriate for column-centric access, whereas a dataset with a compound type would be more appropriate for row-centric access. Finally, data size should also be taken into account. For small tables, performance loss may be an acceptable trade-off for the flexibility of a DynamicTable. - """ - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class AlignedDynamicTable(DynamicTable): - """ - DynamicTable container that supports storing a collection of sub-tables. Each sub-table is a DynamicTable itself that is aligned with the main table by row index. I.e., all DynamicTables stored in this group MUST have the same number of rows. This type effectively defines a 2-level table in which the main data is stored in the main table implemented by this type and additional columns of the table are grouped into categories, with each category being represented by a separate DynamicTable stored within the group. - """ - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class SimpleMultiContainer(Container): - """ - A simple Container for holding onto multiple containers. - """ - Data: Optional[List[Data]] = Field(default_factory=list, description="""Data objects held within this SimpleMultiContainer.""") - Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") - - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -Arraylike.update_forward_refs() -VectorDataArray.update_forward_refs() -VectorIndexArray.update_forward_refs() -ElementIdentifiersArray.update_forward_refs() -DynamicTableRegionArray.update_forward_refs() -DynamicTableIdArray.update_forward_refs() -Data.update_forward_refs() -VectorData.update_forward_refs() -EnumData.update_forward_refs() -VectorIndex.update_forward_refs() -ElementIdentifiers.update_forward_refs() -DynamicTableRegion.update_forward_refs() -DynamicTableId.update_forward_refs() -Container.update_forward_refs() -DynamicTable.update_forward_refs() -AlignedDynamicTable.update_forward_refs() -SimpleMultiContainer.update_forward_refs() diff --git a/nwb_linkml/models/hdmf-experimental.py b/nwb_linkml/models/hdmf-experimental.py deleted file mode 100644 index 06053a7..0000000 --- a/nwb_linkml/models/hdmf-experimental.py +++ /dev/null @@ -1,326 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "0.5.0" - -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): - pass - - -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - -class HERDKeysArray(Arraylike): - - num_rows: Any = Field(...) - - -class HERDFilesArray(Arraylike): - - num_rows: Any = Field(...) - - -class HERDEntitiesArray(Arraylike): - - num_rows: Any = Field(...) - - -class HERDObjectsArray(Arraylike): - - num_rows: Any = Field(...) - - -class HERDObjectKeysArray(Arraylike): - - num_rows: Any = Field(...) - - -class HERDEntityKeysArray(Arraylike): - - num_rows: Any = Field(...) - - -class Data(ConfiguredBaseModel): - """ - An abstract data type for a dataset. - """ - None - - -class HERDKeys(Data): - """ - A table for storing user terms that are used to refer to external resources. - """ - array: Optional[HERDKeysArray] = Field(None) - - -class HERDFiles(Data): - """ - A table for storing object ids of files used in external resources. - """ - array: Optional[HERDFilesArray] = Field(None) - - -class HERDEntities(Data): - """ - A table for mapping user terms (i.e., keys) to resource entities. - """ - array: Optional[HERDEntitiesArray] = Field(None) - - -class HERDObjects(Data): - """ - A table for identifying which objects in a file contain references to external resources. - """ - array: Optional[HERDObjectsArray] = Field(None) - - -class HERDObjectKeys(Data): - """ - A table for identifying which objects use which keys. - """ - array: Optional[HERDObjectKeysArray] = Field(None) - - -class HERDEntityKeys(Data): - """ - A table for identifying which keys use which entity. - """ - array: Optional[HERDEntityKeysArray] = Field(None) - - -class Container(ConfiguredBaseModel): - """ - An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class HERD(Container): - """ - HDMF External Resources Data Structure. A set of six tables for tracking external resource references in a file or across multiple files. - """ - keys: HERDKeys = Field(, description="""A table for storing user terms that are used to refer to external resources.""") - files: HERDFiles = Field(..., description="""A table for storing object ids of files used in external resources.""") - entities: HERDEntities = Field(..., description="""A table for mapping user terms (i.e., keys) to resource entities.""") - objects: HERDObjects = Field(..., description="""A table for identifying which objects in a file contain references to external resources.""") - object_keys: HERDObjectKeys = Field(..., description="""A table for identifying which objects use which keys.""") - entity_keys: HERDEntityKeys = Field(..., description="""A table for identifying which keys use which entity.""") - - -class SimpleMultiContainer(Container): - """ - A simple Container for holding onto multiple containers. - """ - Data: Optional[List[Data]] = Field(default_factory=list, description="""Data objects held within this SimpleMultiContainer.""") - Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") - - -class VectorData(Data): - """ - An n-dimensional dataset representing a column of a DynamicTable. If used without an accompanying VectorIndex, first dimension is along the rows of the DynamicTable and each step along the first dimension is a cell of the larger table. VectorData can also be used to represent a ragged array if paired with a VectorIndex. This allows for storing arrays of varying length in a single cell of the DynamicTable by indexing into this VectorData. The first vector is at VectorData[0:VectorIndex[0]]. The second vector is at VectorData[VectorIndex[0]:VectorIndex[1]], and so on. - """ - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class EnumData(VectorData): - """ - Data that come from a fixed set of values. A data value of i corresponds to the i-th value in the VectorData referenced by the 'elements' attribute. - """ - elements: Optional[VectorData] = Field(None, description="""Reference to the VectorData object that contains the enumerable elements""") - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - array: Optional[VectorDataArray] = Field(None) - - -class VectorDataArray(Arraylike): - - dim0: Any = Field(...) - dim1: Optional[Any] = Field(None) - dim2: Optional[Any] = Field(None) - dim3: Optional[Any] = Field(None) - - -class VectorIndex(VectorData): - """ - Used with VectorData to encode a ragged array. An array of indices into the first dimension of the target VectorData, and forming a map between the rows of a DynamicTable and the indices of the VectorData. The name of the VectorIndex is expected to be the name of the target VectorData object followed by \"_index\". - """ - target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") - array: Optional[VectorIndexArray] = Field(None) - description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") - - -class VectorIndexArray(Arraylike): - - num_rows: int = Field(...) - - -class ElementIdentifiers(Data): - """ - A list of unique identifiers for values within a dataset, e.g. rows of a DynamicTable. - """ - array: Optional[ElementIdentifiersArray] = Field(None) - - -class ElementIdentifiersArray(Arraylike): - - num_elements: int = Field(...) - - -class DynamicTableRegion(VectorData): - """ - DynamicTableRegion provides a link from one table to an index or region of another. The `table` attribute is a link to another `DynamicTable`, indicating which table is referenced, and the data is int(s) indicating the row(s) (0-indexed) of the target array. `DynamicTableRegion`s can be used to associate rows with repeated meta-data without data duplication. They can also be used to create hierarchical relationships between multiple `DynamicTable`s. `DynamicTableRegion` objects may be paired with a `VectorIndex` object to create ragged references, so a single cell of a `DynamicTable` can reference many rows of another `DynamicTable`. - """ - table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") - description: Optional[str] = Field(None, description="""Description of what this table region points to.""") - array: Optional[DynamicTableRegionArray] = Field(None) - - -class DynamicTableRegionArray(Arraylike): - - num_rows: int = Field(...) - - -class DynamicTable(Container): - """ - A group containing multiple datasets that are aligned on the first dimension (Currently, this requirement if left up to APIs to check and enforce). These datasets represent different columns in the table. Apart from a column that contains unique identifiers for each row, there are no other required datasets. Users are free to add any number of custom VectorData objects (columns) here. DynamicTable also supports ragged array columns, where each element can be of a different size. To add a ragged array column, use a VectorIndex type to index the corresponding VectorData type. See documentation for VectorData and VectorIndex for more details. Unlike a compound data type, which is analogous to storing an array-of-structs, a DynamicTable can be thought of as a struct-of-arrays. This provides an alternative structure to choose from when optimizing storage for anticipated access patterns. Additionally, this type provides a way of creating a table without having to define a compound type up front. Although this convenience may be attractive, users should think carefully about how data will be accessed. DynamicTable is more appropriate for column-centric access, whereas a dataset with a compound type would be more appropriate for row-centric access. Finally, data size should also be taken into account. For small tables, performance loss may be an acceptable trade-off for the flexibility of a DynamicTable. - """ - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - -class DynamicTableId(ElementIdentifiers): - """ - Array of unique identifiers for the rows of this dynamic table. - """ - array: Optional[DynamicTableIdArray] = Field(None) - - -class DynamicTableIdArray(Arraylike): - - num_rows: int = Field(...) - - -class AlignedDynamicTable(DynamicTable): - """ - DynamicTable container that supports storing a collection of sub-tables. Each sub-table is a DynamicTable itself that is aligned with the main table by row index. I.e., all DynamicTables stored in this group MUST have the same number of rows. This type effectively defines a 2-level table in which the main data is stored in the main table implemented by this type and additional columns of the table are grouped into categories, with each category being represented by a separate DynamicTable stored within the group. - """ - categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") - DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") - colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") - description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") - id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") - VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") - - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -Arraylike.update_forward_refs() -HERDKeysArray.update_forward_refs() -HERDFilesArray.update_forward_refs() -HERDEntitiesArray.update_forward_refs() -HERDObjectsArray.update_forward_refs() -HERDObjectKeysArray.update_forward_refs() -HERDEntityKeysArray.update_forward_refs() -Data.update_forward_refs() -HERDKeys.update_forward_refs() -HERDFiles.update_forward_refs() -HERDEntities.update_forward_refs() -HERDObjects.update_forward_refs() -HERDObjectKeys.update_forward_refs() -HERDEntityKeys.update_forward_refs() -Container.update_forward_refs() -HERD.update_forward_refs() -SimpleMultiContainer.update_forward_refs() -VectorData.update_forward_refs() -EnumData.update_forward_refs() -VectorDataArray.update_forward_refs() -VectorIndex.update_forward_refs() -VectorIndexArray.update_forward_refs() -ElementIdentifiers.update_forward_refs() -ElementIdentifiersArray.update_forward_refs() -DynamicTableRegion.update_forward_refs() -DynamicTableRegionArray.update_forward_refs() -DynamicTable.update_forward_refs() -DynamicTableId.update_forward_refs() -DynamicTableIdArray.update_forward_refs() -AlignedDynamicTable.update_forward_refs() diff --git a/nwb_linkml/models/hdmf-experimental.resources.py b/nwb_linkml/models/hdmf-experimental.resources.py deleted file mode 100644 index 75fce1b..0000000 --- a/nwb_linkml/models/hdmf-experimental.resources.py +++ /dev/null @@ -1,214 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): - pass - - -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - -class HERDKeysArray(Arraylike): - - num_rows: Any = Field(...) - - -class HERDFilesArray(Arraylike): - - num_rows: Any = Field(...) - - -class HERDEntitiesArray(Arraylike): - - num_rows: Any = Field(...) - - -class HERDObjectsArray(Arraylike): - - num_rows: Any = Field(...) - - -class HERDObjectKeysArray(Arraylike): - - num_rows: Any = Field(...) - - -class HERDEntityKeysArray(Arraylike): - - num_rows: Any = Field(...) - - -class Data(ConfiguredBaseModel): - """ - An abstract data type for a dataset. - """ - None - - -class HERDKeys(Data): - """ - A table for storing user terms that are used to refer to external resources. - """ - array: Optional[HERDKeysArray] = Field(None) - - -class HERDFiles(Data): - """ - A table for storing object ids of files used in external resources. - """ - array: Optional[HERDFilesArray] = Field(None) - - -class HERDEntities(Data): - """ - A table for mapping user terms (i.e., keys) to resource entities. - """ - array: Optional[HERDEntitiesArray] = Field(None) - - -class HERDObjects(Data): - """ - A table for identifying which objects in a file contain references to external resources. - """ - array: Optional[HERDObjectsArray] = Field(None) - - -class HERDObjectKeys(Data): - """ - A table for identifying which objects use which keys. - """ - array: Optional[HERDObjectKeysArray] = Field(None) - - -class HERDEntityKeys(Data): - """ - A table for identifying which keys use which entity. - """ - array: Optional[HERDEntityKeysArray] = Field(None) - - -class Container(ConfiguredBaseModel): - """ - An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers. - """ - None - - -class HERD(Container): - """ - HDMF External Resources Data Structure. A set of six tables for tracking external resource references in a file or across multiple files. - """ - keys: HERDKeys = Field(, description="""A table for storing user terms that are used to refer to external resources.""") - files: HERDFiles = Field(..., description="""A table for storing object ids of files used in external resources.""") - entities: HERDEntities = Field(..., description="""A table for mapping user terms (i.e., keys) to resource entities.""") - objects: HERDObjects = Field(..., description="""A table for identifying which objects in a file contain references to external resources.""") - object_keys: HERDObjectKeys = Field(..., description="""A table for identifying which objects use which keys.""") - entity_keys: HERDEntityKeys = Field(..., description="""A table for identifying which keys use which entity.""") - - -class SimpleMultiContainer(Container): - """ - A simple Container for holding onto multiple containers. - """ - Data: Optional[List[Data]] = Field(default_factory=list, description="""Data objects held within this SimpleMultiContainer.""") - Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") - - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -Arraylike.update_forward_refs() -HERDKeysArray.update_forward_refs() -HERDFilesArray.update_forward_refs() -HERDEntitiesArray.update_forward_refs() -HERDObjectsArray.update_forward_refs() -HERDObjectKeysArray.update_forward_refs() -HERDEntityKeysArray.update_forward_refs() -Data.update_forward_refs() -HERDKeys.update_forward_refs() -HERDFiles.update_forward_refs() -HERDEntities.update_forward_refs() -HERDObjects.update_forward_refs() -HERDObjectKeys.update_forward_refs() -HERDEntityKeys.update_forward_refs() -Container.update_forward_refs() -HERD.update_forward_refs() -SimpleMultiContainer.update_forward_refs() diff --git a/nwb_linkml/models/hdmf_common.py b/nwb_linkml/models/hdmf_common.py new file mode 100644 index 0000000..0802341 --- /dev/null +++ b/nwb_linkml/models/hdmf_common.py @@ -0,0 +1,33 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + + +metamodel_version = "None" +version = "1.8.0" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ diff --git a/nwb_linkml/models/hdmf-common.base.py b/nwb_linkml/models/hdmf_common_base.py similarity index 58% rename from nwb_linkml/models/hdmf-common.base.py rename to nwb_linkml/models/hdmf_common_base.py index 449a566..be2c9e5 100644 --- a/nwb_linkml/models/hdmf-common.base.py +++ b/nwb_linkml/models/hdmf_common_base.py @@ -3,6 +3,7 @@ from datetime import datetime, date from enum import Enum from typing import List, Dict, Optional, Any, Union from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 import sys if sys.version_info >= (3, 8): from typing import Literal @@ -10,6 +11,7 @@ else: from typing_extensions import Literal + metamodel_version = "None" version = "None" @@ -26,59 +28,6 @@ class ConfiguredBaseModel(WeakRefShimBaseModel, pass -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - class Data(ConfiguredBaseModel): """ An abstract data type for a dataset. @@ -101,17 +50,9 @@ class SimpleMultiContainer(Container): Container: Optional[List[Container]] = Field(default_factory=list, description="""Container objects held within this SimpleMultiContainer.""") -class Arraylike(ConfiguredBaseModel): - """ - Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. - """ - None - - # Update forward refs # see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ Data.update_forward_refs() Container.update_forward_refs() SimpleMultiContainer.update_forward_refs() -Arraylike.update_forward_refs() diff --git a/nwb_linkml/models/hdmf_common_base_include.py b/nwb_linkml/models/hdmf_common_base_include.py new file mode 100644 index 0000000..c923ad6 --- /dev/null +++ b/nwb_linkml/models/hdmf_common_base_include.py @@ -0,0 +1,33 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ diff --git a/nwb_linkml/models/hdmf_common_sparse.py b/nwb_linkml/models/hdmf_common_sparse.py new file mode 100644 index 0000000..79fc060 --- /dev/null +++ b/nwb_linkml/models/hdmf_common_sparse.py @@ -0,0 +1,54 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .hdmf_common_sparse_include import ( + CSRMatrixData, + CSRMatrixIndices, + CSRMatrixIndptr +) + +from .hdmf_common_base import ( + Container +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class CSRMatrix(Container): + """ + A compressed sparse row matrix. Data are stored in the standard CSR format, where column indices for row i are stored in indices[indptr[i]:indptr[i+1]] and their corresponding values are stored in data[indptr[i]:indptr[i+1]]. + """ + shape: Optional[int] = Field(None, description="""The shape (number of rows, number of columns) of this sparse matrix.""") + indices: CSRMatrixIndices = Field(..., description="""The column indices.""") + indptr: CSRMatrixIndptr = Field(..., description="""The row index pointer.""") + data: CSRMatrixData = Field(..., description="""The non-zero values in the matrix.""") + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +CSRMatrix.update_forward_refs() diff --git a/nwb_linkml/models/hdmf_common_sparse_include.py b/nwb_linkml/models/hdmf_common_sparse_include.py new file mode 100644 index 0000000..e1e2206 --- /dev/null +++ b/nwb_linkml/models/hdmf_common_sparse_include.py @@ -0,0 +1,57 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class CSRMatrixIndices(ConfiguredBaseModel): + """ + The column indices. + """ + indices: List[int] = Field(default_factory=list, description="""The column indices.""") + + +class CSRMatrixIndptr(ConfiguredBaseModel): + """ + The row index pointer. + """ + indptr: List[int] = Field(default_factory=list, description="""The row index pointer.""") + + +class CSRMatrixData(ConfiguredBaseModel): + """ + The non-zero values in the matrix. + """ + data: List[Any] = Field(default_factory=list, description="""The non-zero values in the matrix.""") + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +CSRMatrixIndices.update_forward_refs() +CSRMatrixIndptr.update_forward_refs() +CSRMatrixData.update_forward_refs() diff --git a/nwb_linkml/models/hdmf_common_table.py b/nwb_linkml/models/hdmf_common_table.py new file mode 100644 index 0000000..5a2971c --- /dev/null +++ b/nwb_linkml/models/hdmf_common_table.py @@ -0,0 +1,105 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +# from .hdmf_common_table_include import ( +# VectorDataArray, +# ElementIdentifiersArray, +# DynamicTableId +# ) + +from .hdmf_common_base import ( + Container, + Data +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class VectorData(Data): + """ + An n-dimensional dataset representing a column of a DynamicTable. If used without an accompanying VectorIndex, first dimension is along the rows of the DynamicTable and each step along the first dimension is a cell of the larger table. VectorData can also be used to represent a ragged array if paired with a VectorIndex. This allows for storing arrays of varying length in a single cell of the DynamicTable by indexing into this VectorData. The first vector is at VectorData[0:VectorIndex[0]]. The second vector is at VectorData[VectorIndex[0]:VectorIndex[1]], and so on. + """ + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], Any]] = Field(None) + + +class VectorIndex(VectorData): + """ + Used with VectorData to encode a ragged array. An array of indices into the first dimension of the target VectorData, and forming a map between the rows of a DynamicTable and the indices of the VectorData. The name of the VectorIndex is expected to be the name of the target VectorData object followed by \"_index\". + """ + target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], Any]] = Field(None) + + +class ElementIdentifiers(Data): + """ + A list of unique identifiers for values within a dataset, e.g. rows of a DynamicTable. + """ + array: Optional[NDArray[Shape["* num_elements"], Int]] = Field(None) + + +# class DynamicTableRegion(VectorData): +# """ +# DynamicTableRegion provides a link from one table to an index or region of another. The `table` attribute is a link to another `DynamicTable`, indicating which table is referenced, and the data is int(s) indicating the row(s) (0-indexed) of the target array. `DynamicTableRegion`s can be used to associate rows with repeated meta-data without data duplication. They can also be used to create hierarchical relationships between multiple `DynamicTable`s. `DynamicTableRegion` objects may be paired with a `VectorIndex` object to create ragged references, so a single cell of a `DynamicTable` can reference many rows of another `DynamicTable`. +# """ +# table: Optional[DynamicTable] = Field(None, description="""Reference to the DynamicTable object that this region applies to.""") +# description: Optional[str] = Field(None, description="""Description of what this table region points to.""") +# array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], Any]] = Field(None) +# + +# class DynamicTable(Container): +# """ +# A group containing multiple datasets that are aligned on the first dimension (Currently, this requirement if left up to APIs to check and enforce). These datasets represent different columns in the table. Apart from a column that contains unique identifiers for each row, there are no other required datasets. Users are free to add any number of custom VectorData objects (columns) here. DynamicTable also supports ragged array columns, where each element can be of a different size. To add a ragged array column, use a VectorIndex type to index the corresponding VectorData type. See documentation for VectorData and VectorIndex for more details. Unlike a compound data type, which is analogous to storing an array-of-structs, a DynamicTable can be thought of as a struct-of-arrays. This provides an alternative structure to choose from when optimizing storage for anticipated access patterns. Additionally, this type provides a way of creating a table without having to define a compound type up front. Although this convenience may be attractive, users should think carefully about how data will be accessed. DynamicTable is more appropriate for column-centric access, whereas a dataset with a compound type would be more appropriate for row-centric access. Finally, data size should also be taken into account. For small tables, performance loss may be an acceptable trade-off for the flexibility of a DynamicTable. +# """ +# colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") +# description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") +# id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") +# VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") +# + +# class AlignedDynamicTable(DynamicTable): +# """ +# DynamicTable container that supports storing a collection of sub-tables. Each sub-table is a DynamicTable itself that is aligned with the main table by row index. I.e., all DynamicTables stored in this group MUST have the same number of rows. This type effectively defines a 2-level table in which the main data is stored in the main table implemented by this type and additional columns of the table are grouped into categories, with each category being represented by a separate DynamicTable stored within the group. +# """ +# categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""") +# DynamicTable: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""") +# colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""") +# description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""") +# id: DynamicTableId = Field(..., description="""Array of unique identifiers for the rows of this dynamic table.""") +# VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""") +# + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +VectorData.update_forward_refs() +VectorIndex.update_forward_refs() +ElementIdentifiers.update_forward_refs() +DynamicTableRegion.update_forward_refs() +# DynamicTable.update_forward_refs() +# AlignedDynamicTable.update_forward_refs() diff --git a/nwb_linkml/models/hdmf_common_table_include.py b/nwb_linkml/models/hdmf_common_table_include.py new file mode 100644 index 0000000..043b0fa --- /dev/null +++ b/nwb_linkml/models/hdmf_common_table_include.py @@ -0,0 +1,65 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +# from .hdmf_common_table import ( +# ElementIdentifiers +# ) + +from .nwb_language import ( + Arraylike +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class VectorDataArray(Arraylike): + + dim0: Any = Field(...) + dim1: Optional[Any] = Field(None) + dim2: Optional[Any] = Field(None) + dim3: Optional[Any] = Field(None) + + +class ElementIdentifiersArray(Arraylike): + + num_elements: int = Field(...) + + +# class DynamicTableId(ElementIdentifiers): +# """ +# Array of unique identifiers for the rows of this dynamic table. +# """ +# id: List[int] = Field(default_factory=list, description="""Array of unique identifiers for the rows of this dynamic table.""") +# array: Optional[NDArray[Shape["* num_elements"], Int]] = Field(None) +# + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +VectorDataArray.update_forward_refs() +ElementIdentifiersArray.update_forward_refs() +DynamicTableId.update_forward_refs() diff --git a/nwb_linkml/models/hdmf_experimental.py b/nwb_linkml/models/hdmf_experimental.py new file mode 100644 index 0000000..42ed1e5 --- /dev/null +++ b/nwb_linkml/models/hdmf_experimental.py @@ -0,0 +1,33 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + + +metamodel_version = "None" +version = "0.5.0" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ diff --git a/nwb_linkml/models/hdmf_experimental_experimental.py b/nwb_linkml/models/hdmf_experimental_experimental.py new file mode 100644 index 0000000..3b6b113 --- /dev/null +++ b/nwb_linkml/models/hdmf_experimental_experimental.py @@ -0,0 +1,47 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .hdmf_common_table import ( + VectorData +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class EnumData(VectorData): + """ + Data that come from a fixed set of values. A data value of i corresponds to the i-th value in the VectorData referenced by the 'elements' attribute. + """ + elements: Optional[VectorData] = Field(None, description="""Reference to the VectorData object that contains the enumerable elements""") + description: Optional[str] = Field(None, description="""Description of what these vectors represent.""") + array: Optional[NDArray[Shape["* dim0, * dim1, * dim2, * dim3"], ]] = Field(None) + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +EnumData.update_forward_refs() diff --git a/nwb_linkml/models/hdmf_experimental_experimental_include.py b/nwb_linkml/models/hdmf_experimental_experimental_include.py new file mode 100644 index 0000000..c923ad6 --- /dev/null +++ b/nwb_linkml/models/hdmf_experimental_experimental_include.py @@ -0,0 +1,33 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ diff --git a/nwb_linkml/models/hdmf_experimental_resources.py b/nwb_linkml/models/hdmf_experimental_resources.py new file mode 100644 index 0000000..4fd7aa1 --- /dev/null +++ b/nwb_linkml/models/hdmf_experimental_resources.py @@ -0,0 +1,59 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .hdmf_common_base import ( + Container +) + +from .hdmf_experimental_resources_include import ( + HERDObjectKeys, + HERDObjects, + HERDEntities, + HERDKeys, + HERDFiles, + HERDEntityKeys +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class HERD(Container): + """ + HDMF External Resources Data Structure. A set of six tables for tracking external resource references in a file or across multiple files. + """ + keys: HERDKeys = Field(, description="""A table for storing user terms that are used to refer to external resources.""") + files: HERDFiles = Field(..., description="""A table for storing object ids of files used in external resources.""") + entities: HERDEntities = Field(..., description="""A table for mapping user terms (i.e., keys) to resource entities.""") + objects: HERDObjects = Field(..., description="""A table for identifying which objects in a file contain references to external resources.""") + object_keys: HERDObjectKeys = Field(..., description="""A table for identifying which objects use which keys.""") + entity_keys: HERDEntityKeys = Field(..., description="""A table for identifying which keys use which entity.""") + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +HERD.update_forward_refs() diff --git a/nwb_linkml/models/hdmf_experimental_resources_include.py b/nwb_linkml/models/hdmf_experimental_resources_include.py new file mode 100644 index 0000000..f4b3937 --- /dev/null +++ b/nwb_linkml/models/hdmf_experimental_resources_include.py @@ -0,0 +1,85 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +from .hdmf_common_base import ( + Data +) + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class HERDKeys(Data): + """ + A table for storing user terms that are used to refer to external resources. + """ + keys: List[Any] = Field(default_factory=list, description="""A table for storing user terms that are used to refer to external resources.""") + + +class HERDFiles(Data): + """ + A table for storing object ids of files used in external resources. + """ + files: List[Any] = Field(default_factory=list, description="""A table for storing object ids of files used in external resources.""") + + +class HERDEntities(Data): + """ + A table for mapping user terms (i.e., keys) to resource entities. + """ + entities: List[Any] = Field(default_factory=list, description="""A table for mapping user terms (i.e., keys) to resource entities.""") + + +class HERDObjects(Data): + """ + A table for identifying which objects in a file contain references to external resources. + """ + objects: List[Any] = Field(default_factory=list, description="""A table for identifying which objects in a file contain references to external resources.""") + + +class HERDObjectKeys(Data): + """ + A table for identifying which objects use which keys. + """ + object_keys: List[Any] = Field(default_factory=list, description="""A table for identifying which objects use which keys.""") + + +class HERDEntityKeys(Data): + """ + A table for identifying which keys use which entity. + """ + entity_keys: List[Any] = Field(default_factory=list, description="""A table for identifying which keys use which entity.""") + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +HERDKeys.update_forward_refs() +HERDFiles.update_forward_refs() +HERDEntities.update_forward_refs() +HERDObjects.update_forward_refs() +HERDObjectKeys.update_forward_refs() +HERDEntityKeys.update_forward_refs() diff --git a/nwb_linkml/models/nwb.language.py b/nwb_linkml/models/nwb_language.py similarity index 67% rename from nwb_linkml/models/nwb.language.py rename to nwb_linkml/models/nwb_language.py index 5da9a24..2709a31 100644 --- a/nwb_linkml/models/nwb.language.py +++ b/nwb_linkml/models/nwb_language.py @@ -3,6 +3,7 @@ from datetime import datetime, date from enum import Enum from typing import List, Dict, Optional, Any, Union from pydantic import BaseModel as BaseModel, Field +from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64 import sys if sys.version_info >= (3, 8): from typing import Literal @@ -10,6 +11,7 @@ else: from typing_extensions import Literal + metamodel_version = "None" version = "None" @@ -26,59 +28,6 @@ class ConfiguredBaseModel(WeakRefShimBaseModel, pass -class FlatDType(str, Enum): - - - float = "float" - - float32 = "float32" - - double = "double" - - float64 = "float64" - - long = "long" - - int64 = "int64" - - int = "int" - - int32 = "int32" - - int16 = "int16" - - short = "short" - - int8 = "int8" - - uint = "uint" - - uint32 = "uint32" - - uint16 = "uint16" - - uint8 = "uint8" - - uint64 = "uint64" - - numeric = "numeric" - - text = "text" - - utf = "utf" - - utf8 = "utf8" - - utf_8 = "utf_8" - - ascii = "ascii" - - bool = "bool" - - isodatetime = "isodatetime" - - - class Arraylike(ConfiguredBaseModel): """ Container for arraylike information held in the dims, shape, and dtype properties.this is a special case to be interpreted by downstream i/o. this class has no slotsand is abstract by default.- Each slot within a subclass indicates a possible dimension.- Only dimensions that are present in all the dimension specifiers in the original schema are required.- Shape requirements are indicated using max/min cardinalities on the slot. diff --git a/nwb_linkml/schema/core.nwb.base.include.yaml b/nwb_linkml/schema/core.nwb.base.include.yaml new file mode 100644 index 0000000..71646b5 --- /dev/null +++ b/nwb_linkml/schema/core.nwb.base.include.yaml @@ -0,0 +1,192 @@ +name: core.nwb.base.include +id: core.nwb.base.include +imports: +- hdmf-common.base +- hdmf-common.table +- nwb.language +- core.nwb.base.include +- core.nwb.base +default_prefix: core.nwb.base.include/ +classes: + Image__Array: + name: Image__Array + is_a: Arraylike + attributes: + x: + name: x + range: numeric + required: true + y: + name: y + range: numeric + required: true + r, g, b: + name: r, g, b + range: numeric + required: false + minimum_cardinality: 3 + maximum_cardinality: 3 + r, g, b, a: + name: r, g, b, a + range: numeric + required: false + minimum_cardinality: 4 + maximum_cardinality: 4 + ImageReferences__Array: + name: ImageReferences__Array + is_a: Arraylike + attributes: + num_images: + name: num_images + range: Image + required: true + TimeSeries__data: + name: TimeSeries__data + description: Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension + should always represent time. This can also be used to store binary data (e.g., + image frames). This can also be a link to data stored in an external file. + attributes: + conversion: + name: conversion + description: Scalar to multiply each element in data to convert it to the + specified 'unit'. If the data are stored in acquisition system units or + other units that require a conversion to be interpretable, multiply the + data by 'conversion' to convert the data to the specified 'unit'. e.g. if + the data acquisition system stores values in this object as signed 16-bit + integers (int16 range -32,768 to 32,767) that correspond to a 5V range (-2.5V + to 2.5V), and the data acquisition system gain is 8000X, then the 'conversion' + multiplier to get from raw data acquisition values to recorded volts is + 2.5/32768/8000 = 9.5367e-9. + range: float32 + offset: + name: offset + description: Scalar to add to the data after scaling by 'conversion' to finalize + its coercion to the specified 'unit'. Two common examples of this include + (a) data stored in an unsigned type that requires a shift after scaling + to re-center the data, and (b) specialized recording devices that naturally + cause a scalar offset with respect to the true units. + range: float32 + resolution: + name: resolution + description: Smallest meaningful difference between values in data, stored + in the specified by unit, e.g., the change in value of the least significant + bit, or a larger number if signal noise is known to be present. If unknown, + use -1.0. + range: float32 + unit: + name: unit + description: Base unit of measurement for working with the data. Actual stored + values are not necessarily stored in these units. To access the data in + these units, multiply 'data' by 'conversion' and add 'offset'. + range: text + continuity: + name: continuity + description: Optionally describe the continuity of the data. Can be "continuous", + "instantaneous", or "step". For example, a voltage trace would be "continuous", + because samples are recorded from a continuous process. An array of lick + times would be "instantaneous", because the data represents distinct moments + in time. Times of image presentations would be "step" because the picture + remains the same until the next timepoint. This field is optional, but is + useful in providing information about the underlying data. It may inform + the way this data is interpreted, the way it is visualized, and what analysis + methods are applicable. + range: text + array: + name: array + range: TimeSeries__data__Array + TimeSeries__data__Array: + name: TimeSeries__data__Array + is_a: Arraylike + attributes: + num_times: + name: num_times + range: AnyType + required: true + num_DIM2: + name: num_DIM2 + range: AnyType + required: false + num_DIM3: + name: num_DIM3 + range: AnyType + required: false + num_DIM4: + name: num_DIM4 + range: AnyType + required: false + TimeSeries__starting_time: + name: TimeSeries__starting_time + description: Timestamp of the first sample in seconds. When timestamps are uniformly + spaced, the timestamp of the first sample can be specified and all subsequent + ones calculated from the sampling rate attribute. + attributes: + rate: + name: rate + description: Sampling rate, in Hz. + range: float32 + unit: + name: unit + description: Unit of measurement for time, which is fixed to 'seconds'. + range: text + TimeSeries__timestamps: + name: TimeSeries__timestamps + description: Timestamps for samples stored in data, in seconds, relative to the + common experiment master-clock stored in NWBFile.timestamps_reference_time. + attributes: + interval: + name: interval + description: Value is '1' + range: int32 + unit: + name: unit + description: Unit of measurement for timestamps, which is fixed to 'seconds'. + range: text + timestamps: + name: timestamps + description: Timestamps for samples stored in data, in seconds, relative to + the common experiment master-clock stored in NWBFile.timestamps_reference_time. + multivalued: true + range: float64 + required: false + TimeSeries__control: + name: TimeSeries__control + description: Numerical labels that apply to each time point in data for the purpose + of querying and slicing data by these values. If present, the length of this + array should be the same size as the first dimension of data. + attributes: + control: + name: control + description: Numerical labels that apply to each time point in data for the + purpose of querying and slicing data by these values. If present, the length + of this array should be the same size as the first dimension of data. + multivalued: true + range: uint8 + required: false + TimeSeries__control_description: + name: TimeSeries__control_description + description: Description of each control value. Must be present if control is + present. If present, control_description[0] should describe time points where + control == 0. + attributes: + control_description: + name: control_description + description: Description of each control value. Must be present if control + is present. If present, control_description[0] should describe time points + where control == 0. + multivalued: true + range: text + required: false + TimeSeries__sync: + name: TimeSeries__sync + description: Lab-specific time and sync information as provided directly from + hardware devices and that is necessary for aligning all acquired time information + to a common timebase. The timestamp array stores time in the common timebase. + This group will usually only be populated in TimeSeries that are stored external + to the NWB file, in files storing raw data. Once timestamp data is calculated, + the contents of 'sync' are mostly for archival purposes. + Images__order_of_images: + name: Images__order_of_images + description: Ordered dataset of references to Image objects stored in the parent + group. Each Image object in the Images group should be stored once and only + once, so the dataset should have the same length as the number of images. + is_a: ImageReferences diff --git a/nwb_linkml/schema/core.nwb.base.yaml b/nwb_linkml/schema/core.nwb.base.yaml index 4f401c8..2a31e48 100644 --- a/nwb_linkml/schema/core.nwb.base.yaml +++ b/nwb_linkml/schema/core.nwb.base.yaml @@ -4,6 +4,8 @@ imports: - hdmf-common.base - hdmf-common.table - nwb.language +- core.nwb.base.include +- core.nwb.base default_prefix: core.nwb.base/ classes: NWBData: @@ -33,31 +35,7 @@ classes: range: text array: name: array - range: Image_Array - Image_Array: - name: Image_Array - is_a: Arraylike - attributes: - x: - name: x - range: numeric - required: true - y: - name: y - range: numeric - required: true - r, g, b: - name: r, g, b - range: numeric - required: false - minimum_cardinality: 3 - maximum_cardinality: 3 - r, g, b, a: - name: r, g, b, a - range: numeric - required: false - minimum_cardinality: 4 - maximum_cardinality: 4 + range: Image__Array ImageReferences: name: ImageReferences description: Ordered dataset of references to Image objects. @@ -65,15 +43,7 @@ classes: attributes: array: name: array - range: ImageReferences_Array - ImageReferences_Array: - name: ImageReferences_Array - is_a: Arraylike - attributes: - num_images: - name: num_images - range: Image - required: true + range: ImageReferences__Array NWBContainer: name: NWBContainer description: An abstract data type for a generic container storing collections @@ -106,7 +76,7 @@ classes: data (e.g., image frames). This can also be a link to data stored in an external file. multivalued: false - range: TimeSeries_data + range: TimeSeries__data required: true starting_time: name: starting_time @@ -114,14 +84,14 @@ classes: uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute. multivalued: false - range: TimeSeries_starting_time + range: TimeSeries__starting_time required: false timestamps: name: timestamps description: Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. multivalued: false - range: TimeSeries_timestamps + range: TimeSeries__timestamps required: false control: name: control @@ -129,7 +99,7 @@ classes: purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data. multivalued: false - range: TimeSeries_control + range: TimeSeries__control required: false control_description: name: control_description @@ -137,7 +107,7 @@ classes: is present. If present, control_description[0] should describe time points where control == 0. multivalued: false - range: TimeSeries_control_description + range: TimeSeries__control_description required: false sync: name: sync @@ -148,162 +118,8 @@ classes: external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes. multivalued: false - range: TimeSeries_sync + range: TimeSeries__sync required: false - TimeSeries_data: - name: TimeSeries_data - description: Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension - should always represent time. This can also be used to store binary data (e.g., - image frames). This can also be a link to data stored in an external file. - attributes: - conversion: - name: conversion - description: Scalar to multiply each element in data to convert it to the - specified 'unit'. If the data are stored in acquisition system units or - other units that require a conversion to be interpretable, multiply the - data by 'conversion' to convert the data to the specified 'unit'. e.g. if - the data acquisition system stores values in this object as signed 16-bit - integers (int16 range -32,768 to 32,767) that correspond to a 5V range (-2.5V - to 2.5V), and the data acquisition system gain is 8000X, then the 'conversion' - multiplier to get from raw data acquisition values to recorded volts is - 2.5/32768/8000 = 9.5367e-9. - range: float32 - offset: - name: offset - description: Scalar to add to the data after scaling by 'conversion' to finalize - its coercion to the specified 'unit'. Two common examples of this include - (a) data stored in an unsigned type that requires a shift after scaling - to re-center the data, and (b) specialized recording devices that naturally - cause a scalar offset with respect to the true units. - range: float32 - resolution: - name: resolution - description: Smallest meaningful difference between values in data, stored - in the specified by unit, e.g., the change in value of the least significant - bit, or a larger number if signal noise is known to be present. If unknown, - use -1.0. - range: float32 - unit: - name: unit - description: Base unit of measurement for working with the data. Actual stored - values are not necessarily stored in these units. To access the data in - these units, multiply 'data' by 'conversion' and add 'offset'. - range: text - continuity: - name: continuity - description: Optionally describe the continuity of the data. Can be "continuous", - "instantaneous", or "step". For example, a voltage trace would be "continuous", - because samples are recorded from a continuous process. An array of lick - times would be "instantaneous", because the data represents distinct moments - in time. Times of image presentations would be "step" because the picture - remains the same until the next timepoint. This field is optional, but is - useful in providing information about the underlying data. It may inform - the way this data is interpreted, the way it is visualized, and what analysis - methods are applicable. - range: text - array: - name: array - range: TimeSeries_data_Array - TimeSeries_data_Array: - name: TimeSeries_data_Array - is_a: Arraylike - attributes: - num_times: - name: num_times - range: AnyType - required: true - num_DIM2: - name: num_DIM2 - range: AnyType - required: false - num_DIM3: - name: num_DIM3 - range: AnyType - required: false - num_DIM4: - name: num_DIM4 - range: AnyType - required: false - TimeSeries_starting_time: - name: TimeSeries_starting_time - description: Timestamp of the first sample in seconds. When timestamps are uniformly - spaced, the timestamp of the first sample can be specified and all subsequent - ones calculated from the sampling rate attribute. - attributes: - rate: - name: rate - description: Sampling rate, in Hz. - range: float32 - unit: - name: unit - description: Unit of measurement for time, which is fixed to 'seconds'. - range: text - TimeSeries_timestamps: - name: TimeSeries_timestamps - description: Timestamps for samples stored in data, in seconds, relative to the - common experiment master-clock stored in NWBFile.timestamps_reference_time. - attributes: - interval: - name: interval - description: Value is '1' - range: int32 - unit: - name: unit - description: Unit of measurement for timestamps, which is fixed to 'seconds'. - range: text - array: - name: array - range: TimeSeries_timestamps_Array - TimeSeries_timestamps_Array: - name: TimeSeries_timestamps_Array - is_a: Arraylike - attributes: - num_times: - name: num_times - range: float64 - required: true - TimeSeries_control: - name: TimeSeries_control - description: Numerical labels that apply to each time point in data for the purpose - of querying and slicing data by these values. If present, the length of this - array should be the same size as the first dimension of data. - attributes: - array: - name: array - range: TimeSeries_control_Array - TimeSeries_control_Array: - name: TimeSeries_control_Array - is_a: Arraylike - attributes: - num_times: - name: num_times - range: uint8 - required: true - TimeSeries_control_description: - name: TimeSeries_control_description - description: Description of each control value. Must be present if control is - present. If present, control_description[0] should describe time points where - control == 0. - attributes: - array: - name: array - range: TimeSeries_control_description_Array - TimeSeries_control_description_Array: - name: TimeSeries_control_description_Array - is_a: Arraylike - attributes: - num_control_values: - name: num_control_values - range: text - required: true - TimeSeries_sync: - name: TimeSeries_sync - description: Lab-specific time and sync information as provided directly from - hardware devices and that is necessary for aligning all acquired time information - to a common timebase. The timestamp array stores time in the common timebase. - This group will usually only be populated in TimeSeries that are stored external - to the NWB file, in files storing raw data. Once timestamp data is calculated, - the contents of 'sync' are mostly for archival purposes. ProcessingModule: name: ProcessingModule description: A collection of processed data. @@ -349,11 +165,5 @@ classes: and only once, so the dataset should have the same length as the number of images. multivalued: false - range: Images_order_of_images + range: Images__order_of_images required: false - Images_order_of_images: - name: Images_order_of_images - description: Ordered dataset of references to Image objects stored in the parent - group. Each Image object in the Images group should be stored once and only - once, so the dataset should have the same length as the number of images. - is_a: ImageReferences diff --git a/nwb_linkml/schema/core.nwb.behavior.include.yaml b/nwb_linkml/schema/core.nwb.behavior.include.yaml new file mode 100644 index 0000000..443d975 --- /dev/null +++ b/nwb_linkml/schema/core.nwb.behavior.include.yaml @@ -0,0 +1,51 @@ +name: core.nwb.behavior.include +id: core.nwb.behavior.include +imports: +- core.nwb.base +- core.nwb.misc +- nwb.language +- core.nwb.behavior.include +- core.nwb.behavior +default_prefix: core.nwb.behavior.include/ +classes: + SpatialSeries__data: + name: SpatialSeries__data + description: 1-D or 2-D array storing position or direction relative to some reference + frame. + attributes: + unit: + name: unit + description: Base unit of measurement for working with the data. The default + value is 'meters'. Actual stored values are not necessarily stored in these + units. To access the data in these units, multiply 'data' by 'conversion' + and add 'offset'. + range: text + array: + name: array + range: SpatialSeries__data__Array + SpatialSeries__data__Array: + name: SpatialSeries__data__Array + is_a: Arraylike + attributes: + num_times: + name: num_times + range: numeric + required: true + x: + name: x + range: numeric + required: false + minimum_cardinality: 1 + maximum_cardinality: 1 + x,y: + name: x,y + range: numeric + required: false + minimum_cardinality: 2 + maximum_cardinality: 2 + x,y,z: + name: x,y,z + range: numeric + required: false + minimum_cardinality: 3 + maximum_cardinality: 3 diff --git a/nwb_linkml/schema/core.nwb.behavior.yaml b/nwb_linkml/schema/core.nwb.behavior.yaml index 6085844..05179cc 100644 --- a/nwb_linkml/schema/core.nwb.behavior.yaml +++ b/nwb_linkml/schema/core.nwb.behavior.yaml @@ -4,6 +4,8 @@ imports: - core.nwb.base - core.nwb.misc - nwb.language +- core.nwb.behavior.include +- core.nwb.behavior default_prefix: core.nwb.behavior/ classes: SpatialSeries: @@ -24,58 +26,14 @@ classes: description: 1-D or 2-D array storing position or direction relative to some reference frame. multivalued: false - range: SpatialSeries_data + range: SpatialSeries__data required: true reference_frame: name: reference_frame description: Description defining what exactly 'straight-ahead' means. multivalued: false - range: SpatialSeries_reference_frame - required: false - SpatialSeries_data: - name: SpatialSeries_data - description: 1-D or 2-D array storing position or direction relative to some reference - frame. - attributes: - unit: - name: unit - description: Base unit of measurement for working with the data. The default - value is 'meters'. Actual stored values are not necessarily stored in these - units. To access the data in these units, multiply 'data' by 'conversion' - and add 'offset'. range: text - array: - name: array - range: SpatialSeries_data_Array - SpatialSeries_data_Array: - name: SpatialSeries_data_Array - is_a: Arraylike - attributes: - num_times: - name: num_times - range: numeric - required: true - x: - name: x - range: numeric required: false - minimum_cardinality: 1 - maximum_cardinality: 1 - x,y: - name: x,y - range: numeric - required: false - minimum_cardinality: 2 - maximum_cardinality: 2 - x,y,z: - name: x,y,z - range: numeric - required: false - minimum_cardinality: 3 - maximum_cardinality: 3 - SpatialSeries_reference_frame: - name: SpatialSeries_reference_frame - description: Description defining what exactly 'straight-ahead' means. BehavioralEpochs: name: BehavioralEpochs description: TimeSeries for storing behavioral epochs. The objective of this diff --git a/nwb_linkml/schema/core.nwb.device.include.yaml b/nwb_linkml/schema/core.nwb.device.include.yaml new file mode 100644 index 0000000..21c602f --- /dev/null +++ b/nwb_linkml/schema/core.nwb.device.include.yaml @@ -0,0 +1,8 @@ +name: core.nwb.device.include +id: core.nwb.device.include +imports: +- core.nwb.base +- nwb.language +- core.nwb.device.include +- core.nwb.device +default_prefix: core.nwb.device.include/ diff --git a/nwb_linkml/schema/core.nwb.device.yaml b/nwb_linkml/schema/core.nwb.device.yaml index 211924a..be9727d 100644 --- a/nwb_linkml/schema/core.nwb.device.yaml +++ b/nwb_linkml/schema/core.nwb.device.yaml @@ -3,6 +3,8 @@ id: core.nwb.device imports: - core.nwb.base - nwb.language +- core.nwb.device.include +- core.nwb.device default_prefix: core.nwb.device/ classes: Device: diff --git a/nwb_linkml/schema/core.nwb.ecephys.include.yaml b/nwb_linkml/schema/core.nwb.ecephys.include.yaml new file mode 100644 index 0000000..bacdea1 --- /dev/null +++ b/nwb_linkml/schema/core.nwb.ecephys.include.yaml @@ -0,0 +1,283 @@ +name: core.nwb.ecephys.include +id: core.nwb.ecephys.include +imports: +- core.nwb.base +- hdmf-common.table +- core.nwb.device +- nwb.language +- core.nwb.ecephys.include +- core.nwb.ecephys +default_prefix: core.nwb.ecephys.include/ +classes: + ElectricalSeries__data: + name: ElectricalSeries__data + description: Recorded voltage data. + attributes: + unit: + name: unit + description: Base unit of measurement for working with the data. This value + is fixed to 'volts'. Actual stored values are not necessarily stored in + these units. To access the data in these units, multiply 'data' by 'conversion', + followed by 'channel_conversion' (if present), and then add 'offset'. + range: text + array: + name: array + range: ElectricalSeries__data__Array + ElectricalSeries__data__Array: + name: ElectricalSeries__data__Array + is_a: Arraylike + attributes: + num_times: + name: num_times + range: numeric + required: true + num_channels: + name: num_channels + range: numeric + required: false + num_samples: + name: num_samples + range: numeric + required: false + ElectricalSeries__electrodes: + name: ElectricalSeries__electrodes + description: DynamicTableRegion pointer to the electrodes that this time series + was generated from. + is_a: DynamicTableRegion + ElectricalSeries__channel_conversion: + name: ElectricalSeries__channel_conversion + description: Channel-specific conversion factor. Multiply the data in the 'data' + dataset by these values along the channel axis (as indicated by axis attribute) + AND by the global conversion factor in the 'conversion' attribute of 'data' + to get the data values in Volts, i.e, data in Volts = data * data.conversion + * channel_conversion. This approach allows for both global and per-channel data + conversion factors needed to support the storage of electrical recordings as + native values generated by data acquisition systems. If this dataset is not + present, then there is no channel-specific conversion factor, i.e. it is 1 for + all channels. + attributes: + axis: + name: axis + description: The zero-indexed axis of the 'data' dataset that the channel-specific + conversion factor corresponds to. This value is fixed to 1. + range: int32 + channel_conversion: + name: channel_conversion + description: Channel-specific conversion factor. Multiply the data in the + 'data' dataset by these values along the channel axis (as indicated by axis + attribute) AND by the global conversion factor in the 'conversion' attribute + of 'data' to get the data values in Volts, i.e, data in Volts = data * data.conversion + * channel_conversion. This approach allows for both global and per-channel + data conversion factors needed to support the storage of electrical recordings + as native values generated by data acquisition systems. If this dataset + is not present, then there is no channel-specific conversion factor, i.e. + it is 1 for all channels. + multivalued: true + range: float32 + required: false + SpikeEventSeries__data: + name: SpikeEventSeries__data + description: Spike waveforms. + attributes: + unit: + name: unit + description: Unit of measurement for waveforms, which is fixed to 'volts'. + range: text + array: + name: array + range: SpikeEventSeries__data__Array + SpikeEventSeries__data__Array: + name: SpikeEventSeries__data__Array + is_a: Arraylike + attributes: + num_events: + name: num_events + range: numeric + required: true + num_samples: + name: num_samples + range: numeric + required: true + num_channels: + name: num_channels + range: numeric + required: false + SpikeEventSeries__timestamps: + name: SpikeEventSeries__timestamps + description: Timestamps for samples stored in data, in seconds, relative to the + common experiment master-clock stored in NWBFile.timestamps_reference_time. + Timestamps are required for the events. Unlike for TimeSeries, timestamps are + required for SpikeEventSeries and are thus re-specified here. + attributes: + interval: + name: interval + description: Value is '1' + range: int32 + unit: + name: unit + description: Unit of measurement for timestamps, which is fixed to 'seconds'. + range: text + timestamps: + name: timestamps + description: Timestamps for samples stored in data, in seconds, relative to + the common experiment master-clock stored in NWBFile.timestamps_reference_time. + Timestamps are required for the events. Unlike for TimeSeries, timestamps + are required for SpikeEventSeries and are thus re-specified here. + multivalued: true + range: float64 + required: true + FeatureExtraction__description: + name: FeatureExtraction__description + description: Description of features (eg, ''PC1'') for each of the extracted features. + attributes: + description: + name: description + description: Description of features (eg, ''PC1'') for each of the extracted + features. + multivalued: true + range: text + required: true + FeatureExtraction__features: + name: FeatureExtraction__features + description: Multi-dimensional array of features extracted from each event. + attributes: + array: + name: array + range: FeatureExtraction__features__Array + FeatureExtraction__features__Array: + name: FeatureExtraction__features__Array + is_a: Arraylike + attributes: + num_events: + name: num_events + range: float32 + required: false + num_channels: + name: num_channels + range: float32 + required: false + num_features: + name: num_features + range: float32 + required: false + FeatureExtraction__times: + name: FeatureExtraction__times + description: Times of events that features correspond to (can be a link). + attributes: + times: + name: times + description: Times of events that features correspond to (can be a link). + multivalued: true + range: float64 + required: true + FeatureExtraction__electrodes: + name: FeatureExtraction__electrodes + description: DynamicTableRegion pointer to the electrodes that this time series + was generated from. + is_a: DynamicTableRegion + EventDetection__source_idx: + name: EventDetection__source_idx + description: Indices (zero-based) into source ElectricalSeries::data array corresponding + to time of event. ''description'' should define what is meant by time of event + (e.g., .25 ms before action potential peak, zero-crossing time, etc). The index + points to each event from the raw data. + attributes: + source_idx: + name: source_idx + description: Indices (zero-based) into source ElectricalSeries::data array + corresponding to time of event. ''description'' should define what is meant + by time of event (e.g., .25 ms before action potential peak, zero-crossing + time, etc). The index points to each event from the raw data. + multivalued: true + range: int32 + required: true + EventDetection__times: + name: EventDetection__times + description: Timestamps of events, in seconds. + attributes: + unit: + name: unit + description: Unit of measurement for event times, which is fixed to 'seconds'. + range: text + times: + name: times + description: Timestamps of events, in seconds. + multivalued: true + range: float64 + required: true + ClusterWaveforms__waveform_mean: + name: ClusterWaveforms__waveform_mean + description: The mean waveform for each cluster, using the same indices for each + wave as cluster numbers in the associated Clustering module (i.e, cluster 3 + is in array slot [3]). Waveforms corresponding to gaps in cluster sequence should + be empty (e.g., zero- filled) + attributes: + array: + name: array + range: ClusterWaveforms__waveform_mean__Array + ClusterWaveforms__waveform_mean__Array: + name: ClusterWaveforms__waveform_mean__Array + is_a: Arraylike + attributes: + num_clusters: + name: num_clusters + range: float32 + required: false + num_samples: + name: num_samples + range: float32 + required: false + ClusterWaveforms__waveform_sd: + name: ClusterWaveforms__waveform_sd + description: Stdev of waveforms for each cluster, using the same indices as in + mean + attributes: + array: + name: array + range: ClusterWaveforms__waveform_sd__Array + ClusterWaveforms__waveform_sd__Array: + name: ClusterWaveforms__waveform_sd__Array + is_a: Arraylike + attributes: + num_clusters: + name: num_clusters + range: float32 + required: false + num_samples: + name: num_samples + range: float32 + required: false + Clustering__num: + name: Clustering__num + description: Cluster number of each event + attributes: + num: + name: num + description: Cluster number of each event + multivalued: true + range: int32 + required: true + Clustering__peak_over_rms: + name: Clustering__peak_over_rms + description: Maximum ratio of waveform peak to RMS on any channel in the cluster + (provides a basic clustering metric). + attributes: + peak_over_rms: + name: peak_over_rms + description: Maximum ratio of waveform peak to RMS on any channel in the cluster + (provides a basic clustering metric). + multivalued: true + range: float32 + required: true + Clustering__times: + name: Clustering__times + description: Times of clustered events, in seconds. This may be a link to times + field in associated FeatureExtraction module. + attributes: + times: + name: times + description: Times of clustered events, in seconds. This may be a link to + times field in associated FeatureExtraction module. + multivalued: true + range: float64 + required: true diff --git a/nwb_linkml/schema/core.nwb.ecephys.yaml b/nwb_linkml/schema/core.nwb.ecephys.yaml index 0ee3375..20d9905 100644 --- a/nwb_linkml/schema/core.nwb.ecephys.yaml +++ b/nwb_linkml/schema/core.nwb.ecephys.yaml @@ -3,7 +3,10 @@ id: core.nwb.ecephys imports: - core.nwb.base - hdmf-common.table +- core.nwb.device - nwb.language +- core.nwb.ecephys.include +- core.nwb.ecephys default_prefix: core.nwb.ecephys/ classes: ElectricalSeries: @@ -28,14 +31,14 @@ classes: name: data description: Recorded voltage data. multivalued: false - range: ElectricalSeries_data + range: ElectricalSeries__data required: true electrodes: name: electrodes description: DynamicTableRegion pointer to the electrodes that this time series was generated from. multivalued: false - range: ElectricalSeries_electrodes + range: ElectricalSeries__electrodes required: true channel_conversion: name: channel_conversion @@ -49,71 +52,8 @@ classes: is not present, then there is no channel-specific conversion factor, i.e. it is 1 for all channels. multivalued: false - range: ElectricalSeries_channel_conversion + range: ElectricalSeries__channel_conversion required: false - ElectricalSeries_data: - name: ElectricalSeries_data - description: Recorded voltage data. - attributes: - unit: - name: unit - description: Base unit of measurement for working with the data. This value - is fixed to 'volts'. Actual stored values are not necessarily stored in - these units. To access the data in these units, multiply 'data' by 'conversion', - followed by 'channel_conversion' (if present), and then add 'offset'. - range: text - array: - name: array - range: ElectricalSeries_data_Array - ElectricalSeries_data_Array: - name: ElectricalSeries_data_Array - is_a: Arraylike - attributes: - num_times: - name: num_times - range: numeric - required: true - num_channels: - name: num_channels - range: numeric - required: false - num_samples: - name: num_samples - range: numeric - required: false - ElectricalSeries_electrodes: - name: ElectricalSeries_electrodes - description: DynamicTableRegion pointer to the electrodes that this time series - was generated from. - is_a: DynamicTableRegion - ElectricalSeries_channel_conversion: - name: ElectricalSeries_channel_conversion - description: Channel-specific conversion factor. Multiply the data in the 'data' - dataset by these values along the channel axis (as indicated by axis attribute) - AND by the global conversion factor in the 'conversion' attribute of 'data' - to get the data values in Volts, i.e, data in Volts = data * data.conversion - * channel_conversion. This approach allows for both global and per-channel data - conversion factors needed to support the storage of electrical recordings as - native values generated by data acquisition systems. If this dataset is not - present, then there is no channel-specific conversion factor, i.e. it is 1 for - all channels. - attributes: - axis: - name: axis - description: The zero-indexed axis of the 'data' dataset that the channel-specific - conversion factor corresponds to. This value is fixed to 1. - range: int32 - array: - name: array - range: ElectricalSeries_channel_conversion_Array - ElectricalSeries_channel_conversion_Array: - name: ElectricalSeries_channel_conversion_Array - is_a: Arraylike - attributes: - num_channels: - name: num_channels - range: float32 - required: true SpikeEventSeries: name: SpikeEventSeries description: 'Stores snapshots/snippets of recorded spike events (i.e., threshold @@ -130,7 +70,7 @@ classes: name: data description: Spike waveforms. multivalued: false - range: SpikeEventSeries_data + range: SpikeEventSeries__data required: true timestamps: name: timestamps @@ -139,60 +79,7 @@ classes: Timestamps are required for the events. Unlike for TimeSeries, timestamps are required for SpikeEventSeries and are thus re-specified here. multivalued: false - range: SpikeEventSeries_timestamps - required: true - SpikeEventSeries_data: - name: SpikeEventSeries_data - description: Spike waveforms. - attributes: - unit: - name: unit - description: Unit of measurement for waveforms, which is fixed to 'volts'. - range: text - array: - name: array - range: SpikeEventSeries_data_Array - SpikeEventSeries_data_Array: - name: SpikeEventSeries_data_Array - is_a: Arraylike - attributes: - num_events: - name: num_events - range: numeric - required: true - num_samples: - name: num_samples - range: numeric - required: true - num_channels: - name: num_channels - range: numeric - required: false - SpikeEventSeries_timestamps: - name: SpikeEventSeries_timestamps - description: Timestamps for samples stored in data, in seconds, relative to the - common experiment master-clock stored in NWBFile.timestamps_reference_time. - Timestamps are required for the events. Unlike for TimeSeries, timestamps are - required for SpikeEventSeries and are thus re-specified here. - attributes: - interval: - name: interval - description: Value is '1' - range: int32 - unit: - name: unit - description: Unit of measurement for timestamps, which is fixed to 'seconds'. - range: text - array: - name: array - range: SpikeEventSeries_timestamps_Array - SpikeEventSeries_timestamps_Array: - name: SpikeEventSeries_timestamps_Array - is_a: Arraylike - attributes: - num_times: - name: num_times - range: float64 + range: SpikeEventSeries__timestamps required: true FeatureExtraction: name: FeatureExtraction @@ -205,85 +92,27 @@ classes: description: Description of features (eg, ''PC1'') for each of the extracted features. multivalued: false - range: FeatureExtraction_description + range: FeatureExtraction__description required: true features: name: features description: Multi-dimensional array of features extracted from each event. multivalued: false - range: FeatureExtraction_features + range: FeatureExtraction__features required: true times: name: times description: Times of events that features correspond to (can be a link). multivalued: false - range: FeatureExtraction_times + range: FeatureExtraction__times required: true electrodes: name: electrodes description: DynamicTableRegion pointer to the electrodes that this time series was generated from. multivalued: false - range: FeatureExtraction_electrodes + range: FeatureExtraction__electrodes required: true - FeatureExtraction_description: - name: FeatureExtraction_description - description: Description of features (eg, ''PC1'') for each of the extracted features. - attributes: - array: - name: array - range: FeatureExtraction_description_Array - FeatureExtraction_description_Array: - name: FeatureExtraction_description_Array - is_a: Arraylike - attributes: - num_features: - name: num_features - range: text - required: true - FeatureExtraction_features: - name: FeatureExtraction_features - description: Multi-dimensional array of features extracted from each event. - attributes: - array: - name: array - range: FeatureExtraction_features_Array - FeatureExtraction_features_Array: - name: FeatureExtraction_features_Array - is_a: Arraylike - attributes: - num_events: - name: num_events - range: float32 - required: false - num_channels: - name: num_channels - range: float32 - required: false - num_features: - name: num_features - range: float32 - required: false - FeatureExtraction_times: - name: FeatureExtraction_times - description: Times of events that features correspond to (can be a link). - attributes: - array: - name: array - range: FeatureExtraction_times_Array - FeatureExtraction_times_Array: - name: FeatureExtraction_times_Array - is_a: Arraylike - attributes: - num_events: - name: num_events - range: float64 - required: true - FeatureExtraction_electrodes: - name: FeatureExtraction_electrodes - description: DynamicTableRegion pointer to the electrodes that this time series - was generated from. - is_a: DynamicTableRegion EventDetection: name: EventDetection description: Detected spike events from voltage trace(s). @@ -294,7 +123,7 @@ classes: description: Description of how events were detected, such as voltage threshold, or dV/dT threshold, as well as relevant values. multivalued: false - range: EventDetection_detection_method + range: text required: true source_idx: name: source_idx @@ -303,54 +132,13 @@ classes: by time of event (e.g., .25 ms before action potential peak, zero-crossing time, etc). The index points to each event from the raw data. multivalued: false - range: EventDetection_source_idx + range: EventDetection__source_idx required: true times: name: times description: Timestamps of events, in seconds. multivalued: false - range: EventDetection_times - required: true - EventDetection_detection_method: - name: EventDetection_detection_method - description: Description of how events were detected, such as voltage threshold, - or dV/dT threshold, as well as relevant values. - EventDetection_source_idx: - name: EventDetection_source_idx - description: Indices (zero-based) into source ElectricalSeries::data array corresponding - to time of event. ''description'' should define what is meant by time of event - (e.g., .25 ms before action potential peak, zero-crossing time, etc). The index - points to each event from the raw data. - attributes: - array: - name: array - range: EventDetection_source_idx_Array - EventDetection_source_idx_Array: - name: EventDetection_source_idx_Array - is_a: Arraylike - attributes: - num_events: - name: num_events - range: int32 - required: true - EventDetection_times: - name: EventDetection_times - description: Timestamps of events, in seconds. - attributes: - unit: - name: unit - description: Unit of measurement for event times, which is fixed to 'seconds'. - range: text - array: - name: array - range: EventDetection_times_Array - EventDetection_times_Array: - name: EventDetection_times_Array - is_a: Arraylike - attributes: - num_events: - name: num_events - range: float64 + range: EventDetection__times required: true EventWaveform: name: EventWaveform @@ -420,11 +208,8 @@ classes: name: position description: stereotaxic or common framework coordinates multivalued: false - range: ElectrodeGroup_position + range: AnyType required: false - ElectrodeGroup_position: - name: ElectrodeGroup_position - description: stereotaxic or common framework coordinates ClusterWaveforms: name: ClusterWaveforms description: DEPRECATED The mean waveform shape, including standard deviation, @@ -439,7 +224,7 @@ classes: name: waveform_filtering description: Filtering applied to data before generating mean/sd multivalued: false - range: ClusterWaveforms_waveform_filtering + range: text required: true waveform_mean: name: waveform_mean @@ -448,60 +233,15 @@ classes: 3 is in array slot [3]). Waveforms corresponding to gaps in cluster sequence should be empty (e.g., zero- filled) multivalued: false - range: ClusterWaveforms_waveform_mean + range: ClusterWaveforms__waveform_mean required: true waveform_sd: name: waveform_sd description: Stdev of waveforms for each cluster, using the same indices as in mean multivalued: false - range: ClusterWaveforms_waveform_sd + range: ClusterWaveforms__waveform_sd required: true - ClusterWaveforms_waveform_filtering: - name: ClusterWaveforms_waveform_filtering - description: Filtering applied to data before generating mean/sd - ClusterWaveforms_waveform_mean: - name: ClusterWaveforms_waveform_mean - description: The mean waveform for each cluster, using the same indices for each - wave as cluster numbers in the associated Clustering module (i.e, cluster 3 - is in array slot [3]). Waveforms corresponding to gaps in cluster sequence should - be empty (e.g., zero- filled) - attributes: - array: - name: array - range: ClusterWaveforms_waveform_mean_Array - ClusterWaveforms_waveform_mean_Array: - name: ClusterWaveforms_waveform_mean_Array - is_a: Arraylike - attributes: - num_clusters: - name: num_clusters - range: float32 - required: false - num_samples: - name: num_samples - range: float32 - required: false - ClusterWaveforms_waveform_sd: - name: ClusterWaveforms_waveform_sd - description: Stdev of waveforms for each cluster, using the same indices as in - mean - attributes: - array: - name: array - range: ClusterWaveforms_waveform_sd_Array - ClusterWaveforms_waveform_sd_Array: - name: ClusterWaveforms_waveform_sd_Array - is_a: Arraylike - attributes: - num_clusters: - name: num_clusters - range: float32 - required: false - num_samples: - name: num_samples - range: float32 - required: false Clustering: name: Clustering description: DEPRECATED Clustered spike data, whether from automatic clustering @@ -513,76 +253,25 @@ classes: description: Description of clusters or clustering, (e.g. cluster 0 is noise, clusters curated using Klusters, etc) multivalued: false - range: Clustering_description + range: text required: true num: name: num description: Cluster number of each event multivalued: false - range: Clustering_num + range: Clustering__num required: true peak_over_rms: name: peak_over_rms description: Maximum ratio of waveform peak to RMS on any channel in the cluster (provides a basic clustering metric). multivalued: false - range: Clustering_peak_over_rms + range: Clustering__peak_over_rms required: true times: name: times description: Times of clustered events, in seconds. This may be a link to times field in associated FeatureExtraction module. multivalued: false - range: Clustering_times - required: true - Clustering_description: - name: Clustering_description - description: Description of clusters or clustering, (e.g. cluster 0 is noise, - clusters curated using Klusters, etc) - Clustering_num: - name: Clustering_num - description: Cluster number of each event - attributes: - array: - name: array - range: Clustering_num_Array - Clustering_num_Array: - name: Clustering_num_Array - is_a: Arraylike - attributes: - num_events: - name: num_events - range: int32 - required: true - Clustering_peak_over_rms: - name: Clustering_peak_over_rms - description: Maximum ratio of waveform peak to RMS on any channel in the cluster - (provides a basic clustering metric). - attributes: - array: - name: array - range: Clustering_peak_over_rms_Array - Clustering_peak_over_rms_Array: - name: Clustering_peak_over_rms_Array - is_a: Arraylike - attributes: - num_clusters: - name: num_clusters - range: float32 - required: true - Clustering_times: - name: Clustering_times - description: Times of clustered events, in seconds. This may be a link to times - field in associated FeatureExtraction module. - attributes: - array: - name: array - range: Clustering_times_Array - Clustering_times_Array: - name: Clustering_times_Array - is_a: Arraylike - attributes: - num_events: - name: num_events - range: float64 + range: Clustering__times required: true diff --git a/nwb_linkml/schema/core.nwb.epoch.include.yaml b/nwb_linkml/schema/core.nwb.epoch.include.yaml new file mode 100644 index 0000000..cfcded2 --- /dev/null +++ b/nwb_linkml/schema/core.nwb.epoch.include.yaml @@ -0,0 +1,22 @@ +name: core.nwb.epoch.include +id: core.nwb.epoch.include +imports: +- hdmf-common.table +- core.nwb.base +- nwb.language +- core.nwb.epoch.include +- core.nwb.epoch +default_prefix: core.nwb.epoch.include/ +classes: + TimeIntervals__tags_index: + name: TimeIntervals__tags_index + description: Index for tags. + is_a: VectorIndex + TimeIntervals__timeseries: + name: TimeIntervals__timeseries + description: An index into a TimeSeries object. + is_a: TimeSeriesReferenceVectorData + TimeIntervals__timeseries_index: + name: TimeIntervals__timeseries_index + description: Index for timeseries. + is_a: VectorIndex diff --git a/nwb_linkml/schema/core.nwb.epoch.yaml b/nwb_linkml/schema/core.nwb.epoch.yaml index 9cc46e8..70e900d 100644 --- a/nwb_linkml/schema/core.nwb.epoch.yaml +++ b/nwb_linkml/schema/core.nwb.epoch.yaml @@ -4,6 +4,8 @@ imports: - hdmf-common.table - core.nwb.base - nwb.language +- core.nwb.epoch.include +- core.nwb.epoch default_prefix: core.nwb.epoch/ classes: TimeIntervals: @@ -15,60 +17,33 @@ classes: start_time: name: start_time description: Start time of epoch, in seconds. - multivalued: false - range: TimeIntervals_start_time - required: true + multivalued: true + range: float32 stop_time: name: stop_time description: Stop time of epoch, in seconds. - multivalued: false - range: TimeIntervals_stop_time - required: true + multivalued: true + range: float32 tags: name: tags description: User-defined tags that identify or categorize events. - multivalued: false - range: TimeIntervals_tags - required: false + multivalued: true + range: text tags_index: name: tags_index description: Index for tags. multivalued: false - range: TimeIntervals_tags_index + range: TimeIntervals__tags_index required: false timeseries: name: timeseries description: An index into a TimeSeries object. multivalued: false - range: TimeIntervals_timeseries + range: TimeIntervals__timeseries required: false timeseries_index: name: timeseries_index description: Index for timeseries. multivalued: false - range: TimeIntervals_timeseries_index + range: TimeIntervals__timeseries_index required: false - TimeIntervals_start_time: - name: TimeIntervals_start_time - description: Start time of epoch, in seconds. - is_a: VectorData - TimeIntervals_stop_time: - name: TimeIntervals_stop_time - description: Stop time of epoch, in seconds. - is_a: VectorData - TimeIntervals_tags: - name: TimeIntervals_tags - description: User-defined tags that identify or categorize events. - is_a: VectorData - TimeIntervals_tags_index: - name: TimeIntervals_tags_index - description: Index for tags. - is_a: VectorIndex - TimeIntervals_timeseries: - name: TimeIntervals_timeseries - description: An index into a TimeSeries object. - is_a: TimeSeriesReferenceVectorData - TimeIntervals_timeseries_index: - name: TimeIntervals_timeseries_index - description: Index for timeseries. - is_a: VectorIndex diff --git a/nwb_linkml/schema/core.nwb.file.include.yaml b/nwb_linkml/schema/core.nwb.file.include.yaml new file mode 100644 index 0000000..1ee679c --- /dev/null +++ b/nwb_linkml/schema/core.nwb.file.include.yaml @@ -0,0 +1,695 @@ +name: core.nwb.file.include +id: core.nwb.file.include +imports: +- core.nwb.base +- hdmf-common.table +- core.nwb.device +- core.nwb.ecephys +- core.nwb.icephys +- core.nwb.ogen +- core.nwb.ophys +- core.nwb.epoch +- core.nwb.misc +- nwb.language +- core.nwb.file.include +- core.nwb.file +default_prefix: core.nwb.file.include/ +classes: + NWBFile__file_create_date: + name: NWBFile__file_create_date + description: 'A record of the date the file was created and of subsequent modifications. + The date is stored in UTC with local timezone offset as ISO 8601 extended formatted + strings: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in "Z" with + no timezone offset. Date accuracy is up to milliseconds. The file can be created + after the experiment was run, so this may differ from the experiment start time. + Each modification to the nwb file adds a new entry to the array.' + attributes: + file_create_date: + name: file_create_date + description: 'A record of the date the file was created and of subsequent + modifications. The date is stored in UTC with local timezone offset as ISO + 8601 extended formatted strings: 2018-09-28T14:43:54.123+02:00. Dates stored + in UTC end in "Z" with no timezone offset. Date accuracy is up to milliseconds. + The file can be created after the experiment was run, so this may differ + from the experiment start time. Each modification to the nwb file adds a + new entry to the array.' + multivalued: true + range: isodatetime + required: true + NWBFile__acquisition: + name: NWBFile__acquisition + description: Data streams recorded from the system, including ephys, ophys, tracking, + etc. This group should be read-only after the experiment is completed and timestamps + are corrected to a common timebase. The data stored here may be links to raw + data stored in external NWB files. This will allow keeping bulky raw data out + of the file while preserving the option of keeping some/all in the file. Acquired + data includes tracking and experimental data streams (i.e., everything measured + from the system). If bulky data is stored in the /acquisition group, the data + can exist in a separate NWB file that is linked to by the file being used for + processing and analysis. + attributes: + NWBDataInterface: + name: NWBDataInterface + description: Acquired, raw data. + multivalued: true + range: NWBDataInterface + required: false + DynamicTable: + name: DynamicTable + description: Tabular data that is relevant to acquisition + multivalued: true + range: DynamicTable + required: false + NWBFile__analysis: + name: NWBFile__analysis + description: Lab-specific and custom scientific analysis of data. There is no + defined format for the content of this group - the format is up to the individual + user/lab. To facilitate sharing analysis data between labs, the contents here + should be stored in standard types (e.g., neurodata_types) and appropriately + documented. The file can store lab-specific and custom data analysis without + restriction on its form or schema, reducing data formatting restrictions on + end users. Such data should be placed in the analysis group. The analysis data + should be documented so that it could be shared with other labs. + attributes: + NWBContainer: + name: NWBContainer + description: Custom analysis results. + multivalued: true + range: NWBContainer + required: false + DynamicTable: + name: DynamicTable + description: Tabular data that is relevant to data stored in analysis + multivalued: true + range: DynamicTable + required: false + NWBFile__scratch: + name: NWBFile__scratch + description: A place to store one-off analysis results. Data placed here is not + intended for sharing. By placing data here, users acknowledge that there is + no guarantee that their data meets any standard. + attributes: + ScratchData: + name: ScratchData + description: Any one-off datasets + multivalued: true + range: ScratchData + required: false + NWBContainer: + name: NWBContainer + description: Any one-off containers + multivalued: true + range: NWBContainer + required: false + DynamicTable: + name: DynamicTable + description: Any one-off tables + multivalued: true + range: DynamicTable + required: false + NWBFile__processing: + name: NWBFile__processing + description: The home for ProcessingModules. These modules perform intermediate + analysis of data that is necessary to perform before scientific analysis. Examples + include spike clustering, extracting position from tracking data, stitching + together image slices. ProcessingModules can be large and express many data + sets from relatively complex analysis (e.g., spike detection and clustering) + or small, representing extraction of position information from tracking video, + or even binary lick/no-lick decisions. Common software tools (e.g., klustakwik, + MClust) are expected to read/write data here. 'Processing' refers to intermediate + analysis of the acquired data to make it more amenable to scientific analysis. + attributes: + ProcessingModule: + name: ProcessingModule + description: Intermediate analysis of acquired data. + multivalued: true + range: ProcessingModule + required: false + NWBFile__stimulus: + name: NWBFile__stimulus + description: Data pushed into the system (eg, video stimulus, sound, voltage, + etc) and secondary representations of that data (eg, measurements of something + used as a stimulus). This group should be made read-only after experiment complete + and timestamps are corrected to common timebase. Stores both presented stimuli + and stimulus templates, the latter in case the same stimulus is presented multiple + times, or is pulled from an external stimulus library. Stimuli are here defined + as any signal that is pushed into the system as part of the experiment (eg, + sound, video, voltage, etc). Many different experiments can use the same stimuli, + and stimuli can be re-used during an experiment. The stimulus group is organized + so that one version of template stimuli can be stored and these be used multiple + times. These templates can exist in the present file or can be linked to a remote + library file. + attributes: + presentation: + name: presentation + description: Stimuli presented during the experiment. + multivalued: false + range: NWBFile__stimulus__presentation + required: true + templates: + name: templates + description: Template stimuli. Timestamps in templates are based on stimulus + design and are relative to the beginning of the stimulus. When templates + are used, the stimulus instances must convert presentation times to the + experiment`s time reference frame. + multivalued: false + range: NWBFile__stimulus__templates + required: true + NWBFile__stimulus__presentation: + name: NWBFile__stimulus__presentation + description: Stimuli presented during the experiment. + attributes: + TimeSeries: + name: TimeSeries + description: TimeSeries objects containing data of presented stimuli. + multivalued: true + range: TimeSeries + required: false + NWBFile__stimulus__templates: + name: NWBFile__stimulus__templates + description: Template stimuli. Timestamps in templates are based on stimulus design + and are relative to the beginning of the stimulus. When templates are used, + the stimulus instances must convert presentation times to the experiment`s time + reference frame. + attributes: + TimeSeries: + name: TimeSeries + description: TimeSeries objects containing template data of presented stimuli. + multivalued: true + range: TimeSeries + required: false + Images: + name: Images + description: Images objects containing images of presented stimuli. + multivalued: true + range: Images + required: false + NWBFile__general: + name: NWBFile__general + description: Experimental metadata, including protocol, notes and description + of hardware device(s). The metadata stored in this section should be used to + describe the experiment. Metadata necessary for interpreting the data is stored + with the data. General experimental metadata, including animal strain, experimental + protocols, experimenter, devices, etc, are stored under 'general'. Core metadata + (e.g., that required to interpret data fields) is stored with the data itself, + and implicitly defined by the file specification (e.g., time is in seconds). + The strategy used here for storing non-core metadata is to use free-form text + fields, such as would appear in sentences or paragraphs from a Methods section. + Metadata fields are text to enable them to be more general, for example to represent + ranges instead of numerical values. Machine-readable metadata is stored as attributes + to these free-form datasets. All entries in the below table are to be included + when data is present. Unused groups (e.g., intracellular_ephys in an optophysiology + experiment) should not be created unless there is data to store within them. + attributes: + data_collection: + name: data_collection + description: Notes about data collection and analysis. + multivalued: false + range: text + required: false + experiment_description: + name: experiment_description + description: General description of the experiment. + multivalued: false + range: text + required: false + experimenter: + name: experimenter + description: Name of person(s) who performed the experiment. Can also specify + roles of different people involved. + multivalued: false + range: NWBFile__general__experimenter + required: false + institution: + name: institution + description: Institution(s) where experiment was performed. + multivalued: false + range: text + required: false + keywords: + name: keywords + description: Terms to search over. + multivalued: false + range: NWBFile__general__keywords + required: false + lab: + name: lab + description: Laboratory where experiment was performed. + multivalued: false + range: text + required: false + notes: + name: notes + description: Notes about the experiment. + multivalued: false + range: text + required: false + pharmacology: + name: pharmacology + description: Description of drugs used, including how and when they were administered. + Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc. + multivalued: false + range: text + required: false + protocol: + name: protocol + description: Experimental protocol, if applicable. e.g., include IACUC protocol + number. + multivalued: false + range: text + required: false + related_publications: + name: related_publications + description: Publication information. PMID, DOI, URL, etc. + multivalued: false + range: NWBFile__general__related_publications + required: false + session_id: + name: session_id + description: Lab-specific ID for the session. + multivalued: false + range: text + required: false + slices: + name: slices + description: Description of slices, including information about preparation + thickness, orientation, temperature, and bath solution. + multivalued: false + range: text + required: false + source_script: + name: source_script + description: Script file or link to public source code used to create this + NWB file. + multivalued: false + range: NWBFile__general__source_script + required: false + stimulus: + name: stimulus + description: Notes about stimuli, such as how and where they were presented. + multivalued: false + range: text + required: false + surgery: + name: surgery + description: Narrative description about surgery/surgeries, including date(s) + and who performed surgery. + multivalued: false + range: text + required: false + virus: + name: virus + description: Information about virus(es) used in experiments, including virus + ID, source, date made, injection location, volume, etc. + multivalued: false + range: text + required: false + LabMetaData: + name: LabMetaData + description: Place-holder than can be extended so that lab-specific meta-data + can be placed in /general. + multivalued: true + range: LabMetaData + required: false + devices: + name: devices + description: Description of hardware devices used during experiment, e.g., + monitors, ADC boards, microscopes, etc. + multivalued: false + range: NWBFile__general__devices + required: false + subject: + name: subject + description: Information about the animal or person from which the data was + measured. + multivalued: false + range: NWBFile__general__subject + required: false + extracellular_ephys: + name: extracellular_ephys + description: Metadata related to extracellular electrophysiology. + multivalued: false + range: NWBFile__general__extracellular_ephys + required: false + intracellular_ephys: + name: intracellular_ephys + description: Metadata related to intracellular electrophysiology. + multivalued: false + range: NWBFile__general__intracellular_ephys + required: false + optogenetics: + name: optogenetics + description: Metadata describing optogenetic stimuluation. + multivalued: false + range: NWBFile__general__optogenetics + required: false + optophysiology: + name: optophysiology + description: Metadata related to optophysiology. + multivalued: false + range: NWBFile__general__optophysiology + required: false + NWBFile__general__experimenter: + name: NWBFile__general__experimenter + description: Name of person(s) who performed the experiment. Can also specify + roles of different people involved. + attributes: + experimenter: + name: experimenter + description: Name of person(s) who performed the experiment. Can also specify + roles of different people involved. + multivalued: true + range: text + required: false + NWBFile__general__keywords: + name: NWBFile__general__keywords + description: Terms to search over. + attributes: + keywords: + name: keywords + description: Terms to search over. + multivalued: true + range: text + required: false + NWBFile__general__related_publications: + name: NWBFile__general__related_publications + description: Publication information. PMID, DOI, URL, etc. + attributes: + related_publications: + name: related_publications + description: Publication information. PMID, DOI, URL, etc. + multivalued: true + range: text + required: false + NWBFile__general__source_script: + name: NWBFile__general__source_script + description: Script file or link to public source code used to create this NWB + file. + attributes: + file_name: + name: file_name + description: Name of script file. + range: text + NWBFile__general__devices: + name: NWBFile__general__devices + description: Description of hardware devices used during experiment, e.g., monitors, + ADC boards, microscopes, etc. + attributes: + Device: + name: Device + description: Data acquisition devices. + multivalued: true + range: Device + required: false + NWBFile__general__subject: + name: NWBFile__general__subject + description: Information about the animal or person from which the data was measured. + is_a: Subject + NWBFile__general__extracellular_ephys: + name: NWBFile__general__extracellular_ephys + description: Metadata related to extracellular electrophysiology. + attributes: + ElectrodeGroup: + name: ElectrodeGroup + description: Physical group of electrodes. + multivalued: true + range: ElectrodeGroup + required: false + electrodes: + name: electrodes + description: A table of all electrodes (i.e. channels) used for recording. + multivalued: false + range: NWBFile__general__extracellular_ephys__electrodes + required: false + NWBFile__general__extracellular_ephys__electrodes: + name: NWBFile__general__extracellular_ephys__electrodes + description: A table of all electrodes (i.e. channels) used for recording. + is_a: DynamicTable + attributes: + x: + name: x + description: x coordinate of the channel location in the brain (+x is posterior). + multivalued: true + range: float32 + y: + name: y + description: y coordinate of the channel location in the brain (+y is inferior). + multivalued: true + range: float32 + z: + name: z + description: z coordinate of the channel location in the brain (+z is right). + multivalued: true + range: float32 + imp: + name: imp + description: Impedance of the channel, in ohms. + multivalued: true + range: float32 + location: + name: location + description: Location of the electrode (channel). Specify the area, layer, + comments on estimation of area/layer, stereotaxic coordinates if in vivo, + etc. Use standard atlas names for anatomical regions when possible. + multivalued: true + range: text + filtering: + name: filtering + description: Description of hardware filtering, including the filter name + and frequency cutoffs. + multivalued: true + range: text + group: + name: group + description: Reference to the ElectrodeGroup this electrode is a part of. + multivalued: true + range: ElectrodeGroup + group_name: + name: group_name + description: Name of the ElectrodeGroup this electrode is a part of. + multivalued: true + range: text + rel_x: + name: rel_x + description: x coordinate in electrode group + multivalued: true + range: float32 + rel_y: + name: rel_y + description: y coordinate in electrode group + multivalued: true + range: float32 + rel_z: + name: rel_z + description: z coordinate in electrode group + multivalued: true + range: float32 + reference: + name: reference + description: Description of the reference electrode and/or reference scheme + used for this electrode, e.g., "stainless steel skull screw" or "online + common average referencing". + multivalued: true + range: text + NWBFile__general__intracellular_ephys: + name: NWBFile__general__intracellular_ephys + description: Metadata related to intracellular electrophysiology. + attributes: + filtering: + name: filtering + description: '[DEPRECATED] Use IntracellularElectrode.filtering instead. Description + of filtering used. Includes filtering type and parameters, frequency fall-off, + etc. If this changes between TimeSeries, filter description should be stored + as a text attribute for each TimeSeries.' + multivalued: false + range: text + required: false + IntracellularElectrode: + name: IntracellularElectrode + description: An intracellular electrode. + multivalued: true + range: IntracellularElectrode + required: false + sweep_table: + name: sweep_table + description: '[DEPRECATED] Table used to group different PatchClampSeries. + SweepTable is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable + tables. Additional SequentialRecordingsTable, RepetitionsTable and ExperimentalConditions + tables provide enhanced support for experiment metadata.' + multivalued: false + range: NWBFile__general__intracellular_ephys__sweep_table + required: false + intracellular_recordings: + name: intracellular_recordings + description: A table to group together a stimulus and response from a single + electrode and a single simultaneous recording. Each row in the table represents + a single recording consisting typically of a stimulus and a corresponding + response. In some cases, however, only a stimulus or a response are recorded + as as part of an experiment. In this case both, the stimulus and response + will point to the same TimeSeries while the idx_start and count of the invalid + column will be set to -1, thus, indicating that no values have been recorded + for the stimulus or response, respectively. Note, a recording MUST contain + at least a stimulus or a response. Typically the stimulus and response are + PatchClampSeries. However, the use of AD/DA channels that are not associated + to an electrode is also common in intracellular electrophysiology, in which + case other TimeSeries may be used. + multivalued: false + range: NWBFile__general__intracellular_ephys__intracellular_recordings + required: false + simultaneous_recordings: + name: simultaneous_recordings + description: A table for grouping different intracellular recordings from + the IntracellularRecordingsTable table together that were recorded simultaneously + from different electrodes + multivalued: false + range: NWBFile__general__intracellular_ephys__simultaneous_recordings + required: false + sequential_recordings: + name: sequential_recordings + description: A table for grouping different sequential recordings from the + SimultaneousRecordingsTable table together. This is typically used to group + together sequential recordings where the a sequence of stimuli of the same + type with varying parameters have been presented in a sequence. + multivalued: false + range: NWBFile__general__intracellular_ephys__sequential_recordings + required: false + repetitions: + name: repetitions + description: A table for grouping different sequential intracellular recordings + together. With each SequentialRecording typically representing a particular + type of stimulus, the RepetitionsTable table is typically used to group + sets of stimuli applied in sequence. + multivalued: false + range: NWBFile__general__intracellular_ephys__repetitions + required: false + experimental_conditions: + name: experimental_conditions + description: A table for grouping different intracellular recording repetitions + together that belong to the same experimental experimental_conditions. + multivalued: false + range: NWBFile__general__intracellular_ephys__experimental_conditions + required: false + NWBFile__general__intracellular_ephys__sweep_table: + name: NWBFile__general__intracellular_ephys__sweep_table + description: '[DEPRECATED] Table used to group different PatchClampSeries. SweepTable + is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable + tables. Additional SequentialRecordingsTable, RepetitionsTable and ExperimentalConditions + tables provide enhanced support for experiment metadata.' + is_a: SweepTable + NWBFile__general__intracellular_ephys__intracellular_recordings: + name: NWBFile__general__intracellular_ephys__intracellular_recordings + description: A table to group together a stimulus and response from a single electrode + and a single simultaneous recording. Each row in the table represents a single + recording consisting typically of a stimulus and a corresponding response. In + some cases, however, only a stimulus or a response are recorded as as part of + an experiment. In this case both, the stimulus and response will point to the + same TimeSeries while the idx_start and count of the invalid column will be + set to -1, thus, indicating that no values have been recorded for the stimulus + or response, respectively. Note, a recording MUST contain at least a stimulus + or a response. Typically the stimulus and response are PatchClampSeries. However, + the use of AD/DA channels that are not associated to an electrode is also common + in intracellular electrophysiology, in which case other TimeSeries may be used. + is_a: IntracellularRecordingsTable + NWBFile__general__intracellular_ephys__simultaneous_recordings: + name: NWBFile__general__intracellular_ephys__simultaneous_recordings + description: A table for grouping different intracellular recordings from the + IntracellularRecordingsTable table together that were recorded simultaneously + from different electrodes + is_a: SimultaneousRecordingsTable + NWBFile__general__intracellular_ephys__sequential_recordings: + name: NWBFile__general__intracellular_ephys__sequential_recordings + description: A table for grouping different sequential recordings from the SimultaneousRecordingsTable + table together. This is typically used to group together sequential recordings + where the a sequence of stimuli of the same type with varying parameters have + been presented in a sequence. + is_a: SequentialRecordingsTable + NWBFile__general__intracellular_ephys__repetitions: + name: NWBFile__general__intracellular_ephys__repetitions + description: A table for grouping different sequential intracellular recordings + together. With each SequentialRecording typically representing a particular + type of stimulus, the RepetitionsTable table is typically used to group sets + of stimuli applied in sequence. + is_a: RepetitionsTable + NWBFile__general__intracellular_ephys__experimental_conditions: + name: NWBFile__general__intracellular_ephys__experimental_conditions + description: A table for grouping different intracellular recording repetitions + together that belong to the same experimental experimental_conditions. + is_a: ExperimentalConditionsTable + NWBFile__general__optogenetics: + name: NWBFile__general__optogenetics + description: Metadata describing optogenetic stimuluation. + attributes: + OptogeneticStimulusSite: + name: OptogeneticStimulusSite + description: An optogenetic stimulation site. + multivalued: true + range: OptogeneticStimulusSite + required: false + NWBFile__general__optophysiology: + name: NWBFile__general__optophysiology + description: Metadata related to optophysiology. + attributes: + ImagingPlane: + name: ImagingPlane + description: An imaging plane. + multivalued: true + range: ImagingPlane + required: false + NWBFile__intervals: + name: NWBFile__intervals + description: Experimental intervals, whether that be logically distinct sub-experiments + having a particular scientific goal, trials (see trials subgroup) during an + experiment, or epochs (see epochs subgroup) deriving from analysis of data. + attributes: + epochs: + name: epochs + description: Divisions in time marking experimental stages or sub-divisions + of a single recording session. + multivalued: false + range: NWBFile__intervals__epochs + required: false + trials: + name: trials + description: Repeated experimental events that have a logical grouping. + multivalued: false + range: NWBFile__intervals__trials + required: false + invalid_times: + name: invalid_times + description: Time intervals that should be removed from analysis. + multivalued: false + range: NWBFile__intervals__invalid_times + required: false + TimeIntervals: + name: TimeIntervals + description: Optional additional table(s) for describing other experimental + time intervals. + multivalued: true + range: TimeIntervals + required: false + NWBFile__intervals__epochs: + name: NWBFile__intervals__epochs + description: Divisions in time marking experimental stages or sub-divisions of + a single recording session. + is_a: TimeIntervals + NWBFile__intervals__trials: + name: NWBFile__intervals__trials + description: Repeated experimental events that have a logical grouping. + is_a: TimeIntervals + NWBFile__intervals__invalid_times: + name: NWBFile__intervals__invalid_times + description: Time intervals that should be removed from analysis. + is_a: TimeIntervals + NWBFile__units: + name: NWBFile__units + description: Data about sorted spike units. + is_a: Units + Subject__age: + name: Subject__age + description: Age of subject. Can be supplied instead of 'date_of_birth'. + attributes: + reference: + name: reference + description: Age is with reference to this event. Can be 'birth' or 'gestational'. + If reference is omitted, 'birth' is implied. + range: text diff --git a/nwb_linkml/schema/core.nwb.file.yaml b/nwb_linkml/schema/core.nwb.file.yaml index 2bb38bd..2772059 100644 --- a/nwb_linkml/schema/core.nwb.file.yaml +++ b/nwb_linkml/schema/core.nwb.file.yaml @@ -11,6 +11,8 @@ imports: - core.nwb.epoch - core.nwb.misc - nwb.language +- core.nwb.file.include +- core.nwb.file default_prefix: core.nwb.file/ classes: ScratchData: @@ -43,7 +45,7 @@ classes: from the experiment start time. Each modification to the nwb file adds a new entry to the array.' multivalued: false - range: NWBFile_file_create_date + range: NWBFile__file_create_date required: true identifier: name: identifier @@ -52,13 +54,13 @@ classes: and/or other values. The goal is that the string should be unique to all other files. multivalued: false - range: NWBFile_identifier + range: text required: true session_description: name: session_description description: A description of the experimental session and data in the file. multivalued: false - range: NWBFile_session_description + range: text required: true session_start_time: name: session_start_time @@ -67,7 +69,7 @@ classes: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in "Z" with no timezone offset. Date accuracy is up to milliseconds.' multivalued: false - range: NWBFile_session_start_time + range: isodatetime required: true timestamps_reference_time: name: timestamps_reference_time @@ -77,7 +79,7 @@ classes: in "Z" with no timezone offset. Date accuracy is up to milliseconds. All times stored in the file use this time as reference (i.e., time zero).' multivalued: false - range: NWBFile_timestamps_reference_time + range: isodatetime required: true acquisition: name: acquisition @@ -91,7 +93,7 @@ classes: the /acquisition group, the data can exist in a separate NWB file that is linked to by the file being used for processing and analysis. multivalued: false - range: NWBFile_acquisition + range: NWBFile__acquisition required: true analysis: name: analysis @@ -105,7 +107,7 @@ classes: The analysis data should be documented so that it could be shared with other labs. multivalued: false - range: NWBFile_analysis + range: NWBFile__analysis required: true scratch: name: scratch @@ -113,7 +115,7 @@ classes: not intended for sharing. By placing data here, users acknowledge that there is no guarantee that their data meets any standard. multivalued: false - range: NWBFile_scratch + range: NWBFile__scratch required: false processing: name: processing @@ -128,7 +130,7 @@ classes: refers to intermediate analysis of the acquired data to make it more amenable to scientific analysis. multivalued: false - range: NWBFile_processing + range: NWBFile__processing required: true stimulus: name: stimulus @@ -145,7 +147,7 @@ classes: stimuli can be stored and these be used multiple times. These templates can exist in the present file or can be linked to a remote library file. multivalued: false - range: NWBFile_stimulus + range: NWBFile__stimulus required: true general: name: general @@ -165,7 +167,7 @@ classes: present. Unused groups (e.g., intracellular_ephys in an optophysiology experiment) should not be created unless there is data to store within them. multivalued: false - range: NWBFile_general + range: NWBFile__general required: true intervals: name: intervals @@ -174,829 +176,14 @@ classes: an experiment, or epochs (see epochs subgroup) deriving from analysis of data. multivalued: false - range: NWBFile_intervals + range: NWBFile__intervals required: false units: name: units description: Data about sorted spike units. multivalued: false - range: NWBFile_units + range: NWBFile__units required: false - NWBFile_file_create_date: - name: NWBFile_file_create_date - description: 'A record of the date the file was created and of subsequent modifications. - The date is stored in UTC with local timezone offset as ISO 8601 extended formatted - strings: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in "Z" with - no timezone offset. Date accuracy is up to milliseconds. The file can be created - after the experiment was run, so this may differ from the experiment start time. - Each modification to the nwb file adds a new entry to the array.' - attributes: - array: - name: array - range: NWBFile_file_create_date_Array - NWBFile_file_create_date_Array: - name: NWBFile_file_create_date_Array - is_a: Arraylike - attributes: - num_modifications: - name: num_modifications - range: isodatetime - required: true - NWBFile_identifier: - name: NWBFile_identifier - description: A unique text identifier for the file. For example, concatenated - lab name, file creation date/time and experimentalist, or a hash of these and/or - other values. The goal is that the string should be unique to all other files. - NWBFile_session_description: - name: NWBFile_session_description - description: A description of the experimental session and data in the file. - NWBFile_session_start_time: - name: NWBFile_session_start_time - description: 'Date and time of the experiment/session start. The date is stored - in UTC with local timezone offset as ISO 8601 extended formatted string: 2018-09-28T14:43:54.123+02:00. - Dates stored in UTC end in "Z" with no timezone offset. Date accuracy is up - to milliseconds.' - NWBFile_timestamps_reference_time: - name: NWBFile_timestamps_reference_time - description: 'Date and time corresponding to time zero of all timestamps. The - date is stored in UTC with local timezone offset as ISO 8601 extended formatted - string: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in "Z" with no - timezone offset. Date accuracy is up to milliseconds. All times stored in the - file use this time as reference (i.e., time zero).' - NWBFile_acquisition: - name: NWBFile_acquisition - description: Data streams recorded from the system, including ephys, ophys, tracking, - etc. This group should be read-only after the experiment is completed and timestamps - are corrected to a common timebase. The data stored here may be links to raw - data stored in external NWB files. This will allow keeping bulky raw data out - of the file while preserving the option of keeping some/all in the file. Acquired - data includes tracking and experimental data streams (i.e., everything measured - from the system). If bulky data is stored in the /acquisition group, the data - can exist in a separate NWB file that is linked to by the file being used for - processing and analysis. - attributes: - NWBDataInterface: - name: NWBDataInterface - description: Acquired, raw data. - multivalued: true - range: NWBDataInterface - required: false - DynamicTable: - name: DynamicTable - description: Tabular data that is relevant to acquisition - multivalued: true - range: DynamicTable - required: false - NWBFile_analysis: - name: NWBFile_analysis - description: Lab-specific and custom scientific analysis of data. There is no - defined format for the content of this group - the format is up to the individual - user/lab. To facilitate sharing analysis data between labs, the contents here - should be stored in standard types (e.g., neurodata_types) and appropriately - documented. The file can store lab-specific and custom data analysis without - restriction on its form or schema, reducing data formatting restrictions on - end users. Such data should be placed in the analysis group. The analysis data - should be documented so that it could be shared with other labs. - attributes: - NWBContainer: - name: NWBContainer - description: Custom analysis results. - multivalued: true - range: NWBContainer - required: false - DynamicTable: - name: DynamicTable - description: Tabular data that is relevant to data stored in analysis - multivalued: true - range: DynamicTable - required: false - NWBFile_scratch: - name: NWBFile_scratch - description: A place to store one-off analysis results. Data placed here is not - intended for sharing. By placing data here, users acknowledge that there is - no guarantee that their data meets any standard. - attributes: - ScratchData: - name: ScratchData - description: Any one-off datasets - multivalued: true - range: ScratchData - required: false - NWBContainer: - name: NWBContainer - description: Any one-off containers - multivalued: true - range: NWBContainer - required: false - DynamicTable: - name: DynamicTable - description: Any one-off tables - multivalued: true - range: DynamicTable - required: false - NWBFile_processing: - name: NWBFile_processing - description: The home for ProcessingModules. These modules perform intermediate - analysis of data that is necessary to perform before scientific analysis. Examples - include spike clustering, extracting position from tracking data, stitching - together image slices. ProcessingModules can be large and express many data - sets from relatively complex analysis (e.g., spike detection and clustering) - or small, representing extraction of position information from tracking video, - or even binary lick/no-lick decisions. Common software tools (e.g., klustakwik, - MClust) are expected to read/write data here. 'Processing' refers to intermediate - analysis of the acquired data to make it more amenable to scientific analysis. - attributes: - ProcessingModule: - name: ProcessingModule - description: Intermediate analysis of acquired data. - multivalued: true - range: ProcessingModule - required: false - NWBFile_stimulus: - name: NWBFile_stimulus - description: Data pushed into the system (eg, video stimulus, sound, voltage, - etc) and secondary representations of that data (eg, measurements of something - used as a stimulus). This group should be made read-only after experiment complete - and timestamps are corrected to common timebase. Stores both presented stimuli - and stimulus templates, the latter in case the same stimulus is presented multiple - times, or is pulled from an external stimulus library. Stimuli are here defined - as any signal that is pushed into the system as part of the experiment (eg, - sound, video, voltage, etc). Many different experiments can use the same stimuli, - and stimuli can be re-used during an experiment. The stimulus group is organized - so that one version of template stimuli can be stored and these be used multiple - times. These templates can exist in the present file or can be linked to a remote - library file. - attributes: - presentation: - name: presentation - description: Stimuli presented during the experiment. - multivalued: false - range: NWBFile_stimulus_presentation - required: true - templates: - name: templates - description: Template stimuli. Timestamps in templates are based on stimulus - design and are relative to the beginning of the stimulus. When templates - are used, the stimulus instances must convert presentation times to the - experiment`s time reference frame. - multivalued: false - range: NWBFile_stimulus_templates - required: true - NWBFile_stimulus_presentation: - name: NWBFile_stimulus_presentation - description: Stimuli presented during the experiment. - attributes: - TimeSeries: - name: TimeSeries - description: TimeSeries objects containing data of presented stimuli. - multivalued: true - range: TimeSeries - required: false - NWBFile_stimulus_templates: - name: NWBFile_stimulus_templates - description: Template stimuli. Timestamps in templates are based on stimulus design - and are relative to the beginning of the stimulus. When templates are used, - the stimulus instances must convert presentation times to the experiment`s time - reference frame. - attributes: - TimeSeries: - name: TimeSeries - description: TimeSeries objects containing template data of presented stimuli. - multivalued: true - range: TimeSeries - required: false - Images: - name: Images - description: Images objects containing images of presented stimuli. - multivalued: true - range: Images - required: false - NWBFile_general: - name: NWBFile_general - description: Experimental metadata, including protocol, notes and description - of hardware device(s). The metadata stored in this section should be used to - describe the experiment. Metadata necessary for interpreting the data is stored - with the data. General experimental metadata, including animal strain, experimental - protocols, experimenter, devices, etc, are stored under 'general'. Core metadata - (e.g., that required to interpret data fields) is stored with the data itself, - and implicitly defined by the file specification (e.g., time is in seconds). - The strategy used here for storing non-core metadata is to use free-form text - fields, such as would appear in sentences or paragraphs from a Methods section. - Metadata fields are text to enable them to be more general, for example to represent - ranges instead of numerical values. Machine-readable metadata is stored as attributes - to these free-form datasets. All entries in the below table are to be included - when data is present. Unused groups (e.g., intracellular_ephys in an optophysiology - experiment) should not be created unless there is data to store within them. - attributes: - data_collection: - name: data_collection - description: Notes about data collection and analysis. - multivalued: false - range: NWBFile_general_data_collection - required: false - experiment_description: - name: experiment_description - description: General description of the experiment. - multivalued: false - range: NWBFile_general_experiment_description - required: false - experimenter: - name: experimenter - description: Name of person(s) who performed the experiment. Can also specify - roles of different people involved. - multivalued: false - range: NWBFile_general_experimenter - required: false - institution: - name: institution - description: Institution(s) where experiment was performed. - multivalued: false - range: NWBFile_general_institution - required: false - keywords: - name: keywords - description: Terms to search over. - multivalued: false - range: NWBFile_general_keywords - required: false - lab: - name: lab - description: Laboratory where experiment was performed. - multivalued: false - range: NWBFile_general_lab - required: false - notes: - name: notes - description: Notes about the experiment. - multivalued: false - range: NWBFile_general_notes - required: false - pharmacology: - name: pharmacology - description: Description of drugs used, including how and when they were administered. - Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc. - multivalued: false - range: NWBFile_general_pharmacology - required: false - protocol: - name: protocol - description: Experimental protocol, if applicable. e.g., include IACUC protocol - number. - multivalued: false - range: NWBFile_general_protocol - required: false - related_publications: - name: related_publications - description: Publication information. PMID, DOI, URL, etc. - multivalued: false - range: NWBFile_general_related_publications - required: false - session_id: - name: session_id - description: Lab-specific ID for the session. - multivalued: false - range: NWBFile_general_session_id - required: false - slices: - name: slices - description: Description of slices, including information about preparation - thickness, orientation, temperature, and bath solution. - multivalued: false - range: NWBFile_general_slices - required: false - source_script: - name: source_script - description: Script file or link to public source code used to create this - NWB file. - multivalued: false - range: NWBFile_general_source_script - required: false - stimulus: - name: stimulus - description: Notes about stimuli, such as how and where they were presented. - multivalued: false - range: NWBFile_general_stimulus - required: false - surgery: - name: surgery - description: Narrative description about surgery/surgeries, including date(s) - and who performed surgery. - multivalued: false - range: NWBFile_general_surgery - required: false - virus: - name: virus - description: Information about virus(es) used in experiments, including virus - ID, source, date made, injection location, volume, etc. - multivalued: false - range: NWBFile_general_virus - required: false - LabMetaData: - name: LabMetaData - description: Place-holder than can be extended so that lab-specific meta-data - can be placed in /general. - multivalued: true - range: LabMetaData - required: false - devices: - name: devices - description: Description of hardware devices used during experiment, e.g., - monitors, ADC boards, microscopes, etc. - multivalued: false - range: NWBFile_general_devices - required: false - subject: - name: subject - description: Information about the animal or person from which the data was - measured. - multivalued: false - range: NWBFile_general_subject - required: false - extracellular_ephys: - name: extracellular_ephys - description: Metadata related to extracellular electrophysiology. - multivalued: false - range: NWBFile_general_extracellular_ephys - required: false - intracellular_ephys: - name: intracellular_ephys - description: Metadata related to intracellular electrophysiology. - multivalued: false - range: NWBFile_general_intracellular_ephys - required: false - optogenetics: - name: optogenetics - description: Metadata describing optogenetic stimuluation. - multivalued: false - range: NWBFile_general_optogenetics - required: false - optophysiology: - name: optophysiology - description: Metadata related to optophysiology. - multivalued: false - range: NWBFile_general_optophysiology - required: false - NWBFile_general_data_collection: - name: NWBFile_general_data_collection - description: Notes about data collection and analysis. - NWBFile_general_experiment_description: - name: NWBFile_general_experiment_description - description: General description of the experiment. - NWBFile_general_experimenter: - name: NWBFile_general_experimenter - description: Name of person(s) who performed the experiment. Can also specify - roles of different people involved. - attributes: - array: - name: array - range: NWBFile_general_experimenter_Array - NWBFile_general_experimenter_Array: - name: NWBFile_general_experimenter_Array - is_a: Arraylike - attributes: - num_experimenters: - name: num_experimenters - range: text - required: true - NWBFile_general_institution: - name: NWBFile_general_institution - description: Institution(s) where experiment was performed. - NWBFile_general_keywords: - name: NWBFile_general_keywords - description: Terms to search over. - attributes: - array: - name: array - range: NWBFile_general_keywords_Array - NWBFile_general_keywords_Array: - name: NWBFile_general_keywords_Array - is_a: Arraylike - attributes: - num_keywords: - name: num_keywords - range: text - required: true - NWBFile_general_lab: - name: NWBFile_general_lab - description: Laboratory where experiment was performed. - NWBFile_general_notes: - name: NWBFile_general_notes - description: Notes about the experiment. - NWBFile_general_pharmacology: - name: NWBFile_general_pharmacology - description: Description of drugs used, including how and when they were administered. - Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc. - NWBFile_general_protocol: - name: NWBFile_general_protocol - description: Experimental protocol, if applicable. e.g., include IACUC protocol - number. - NWBFile_general_related_publications: - name: NWBFile_general_related_publications - description: Publication information. PMID, DOI, URL, etc. - attributes: - array: - name: array - range: NWBFile_general_related_publications_Array - NWBFile_general_related_publications_Array: - name: NWBFile_general_related_publications_Array - is_a: Arraylike - attributes: - num_publications: - name: num_publications - range: text - required: true - NWBFile_general_session_id: - name: NWBFile_general_session_id - description: Lab-specific ID for the session. - NWBFile_general_slices: - name: NWBFile_general_slices - description: Description of slices, including information about preparation thickness, - orientation, temperature, and bath solution. - NWBFile_general_source_script: - name: NWBFile_general_source_script - description: Script file or link to public source code used to create this NWB - file. - attributes: - file_name: - name: file_name - description: Name of script file. - range: text - NWBFile_general_stimulus: - name: NWBFile_general_stimulus - description: Notes about stimuli, such as how and where they were presented. - NWBFile_general_surgery: - name: NWBFile_general_surgery - description: Narrative description about surgery/surgeries, including date(s) - and who performed surgery. - NWBFile_general_virus: - name: NWBFile_general_virus - description: Information about virus(es) used in experiments, including virus - ID, source, date made, injection location, volume, etc. - NWBFile_general_devices: - name: NWBFile_general_devices - description: Description of hardware devices used during experiment, e.g., monitors, - ADC boards, microscopes, etc. - attributes: - Device: - name: Device - description: Data acquisition devices. - multivalued: true - range: Device - required: false - NWBFile_general_subject: - name: NWBFile_general_subject - description: Information about the animal or person from which the data was measured. - is_a: Subject - NWBFile_general_extracellular_ephys: - name: NWBFile_general_extracellular_ephys - description: Metadata related to extracellular electrophysiology. - attributes: - ElectrodeGroup: - name: ElectrodeGroup - description: Physical group of electrodes. - multivalued: true - range: ElectrodeGroup - required: false - electrodes: - name: electrodes - description: A table of all electrodes (i.e. channels) used for recording. - multivalued: false - range: NWBFile_general_extracellular_ephys_electrodes - required: false - NWBFile_general_extracellular_ephys_electrodes: - name: NWBFile_general_extracellular_ephys_electrodes - description: A table of all electrodes (i.e. channels) used for recording. - is_a: DynamicTable - attributes: - x: - name: x - description: x coordinate of the channel location in the brain (+x is posterior). - multivalued: false - range: NWBFile_general_extracellular_ephys_electrodes_x - required: false - y: - name: y - description: y coordinate of the channel location in the brain (+y is inferior). - multivalued: false - range: NWBFile_general_extracellular_ephys_electrodes_y - required: false - z: - name: z - description: z coordinate of the channel location in the brain (+z is right). - multivalued: false - range: NWBFile_general_extracellular_ephys_electrodes_z - required: false - imp: - name: imp - description: Impedance of the channel, in ohms. - multivalued: false - range: NWBFile_general_extracellular_ephys_electrodes_imp - required: false - location: - name: location - description: Location of the electrode (channel). Specify the area, layer, - comments on estimation of area/layer, stereotaxic coordinates if in vivo, - etc. Use standard atlas names for anatomical regions when possible. - multivalued: false - range: NWBFile_general_extracellular_ephys_electrodes_location - required: true - filtering: - name: filtering - description: Description of hardware filtering, including the filter name - and frequency cutoffs. - multivalued: false - range: NWBFile_general_extracellular_ephys_electrodes_filtering - required: false - group: - name: group - description: Reference to the ElectrodeGroup this electrode is a part of. - multivalued: false - range: NWBFile_general_extracellular_ephys_electrodes_group - required: true - group_name: - name: group_name - description: Name of the ElectrodeGroup this electrode is a part of. - multivalued: false - range: NWBFile_general_extracellular_ephys_electrodes_group_name - required: true - rel_x: - name: rel_x - description: x coordinate in electrode group - multivalued: false - range: NWBFile_general_extracellular_ephys_electrodes_rel_x - required: false - rel_y: - name: rel_y - description: y coordinate in electrode group - multivalued: false - range: NWBFile_general_extracellular_ephys_electrodes_rel_y - required: false - rel_z: - name: rel_z - description: z coordinate in electrode group - multivalued: false - range: NWBFile_general_extracellular_ephys_electrodes_rel_z - required: false - reference: - name: reference - description: Description of the reference electrode and/or reference scheme - used for this electrode, e.g., "stainless steel skull screw" or "online - common average referencing". - multivalued: false - range: NWBFile_general_extracellular_ephys_electrodes_reference - required: false - NWBFile_general_extracellular_ephys_electrodes_x: - name: NWBFile_general_extracellular_ephys_electrodes_x - description: x coordinate of the channel location in the brain (+x is posterior). - is_a: VectorData - NWBFile_general_extracellular_ephys_electrodes_y: - name: NWBFile_general_extracellular_ephys_electrodes_y - description: y coordinate of the channel location in the brain (+y is inferior). - is_a: VectorData - NWBFile_general_extracellular_ephys_electrodes_z: - name: NWBFile_general_extracellular_ephys_electrodes_z - description: z coordinate of the channel location in the brain (+z is right). - is_a: VectorData - NWBFile_general_extracellular_ephys_electrodes_imp: - name: NWBFile_general_extracellular_ephys_electrodes_imp - description: Impedance of the channel, in ohms. - is_a: VectorData - NWBFile_general_extracellular_ephys_electrodes_location: - name: NWBFile_general_extracellular_ephys_electrodes_location - description: Location of the electrode (channel). Specify the area, layer, comments - on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard - atlas names for anatomical regions when possible. - is_a: VectorData - NWBFile_general_extracellular_ephys_electrodes_filtering: - name: NWBFile_general_extracellular_ephys_electrodes_filtering - description: Description of hardware filtering, including the filter name and - frequency cutoffs. - is_a: VectorData - NWBFile_general_extracellular_ephys_electrodes_group: - name: NWBFile_general_extracellular_ephys_electrodes_group - description: Reference to the ElectrodeGroup this electrode is a part of. - is_a: VectorData - NWBFile_general_extracellular_ephys_electrodes_group_name: - name: NWBFile_general_extracellular_ephys_electrodes_group_name - description: Name of the ElectrodeGroup this electrode is a part of. - is_a: VectorData - NWBFile_general_extracellular_ephys_electrodes_rel_x: - name: NWBFile_general_extracellular_ephys_electrodes_rel_x - description: x coordinate in electrode group - is_a: VectorData - NWBFile_general_extracellular_ephys_electrodes_rel_y: - name: NWBFile_general_extracellular_ephys_electrodes_rel_y - description: y coordinate in electrode group - is_a: VectorData - NWBFile_general_extracellular_ephys_electrodes_rel_z: - name: NWBFile_general_extracellular_ephys_electrodes_rel_z - description: z coordinate in electrode group - is_a: VectorData - NWBFile_general_extracellular_ephys_electrodes_reference: - name: NWBFile_general_extracellular_ephys_electrodes_reference - description: Description of the reference electrode and/or reference scheme used - for this electrode, e.g., "stainless steel skull screw" or "online common average - referencing". - is_a: VectorData - NWBFile_general_intracellular_ephys: - name: NWBFile_general_intracellular_ephys - description: Metadata related to intracellular electrophysiology. - attributes: - filtering: - name: filtering - description: '[DEPRECATED] Use IntracellularElectrode.filtering instead. Description - of filtering used. Includes filtering type and parameters, frequency fall-off, - etc. If this changes between TimeSeries, filter description should be stored - as a text attribute for each TimeSeries.' - multivalued: false - range: NWBFile_general_intracellular_ephys_filtering - required: false - IntracellularElectrode: - name: IntracellularElectrode - description: An intracellular electrode. - multivalued: true - range: IntracellularElectrode - required: false - sweep_table: - name: sweep_table - description: '[DEPRECATED] Table used to group different PatchClampSeries. - SweepTable is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable - tables. Additional SequentialRecordingsTable, RepetitionsTable and ExperimentalConditions - tables provide enhanced support for experiment metadata.' - multivalued: false - range: NWBFile_general_intracellular_ephys_sweep_table - required: false - intracellular_recordings: - name: intracellular_recordings - description: A table to group together a stimulus and response from a single - electrode and a single simultaneous recording. Each row in the table represents - a single recording consisting typically of a stimulus and a corresponding - response. In some cases, however, only a stimulus or a response are recorded - as as part of an experiment. In this case both, the stimulus and response - will point to the same TimeSeries while the idx_start and count of the invalid - column will be set to -1, thus, indicating that no values have been recorded - for the stimulus or response, respectively. Note, a recording MUST contain - at least a stimulus or a response. Typically the stimulus and response are - PatchClampSeries. However, the use of AD/DA channels that are not associated - to an electrode is also common in intracellular electrophysiology, in which - case other TimeSeries may be used. - multivalued: false - range: NWBFile_general_intracellular_ephys_intracellular_recordings - required: false - simultaneous_recordings: - name: simultaneous_recordings - description: A table for grouping different intracellular recordings from - the IntracellularRecordingsTable table together that were recorded simultaneously - from different electrodes - multivalued: false - range: NWBFile_general_intracellular_ephys_simultaneous_recordings - required: false - sequential_recordings: - name: sequential_recordings - description: A table for grouping different sequential recordings from the - SimultaneousRecordingsTable table together. This is typically used to group - together sequential recordings where the a sequence of stimuli of the same - type with varying parameters have been presented in a sequence. - multivalued: false - range: NWBFile_general_intracellular_ephys_sequential_recordings - required: false - repetitions: - name: repetitions - description: A table for grouping different sequential intracellular recordings - together. With each SequentialRecording typically representing a particular - type of stimulus, the RepetitionsTable table is typically used to group - sets of stimuli applied in sequence. - multivalued: false - range: NWBFile_general_intracellular_ephys_repetitions - required: false - experimental_conditions: - name: experimental_conditions - description: A table for grouping different intracellular recording repetitions - together that belong to the same experimental experimental_conditions. - multivalued: false - range: NWBFile_general_intracellular_ephys_experimental_conditions - required: false - NWBFile_general_intracellular_ephys_filtering: - name: NWBFile_general_intracellular_ephys_filtering - description: '[DEPRECATED] Use IntracellularElectrode.filtering instead. Description - of filtering used. Includes filtering type and parameters, frequency fall-off, - etc. If this changes between TimeSeries, filter description should be stored - as a text attribute for each TimeSeries.' - NWBFile_general_intracellular_ephys_sweep_table: - name: NWBFile_general_intracellular_ephys_sweep_table - description: '[DEPRECATED] Table used to group different PatchClampSeries. SweepTable - is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable - tables. Additional SequentialRecordingsTable, RepetitionsTable and ExperimentalConditions - tables provide enhanced support for experiment metadata.' - is_a: SweepTable - NWBFile_general_intracellular_ephys_intracellular_recordings: - name: NWBFile_general_intracellular_ephys_intracellular_recordings - description: A table to group together a stimulus and response from a single electrode - and a single simultaneous recording. Each row in the table represents a single - recording consisting typically of a stimulus and a corresponding response. In - some cases, however, only a stimulus or a response are recorded as as part of - an experiment. In this case both, the stimulus and response will point to the - same TimeSeries while the idx_start and count of the invalid column will be - set to -1, thus, indicating that no values have been recorded for the stimulus - or response, respectively. Note, a recording MUST contain at least a stimulus - or a response. Typically the stimulus and response are PatchClampSeries. However, - the use of AD/DA channels that are not associated to an electrode is also common - in intracellular electrophysiology, in which case other TimeSeries may be used. - is_a: IntracellularRecordingsTable - NWBFile_general_intracellular_ephys_simultaneous_recordings: - name: NWBFile_general_intracellular_ephys_simultaneous_recordings - description: A table for grouping different intracellular recordings from the - IntracellularRecordingsTable table together that were recorded simultaneously - from different electrodes - is_a: SimultaneousRecordingsTable - NWBFile_general_intracellular_ephys_sequential_recordings: - name: NWBFile_general_intracellular_ephys_sequential_recordings - description: A table for grouping different sequential recordings from the SimultaneousRecordingsTable - table together. This is typically used to group together sequential recordings - where the a sequence of stimuli of the same type with varying parameters have - been presented in a sequence. - is_a: SequentialRecordingsTable - NWBFile_general_intracellular_ephys_repetitions: - name: NWBFile_general_intracellular_ephys_repetitions - description: A table for grouping different sequential intracellular recordings - together. With each SequentialRecording typically representing a particular - type of stimulus, the RepetitionsTable table is typically used to group sets - of stimuli applied in sequence. - is_a: RepetitionsTable - NWBFile_general_intracellular_ephys_experimental_conditions: - name: NWBFile_general_intracellular_ephys_experimental_conditions - description: A table for grouping different intracellular recording repetitions - together that belong to the same experimental experimental_conditions. - is_a: ExperimentalConditionsTable - NWBFile_general_optogenetics: - name: NWBFile_general_optogenetics - description: Metadata describing optogenetic stimuluation. - attributes: - OptogeneticStimulusSite: - name: OptogeneticStimulusSite - description: An optogenetic stimulation site. - multivalued: true - range: OptogeneticStimulusSite - required: false - NWBFile_general_optophysiology: - name: NWBFile_general_optophysiology - description: Metadata related to optophysiology. - attributes: - ImagingPlane: - name: ImagingPlane - description: An imaging plane. - multivalued: true - range: ImagingPlane - required: false - NWBFile_intervals: - name: NWBFile_intervals - description: Experimental intervals, whether that be logically distinct sub-experiments - having a particular scientific goal, trials (see trials subgroup) during an - experiment, or epochs (see epochs subgroup) deriving from analysis of data. - attributes: - epochs: - name: epochs - description: Divisions in time marking experimental stages or sub-divisions - of a single recording session. - multivalued: false - range: NWBFile_intervals_epochs - required: false - trials: - name: trials - description: Repeated experimental events that have a logical grouping. - multivalued: false - range: NWBFile_intervals_trials - required: false - invalid_times: - name: invalid_times - description: Time intervals that should be removed from analysis. - multivalued: false - range: NWBFile_intervals_invalid_times - required: false - TimeIntervals: - name: TimeIntervals - description: Optional additional table(s) for describing other experimental - time intervals. - multivalued: true - range: TimeIntervals - required: false - NWBFile_intervals_epochs: - name: NWBFile_intervals_epochs - description: Divisions in time marking experimental stages or sub-divisions of - a single recording session. - is_a: TimeIntervals - NWBFile_intervals_trials: - name: NWBFile_intervals_trials - description: Repeated experimental events that have a logical grouping. - is_a: TimeIntervals - NWBFile_intervals_invalid_times: - name: NWBFile_intervals_invalid_times - description: Time intervals that should be removed from analysis. - is_a: TimeIntervals - NWBFile_units: - name: NWBFile_units - description: Data about sorted spike units. - is_a: Units LabMetaData: name: LabMetaData description: Lab-specific meta-data. @@ -1010,90 +197,55 @@ classes: name: age description: Age of subject. Can be supplied instead of 'date_of_birth'. multivalued: false - range: Subject_age + range: Subject__age required: false date_of_birth: name: date_of_birth description: Date of birth of subject. Can be supplied instead of 'age'. multivalued: false - range: Subject_date_of_birth + range: isodatetime required: false description: name: description description: Description of subject and where subject came from (e.g., breeder, if animal). multivalued: false - range: Subject_description + range: text required: false genotype: name: genotype description: Genetic strain. If absent, assume Wild Type (WT). multivalued: false - range: Subject_genotype + range: text required: false sex: name: sex description: Gender of subject. multivalued: false - range: Subject_sex + range: text required: false species: name: species description: Species of subject. multivalued: false - range: Subject_species + range: text required: false strain: name: strain description: Strain of subject. multivalued: false - range: Subject_strain + range: text required: false subject_id: name: subject_id description: ID of animal/person used/participating in experiment (lab convention). multivalued: false - range: Subject_subject_id + range: text required: false weight: name: weight description: Weight at time of experiment, at time of surgery and at other important times. multivalued: false - range: Subject_weight - required: false - Subject_age: - name: Subject_age - description: Age of subject. Can be supplied instead of 'date_of_birth'. - attributes: - reference: - name: reference - description: Age is with reference to this event. Can be 'birth' or 'gestational'. - If reference is omitted, 'birth' is implied. range: text - Subject_date_of_birth: - name: Subject_date_of_birth - description: Date of birth of subject. Can be supplied instead of 'age'. - Subject_description: - name: Subject_description - description: Description of subject and where subject came from (e.g., breeder, - if animal). - Subject_genotype: - name: Subject_genotype - description: Genetic strain. If absent, assume Wild Type (WT). - Subject_sex: - name: Subject_sex - description: Gender of subject. - Subject_species: - name: Subject_species - description: Species of subject. - Subject_strain: - name: Subject_strain - description: Strain of subject. - Subject_subject_id: - name: Subject_subject_id - description: ID of animal/person used/participating in experiment (lab convention). - Subject_weight: - name: Subject_weight - description: Weight at time of experiment, at time of surgery and at other important - times. + required: false diff --git a/nwb_linkml/schema/core.nwb.icephys.include.yaml b/nwb_linkml/schema/core.nwb.icephys.include.yaml new file mode 100644 index 0000000..c18a818 --- /dev/null +++ b/nwb_linkml/schema/core.nwb.icephys.include.yaml @@ -0,0 +1,221 @@ +name: core.nwb.icephys.include +id: core.nwb.icephys.include +imports: +- core.nwb.base +- core.nwb.device +- hdmf-common.table +- nwb.language +- core.nwb.icephys.include +- core.nwb.icephys +default_prefix: core.nwb.icephys.include/ +classes: + PatchClampSeries__data: + name: PatchClampSeries__data + description: Recorded voltage or current. + attributes: + unit: + name: unit + description: Base unit of measurement for working with the data. Actual stored + values are not necessarily stored in these units. To access the data in + these units, multiply 'data' by 'conversion' and add 'offset'. + range: text + data: + name: data + description: Recorded voltage or current. + multivalued: true + range: numeric + required: true + CurrentClampSeries__data: + name: CurrentClampSeries__data + description: Recorded voltage. + attributes: + unit: + name: unit + description: Base unit of measurement for working with the data. which is + fixed to 'volts'. Actual stored values are not necessarily stored in these + units. To access the data in these units, multiply 'data' by 'conversion' + and add 'offset'. + range: text + CurrentClampStimulusSeries__data: + name: CurrentClampStimulusSeries__data + description: Stimulus current applied. + attributes: + unit: + name: unit + description: Base unit of measurement for working with the data. which is + fixed to 'amperes'. Actual stored values are not necessarily stored in these + units. To access the data in these units, multiply 'data' by 'conversion' + and add 'offset'. + range: text + VoltageClampSeries__data: + name: VoltageClampSeries__data + description: Recorded current. + attributes: + unit: + name: unit + description: Base unit of measurement for working with the data. which is + fixed to 'amperes'. Actual stored values are not necessarily stored in these + units. To access the data in these units, multiply 'data' by 'conversion' + and add 'offset'. + range: text + VoltageClampSeries__capacitance_fast: + name: VoltageClampSeries__capacitance_fast + description: Fast capacitance, in farads. + attributes: + unit: + name: unit + description: Unit of measurement for capacitance_fast, which is fixed to 'farads'. + range: text + VoltageClampSeries__capacitance_slow: + name: VoltageClampSeries__capacitance_slow + description: Slow capacitance, in farads. + attributes: + unit: + name: unit + description: Unit of measurement for capacitance_fast, which is fixed to 'farads'. + range: text + VoltageClampSeries__resistance_comp_bandwidth: + name: VoltageClampSeries__resistance_comp_bandwidth + description: Resistance compensation bandwidth, in hertz. + attributes: + unit: + name: unit + description: Unit of measurement for resistance_comp_bandwidth, which is fixed + to 'hertz'. + range: text + VoltageClampSeries__resistance_comp_correction: + name: VoltageClampSeries__resistance_comp_correction + description: Resistance compensation correction, in percent. + attributes: + unit: + name: unit + description: Unit of measurement for resistance_comp_correction, which is + fixed to 'percent'. + range: text + VoltageClampSeries__resistance_comp_prediction: + name: VoltageClampSeries__resistance_comp_prediction + description: Resistance compensation prediction, in percent. + attributes: + unit: + name: unit + description: Unit of measurement for resistance_comp_prediction, which is + fixed to 'percent'. + range: text + VoltageClampSeries__whole_cell_capacitance_comp: + name: VoltageClampSeries__whole_cell_capacitance_comp + description: Whole cell capacitance compensation, in farads. + attributes: + unit: + name: unit + description: Unit of measurement for whole_cell_capacitance_comp, which is + fixed to 'farads'. + range: text + VoltageClampSeries__whole_cell_series_resistance_comp: + name: VoltageClampSeries__whole_cell_series_resistance_comp + description: Whole cell series resistance compensation, in ohms. + attributes: + unit: + name: unit + description: Unit of measurement for whole_cell_series_resistance_comp, which + is fixed to 'ohms'. + range: text + VoltageClampStimulusSeries__data: + name: VoltageClampStimulusSeries__data + description: Stimulus voltage applied. + attributes: + unit: + name: unit + description: Base unit of measurement for working with the data. which is + fixed to 'volts'. Actual stored values are not necessarily stored in these + units. To access the data in these units, multiply 'data' by 'conversion' + and add 'offset'. + range: text + SweepTable__series_index: + name: SweepTable__series_index + description: Index for series. + is_a: VectorIndex + IntracellularStimuliTable__stimulus: + name: IntracellularStimuliTable__stimulus + description: Column storing the reference to the recorded stimulus for the recording + (rows). + is_a: TimeSeriesReferenceVectorData + IntracellularResponsesTable__response: + name: IntracellularResponsesTable__response + description: Column storing the reference to the recorded response for the recording + (rows) + is_a: TimeSeriesReferenceVectorData + IntracellularRecordingsTable__electrodes: + name: IntracellularRecordingsTable__electrodes + description: Table for storing intracellular electrode related metadata. + is_a: IntracellularElectrodesTable + IntracellularRecordingsTable__stimuli: + name: IntracellularRecordingsTable__stimuli + description: Table for storing intracellular stimulus related metadata. + is_a: IntracellularStimuliTable + IntracellularRecordingsTable__responses: + name: IntracellularRecordingsTable__responses + description: Table for storing intracellular response related metadata. + is_a: IntracellularResponsesTable + SimultaneousRecordingsTable__recordings: + name: SimultaneousRecordingsTable__recordings + description: A reference to one or more rows in the IntracellularRecordingsTable + table. + is_a: DynamicTableRegion + attributes: + table: + name: table + description: Reference to the IntracellularRecordingsTable table that this + table region applies to. This specializes the attribute inherited from DynamicTableRegion + to fix the type of table that can be referenced here. + range: IntracellularRecordingsTable + SimultaneousRecordingsTable__recordings_index: + name: SimultaneousRecordingsTable__recordings_index + description: Index dataset for the recordings column. + is_a: VectorIndex + SequentialRecordingsTable__simultaneous_recordings: + name: SequentialRecordingsTable__simultaneous_recordings + description: A reference to one or more rows in the SimultaneousRecordingsTable + table. + is_a: DynamicTableRegion + attributes: + table: + name: table + description: Reference to the SimultaneousRecordingsTable table that this + table region applies to. This specializes the attribute inherited from DynamicTableRegion + to fix the type of table that can be referenced here. + range: SimultaneousRecordingsTable + SequentialRecordingsTable__simultaneous_recordings_index: + name: SequentialRecordingsTable__simultaneous_recordings_index + description: Index dataset for the simultaneous_recordings column. + is_a: VectorIndex + RepetitionsTable__sequential_recordings: + name: RepetitionsTable__sequential_recordings + description: A reference to one or more rows in the SequentialRecordingsTable + table. + is_a: DynamicTableRegion + attributes: + table: + name: table + description: Reference to the SequentialRecordingsTable table that this table + region applies to. This specializes the attribute inherited from DynamicTableRegion + to fix the type of table that can be referenced here. + range: SequentialRecordingsTable + RepetitionsTable__sequential_recordings_index: + name: RepetitionsTable__sequential_recordings_index + description: Index dataset for the sequential_recordings column. + is_a: VectorIndex + ExperimentalConditionsTable__repetitions: + name: ExperimentalConditionsTable__repetitions + description: A reference to one or more rows in the RepetitionsTable table. + is_a: DynamicTableRegion + attributes: + table: + name: table + description: Reference to the RepetitionsTable table that this table region + applies to. This specializes the attribute inherited from DynamicTableRegion + to fix the type of table that can be referenced here. + range: RepetitionsTable + ExperimentalConditionsTable__repetitions_index: + name: ExperimentalConditionsTable__repetitions_index + description: Index dataset for the repetitions column. + is_a: VectorIndex diff --git a/nwb_linkml/schema/core.nwb.icephys.yaml b/nwb_linkml/schema/core.nwb.icephys.yaml index 019cd8a..0dabfe2 100644 --- a/nwb_linkml/schema/core.nwb.icephys.yaml +++ b/nwb_linkml/schema/core.nwb.icephys.yaml @@ -2,8 +2,11 @@ name: core.nwb.icephys id: core.nwb.icephys imports: - core.nwb.base +- core.nwb.device - hdmf-common.table - nwb.language +- core.nwb.icephys.include +- core.nwb.icephys default_prefix: core.nwb.icephys/ classes: PatchClampSeries: @@ -24,39 +27,15 @@ classes: name: data description: Recorded voltage or current. multivalued: false - range: PatchClampSeries_data + range: PatchClampSeries__data required: true gain: name: gain description: Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp). multivalued: false - range: PatchClampSeries_gain + range: float32 required: false - PatchClampSeries_data: - name: PatchClampSeries_data - description: Recorded voltage or current. - attributes: - unit: - name: unit - description: Base unit of measurement for working with the data. Actual stored - values are not necessarily stored in these units. To access the data in - these units, multiply 'data' by 'conversion' and add 'offset'. - range: text - array: - name: array - range: PatchClampSeries_data_Array - PatchClampSeries_data_Array: - name: PatchClampSeries_data_Array - is_a: Arraylike - attributes: - num_times: - name: num_times - range: numeric - required: true - PatchClampSeries_gain: - name: PatchClampSeries_gain - description: Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp). CurrentClampSeries: name: CurrentClampSeries description: Voltage data from an intracellular current-clamp recording. A corresponding @@ -68,46 +47,26 @@ classes: name: data description: Recorded voltage. multivalued: false - range: CurrentClampSeries_data + range: CurrentClampSeries__data required: true bias_current: name: bias_current description: Bias current, in amps. multivalued: false - range: CurrentClampSeries_bias_current + range: float32 required: false bridge_balance: name: bridge_balance description: Bridge balance, in ohms. multivalued: false - range: CurrentClampSeries_bridge_balance + range: float32 required: false capacitance_compensation: name: capacitance_compensation description: Capacitance compensation, in farads. multivalued: false - range: CurrentClampSeries_capacitance_compensation + range: float32 required: false - CurrentClampSeries_data: - name: CurrentClampSeries_data - description: Recorded voltage. - attributes: - unit: - name: unit - description: Base unit of measurement for working with the data. which is - fixed to 'volts'. Actual stored values are not necessarily stored in these - units. To access the data in these units, multiply 'data' by 'conversion' - and add 'offset'. - range: text - CurrentClampSeries_bias_current: - name: CurrentClampSeries_bias_current - description: Bias current, in amps. - CurrentClampSeries_bridge_balance: - name: CurrentClampSeries_bridge_balance - description: Bridge balance, in ohms. - CurrentClampSeries_capacitance_compensation: - name: CurrentClampSeries_capacitance_compensation - description: Capacitance compensation, in farads. IZeroClampSeries: name: IZeroClampSeries description: Voltage data from an intracellular recording when all current and @@ -125,29 +84,20 @@ classes: name: bias_current description: Bias current, in amps, fixed to 0.0. multivalued: false - range: IZeroClampSeries_bias_current + range: float32 required: true bridge_balance: name: bridge_balance description: Bridge balance, in ohms, fixed to 0.0. multivalued: false - range: IZeroClampSeries_bridge_balance + range: float32 required: true capacitance_compensation: name: capacitance_compensation description: Capacitance compensation, in farads, fixed to 0.0. multivalued: false - range: IZeroClampSeries_capacitance_compensation + range: float32 required: true - IZeroClampSeries_bias_current: - name: IZeroClampSeries_bias_current - description: Bias current, in amps, fixed to 0.0. - IZeroClampSeries_bridge_balance: - name: IZeroClampSeries_bridge_balance - description: Bridge balance, in ohms, fixed to 0.0. - IZeroClampSeries_capacitance_compensation: - name: IZeroClampSeries_capacitance_compensation - description: Capacitance compensation, in farads, fixed to 0.0. CurrentClampStimulusSeries: name: CurrentClampStimulusSeries description: Stimulus current applied during current clamp recording. @@ -157,19 +107,8 @@ classes: name: data description: Stimulus current applied. multivalued: false - range: CurrentClampStimulusSeries_data + range: CurrentClampStimulusSeries__data required: true - CurrentClampStimulusSeries_data: - name: CurrentClampStimulusSeries_data - description: Stimulus current applied. - attributes: - unit: - name: unit - description: Base unit of measurement for working with the data. which is - fixed to 'amperes'. Actual stored values are not necessarily stored in these - units. To access the data in these units, multiply 'data' by 'conversion' - and add 'offset'. - range: text VoltageClampSeries: name: VoltageClampSeries description: Current data from an intracellular voltage-clamp recording. A corresponding @@ -181,122 +120,50 @@ classes: name: data description: Recorded current. multivalued: false - range: VoltageClampSeries_data + range: VoltageClampSeries__data required: true capacitance_fast: name: capacitance_fast description: Fast capacitance, in farads. multivalued: false - range: VoltageClampSeries_capacitance_fast + range: VoltageClampSeries__capacitance_fast required: false capacitance_slow: name: capacitance_slow description: Slow capacitance, in farads. multivalued: false - range: VoltageClampSeries_capacitance_slow + range: VoltageClampSeries__capacitance_slow required: false resistance_comp_bandwidth: name: resistance_comp_bandwidth description: Resistance compensation bandwidth, in hertz. multivalued: false - range: VoltageClampSeries_resistance_comp_bandwidth + range: VoltageClampSeries__resistance_comp_bandwidth required: false resistance_comp_correction: name: resistance_comp_correction description: Resistance compensation correction, in percent. multivalued: false - range: VoltageClampSeries_resistance_comp_correction + range: VoltageClampSeries__resistance_comp_correction required: false resistance_comp_prediction: name: resistance_comp_prediction description: Resistance compensation prediction, in percent. multivalued: false - range: VoltageClampSeries_resistance_comp_prediction + range: VoltageClampSeries__resistance_comp_prediction required: false whole_cell_capacitance_comp: name: whole_cell_capacitance_comp description: Whole cell capacitance compensation, in farads. multivalued: false - range: VoltageClampSeries_whole_cell_capacitance_comp + range: VoltageClampSeries__whole_cell_capacitance_comp required: false whole_cell_series_resistance_comp: name: whole_cell_series_resistance_comp description: Whole cell series resistance compensation, in ohms. multivalued: false - range: VoltageClampSeries_whole_cell_series_resistance_comp + range: VoltageClampSeries__whole_cell_series_resistance_comp required: false - VoltageClampSeries_data: - name: VoltageClampSeries_data - description: Recorded current. - attributes: - unit: - name: unit - description: Base unit of measurement for working with the data. which is - fixed to 'amperes'. Actual stored values are not necessarily stored in these - units. To access the data in these units, multiply 'data' by 'conversion' - and add 'offset'. - range: text - VoltageClampSeries_capacitance_fast: - name: VoltageClampSeries_capacitance_fast - description: Fast capacitance, in farads. - attributes: - unit: - name: unit - description: Unit of measurement for capacitance_fast, which is fixed to 'farads'. - range: text - VoltageClampSeries_capacitance_slow: - name: VoltageClampSeries_capacitance_slow - description: Slow capacitance, in farads. - attributes: - unit: - name: unit - description: Unit of measurement for capacitance_fast, which is fixed to 'farads'. - range: text - VoltageClampSeries_resistance_comp_bandwidth: - name: VoltageClampSeries_resistance_comp_bandwidth - description: Resistance compensation bandwidth, in hertz. - attributes: - unit: - name: unit - description: Unit of measurement for resistance_comp_bandwidth, which is fixed - to 'hertz'. - range: text - VoltageClampSeries_resistance_comp_correction: - name: VoltageClampSeries_resistance_comp_correction - description: Resistance compensation correction, in percent. - attributes: - unit: - name: unit - description: Unit of measurement for resistance_comp_correction, which is - fixed to 'percent'. - range: text - VoltageClampSeries_resistance_comp_prediction: - name: VoltageClampSeries_resistance_comp_prediction - description: Resistance compensation prediction, in percent. - attributes: - unit: - name: unit - description: Unit of measurement for resistance_comp_prediction, which is - fixed to 'percent'. - range: text - VoltageClampSeries_whole_cell_capacitance_comp: - name: VoltageClampSeries_whole_cell_capacitance_comp - description: Whole cell capacitance compensation, in farads. - attributes: - unit: - name: unit - description: Unit of measurement for whole_cell_capacitance_comp, which is - fixed to 'farads'. - range: text - VoltageClampSeries_whole_cell_series_resistance_comp: - name: VoltageClampSeries_whole_cell_series_resistance_comp - description: Whole cell series resistance compensation, in ohms. - attributes: - unit: - name: unit - description: Unit of measurement for whole_cell_series_resistance_comp, which - is fixed to 'ohms'. - range: text VoltageClampStimulusSeries: name: VoltageClampStimulusSeries description: Stimulus voltage applied during a voltage clamp recording. @@ -306,19 +173,8 @@ classes: name: data description: Stimulus voltage applied. multivalued: false - range: VoltageClampStimulusSeries_data + range: VoltageClampStimulusSeries__data required: true - VoltageClampStimulusSeries_data: - name: VoltageClampStimulusSeries_data - description: Stimulus voltage applied. - attributes: - unit: - name: unit - description: Base unit of measurement for working with the data. which is - fixed to 'volts'. Actual stored values are not necessarily stored in these - units. To access the data in these units, multiply 'data' by 'conversion' - and add 'offset'. - range: text IntracellularElectrode: name: IntracellularElectrode description: An intracellular electrode and its metadata. @@ -328,25 +184,25 @@ classes: name: cell_id description: unique ID of the cell multivalued: false - range: IntracellularElectrode_cell_id + range: text required: false description: name: description description: Description of electrode (e.g., whole-cell, sharp, etc.). multivalued: false - range: IntracellularElectrode_description + range: text required: true filtering: name: filtering description: Electrode specific filtering. multivalued: false - range: IntracellularElectrode_filtering + range: text required: false initial_access_resistance: name: initial_access_resistance description: Initial access resistance. multivalued: false - range: IntracellularElectrode_initial_access_resistance + range: text required: false location: name: location @@ -354,52 +210,26 @@ classes: on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible. multivalued: false - range: IntracellularElectrode_location + range: text required: false resistance: name: resistance description: Electrode resistance, in ohms. multivalued: false - range: IntracellularElectrode_resistance + range: text required: false seal: name: seal description: Information about seal used for recording. multivalued: false - range: IntracellularElectrode_seal + range: text required: false slice: name: slice description: Information about slice used for recording. multivalued: false - range: IntracellularElectrode_slice + range: text required: false - IntracellularElectrode_cell_id: - name: IntracellularElectrode_cell_id - description: unique ID of the cell - IntracellularElectrode_description: - name: IntracellularElectrode_description - description: Description of electrode (e.g., whole-cell, sharp, etc.). - IntracellularElectrode_filtering: - name: IntracellularElectrode_filtering - description: Electrode specific filtering. - IntracellularElectrode_initial_access_resistance: - name: IntracellularElectrode_initial_access_resistance - description: Initial access resistance. - IntracellularElectrode_location: - name: IntracellularElectrode_location - description: Location of the electrode. Specify the area, layer, comments on estimation - of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names - for anatomical regions when possible. - IntracellularElectrode_resistance: - name: IntracellularElectrode_resistance - description: Electrode resistance, in ohms. - IntracellularElectrode_seal: - name: IntracellularElectrode_seal - description: Information about seal used for recording. - IntracellularElectrode_slice: - name: IntracellularElectrode_slice - description: Information about slice used for recording. SweepTable: name: SweepTable description: '[DEPRECATED] Table used to group different PatchClampSeries. SweepTable @@ -411,33 +241,19 @@ classes: sweep_number: name: sweep_number description: Sweep number of the PatchClampSeries in that row. - multivalued: false - range: SweepTable_sweep_number - required: true + multivalued: true + range: uint32 series: name: series description: The PatchClampSeries with the sweep number in that row. - multivalued: false - range: SweepTable_series - required: true + multivalued: true + range: PatchClampSeries series_index: name: series_index description: Index for series. multivalued: false - range: SweepTable_series_index + range: SweepTable__series_index required: true - SweepTable_sweep_number: - name: SweepTable_sweep_number - description: Sweep number of the PatchClampSeries in that row. - is_a: VectorData - SweepTable_series: - name: SweepTable_series - description: The PatchClampSeries with the sweep number in that row. - is_a: VectorData - SweepTable_series_index: - name: SweepTable_series_index - description: Index for series. - is_a: VectorIndex IntracellularElectrodesTable: name: IntracellularElectrodesTable description: Table for storing intracellular electrode related metadata. @@ -450,13 +266,8 @@ classes: electrode: name: electrode description: Column for storing the reference to the intracellular electrode. - multivalued: false - range: IntracellularElectrodesTable_electrode - required: true - IntracellularElectrodesTable_electrode: - name: IntracellularElectrodesTable_electrode - description: Column for storing the reference to the intracellular electrode. - is_a: VectorData + multivalued: true + range: IntracellularElectrode IntracellularStimuliTable: name: IntracellularStimuliTable description: Table for storing intracellular stimulus related metadata. @@ -471,13 +282,8 @@ classes: description: Column storing the reference to the recorded stimulus for the recording (rows). multivalued: false - range: IntracellularStimuliTable_stimulus + range: IntracellularStimuliTable__stimulus required: true - IntracellularStimuliTable_stimulus: - name: IntracellularStimuliTable_stimulus - description: Column storing the reference to the recorded stimulus for the recording - (rows). - is_a: TimeSeriesReferenceVectorData IntracellularResponsesTable: name: IntracellularResponsesTable description: Table for storing intracellular response related metadata. @@ -492,13 +298,8 @@ classes: description: Column storing the reference to the recorded response for the recording (rows) multivalued: false - range: IntracellularResponsesTable_response + range: IntracellularResponsesTable__response required: true - IntracellularResponsesTable_response: - name: IntracellularResponsesTable_response - description: Column storing the reference to the recorded response for the recording - (rows) - is_a: TimeSeriesReferenceVectorData IntracellularRecordingsTable: name: IntracellularRecordingsTable description: A table to group together a stimulus and response from a single electrode @@ -523,32 +324,20 @@ classes: name: electrodes description: Table for storing intracellular electrode related metadata. multivalued: false - range: IntracellularRecordingsTable_electrodes + range: IntracellularRecordingsTable__electrodes required: true stimuli: name: stimuli description: Table for storing intracellular stimulus related metadata. multivalued: false - range: IntracellularRecordingsTable_stimuli + range: IntracellularRecordingsTable__stimuli required: true responses: name: responses description: Table for storing intracellular response related metadata. multivalued: false - range: IntracellularRecordingsTable_responses + range: IntracellularRecordingsTable__responses required: true - IntracellularRecordingsTable_electrodes: - name: IntracellularRecordingsTable_electrodes - description: Table for storing intracellular electrode related metadata. - is_a: IntracellularElectrodesTable - IntracellularRecordingsTable_stimuli: - name: IntracellularRecordingsTable_stimuli - description: Table for storing intracellular stimulus related metadata. - is_a: IntracellularStimuliTable - IntracellularRecordingsTable_responses: - name: IntracellularRecordingsTable_responses - description: Table for storing intracellular response related metadata. - is_a: IntracellularResponsesTable SimultaneousRecordingsTable: name: SimultaneousRecordingsTable description: A table for grouping different intracellular recordings from the @@ -561,30 +350,14 @@ classes: description: A reference to one or more rows in the IntracellularRecordingsTable table. multivalued: false - range: SimultaneousRecordingsTable_recordings + range: SimultaneousRecordingsTable__recordings required: true recordings_index: name: recordings_index description: Index dataset for the recordings column. multivalued: false - range: SimultaneousRecordingsTable_recordings_index + range: SimultaneousRecordingsTable__recordings_index required: true - SimultaneousRecordingsTable_recordings: - name: SimultaneousRecordingsTable_recordings - description: A reference to one or more rows in the IntracellularRecordingsTable - table. - is_a: DynamicTableRegion - attributes: - table: - name: table - description: Reference to the IntracellularRecordingsTable table that this - table region applies to. This specializes the attribute inherited from DynamicTableRegion - to fix the type of table that can be referenced here. - range: IntracellularRecordingsTable - SimultaneousRecordingsTable_recordings_index: - name: SimultaneousRecordingsTable_recordings_index - description: Index dataset for the recordings column. - is_a: VectorIndex SequentialRecordingsTable: name: SequentialRecordingsTable description: A table for grouping different sequential recordings from the SimultaneousRecordingsTable @@ -598,40 +371,19 @@ classes: description: A reference to one or more rows in the SimultaneousRecordingsTable table. multivalued: false - range: SequentialRecordingsTable_simultaneous_recordings + range: SequentialRecordingsTable__simultaneous_recordings required: true simultaneous_recordings_index: name: simultaneous_recordings_index description: Index dataset for the simultaneous_recordings column. multivalued: false - range: SequentialRecordingsTable_simultaneous_recordings_index + range: SequentialRecordingsTable__simultaneous_recordings_index required: true stimulus_type: name: stimulus_type description: The type of stimulus used for the sequential recording. - multivalued: false - range: SequentialRecordingsTable_stimulus_type - required: true - SequentialRecordingsTable_simultaneous_recordings: - name: SequentialRecordingsTable_simultaneous_recordings - description: A reference to one or more rows in the SimultaneousRecordingsTable - table. - is_a: DynamicTableRegion - attributes: - table: - name: table - description: Reference to the SimultaneousRecordingsTable table that this - table region applies to. This specializes the attribute inherited from DynamicTableRegion - to fix the type of table that can be referenced here. - range: SimultaneousRecordingsTable - SequentialRecordingsTable_simultaneous_recordings_index: - name: SequentialRecordingsTable_simultaneous_recordings_index - description: Index dataset for the simultaneous_recordings column. - is_a: VectorIndex - SequentialRecordingsTable_stimulus_type: - name: SequentialRecordingsTable_stimulus_type - description: The type of stimulus used for the sequential recording. - is_a: VectorData + multivalued: true + range: text RepetitionsTable: name: RepetitionsTable description: A table for grouping different sequential intracellular recordings @@ -645,30 +397,14 @@ classes: description: A reference to one or more rows in the SequentialRecordingsTable table. multivalued: false - range: RepetitionsTable_sequential_recordings + range: RepetitionsTable__sequential_recordings required: true sequential_recordings_index: name: sequential_recordings_index description: Index dataset for the sequential_recordings column. multivalued: false - range: RepetitionsTable_sequential_recordings_index + range: RepetitionsTable__sequential_recordings_index required: true - RepetitionsTable_sequential_recordings: - name: RepetitionsTable_sequential_recordings - description: A reference to one or more rows in the SequentialRecordingsTable - table. - is_a: DynamicTableRegion - attributes: - table: - name: table - description: Reference to the SequentialRecordingsTable table that this table - region applies to. This specializes the attribute inherited from DynamicTableRegion - to fix the type of table that can be referenced here. - range: SequentialRecordingsTable - RepetitionsTable_sequential_recordings_index: - name: RepetitionsTable_sequential_recordings_index - description: Index dataset for the sequential_recordings column. - is_a: VectorIndex ExperimentalConditionsTable: name: ExperimentalConditionsTable description: A table for grouping different intracellular recording repetitions @@ -679,26 +415,11 @@ classes: name: repetitions description: A reference to one or more rows in the RepetitionsTable table. multivalued: false - range: ExperimentalConditionsTable_repetitions + range: ExperimentalConditionsTable__repetitions required: true repetitions_index: name: repetitions_index description: Index dataset for the repetitions column. multivalued: false - range: ExperimentalConditionsTable_repetitions_index + range: ExperimentalConditionsTable__repetitions_index required: true - ExperimentalConditionsTable_repetitions: - name: ExperimentalConditionsTable_repetitions - description: A reference to one or more rows in the RepetitionsTable table. - is_a: DynamicTableRegion - attributes: - table: - name: table - description: Reference to the RepetitionsTable table that this table region - applies to. This specializes the attribute inherited from DynamicTableRegion - to fix the type of table that can be referenced here. - range: RepetitionsTable - ExperimentalConditionsTable_repetitions_index: - name: ExperimentalConditionsTable_repetitions_index - description: Index dataset for the repetitions column. - is_a: VectorIndex diff --git a/nwb_linkml/schema/core.nwb.image.include.yaml b/nwb_linkml/schema/core.nwb.image.include.yaml new file mode 100644 index 0000000..5c14f9d --- /dev/null +++ b/nwb_linkml/schema/core.nwb.image.include.yaml @@ -0,0 +1,207 @@ +name: core.nwb.image.include +id: core.nwb.image.include +imports: +- core.nwb.base +- core.nwb.device +- nwb.language +- core.nwb.image.include +- core.nwb.image +default_prefix: core.nwb.image.include/ +classes: + GrayscaleImage__Array: + name: GrayscaleImage__Array + is_a: Arraylike + attributes: + x: + name: x + range: numeric + required: false + y: + name: y + range: numeric + required: false + RGBImage__Array: + name: RGBImage__Array + is_a: Arraylike + attributes: + x: + name: x + range: numeric + required: false + y: + name: y + range: numeric + required: false + r, g, b: + name: r, g, b + range: numeric + required: false + minimum_cardinality: 3 + maximum_cardinality: 3 + RGBAImage__Array: + name: RGBAImage__Array + is_a: Arraylike + attributes: + x: + name: x + range: numeric + required: false + y: + name: y + range: numeric + required: false + r, g, b, a: + name: r, g, b, a + range: numeric + required: false + minimum_cardinality: 4 + maximum_cardinality: 4 + ImageSeries__data: + name: ImageSeries__data + description: Binary data representing images across frames. If data are stored + in an external file, this should be an empty 3D array. + attributes: + array: + name: array + range: ImageSeries__data__Array + ImageSeries__data__Array: + name: ImageSeries__data__Array + is_a: Arraylike + attributes: + frame: + name: frame + range: numeric + required: true + x: + name: x + range: numeric + required: true + y: + name: y + range: numeric + required: true + z: + name: z + range: numeric + required: false + ImageSeries__dimension: + name: ImageSeries__dimension + description: Number of pixels on x, y, (and z) axes. + attributes: + dimension: + name: dimension + description: Number of pixels on x, y, (and z) axes. + multivalued: true + range: int32 + required: false + ImageSeries__external_file: + name: ImageSeries__external_file + description: Paths to one or more external file(s). The field is only present + if format='external'. This is only relevant if the image series is stored in + the file system as one or more image file(s). This field should NOT be used + if the image is stored in another NWB file and that file is linked to this file. + attributes: + starting_frame: + name: starting_frame + description: Each external image may contain one or more consecutive frames + of the full ImageSeries. This attribute serves as an index to indicate which + frames each file contains, to facilitate random access. The 'starting_frame' + attribute, hence, contains a list of frame numbers within the full ImageSeries + of the first frame of each file listed in the parent 'external_file' dataset. + Zero-based indexing is used (hence, the first element will always be zero). + For example, if the 'external_file' dataset has three paths to files and + the first file has 5 frames, the second file has 10 frames, and the third + file has 20 frames, then this attribute will have values [0, 5, 15]. If + there is a single external file that holds all of the frames of the ImageSeries + (and so there is a single element in the 'external_file' dataset), then + this attribute should have value [0]. + range: int32 + external_file: + name: external_file + description: Paths to one or more external file(s). The field is only present + if format='external'. This is only relevant if the image series is stored + in the file system as one or more image file(s). This field should NOT be + used if the image is stored in another NWB file and that file is linked + to this file. + multivalued: true + range: text + required: false + OpticalSeries__field_of_view: + name: OpticalSeries__field_of_view + description: Width, height and depth of image, or imaged area, in meters. + attributes: + array: + name: array + range: OpticalSeries__field_of_view__Array + OpticalSeries__field_of_view__Array: + name: OpticalSeries__field_of_view__Array + is_a: Arraylike + attributes: + width, height: + name: width, height + range: float32 + required: false + minimum_cardinality: 2 + maximum_cardinality: 2 + width, height, depth: + name: width, height, depth + range: float32 + required: false + minimum_cardinality: 3 + maximum_cardinality: 3 + OpticalSeries__data: + name: OpticalSeries__data + description: Images presented to subject, either grayscale or RGB + attributes: + array: + name: array + range: OpticalSeries__data__Array + OpticalSeries__data__Array: + name: OpticalSeries__data__Array + is_a: Arraylike + attributes: + frame: + name: frame + range: numeric + required: true + x: + name: x + range: numeric + required: true + y: + name: y + range: numeric + required: true + r, g, b: + name: r, g, b + range: numeric + required: false + minimum_cardinality: 3 + maximum_cardinality: 3 + IndexSeries__data: + name: IndexSeries__data + description: Index of the image (using zero-indexing) in the linked Images object. + attributes: + conversion: + name: conversion + description: This field is unused by IndexSeries. + range: float32 + resolution: + name: resolution + description: This field is unused by IndexSeries. + range: float32 + offset: + name: offset + description: This field is unused by IndexSeries. + range: float32 + unit: + name: unit + description: This field is unused by IndexSeries and has the value N/A. + range: text + data: + name: data + description: Index of the image (using zero-indexing) in the linked Images + object. + multivalued: true + range: uint32 + required: true diff --git a/nwb_linkml/schema/core.nwb.image.yaml b/nwb_linkml/schema/core.nwb.image.yaml index 16bf0c7..c3c9131 100644 --- a/nwb_linkml/schema/core.nwb.image.yaml +++ b/nwb_linkml/schema/core.nwb.image.yaml @@ -2,7 +2,10 @@ name: core.nwb.image id: core.nwb.image imports: - core.nwb.base +- core.nwb.device - nwb.language +- core.nwb.image.include +- core.nwb.image default_prefix: core.nwb.image/ classes: GrayscaleImage: @@ -12,19 +15,7 @@ classes: attributes: array: name: array - range: GrayscaleImage_Array - GrayscaleImage_Array: - name: GrayscaleImage_Array - is_a: Arraylike - attributes: - x: - name: x - range: numeric - required: false - y: - name: y - range: numeric - required: false + range: GrayscaleImage__Array RGBImage: name: RGBImage description: A color image. @@ -32,25 +23,7 @@ classes: attributes: array: name: array - range: RGBImage_Array - RGBImage_Array: - name: RGBImage_Array - is_a: Arraylike - attributes: - x: - name: x - range: numeric - required: false - y: - name: y - range: numeric - required: false - r, g, b: - name: r, g, b - range: numeric - required: false - minimum_cardinality: 3 - maximum_cardinality: 3 + range: RGBImage__Array RGBAImage: name: RGBAImage description: A color image with transparency. @@ -58,25 +31,7 @@ classes: attributes: array: name: array - range: RGBAImage_Array - RGBAImage_Array: - name: RGBAImage_Array - is_a: Arraylike - attributes: - x: - name: x - range: numeric - required: false - y: - name: y - range: numeric - required: false - r, g, b, a: - name: r, g, b, a - range: numeric - required: false - minimum_cardinality: 4 - maximum_cardinality: 4 + range: RGBAImage__Array ImageSeries: name: ImageSeries description: General image data that is common between acquisition and stimulus @@ -92,13 +47,13 @@ classes: description: Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array. multivalued: false - range: ImageSeries_data + range: ImageSeries__data required: true dimension: name: dimension description: Number of pixels on x, y, (and z) axes. multivalued: false - range: ImageSeries_dimension + range: ImageSeries__dimension required: false external_file: name: external_file @@ -108,7 +63,7 @@ classes: used if the image is stored in another NWB file and that file is linked to this file. multivalued: false - range: ImageSeries_external_file + range: ImageSeries__external_file required: false format: name: format @@ -117,90 +72,8 @@ classes: the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed. multivalued: false - range: ImageSeries_format - required: false - ImageSeries_data: - name: ImageSeries_data - description: Binary data representing images across frames. If data are stored - in an external file, this should be an empty 3D array. - attributes: - array: - name: array - range: ImageSeries_data_Array - ImageSeries_data_Array: - name: ImageSeries_data_Array - is_a: Arraylike - attributes: - frame: - name: frame - range: numeric - required: true - x: - name: x - range: numeric - required: true - y: - name: y - range: numeric - required: true - z: - name: z - range: numeric - required: false - ImageSeries_dimension: - name: ImageSeries_dimension - description: Number of pixels on x, y, (and z) axes. - attributes: - array: - name: array - range: ImageSeries_dimension_Array - ImageSeries_dimension_Array: - name: ImageSeries_dimension_Array - is_a: Arraylike - attributes: - rank: - name: rank - range: int32 - required: true - ImageSeries_external_file: - name: ImageSeries_external_file - description: Paths to one or more external file(s). The field is only present - if format='external'. This is only relevant if the image series is stored in - the file system as one or more image file(s). This field should NOT be used - if the image is stored in another NWB file and that file is linked to this file. - attributes: - starting_frame: - name: starting_frame - description: Each external image may contain one or more consecutive frames - of the full ImageSeries. This attribute serves as an index to indicate which - frames each file contains, to facilitate random access. The 'starting_frame' - attribute, hence, contains a list of frame numbers within the full ImageSeries - of the first frame of each file listed in the parent 'external_file' dataset. - Zero-based indexing is used (hence, the first element will always be zero). - For example, if the 'external_file' dataset has three paths to files and - the first file has 5 frames, the second file has 10 frames, and the third - file has 20 frames, then this attribute will have values [0, 5, 15]. If - there is a single external file that holds all of the frames of the ImageSeries - (and so there is a single element in the 'external_file' dataset), then - this attribute should have value [0]. - range: int32 - array: - name: array - range: ImageSeries_external_file_Array - ImageSeries_external_file_Array: - name: ImageSeries_external_file_Array - is_a: Arraylike - attributes: - num_files: - name: num_files range: text - required: true - ImageSeries_format: - name: ImageSeries_format - description: Format of image. If this is 'external', then the attribute 'external_file' - contains the path information to the image files. If this is 'raw', then the - raw (single-channel) binary data is stored in the 'data' dataset. If this attribute - is not present, then the default format='raw' case is assumed. + required: false ImageMaskSeries: name: ImageMaskSeries description: An alpha mask that is applied to a presented visual stimulus. The @@ -222,86 +95,27 @@ classes: name: distance description: Distance from camera/monitor to target/eye. multivalued: false - range: OpticalSeries_distance + range: float32 required: false field_of_view: name: field_of_view description: Width, height and depth of image, or imaged area, in meters. multivalued: false - range: OpticalSeries_field_of_view + range: OpticalSeries__field_of_view required: false data: name: data description: Images presented to subject, either grayscale or RGB multivalued: false - range: OpticalSeries_data + range: OpticalSeries__data required: true orientation: name: orientation description: Description of image relative to some reference frame (e.g., which way is up). Must also specify frame of reference. multivalued: false - range: OpticalSeries_orientation + range: text required: false - OpticalSeries_distance: - name: OpticalSeries_distance - description: Distance from camera/monitor to target/eye. - OpticalSeries_field_of_view: - name: OpticalSeries_field_of_view - description: Width, height and depth of image, or imaged area, in meters. - attributes: - array: - name: array - range: OpticalSeries_field_of_view_Array - OpticalSeries_field_of_view_Array: - name: OpticalSeries_field_of_view_Array - is_a: Arraylike - attributes: - width, height: - name: width, height - range: float32 - required: false - minimum_cardinality: 2 - maximum_cardinality: 2 - width, height, depth: - name: width, height, depth - range: float32 - required: false - minimum_cardinality: 3 - maximum_cardinality: 3 - OpticalSeries_data: - name: OpticalSeries_data - description: Images presented to subject, either grayscale or RGB - attributes: - array: - name: array - range: OpticalSeries_data_Array - OpticalSeries_data_Array: - name: OpticalSeries_data_Array - is_a: Arraylike - attributes: - frame: - name: frame - range: numeric - required: true - x: - name: x - range: numeric - required: true - y: - name: y - range: numeric - required: true - r, g, b: - name: r, g, b - range: numeric - required: false - minimum_cardinality: 3 - maximum_cardinality: 3 - OpticalSeries_orientation: - name: OpticalSeries_orientation - description: Description of image relative to some reference frame (e.g., which - way is up). Must also specify frame of reference. IndexSeries: name: IndexSeries description: Stores indices to image frames stored in an ImageSeries. The purpose @@ -318,36 +132,5 @@ classes: description: Index of the image (using zero-indexing) in the linked Images object. multivalued: false - range: IndexSeries_data - required: true - IndexSeries_data: - name: IndexSeries_data - description: Index of the image (using zero-indexing) in the linked Images object. - attributes: - conversion: - name: conversion - description: This field is unused by IndexSeries. - range: float32 - resolution: - name: resolution - description: This field is unused by IndexSeries. - range: float32 - offset: - name: offset - description: This field is unused by IndexSeries. - range: float32 - unit: - name: unit - description: This field is unused by IndexSeries and has the value N/A. - range: text - array: - name: array - range: IndexSeries_data_Array - IndexSeries_data_Array: - name: IndexSeries_data_Array - is_a: Arraylike - attributes: - num_times: - name: num_times - range: uint32 + range: IndexSeries__data required: true diff --git a/nwb_linkml/schema/core.nwb.misc.include.yaml b/nwb_linkml/schema/core.nwb.misc.include.yaml new file mode 100644 index 0000000..943bde5 --- /dev/null +++ b/nwb_linkml/schema/core.nwb.misc.include.yaml @@ -0,0 +1,277 @@ +name: core.nwb.misc.include +id: core.nwb.misc.include +imports: +- core.nwb.base +- hdmf-common.table +- core.nwb.ecephys +- nwb.language +- core.nwb.misc.include +- core.nwb.misc +default_prefix: core.nwb.misc.include/ +classes: + AbstractFeatureSeries__data: + name: AbstractFeatureSeries__data + description: Values of each feature at each time. + attributes: + unit: + name: unit + description: Since there can be different units for different features, store + the units in 'feature_units'. The default value for this attribute is "see + 'feature_units'". + range: text + array: + name: array + range: AbstractFeatureSeries__data__Array + AbstractFeatureSeries__data__Array: + name: AbstractFeatureSeries__data__Array + is_a: Arraylike + attributes: + num_times: + name: num_times + range: numeric + required: true + num_features: + name: num_features + range: numeric + required: false + AbstractFeatureSeries__feature_units: + name: AbstractFeatureSeries__feature_units + description: Units of each feature. + attributes: + feature_units: + name: feature_units + description: Units of each feature. + multivalued: true + range: text + required: false + AbstractFeatureSeries__features: + name: AbstractFeatureSeries__features + description: Description of the features represented in TimeSeries::data. + attributes: + features: + name: features + description: Description of the features represented in TimeSeries::data. + multivalued: true + range: text + required: true + AnnotationSeries__data: + name: AnnotationSeries__data + description: Annotations made during an experiment. + attributes: + resolution: + name: resolution + description: Smallest meaningful difference between values in data. Annotations + have no units, so the value is fixed to -1.0. + range: float32 + unit: + name: unit + description: Base unit of measurement for working with the data. Annotations + have no units, so the value is fixed to 'n/a'. + range: text + data: + name: data + description: Annotations made during an experiment. + multivalued: true + range: text + required: true + IntervalSeries__data: + name: IntervalSeries__data + description: Use values >0 if interval started, <0 if interval ended. + attributes: + resolution: + name: resolution + description: Smallest meaningful difference between values in data. Annotations + have no units, so the value is fixed to -1.0. + range: float32 + unit: + name: unit + description: Base unit of measurement for working with the data. Annotations + have no units, so the value is fixed to 'n/a'. + range: text + data: + name: data + description: Use values >0 if interval started, <0 if interval ended. + multivalued: true + range: int8 + required: true + DecompositionSeries__data: + name: DecompositionSeries__data + description: Data decomposed into frequency bands. + attributes: + unit: + name: unit + description: Base unit of measurement for working with the data. Actual stored + values are not necessarily stored in these units. To access the data in + these units, multiply 'data' by 'conversion'. + range: text + array: + name: array + range: DecompositionSeries__data__Array + DecompositionSeries__data__Array: + name: DecompositionSeries__data__Array + is_a: Arraylike + attributes: + num_times: + name: num_times + range: numeric + required: false + num_channels: + name: num_channels + range: numeric + required: false + num_bands: + name: num_bands + range: numeric + required: false + DecompositionSeries__source_channels: + name: DecompositionSeries__source_channels + description: DynamicTableRegion pointer to the channels that this decomposition + series was generated from. + is_a: DynamicTableRegion + DecompositionSeries__bands: + name: DecompositionSeries__bands + description: Table for describing the bands that this series was generated from. + There should be one row in this table for each band. + is_a: DynamicTable + attributes: + band_name: + name: band_name + description: Name of the band, e.g. theta. + multivalued: true + range: text + band_limits: + name: band_limits + description: Low and high limit of each band in Hz. If it is a Gaussian filter, + use 2 SD on either side of the center. + multivalued: false + range: DecompositionSeries__bands__band_limits + required: true + band_mean: + name: band_mean + description: The mean Gaussian filters, in Hz. + multivalued: false + range: DecompositionSeries__bands__band_mean + required: true + band_stdev: + name: band_stdev + description: The standard deviation of Gaussian filters, in Hz. + multivalued: false + range: DecompositionSeries__bands__band_stdev + required: true + DecompositionSeries__bands__band_limits: + name: DecompositionSeries__bands__band_limits + description: Low and high limit of each band in Hz. If it is a Gaussian filter, + use 2 SD on either side of the center. + is_a: VectorData + DecompositionSeries__bands__band_mean: + name: DecompositionSeries__bands__band_mean + description: The mean Gaussian filters, in Hz. + is_a: VectorData + DecompositionSeries__bands__band_stdev: + name: DecompositionSeries__bands__band_stdev + description: The standard deviation of Gaussian filters, in Hz. + is_a: VectorData + Units__spike_times_index: + name: Units__spike_times_index + description: Index into the spike_times dataset. + is_a: VectorIndex + Units__spike_times: + name: Units__spike_times + description: Spike times for each unit in seconds. + is_a: VectorData + attributes: + resolution: + name: resolution + description: The smallest possible difference between two spike times. Usually + 1 divided by the acquisition sampling rate from which spike times were extracted, + but could be larger if the acquisition time series was downsampled or smaller + if the acquisition time series was smoothed/interpolated and it is possible + for the spike time to be between samples. + range: float64 + Units__obs_intervals_index: + name: Units__obs_intervals_index + description: Index into the obs_intervals dataset. + is_a: VectorIndex + Units__obs_intervals: + name: Units__obs_intervals + description: Observation intervals for each unit. + is_a: VectorData + Units__electrodes_index: + name: Units__electrodes_index + description: Index into electrodes. + is_a: VectorIndex + Units__electrodes: + name: Units__electrodes + description: Electrode that each spike unit came from, specified using a DynamicTableRegion. + is_a: DynamicTableRegion + Units__waveform_mean: + name: Units__waveform_mean + description: Spike waveform mean for each spike unit. + is_a: VectorData + attributes: + sampling_rate: + name: sampling_rate + description: Sampling rate, in hertz. + range: float32 + unit: + name: unit + description: Unit of measurement. This value is fixed to 'volts'. + range: text + Units__waveform_sd: + name: Units__waveform_sd + description: Spike waveform standard deviation for each spike unit. + is_a: VectorData + attributes: + sampling_rate: + name: sampling_rate + description: Sampling rate, in hertz. + range: float32 + unit: + name: unit + description: Unit of measurement. This value is fixed to 'volts'. + range: text + Units__waveforms: + name: Units__waveforms + description: Individual waveforms for each spike on each electrode. This is a + doubly indexed column. The 'waveforms_index' column indexes which waveforms + in this column belong to the same spike event for a given unit, where each waveform + was recorded from a different electrode. The 'waveforms_index_index' column + indexes the 'waveforms_index' column to indicate which spike events belong to + a given unit. For example, if the 'waveforms_index_index' column has values + [2, 5, 6], then the first 2 elements of the 'waveforms_index' column correspond + to the 2 spike events of the first unit, the next 3 elements of the 'waveforms_index' + column correspond to the 3 spike events of the second unit, and the next 1 element + of the 'waveforms_index' column corresponds to the 1 spike event of the third + unit. If the 'waveforms_index' column has values [3, 6, 8, 10, 12, 13], then + the first 3 elements of the 'waveforms' column contain the 3 spike waveforms + that were recorded from 3 different electrodes for the first spike time of the + first unit. See https://nwb-schema.readthedocs.io/en/stable/format_description.html#doubly-ragged-arrays + for a graphical representation of this example. When there is only one electrode + for each unit (i.e., each spike time is associated with a single waveform), + then the 'waveforms_index' column will have values 1, 2, ..., N, where N is + the number of spike events. The number of electrodes for each spike event should + be the same within a given unit. The 'electrodes' column should be used to indicate + which electrodes are associated with each unit, and the order of the waveforms + within a given unit x spike event should be in the same order as the electrodes + referenced in the 'electrodes' column of this table. The number of samples for + each waveform must be the same. + is_a: VectorData + attributes: + sampling_rate: + name: sampling_rate + description: Sampling rate, in hertz. + range: float32 + unit: + name: unit + description: Unit of measurement. This value is fixed to 'volts'. + range: text + Units__waveforms_index: + name: Units__waveforms_index + description: Index into the waveforms dataset. One value for every spike event. + See 'waveforms' for more detail. + is_a: VectorIndex + Units__waveforms_index_index: + name: Units__waveforms_index_index + description: Index into the waveforms_index dataset. One value for every unit + (row in the table). See 'waveforms' for more detail. + is_a: VectorIndex diff --git a/nwb_linkml/schema/core.nwb.misc.yaml b/nwb_linkml/schema/core.nwb.misc.yaml index d71a3d5..06559d5 100644 --- a/nwb_linkml/schema/core.nwb.misc.yaml +++ b/nwb_linkml/schema/core.nwb.misc.yaml @@ -3,7 +3,10 @@ id: core.nwb.misc imports: - core.nwb.base - hdmf-common.table +- core.nwb.ecephys - nwb.language +- core.nwb.misc.include +- core.nwb.misc default_prefix: core.nwb.misc/ classes: AbstractFeatureSeries: @@ -23,74 +26,19 @@ classes: name: data description: Values of each feature at each time. multivalued: false - range: AbstractFeatureSeries_data + range: AbstractFeatureSeries__data required: true feature_units: name: feature_units description: Units of each feature. multivalued: false - range: AbstractFeatureSeries_feature_units + range: AbstractFeatureSeries__feature_units required: false features: name: features description: Description of the features represented in TimeSeries::data. multivalued: false - range: AbstractFeatureSeries_features - required: true - AbstractFeatureSeries_data: - name: AbstractFeatureSeries_data - description: Values of each feature at each time. - attributes: - unit: - name: unit - description: Since there can be different units for different features, store - the units in 'feature_units'. The default value for this attribute is "see - 'feature_units'". - range: text - array: - name: array - range: AbstractFeatureSeries_data_Array - AbstractFeatureSeries_data_Array: - name: AbstractFeatureSeries_data_Array - is_a: Arraylike - attributes: - num_times: - name: num_times - range: numeric - required: true - num_features: - name: num_features - range: numeric - required: false - AbstractFeatureSeries_feature_units: - name: AbstractFeatureSeries_feature_units - description: Units of each feature. - attributes: - array: - name: array - range: AbstractFeatureSeries_feature_units_Array - AbstractFeatureSeries_feature_units_Array: - name: AbstractFeatureSeries_feature_units_Array - is_a: Arraylike - attributes: - num_features: - name: num_features - range: text - required: true - AbstractFeatureSeries_features: - name: AbstractFeatureSeries_features - description: Description of the features represented in TimeSeries::data. - attributes: - array: - name: array - range: AbstractFeatureSeries_features_Array - AbstractFeatureSeries_features_Array: - name: AbstractFeatureSeries_features_Array - is_a: Arraylike - attributes: - num_features: - name: num_features - range: text + range: AbstractFeatureSeries__features required: true AnnotationSeries: name: AnnotationSeries @@ -104,32 +52,7 @@ classes: name: data description: Annotations made during an experiment. multivalued: false - range: AnnotationSeries_data - required: true - AnnotationSeries_data: - name: AnnotationSeries_data - description: Annotations made during an experiment. - attributes: - resolution: - name: resolution - description: Smallest meaningful difference between values in data. Annotations - have no units, so the value is fixed to -1.0. - range: float32 - unit: - name: unit - description: Base unit of measurement for working with the data. Annotations - have no units, so the value is fixed to 'n/a'. - range: text - array: - name: array - range: AnnotationSeries_data_Array - AnnotationSeries_data_Array: - name: AnnotationSeries_data_Array - is_a: Arraylike - attributes: - num_times: - name: num_times - range: text + range: AnnotationSeries__data required: true IntervalSeries: name: IntervalSeries @@ -146,32 +69,7 @@ classes: name: data description: Use values >0 if interval started, <0 if interval ended. multivalued: false - range: IntervalSeries_data - required: true - IntervalSeries_data: - name: IntervalSeries_data - description: Use values >0 if interval started, <0 if interval ended. - attributes: - resolution: - name: resolution - description: Smallest meaningful difference between values in data. Annotations - have no units, so the value is fixed to -1.0. - range: float32 - unit: - name: unit - description: Base unit of measurement for working with the data. Annotations - have no units, so the value is fixed to 'n/a'. - range: text - array: - name: array - range: IntervalSeries_data_Array - IntervalSeries_data_Array: - name: IntervalSeries_data_Array - is_a: Arraylike - attributes: - num_times: - name: num_times - range: int8 + range: IntervalSeries__data required: true DecompositionSeries: name: DecompositionSeries @@ -182,154 +80,27 @@ classes: name: data description: Data decomposed into frequency bands. multivalued: false - range: DecompositionSeries_data + range: DecompositionSeries__data required: true metric: name: metric description: The metric used, e.g. phase, amplitude, power. multivalued: false - range: DecompositionSeries_metric + range: text required: true source_channels: name: source_channels description: DynamicTableRegion pointer to the channels that this decomposition series was generated from. multivalued: false - range: DecompositionSeries_source_channels + range: DecompositionSeries__source_channels required: false bands: name: bands description: Table for describing the bands that this series was generated from. There should be one row in this table for each band. multivalued: false - range: DecompositionSeries_bands - required: true - DecompositionSeries_data: - name: DecompositionSeries_data - description: Data decomposed into frequency bands. - attributes: - unit: - name: unit - description: Base unit of measurement for working with the data. Actual stored - values are not necessarily stored in these units. To access the data in - these units, multiply 'data' by 'conversion'. - range: text - array: - name: array - range: DecompositionSeries_data_Array - DecompositionSeries_data_Array: - name: DecompositionSeries_data_Array - is_a: Arraylike - attributes: - num_times: - name: num_times - range: numeric - required: false - num_channels: - name: num_channels - range: numeric - required: false - num_bands: - name: num_bands - range: numeric - required: false - DecompositionSeries_metric: - name: DecompositionSeries_metric - description: The metric used, e.g. phase, amplitude, power. - DecompositionSeries_source_channels: - name: DecompositionSeries_source_channels - description: DynamicTableRegion pointer to the channels that this decomposition - series was generated from. - is_a: DynamicTableRegion - DecompositionSeries_bands: - name: DecompositionSeries_bands - description: Table for describing the bands that this series was generated from. - There should be one row in this table for each band. - is_a: DynamicTable - attributes: - band_name: - name: band_name - description: Name of the band, e.g. theta. - multivalued: false - range: DecompositionSeries_bands_band_name - required: true - band_limits: - name: band_limits - description: Low and high limit of each band in Hz. If it is a Gaussian filter, - use 2 SD on either side of the center. - multivalued: false - range: DecompositionSeries_bands_band_limits - required: true - band_mean: - name: band_mean - description: The mean Gaussian filters, in Hz. - multivalued: false - range: DecompositionSeries_bands_band_mean - required: true - band_stdev: - name: band_stdev - description: The standard deviation of Gaussian filters, in Hz. - multivalued: false - range: DecompositionSeries_bands_band_stdev - required: true - DecompositionSeries_bands_band_name: - name: DecompositionSeries_bands_band_name - description: Name of the band, e.g. theta. - is_a: VectorData - DecompositionSeries_bands_band_limits: - name: DecompositionSeries_bands_band_limits - description: Low and high limit of each band in Hz. If it is a Gaussian filter, - use 2 SD on either side of the center. - is_a: VectorData - attributes: - array: - name: array - range: DecompositionSeries_bands_band_limits_Array - DecompositionSeries_bands_band_limits_Array: - name: DecompositionSeries_bands_band_limits_Array - is_a: Arraylike - attributes: - num_bands: - name: num_bands - range: float32 - required: false - low, high: - name: low, high - range: float32 - required: false - minimum_cardinality: 2 - maximum_cardinality: 2 - DecompositionSeries_bands_band_mean: - name: DecompositionSeries_bands_band_mean - description: The mean Gaussian filters, in Hz. - is_a: VectorData - attributes: - array: - name: array - range: DecompositionSeries_bands_band_mean_Array - DecompositionSeries_bands_band_mean_Array: - name: DecompositionSeries_bands_band_mean_Array - is_a: Arraylike - attributes: - num_bands: - name: num_bands - range: float32 - required: true - DecompositionSeries_bands_band_stdev: - name: DecompositionSeries_bands_band_stdev - description: The standard deviation of Gaussian filters, in Hz. - is_a: VectorData - attributes: - array: - name: array - range: DecompositionSeries_bands_band_stdev_Array - DecompositionSeries_bands_band_stdev_Array: - name: DecompositionSeries_bands_band_stdev_Array - is_a: Arraylike - attributes: - num_bands: - name: num_bands - range: float32 + range: DecompositionSeries__bands required: true Units: name: Units @@ -341,55 +112,54 @@ classes: name: spike_times_index description: Index into the spike_times dataset. multivalued: false - range: Units_spike_times_index + range: Units__spike_times_index required: false spike_times: name: spike_times description: Spike times for each unit in seconds. multivalued: false - range: Units_spike_times + range: Units__spike_times required: false obs_intervals_index: name: obs_intervals_index description: Index into the obs_intervals dataset. multivalued: false - range: Units_obs_intervals_index + range: Units__obs_intervals_index required: false obs_intervals: name: obs_intervals description: Observation intervals for each unit. multivalued: false - range: Units_obs_intervals + range: Units__obs_intervals required: false electrodes_index: name: electrodes_index description: Index into electrodes. multivalued: false - range: Units_electrodes_index + range: Units__electrodes_index required: false electrodes: name: electrodes description: Electrode that each spike unit came from, specified using a DynamicTableRegion. multivalued: false - range: Units_electrodes + range: Units__electrodes required: false electrode_group: name: electrode_group description: Electrode group that each spike unit came from. - multivalued: false - range: Units_electrode_group - required: false + multivalued: true + range: ElectrodeGroup waveform_mean: name: waveform_mean description: Spike waveform mean for each spike unit. multivalued: false - range: Units_waveform_mean + range: Units__waveform_mean required: false waveform_sd: name: waveform_sd description: Spike waveform standard deviation for each spike unit. multivalued: false - range: Units_waveform_sd + range: Units__waveform_sd required: false waveforms: name: waveforms @@ -417,198 +187,19 @@ classes: same order as the electrodes referenced in the 'electrodes' column of this table. The number of samples for each waveform must be the same. multivalued: false - range: Units_waveforms + range: Units__waveforms required: false waveforms_index: name: waveforms_index description: Index into the waveforms dataset. One value for every spike event. See 'waveforms' for more detail. multivalued: false - range: Units_waveforms_index + range: Units__waveforms_index required: false waveforms_index_index: name: waveforms_index_index description: Index into the waveforms_index dataset. One value for every unit (row in the table). See 'waveforms' for more detail. multivalued: false - range: Units_waveforms_index_index + range: Units__waveforms_index_index required: false - Units_spike_times_index: - name: Units_spike_times_index - description: Index into the spike_times dataset. - is_a: VectorIndex - Units_spike_times: - name: Units_spike_times - description: Spike times for each unit in seconds. - is_a: VectorData - attributes: - resolution: - name: resolution - description: The smallest possible difference between two spike times. Usually - 1 divided by the acquisition sampling rate from which spike times were extracted, - but could be larger if the acquisition time series was downsampled or smaller - if the acquisition time series was smoothed/interpolated and it is possible - for the spike time to be between samples. - range: float64 - Units_obs_intervals_index: - name: Units_obs_intervals_index - description: Index into the obs_intervals dataset. - is_a: VectorIndex - Units_obs_intervals: - name: Units_obs_intervals - description: Observation intervals for each unit. - is_a: VectorData - attributes: - array: - name: array - range: Units_obs_intervals_Array - Units_obs_intervals_Array: - name: Units_obs_intervals_Array - is_a: Arraylike - attributes: - num_intervals: - name: num_intervals - range: float64 - required: false - start|end: - name: start|end - range: float64 - required: false - minimum_cardinality: 2 - maximum_cardinality: 2 - Units_electrodes_index: - name: Units_electrodes_index - description: Index into electrodes. - is_a: VectorIndex - Units_electrodes: - name: Units_electrodes - description: Electrode that each spike unit came from, specified using a DynamicTableRegion. - is_a: DynamicTableRegion - Units_electrode_group: - name: Units_electrode_group - description: Electrode group that each spike unit came from. - is_a: VectorData - Units_waveform_mean: - name: Units_waveform_mean - description: Spike waveform mean for each spike unit. - is_a: VectorData - attributes: - sampling_rate: - name: sampling_rate - description: Sampling rate, in hertz. - range: float32 - unit: - name: unit - description: Unit of measurement. This value is fixed to 'volts'. - range: text - array: - name: array - range: Units_waveform_mean_Array - Units_waveform_mean_Array: - name: Units_waveform_mean_Array - is_a: Arraylike - attributes: - num_units: - name: num_units - range: float32 - required: true - num_samples: - name: num_samples - range: float32 - required: true - num_electrodes: - name: num_electrodes - range: float32 - required: false - Units_waveform_sd: - name: Units_waveform_sd - description: Spike waveform standard deviation for each spike unit. - is_a: VectorData - attributes: - sampling_rate: - name: sampling_rate - description: Sampling rate, in hertz. - range: float32 - unit: - name: unit - description: Unit of measurement. This value is fixed to 'volts'. - range: text - array: - name: array - range: Units_waveform_sd_Array - Units_waveform_sd_Array: - name: Units_waveform_sd_Array - is_a: Arraylike - attributes: - num_units: - name: num_units - range: float32 - required: true - num_samples: - name: num_samples - range: float32 - required: true - num_electrodes: - name: num_electrodes - range: float32 - required: false - Units_waveforms: - name: Units_waveforms - description: Individual waveforms for each spike on each electrode. This is a - doubly indexed column. The 'waveforms_index' column indexes which waveforms - in this column belong to the same spike event for a given unit, where each waveform - was recorded from a different electrode. The 'waveforms_index_index' column - indexes the 'waveforms_index' column to indicate which spike events belong to - a given unit. For example, if the 'waveforms_index_index' column has values - [2, 5, 6], then the first 2 elements of the 'waveforms_index' column correspond - to the 2 spike events of the first unit, the next 3 elements of the 'waveforms_index' - column correspond to the 3 spike events of the second unit, and the next 1 element - of the 'waveforms_index' column corresponds to the 1 spike event of the third - unit. If the 'waveforms_index' column has values [3, 6, 8, 10, 12, 13], then - the first 3 elements of the 'waveforms' column contain the 3 spike waveforms - that were recorded from 3 different electrodes for the first spike time of the - first unit. See https://nwb-schema.readthedocs.io/en/stable/format_description.html#doubly-ragged-arrays - for a graphical representation of this example. When there is only one electrode - for each unit (i.e., each spike time is associated with a single waveform), - then the 'waveforms_index' column will have values 1, 2, ..., N, where N is - the number of spike events. The number of electrodes for each spike event should - be the same within a given unit. The 'electrodes' column should be used to indicate - which electrodes are associated with each unit, and the order of the waveforms - within a given unit x spike event should be in the same order as the electrodes - referenced in the 'electrodes' column of this table. The number of samples for - each waveform must be the same. - is_a: VectorData - attributes: - sampling_rate: - name: sampling_rate - description: Sampling rate, in hertz. - range: float32 - unit: - name: unit - description: Unit of measurement. This value is fixed to 'volts'. - range: text - array: - name: array - range: Units_waveforms_Array - Units_waveforms_Array: - name: Units_waveforms_Array - is_a: Arraylike - attributes: - num_waveforms: - name: num_waveforms - range: numeric - required: false - num_samples: - name: num_samples - range: numeric - required: false - Units_waveforms_index: - name: Units_waveforms_index - description: Index into the waveforms dataset. One value for every spike event. - See 'waveforms' for more detail. - is_a: VectorIndex - Units_waveforms_index_index: - name: Units_waveforms_index_index - description: Index into the waveforms_index dataset. One value for every unit - (row in the table). See 'waveforms' for more detail. - is_a: VectorIndex diff --git a/nwb_linkml/schema/core.nwb.ogen.include.yaml b/nwb_linkml/schema/core.nwb.ogen.include.yaml new file mode 100644 index 0000000..575659b --- /dev/null +++ b/nwb_linkml/schema/core.nwb.ogen.include.yaml @@ -0,0 +1,24 @@ +name: core.nwb.ogen.include +id: core.nwb.ogen.include +imports: +- core.nwb.base +- core.nwb.device +- nwb.language +- core.nwb.ogen.include +- core.nwb.ogen +default_prefix: core.nwb.ogen.include/ +classes: + OptogeneticSeries__data: + name: OptogeneticSeries__data + description: Applied power for optogenetic stimulus, in watts. + attributes: + unit: + name: unit + description: Unit of measurement for data, which is fixed to 'watts'. + range: text + data: + name: data + description: Applied power for optogenetic stimulus, in watts. + multivalued: true + range: numeric + required: true diff --git a/nwb_linkml/schema/core.nwb.ogen.yaml b/nwb_linkml/schema/core.nwb.ogen.yaml index 4d3a44d..328fbe5 100644 --- a/nwb_linkml/schema/core.nwb.ogen.yaml +++ b/nwb_linkml/schema/core.nwb.ogen.yaml @@ -2,7 +2,10 @@ name: core.nwb.ogen id: core.nwb.ogen imports: - core.nwb.base +- core.nwb.device - nwb.language +- core.nwb.ogen.include +- core.nwb.ogen default_prefix: core.nwb.ogen/ classes: OptogeneticSeries: @@ -14,26 +17,7 @@ classes: name: data description: Applied power for optogenetic stimulus, in watts. multivalued: false - range: OptogeneticSeries_data - required: true - OptogeneticSeries_data: - name: OptogeneticSeries_data - description: Applied power for optogenetic stimulus, in watts. - attributes: - unit: - name: unit - description: Unit of measurement for data, which is fixed to 'watts'. - range: text - array: - name: array - range: OptogeneticSeries_data_Array - OptogeneticSeries_data_Array: - name: OptogeneticSeries_data_Array - is_a: Arraylike - attributes: - num_times: - name: num_times - range: numeric + range: OptogeneticSeries__data required: true OptogeneticStimulusSite: name: OptogeneticStimulusSite @@ -44,13 +28,13 @@ classes: name: description description: Description of stimulation site. multivalued: false - range: OptogeneticStimulusSite_description + range: text required: true excitation_lambda: name: excitation_lambda description: Excitation wavelength, in nm. multivalued: false - range: OptogeneticStimulusSite_excitation_lambda + range: float32 required: true location: name: location @@ -58,16 +42,5 @@ classes: on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible. multivalued: false - range: OptogeneticStimulusSite_location + range: text required: true - OptogeneticStimulusSite_description: - name: OptogeneticStimulusSite_description - description: Description of stimulation site. - OptogeneticStimulusSite_excitation_lambda: - name: OptogeneticStimulusSite_excitation_lambda - description: Excitation wavelength, in nm. - OptogeneticStimulusSite_location: - name: OptogeneticStimulusSite_location - description: Location of the stimulation site. Specify the area, layer, comments - on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard - atlas names for anatomical regions when possible. diff --git a/nwb_linkml/schema/core.nwb.ophys.include.yaml b/nwb_linkml/schema/core.nwb.ophys.include.yaml new file mode 100644 index 0000000..21e9b8d --- /dev/null +++ b/nwb_linkml/schema/core.nwb.ophys.include.yaml @@ -0,0 +1,197 @@ +name: core.nwb.ophys.include +id: core.nwb.ophys.include +imports: +- core.nwb.image +- core.nwb.base +- hdmf-common.table +- core.nwb.device +- nwb.language +- core.nwb.ophys.include +- core.nwb.ophys +default_prefix: core.nwb.ophys.include/ +classes: + TwoPhotonSeries__field_of_view: + name: TwoPhotonSeries__field_of_view + description: Width, height and depth of image, or imaged area, in meters. + attributes: + array: + name: array + range: TwoPhotonSeries__field_of_view__Array + TwoPhotonSeries__field_of_view__Array: + name: TwoPhotonSeries__field_of_view__Array + is_a: Arraylike + attributes: + width|height: + name: width|height + range: float32 + required: false + minimum_cardinality: 2 + maximum_cardinality: 2 + width|height|depth: + name: width|height|depth + range: float32 + required: false + minimum_cardinality: 3 + maximum_cardinality: 3 + RoiResponseSeries__data: + name: RoiResponseSeries__data + description: Signals from ROIs. + attributes: + array: + name: array + range: RoiResponseSeries__data__Array + RoiResponseSeries__data__Array: + name: RoiResponseSeries__data__Array + is_a: Arraylike + attributes: + num_times: + name: num_times + range: numeric + required: true + num_ROIs: + name: num_ROIs + range: numeric + required: false + RoiResponseSeries__rois: + name: RoiResponseSeries__rois + description: DynamicTableRegion referencing into an ROITable containing information + on the ROIs stored in this timeseries. + is_a: DynamicTableRegion + PlaneSegmentation__image_mask: + name: PlaneSegmentation__image_mask + description: ROI masks for each ROI. Each image mask is the size of the original + imaging plane (or volume) and members of the ROI are finite non-zero. + is_a: VectorData + PlaneSegmentation__pixel_mask_index: + name: PlaneSegmentation__pixel_mask_index + description: Index into pixel_mask. + is_a: VectorIndex + PlaneSegmentation__voxel_mask_index: + name: PlaneSegmentation__voxel_mask_index + description: Index into voxel_mask. + is_a: VectorIndex + PlaneSegmentation__reference_images: + name: PlaneSegmentation__reference_images + description: Image stacks that the segmentation masks apply to. + attributes: + ImageSeries: + name: ImageSeries + description: One or more image stacks that the masks apply to (can be one-element + stack). + multivalued: true + range: ImageSeries + required: false + ImagingPlane__manifold: + name: ImagingPlane__manifold + description: DEPRECATED Physical position of each pixel. 'xyz' represents the + position of the pixel relative to the defined coordinate space. Deprecated in + favor of origin_coords and grid_spacing. + attributes: + conversion: + name: conversion + description: Scalar to multiply each element in data to convert it to the + specified 'unit'. If the data are stored in acquisition system units or + other units that require a conversion to be interpretable, multiply the + data by 'conversion' to convert the data to the specified 'unit'. e.g. if + the data acquisition system stores values in this object as pixels from + x = -500 to 499, y = -500 to 499 that correspond to a 2 m x 2 m range, then + the 'conversion' multiplier to get from raw data acquisition pixel units + to meters is 2/1000. + range: float32 + unit: + name: unit + description: Base unit of measurement for working with the data. The default + value is 'meters'. + range: text + array: + name: array + range: ImagingPlane__manifold__Array + ImagingPlane__manifold__Array: + name: ImagingPlane__manifold__Array + is_a: Arraylike + attributes: + height: + name: height + range: float32 + required: true + width: + name: width + range: float32 + required: true + x, y, z: + name: x, y, z + range: float32 + required: true + minimum_cardinality: 3 + maximum_cardinality: 3 + depth: + name: depth + range: float32 + required: false + ImagingPlane__origin_coords: + name: ImagingPlane__origin_coords + description: Physical location of the first element of the imaging plane (0, 0) + for 2-D data or (0, 0, 0) for 3-D data. See also reference_frame for what the + physical location is relative to (e.g., bregma). + attributes: + unit: + name: unit + description: Measurement units for origin_coords. The default value is 'meters'. + range: text + array: + name: array + range: ImagingPlane__origin_coords__Array + ImagingPlane__origin_coords__Array: + name: ImagingPlane__origin_coords__Array + is_a: Arraylike + attributes: + x, y: + name: x, y + range: float32 + required: false + minimum_cardinality: 2 + maximum_cardinality: 2 + x, y, z: + name: x, y, z + range: float32 + required: false + minimum_cardinality: 3 + maximum_cardinality: 3 + ImagingPlane__grid_spacing: + name: ImagingPlane__grid_spacing + description: Space between pixels in (x, y) or voxels in (x, y, z) directions, + in the specified unit. Assumes imaging plane is a regular grid. See also reference_frame + to interpret the grid. + attributes: + unit: + name: unit + description: Measurement units for grid_spacing. The default value is 'meters'. + range: text + array: + name: array + range: ImagingPlane__grid_spacing__Array + ImagingPlane__grid_spacing__Array: + name: ImagingPlane__grid_spacing__Array + is_a: Arraylike + attributes: + x, y: + name: x, y + range: float32 + required: false + minimum_cardinality: 2 + maximum_cardinality: 2 + x, y, z: + name: x, y, z + range: float32 + required: false + minimum_cardinality: 3 + maximum_cardinality: 3 + CorrectedImageStack__corrected: + name: CorrectedImageStack__corrected + description: Image stack with frames shifted to the common coordinates. + is_a: ImageSeries + CorrectedImageStack__xy_translation: + name: CorrectedImageStack__xy_translation + description: Stores the x,y delta necessary to align each frame to the common + coordinates, for example, to align each frame to a reference image. + is_a: TimeSeries diff --git a/nwb_linkml/schema/core.nwb.ophys.yaml b/nwb_linkml/schema/core.nwb.ophys.yaml index e1ad2bd..0720056 100644 --- a/nwb_linkml/schema/core.nwb.ophys.yaml +++ b/nwb_linkml/schema/core.nwb.ophys.yaml @@ -4,7 +4,10 @@ imports: - core.nwb.image - core.nwb.base - hdmf-common.table +- core.nwb.device - nwb.language +- core.nwb.ophys.include +- core.nwb.ophys default_prefix: core.nwb.ophys/ classes: OnePhotonSeries: @@ -57,31 +60,8 @@ classes: name: field_of_view description: Width, height and depth of image, or imaged area, in meters. multivalued: false - range: TwoPhotonSeries_field_of_view + range: TwoPhotonSeries__field_of_view required: false - TwoPhotonSeries_field_of_view: - name: TwoPhotonSeries_field_of_view - description: Width, height and depth of image, or imaged area, in meters. - attributes: - array: - name: array - range: TwoPhotonSeries_field_of_view_Array - TwoPhotonSeries_field_of_view_Array: - name: TwoPhotonSeries_field_of_view_Array - is_a: Arraylike - attributes: - width|height: - name: width|height - range: float32 - required: false - minimum_cardinality: 2 - maximum_cardinality: 2 - width|height|depth: - name: width|height|depth - range: float32 - required: false - minimum_cardinality: 3 - maximum_cardinality: 3 RoiResponseSeries: name: RoiResponseSeries description: ROI responses over an imaging plane. The first dimension represents @@ -92,39 +72,15 @@ classes: name: data description: Signals from ROIs. multivalued: false - range: RoiResponseSeries_data + range: RoiResponseSeries__data required: true rois: name: rois description: DynamicTableRegion referencing into an ROITable containing information on the ROIs stored in this timeseries. multivalued: false - range: RoiResponseSeries_rois + range: RoiResponseSeries__rois required: true - RoiResponseSeries_data: - name: RoiResponseSeries_data - description: Signals from ROIs. - attributes: - array: - name: array - range: RoiResponseSeries_data_Array - RoiResponseSeries_data_Array: - name: RoiResponseSeries_data_Array - is_a: Arraylike - attributes: - num_times: - name: num_times - range: numeric - required: true - num_ROIs: - name: num_ROIs - range: numeric - required: false - RoiResponseSeries_rois: - name: RoiResponseSeries_rois - description: DynamicTableRegion referencing into an ROITable containing information - on the ROIs stored in this timeseries. - is_a: DynamicTableRegion DfOverF: name: DfOverF description: dF/F information about a region of interest (ROI). Storage hierarchy @@ -179,102 +135,40 @@ classes: description: ROI masks for each ROI. Each image mask is the size of the original imaging plane (or volume) and members of the ROI are finite non-zero. multivalued: false - range: PlaneSegmentation_image_mask + range: PlaneSegmentation__image_mask required: false pixel_mask_index: name: pixel_mask_index description: Index into pixel_mask. multivalued: false - range: PlaneSegmentation_pixel_mask_index + range: PlaneSegmentation__pixel_mask_index required: false pixel_mask: name: pixel_mask description: 'Pixel masks for each ROI: a list of indices and weights for the ROI. Pixel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation' - multivalued: false - range: PlaneSegmentation_pixel_mask - required: false + multivalued: true + range: AnyType voxel_mask_index: name: voxel_mask_index description: Index into voxel_mask. multivalued: false - range: PlaneSegmentation_voxel_mask_index + range: PlaneSegmentation__voxel_mask_index required: false voxel_mask: name: voxel_mask description: 'Voxel masks for each ROI: a list of indices and weights for the ROI. Voxel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation' - multivalued: false - range: PlaneSegmentation_voxel_mask - required: false + multivalued: true + range: AnyType reference_images: name: reference_images description: Image stacks that the segmentation masks apply to. multivalued: false - range: PlaneSegmentation_reference_images + range: PlaneSegmentation__reference_images required: true - PlaneSegmentation_image_mask: - name: PlaneSegmentation_image_mask - description: ROI masks for each ROI. Each image mask is the size of the original - imaging plane (or volume) and members of the ROI are finite non-zero. - is_a: VectorData - attributes: - array: - name: array - range: PlaneSegmentation_image_mask_Array - PlaneSegmentation_image_mask_Array: - name: PlaneSegmentation_image_mask_Array - is_a: Arraylike - attributes: - num_roi: - name: num_roi - range: AnyType - required: true - num_x: - name: num_x - range: AnyType - required: true - num_y: - name: num_y - range: AnyType - required: true - num_z: - name: num_z - range: AnyType - required: false - PlaneSegmentation_pixel_mask_index: - name: PlaneSegmentation_pixel_mask_index - description: Index into pixel_mask. - is_a: VectorIndex - PlaneSegmentation_pixel_mask: - name: PlaneSegmentation_pixel_mask - description: 'Pixel masks for each ROI: a list of indices and weights for the - ROI. Pixel masks are concatenated and parsing of this dataset is maintained - by the PlaneSegmentation' - is_a: VectorData - PlaneSegmentation_voxel_mask_index: - name: PlaneSegmentation_voxel_mask_index - description: Index into voxel_mask. - is_a: VectorIndex - PlaneSegmentation_voxel_mask: - name: PlaneSegmentation_voxel_mask - description: 'Voxel masks for each ROI: a list of indices and weights for the - ROI. Voxel masks are concatenated and parsing of this dataset is maintained - by the PlaneSegmentation' - is_a: VectorData - PlaneSegmentation_reference_images: - name: PlaneSegmentation_reference_images - description: Image stacks that the segmentation masks apply to. - attributes: - ImageSeries: - name: ImageSeries - description: One or more image stacks that the masks apply to (can be one-element - stack). - multivalued: true - range: ImageSeries - required: false ImagingPlane: name: ImagingPlane description: An imaging plane and its metadata. @@ -284,26 +178,26 @@ classes: name: description description: Description of the imaging plane. multivalued: false - range: ImagingPlane_description + range: text required: false excitation_lambda: name: excitation_lambda description: Excitation wavelength, in nm. multivalued: false - range: ImagingPlane_excitation_lambda + range: float32 required: true imaging_rate: name: imaging_rate description: Rate that images are acquired, in Hz. If the corresponding TimeSeries is present, the rate should be stored there instead. multivalued: false - range: ImagingPlane_imaging_rate + range: float32 required: false indicator: name: indicator description: Calcium indicator. multivalued: false - range: ImagingPlane_indicator + range: text required: true location: name: location @@ -311,7 +205,7 @@ classes: on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible. multivalued: false - range: ImagingPlane_location + range: text required: true manifold: name: manifold @@ -319,7 +213,7 @@ classes: the position of the pixel relative to the defined coordinate space. Deprecated in favor of origin_coords and grid_spacing. multivalued: false - range: ImagingPlane_manifold + range: ImagingPlane__manifold required: false origin_coords: name: origin_coords @@ -327,7 +221,7 @@ classes: 0) for 2-D data or (0, 0, 0) for 3-D data. See also reference_frame for what the physical location is relative to (e.g., bregma). multivalued: false - range: ImagingPlane_origin_coords + range: ImagingPlane__origin_coords required: false grid_spacing: name: grid_spacing @@ -335,7 +229,7 @@ classes: in the specified unit. Assumes imaging plane is a regular grid. See also reference_frame to interpret the grid. multivalued: false - range: ImagingPlane_grid_spacing + range: ImagingPlane__grid_spacing required: false reference_frame: name: reference_frame @@ -357,7 +251,7 @@ classes: axis (larger index = more rightward). Third dimension corresponds to dorsal-ventral axis (larger index = more ventral)." multivalued: false - range: ImagingPlane_reference_frame + range: text required: false OpticalChannel: name: OpticalChannel @@ -365,147 +259,6 @@ classes: multivalued: true range: OpticalChannel required: true - ImagingPlane_description: - name: ImagingPlane_description - description: Description of the imaging plane. - ImagingPlane_excitation_lambda: - name: ImagingPlane_excitation_lambda - description: Excitation wavelength, in nm. - ImagingPlane_imaging_rate: - name: ImagingPlane_imaging_rate - description: Rate that images are acquired, in Hz. If the corresponding TimeSeries - is present, the rate should be stored there instead. - ImagingPlane_indicator: - name: ImagingPlane_indicator - description: Calcium indicator. - ImagingPlane_location: - name: ImagingPlane_location - description: Location of the imaging plane. Specify the area, layer, comments - on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard - atlas names for anatomical regions when possible. - ImagingPlane_manifold: - name: ImagingPlane_manifold - description: DEPRECATED Physical position of each pixel. 'xyz' represents the - position of the pixel relative to the defined coordinate space. Deprecated in - favor of origin_coords and grid_spacing. - attributes: - conversion: - name: conversion - description: Scalar to multiply each element in data to convert it to the - specified 'unit'. If the data are stored in acquisition system units or - other units that require a conversion to be interpretable, multiply the - data by 'conversion' to convert the data to the specified 'unit'. e.g. if - the data acquisition system stores values in this object as pixels from - x = -500 to 499, y = -500 to 499 that correspond to a 2 m x 2 m range, then - the 'conversion' multiplier to get from raw data acquisition pixel units - to meters is 2/1000. - range: float32 - unit: - name: unit - description: Base unit of measurement for working with the data. The default - value is 'meters'. - range: text - array: - name: array - range: ImagingPlane_manifold_Array - ImagingPlane_manifold_Array: - name: ImagingPlane_manifold_Array - is_a: Arraylike - attributes: - height: - name: height - range: float32 - required: true - width: - name: width - range: float32 - required: true - x, y, z: - name: x, y, z - range: float32 - required: true - minimum_cardinality: 3 - maximum_cardinality: 3 - depth: - name: depth - range: float32 - required: false - ImagingPlane_origin_coords: - name: ImagingPlane_origin_coords - description: Physical location of the first element of the imaging plane (0, 0) - for 2-D data or (0, 0, 0) for 3-D data. See also reference_frame for what the - physical location is relative to (e.g., bregma). - attributes: - unit: - name: unit - description: Measurement units for origin_coords. The default value is 'meters'. - range: text - array: - name: array - range: ImagingPlane_origin_coords_Array - ImagingPlane_origin_coords_Array: - name: ImagingPlane_origin_coords_Array - is_a: Arraylike - attributes: - x, y: - name: x, y - range: float32 - required: false - minimum_cardinality: 2 - maximum_cardinality: 2 - x, y, z: - name: x, y, z - range: float32 - required: false - minimum_cardinality: 3 - maximum_cardinality: 3 - ImagingPlane_grid_spacing: - name: ImagingPlane_grid_spacing - description: Space between pixels in (x, y) or voxels in (x, y, z) directions, - in the specified unit. Assumes imaging plane is a regular grid. See also reference_frame - to interpret the grid. - attributes: - unit: - name: unit - description: Measurement units for grid_spacing. The default value is 'meters'. - range: text - array: - name: array - range: ImagingPlane_grid_spacing_Array - ImagingPlane_grid_spacing_Array: - name: ImagingPlane_grid_spacing_Array - is_a: Arraylike - attributes: - x, y: - name: x, y - range: float32 - required: false - minimum_cardinality: 2 - maximum_cardinality: 2 - x, y, z: - name: x, y, z - range: float32 - required: false - minimum_cardinality: 3 - maximum_cardinality: 3 - ImagingPlane_reference_frame: - name: ImagingPlane_reference_frame - description: Describes reference frame of origin_coords and grid_spacing. For - example, this can be a text description of the anatomical location and orientation - of the grid defined by origin_coords and grid_spacing or the vectors needed - to transform or rotate the grid to a common anatomical axis (e.g., AP/DV/ML). - This field is necessary to interpret origin_coords and grid_spacing. If origin_coords - and grid_spacing are not present, then this field is not required. For example, - if the microscope takes 10 x 10 x 2 images, where the first value of the data - matrix (index (0, 0, 0)) corresponds to (-1.2, -0.6, -2) mm relative to bregma, - the spacing between pixels is 0.2 mm in x, 0.2 mm in y and 0.5 mm in z, and - larger numbers in x means more anterior, larger numbers in y means more rightward, - and larger numbers in z means more ventral, then enter the following -- origin_coords - = (-1.2, -0.6, -2) grid_spacing = (0.2, 0.2, 0.5) reference_frame = "Origin - coordinates are relative to bregma. First dimension corresponds to anterior-posterior - axis (larger index = more anterior). Second dimension corresponds to medial-lateral - axis (larger index = more rightward). Third dimension corresponds to dorsal-ventral - axis (larger index = more ventral)." OpticalChannel: name: OpticalChannel description: An optical channel used to record from an imaging plane. @@ -515,20 +268,14 @@ classes: name: description description: Description or other notes about the channel. multivalued: false - range: OpticalChannel_description + range: text required: true emission_lambda: name: emission_lambda description: Emission wavelength for channel, in nm. multivalued: false - range: OpticalChannel_emission_lambda + range: float32 required: true - OpticalChannel_description: - name: OpticalChannel_description - description: Description or other notes about the channel. - OpticalChannel_emission_lambda: - name: OpticalChannel_emission_lambda - description: Emission wavelength for channel, in nm. MotionCorrection: name: MotionCorrection description: 'An image stack where all frames are shifted (registered) to a common @@ -551,21 +298,12 @@ classes: name: corrected description: Image stack with frames shifted to the common coordinates. multivalued: false - range: CorrectedImageStack_corrected + range: CorrectedImageStack__corrected required: true xy_translation: name: xy_translation description: Stores the x,y delta necessary to align each frame to the common coordinates, for example, to align each frame to a reference image. multivalued: false - range: CorrectedImageStack_xy_translation + range: CorrectedImageStack__xy_translation required: true - CorrectedImageStack_corrected: - name: CorrectedImageStack_corrected - description: Image stack with frames shifted to the common coordinates. - is_a: ImageSeries - CorrectedImageStack_xy_translation: - name: CorrectedImageStack_xy_translation - description: Stores the x,y delta necessary to align each frame to the common - coordinates, for example, to align each frame to a reference image. - is_a: TimeSeries diff --git a/nwb_linkml/schema/core.nwb.retinotopy.include.yaml b/nwb_linkml/schema/core.nwb.retinotopy.include.yaml new file mode 100644 index 0000000..7b9460d --- /dev/null +++ b/nwb_linkml/schema/core.nwb.retinotopy.include.yaml @@ -0,0 +1,262 @@ +name: core.nwb.retinotopy.include +id: core.nwb.retinotopy.include +imports: +- core.nwb.base +- nwb.language +- core.nwb.retinotopy.include +- core.nwb.retinotopy +default_prefix: core.nwb.retinotopy.include/ +classes: + ImagingRetinotopy__axis_1_phase_map: + name: ImagingRetinotopy__axis_1_phase_map + description: Phase response to stimulus on the first measured axis. + attributes: + dimension: + name: dimension + description: 'Number of rows and columns in the image. NOTE: row, column representation + is equivalent to height, width.' + range: int32 + field_of_view: + name: field_of_view + description: Size of viewing area, in meters. + range: float32 + unit: + name: unit + description: Unit that axis data is stored in (e.g., degrees). + range: text + array: + name: array + range: ImagingRetinotopy__axis_1_phase_map__Array + ImagingRetinotopy__axis_1_phase_map__Array: + name: ImagingRetinotopy__axis_1_phase_map__Array + is_a: Arraylike + attributes: + num_rows: + name: num_rows + range: float32 + required: false + num_cols: + name: num_cols + range: float32 + required: false + ImagingRetinotopy__axis_1_power_map: + name: ImagingRetinotopy__axis_1_power_map + description: Power response on the first measured axis. Response is scaled so + 0.0 is no power in the response and 1.0 is maximum relative power. + attributes: + dimension: + name: dimension + description: 'Number of rows and columns in the image. NOTE: row, column representation + is equivalent to height, width.' + range: int32 + field_of_view: + name: field_of_view + description: Size of viewing area, in meters. + range: float32 + unit: + name: unit + description: Unit that axis data is stored in (e.g., degrees). + range: text + array: + name: array + range: ImagingRetinotopy__axis_1_power_map__Array + ImagingRetinotopy__axis_1_power_map__Array: + name: ImagingRetinotopy__axis_1_power_map__Array + is_a: Arraylike + attributes: + num_rows: + name: num_rows + range: float32 + required: false + num_cols: + name: num_cols + range: float32 + required: false + ImagingRetinotopy__axis_2_phase_map: + name: ImagingRetinotopy__axis_2_phase_map + description: Phase response to stimulus on the second measured axis. + attributes: + dimension: + name: dimension + description: 'Number of rows and columns in the image. NOTE: row, column representation + is equivalent to height, width.' + range: int32 + field_of_view: + name: field_of_view + description: Size of viewing area, in meters. + range: float32 + unit: + name: unit + description: Unit that axis data is stored in (e.g., degrees). + range: text + array: + name: array + range: ImagingRetinotopy__axis_2_phase_map__Array + ImagingRetinotopy__axis_2_phase_map__Array: + name: ImagingRetinotopy__axis_2_phase_map__Array + is_a: Arraylike + attributes: + num_rows: + name: num_rows + range: float32 + required: false + num_cols: + name: num_cols + range: float32 + required: false + ImagingRetinotopy__axis_2_power_map: + name: ImagingRetinotopy__axis_2_power_map + description: Power response on the second measured axis. Response is scaled so + 0.0 is no power in the response and 1.0 is maximum relative power. + attributes: + dimension: + name: dimension + description: 'Number of rows and columns in the image. NOTE: row, column representation + is equivalent to height, width.' + range: int32 + field_of_view: + name: field_of_view + description: Size of viewing area, in meters. + range: float32 + unit: + name: unit + description: Unit that axis data is stored in (e.g., degrees). + range: text + array: + name: array + range: ImagingRetinotopy__axis_2_power_map__Array + ImagingRetinotopy__axis_2_power_map__Array: + name: ImagingRetinotopy__axis_2_power_map__Array + is_a: Arraylike + attributes: + num_rows: + name: num_rows + range: float32 + required: false + num_cols: + name: num_cols + range: float32 + required: false + ImagingRetinotopy__axis_descriptions: + name: ImagingRetinotopy__axis_descriptions + description: Two-element array describing the contents of the two response axis + fields. Description should be something like ['altitude', 'azimuth'] or '['radius', + 'theta']. + attributes: + axis_descriptions: + name: axis_descriptions + description: Two-element array describing the contents of the two response + axis fields. Description should be something like ['altitude', 'azimuth'] + or '['radius', 'theta']. + multivalued: true + range: text + required: true + ImagingRetinotopy__focal_depth_image: + name: ImagingRetinotopy__focal_depth_image + description: 'Gray-scale image taken with same settings/parameters (e.g., focal + depth, wavelength) as data collection. Array format: [rows][columns].' + attributes: + bits_per_pixel: + name: bits_per_pixel + description: Number of bits used to represent each value. This is necessary + to determine maximum (white) pixel value. + range: int32 + dimension: + name: dimension + description: 'Number of rows and columns in the image. NOTE: row, column representation + is equivalent to height, width.' + range: int32 + field_of_view: + name: field_of_view + description: Size of viewing area, in meters. + range: float32 + focal_depth: + name: focal_depth + description: Focal depth offset, in meters. + range: float32 + format: + name: format + description: Format of image. Right now only 'raw' is supported. + range: text + array: + name: array + range: ImagingRetinotopy__focal_depth_image__Array + ImagingRetinotopy__focal_depth_image__Array: + name: ImagingRetinotopy__focal_depth_image__Array + is_a: Arraylike + attributes: + num_rows: + name: num_rows + range: uint16 + required: false + num_cols: + name: num_cols + range: uint16 + required: false + ImagingRetinotopy__sign_map: + name: ImagingRetinotopy__sign_map + description: Sine of the angle between the direction of the gradient in axis_1 + and axis_2. + attributes: + dimension: + name: dimension + description: 'Number of rows and columns in the image. NOTE: row, column representation + is equivalent to height, width.' + range: int32 + field_of_view: + name: field_of_view + description: Size of viewing area, in meters. + range: float32 + array: + name: array + range: ImagingRetinotopy__sign_map__Array + ImagingRetinotopy__sign_map__Array: + name: ImagingRetinotopy__sign_map__Array + is_a: Arraylike + attributes: + num_rows: + name: num_rows + range: float32 + required: false + num_cols: + name: num_cols + range: float32 + required: false + ImagingRetinotopy__vasculature_image: + name: ImagingRetinotopy__vasculature_image + description: 'Gray-scale anatomical image of cortical surface. Array structure: + [rows][columns]' + attributes: + bits_per_pixel: + name: bits_per_pixel + description: Number of bits used to represent each value. This is necessary + to determine maximum (white) pixel value + range: int32 + dimension: + name: dimension + description: 'Number of rows and columns in the image. NOTE: row, column representation + is equivalent to height, width.' + range: int32 + field_of_view: + name: field_of_view + description: Size of viewing area, in meters. + range: float32 + format: + name: format + description: Format of image. Right now only 'raw' is supported. + range: text + array: + name: array + range: ImagingRetinotopy__vasculature_image__Array + ImagingRetinotopy__vasculature_image__Array: + name: ImagingRetinotopy__vasculature_image__Array + is_a: Arraylike + attributes: + num_rows: + name: num_rows + range: uint16 + required: false + num_cols: + name: num_cols + range: uint16 + required: false diff --git a/nwb_linkml/schema/core.nwb.retinotopy.yaml b/nwb_linkml/schema/core.nwb.retinotopy.yaml index 3c7afa0..1fda29d 100644 --- a/nwb_linkml/schema/core.nwb.retinotopy.yaml +++ b/nwb_linkml/schema/core.nwb.retinotopy.yaml @@ -3,6 +3,8 @@ id: core.nwb.retinotopy imports: - core.nwb.base - nwb.language +- core.nwb.retinotopy.include +- core.nwb.retinotopy default_prefix: core.nwb.retinotopy/ classes: ImagingRetinotopy: @@ -22,27 +24,27 @@ classes: name: axis_1_phase_map description: Phase response to stimulus on the first measured axis. multivalued: false - range: ImagingRetinotopy_axis_1_phase_map + range: ImagingRetinotopy__axis_1_phase_map required: true axis_1_power_map: name: axis_1_power_map description: Power response on the first measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power. multivalued: false - range: ImagingRetinotopy_axis_1_power_map + range: ImagingRetinotopy__axis_1_power_map required: false axis_2_phase_map: name: axis_2_phase_map description: Phase response to stimulus on the second measured axis. multivalued: false - range: ImagingRetinotopy_axis_2_phase_map + range: ImagingRetinotopy__axis_2_phase_map required: true axis_2_power_map: name: axis_2_power_map description: Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power. multivalued: false - range: ImagingRetinotopy_axis_2_power_map + range: ImagingRetinotopy__axis_2_power_map required: false axis_descriptions: name: axis_descriptions @@ -50,284 +52,26 @@ classes: axis fields. Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta']. multivalued: false - range: ImagingRetinotopy_axis_descriptions + range: ImagingRetinotopy__axis_descriptions required: true focal_depth_image: name: focal_depth_image description: 'Gray-scale image taken with same settings/parameters (e.g., focal depth, wavelength) as data collection. Array format: [rows][columns].' multivalued: false - range: ImagingRetinotopy_focal_depth_image + range: ImagingRetinotopy__focal_depth_image required: false sign_map: name: sign_map description: Sine of the angle between the direction of the gradient in axis_1 and axis_2. multivalued: false - range: ImagingRetinotopy_sign_map + range: ImagingRetinotopy__sign_map required: false vasculature_image: name: vasculature_image description: 'Gray-scale anatomical image of cortical surface. Array structure: [rows][columns]' multivalued: false - range: ImagingRetinotopy_vasculature_image + range: ImagingRetinotopy__vasculature_image required: true - ImagingRetinotopy_axis_1_phase_map: - name: ImagingRetinotopy_axis_1_phase_map - description: Phase response to stimulus on the first measured axis. - attributes: - dimension: - name: dimension - description: 'Number of rows and columns in the image. NOTE: row, column representation - is equivalent to height, width.' - range: int32 - field_of_view: - name: field_of_view - description: Size of viewing area, in meters. - range: float32 - unit: - name: unit - description: Unit that axis data is stored in (e.g., degrees). - range: text - array: - name: array - range: ImagingRetinotopy_axis_1_phase_map_Array - ImagingRetinotopy_axis_1_phase_map_Array: - name: ImagingRetinotopy_axis_1_phase_map_Array - is_a: Arraylike - attributes: - num_rows: - name: num_rows - range: float32 - required: false - num_cols: - name: num_cols - range: float32 - required: false - ImagingRetinotopy_axis_1_power_map: - name: ImagingRetinotopy_axis_1_power_map - description: Power response on the first measured axis. Response is scaled so - 0.0 is no power in the response and 1.0 is maximum relative power. - attributes: - dimension: - name: dimension - description: 'Number of rows and columns in the image. NOTE: row, column representation - is equivalent to height, width.' - range: int32 - field_of_view: - name: field_of_view - description: Size of viewing area, in meters. - range: float32 - unit: - name: unit - description: Unit that axis data is stored in (e.g., degrees). - range: text - array: - name: array - range: ImagingRetinotopy_axis_1_power_map_Array - ImagingRetinotopy_axis_1_power_map_Array: - name: ImagingRetinotopy_axis_1_power_map_Array - is_a: Arraylike - attributes: - num_rows: - name: num_rows - range: float32 - required: false - num_cols: - name: num_cols - range: float32 - required: false - ImagingRetinotopy_axis_2_phase_map: - name: ImagingRetinotopy_axis_2_phase_map - description: Phase response to stimulus on the second measured axis. - attributes: - dimension: - name: dimension - description: 'Number of rows and columns in the image. NOTE: row, column representation - is equivalent to height, width.' - range: int32 - field_of_view: - name: field_of_view - description: Size of viewing area, in meters. - range: float32 - unit: - name: unit - description: Unit that axis data is stored in (e.g., degrees). - range: text - array: - name: array - range: ImagingRetinotopy_axis_2_phase_map_Array - ImagingRetinotopy_axis_2_phase_map_Array: - name: ImagingRetinotopy_axis_2_phase_map_Array - is_a: Arraylike - attributes: - num_rows: - name: num_rows - range: float32 - required: false - num_cols: - name: num_cols - range: float32 - required: false - ImagingRetinotopy_axis_2_power_map: - name: ImagingRetinotopy_axis_2_power_map - description: Power response on the second measured axis. Response is scaled so - 0.0 is no power in the response and 1.0 is maximum relative power. - attributes: - dimension: - name: dimension - description: 'Number of rows and columns in the image. NOTE: row, column representation - is equivalent to height, width.' - range: int32 - field_of_view: - name: field_of_view - description: Size of viewing area, in meters. - range: float32 - unit: - name: unit - description: Unit that axis data is stored in (e.g., degrees). - range: text - array: - name: array - range: ImagingRetinotopy_axis_2_power_map_Array - ImagingRetinotopy_axis_2_power_map_Array: - name: ImagingRetinotopy_axis_2_power_map_Array - is_a: Arraylike - attributes: - num_rows: - name: num_rows - range: float32 - required: false - num_cols: - name: num_cols - range: float32 - required: false - ImagingRetinotopy_axis_descriptions: - name: ImagingRetinotopy_axis_descriptions - description: Two-element array describing the contents of the two response axis - fields. Description should be something like ['altitude', 'azimuth'] or '['radius', - 'theta']. - attributes: - array: - name: array - range: ImagingRetinotopy_axis_descriptions_Array - ImagingRetinotopy_axis_descriptions_Array: - name: ImagingRetinotopy_axis_descriptions_Array - is_a: Arraylike - attributes: - axis_1, axis_2: - name: axis_1, axis_2 - range: text - required: true - minimum_cardinality: 2 - maximum_cardinality: 2 - ImagingRetinotopy_focal_depth_image: - name: ImagingRetinotopy_focal_depth_image - description: 'Gray-scale image taken with same settings/parameters (e.g., focal - depth, wavelength) as data collection. Array format: [rows][columns].' - attributes: - bits_per_pixel: - name: bits_per_pixel - description: Number of bits used to represent each value. This is necessary - to determine maximum (white) pixel value. - range: int32 - dimension: - name: dimension - description: 'Number of rows and columns in the image. NOTE: row, column representation - is equivalent to height, width.' - range: int32 - field_of_view: - name: field_of_view - description: Size of viewing area, in meters. - range: float32 - focal_depth: - name: focal_depth - description: Focal depth offset, in meters. - range: float32 - format: - name: format - description: Format of image. Right now only 'raw' is supported. - range: text - array: - name: array - range: ImagingRetinotopy_focal_depth_image_Array - ImagingRetinotopy_focal_depth_image_Array: - name: ImagingRetinotopy_focal_depth_image_Array - is_a: Arraylike - attributes: - num_rows: - name: num_rows - range: uint16 - required: false - num_cols: - name: num_cols - range: uint16 - required: false - ImagingRetinotopy_sign_map: - name: ImagingRetinotopy_sign_map - description: Sine of the angle between the direction of the gradient in axis_1 - and axis_2. - attributes: - dimension: - name: dimension - description: 'Number of rows and columns in the image. NOTE: row, column representation - is equivalent to height, width.' - range: int32 - field_of_view: - name: field_of_view - description: Size of viewing area, in meters. - range: float32 - array: - name: array - range: ImagingRetinotopy_sign_map_Array - ImagingRetinotopy_sign_map_Array: - name: ImagingRetinotopy_sign_map_Array - is_a: Arraylike - attributes: - num_rows: - name: num_rows - range: float32 - required: false - num_cols: - name: num_cols - range: float32 - required: false - ImagingRetinotopy_vasculature_image: - name: ImagingRetinotopy_vasculature_image - description: 'Gray-scale anatomical image of cortical surface. Array structure: - [rows][columns]' - attributes: - bits_per_pixel: - name: bits_per_pixel - description: Number of bits used to represent each value. This is necessary - to determine maximum (white) pixel value - range: int32 - dimension: - name: dimension - description: 'Number of rows and columns in the image. NOTE: row, column representation - is equivalent to height, width.' - range: int32 - field_of_view: - name: field_of_view - description: Size of viewing area, in meters. - range: float32 - format: - name: format - description: Format of image. Right now only 'raw' is supported. - range: text - array: - name: array - range: ImagingRetinotopy_vasculature_image_Array - ImagingRetinotopy_vasculature_image_Array: - name: ImagingRetinotopy_vasculature_image_Array - is_a: Arraylike - attributes: - num_rows: - name: num_rows - range: uint16 - required: false - num_cols: - name: num_cols - range: uint16 - required: false diff --git a/nwb_linkml/schema/hdmf-common.base.include.yaml b/nwb_linkml/schema/hdmf-common.base.include.yaml new file mode 100644 index 0000000..25fef03 --- /dev/null +++ b/nwb_linkml/schema/hdmf-common.base.include.yaml @@ -0,0 +1,7 @@ +name: hdmf-common.base.include +id: hdmf-common.base.include +imports: +- nwb.language +- hdmf-common.base.include +- hdmf-common.base +default_prefix: hdmf-common.base.include/ diff --git a/nwb_linkml/schema/hdmf-common.base.yaml b/nwb_linkml/schema/hdmf-common.base.yaml index 04204f0..cd0f04c 100644 --- a/nwb_linkml/schema/hdmf-common.base.yaml +++ b/nwb_linkml/schema/hdmf-common.base.yaml @@ -2,6 +2,8 @@ name: hdmf-common.base id: hdmf-common.base imports: - nwb.language +- hdmf-common.base.include +- hdmf-common.base default_prefix: hdmf-common.base/ classes: Data: diff --git a/nwb_linkml/schema/hdmf-common.sparse.include.yaml b/nwb_linkml/schema/hdmf-common.sparse.include.yaml new file mode 100644 index 0000000..33afefc --- /dev/null +++ b/nwb_linkml/schema/hdmf-common.sparse.include.yaml @@ -0,0 +1,39 @@ +name: hdmf-common.sparse.include +id: hdmf-common.sparse.include +imports: +- hdmf-common.base +- nwb.language +- hdmf-common.sparse.include +- hdmf-common.sparse +default_prefix: hdmf-common.sparse.include/ +classes: + CSRMatrix__indices: + name: CSRMatrix__indices + description: The column indices. + attributes: + indices: + name: indices + description: The column indices. + multivalued: true + range: uint + required: true + CSRMatrix__indptr: + name: CSRMatrix__indptr + description: The row index pointer. + attributes: + indptr: + name: indptr + description: The row index pointer. + multivalued: true + range: uint + required: true + CSRMatrix__data: + name: CSRMatrix__data + description: The non-zero values in the matrix. + attributes: + data: + name: data + description: The non-zero values in the matrix. + multivalued: true + range: AnyType + required: true diff --git a/nwb_linkml/schema/hdmf-common.sparse.yaml b/nwb_linkml/schema/hdmf-common.sparse.yaml index d2da441..aeb171e 100644 --- a/nwb_linkml/schema/hdmf-common.sparse.yaml +++ b/nwb_linkml/schema/hdmf-common.sparse.yaml @@ -3,6 +3,8 @@ id: hdmf-common.sparse imports: - hdmf-common.base - nwb.language +- hdmf-common.sparse.include +- hdmf-common.sparse default_prefix: hdmf-common.sparse/ classes: CSRMatrix: @@ -21,62 +23,17 @@ classes: name: indices description: The column indices. multivalued: false - range: CSRMatrix_indices + range: CSRMatrix__indices required: true indptr: name: indptr description: The row index pointer. multivalued: false - range: CSRMatrix_indptr + range: CSRMatrix__indptr required: true data: name: data description: The non-zero values in the matrix. multivalued: false - range: CSRMatrix_data - required: true - CSRMatrix_indices: - name: CSRMatrix_indices - description: The column indices. - attributes: - array: - name: array - range: CSRMatrix_indices_Array - CSRMatrix_indices_Array: - name: CSRMatrix_indices_Array - is_a: Arraylike - attributes: - number of non-zero values: - name: number of non-zero values - range: uint - required: true - CSRMatrix_indptr: - name: CSRMatrix_indptr - description: The row index pointer. - attributes: - array: - name: array - range: CSRMatrix_indptr_Array - CSRMatrix_indptr_Array: - name: CSRMatrix_indptr_Array - is_a: Arraylike - attributes: - number of rows in the matrix + 1: - name: number of rows in the matrix + 1 - range: uint - required: true - CSRMatrix_data: - name: CSRMatrix_data - description: The non-zero values in the matrix. - attributes: - array: - name: array - range: CSRMatrix_data_Array - CSRMatrix_data_Array: - name: CSRMatrix_data_Array - is_a: Arraylike - attributes: - number of non-zero values: - name: number of non-zero values - range: AnyType + range: CSRMatrix__data required: true diff --git a/nwb_linkml/schema/hdmf-common.table.include.yaml b/nwb_linkml/schema/hdmf-common.table.include.yaml new file mode 100644 index 0000000..c5e3786 --- /dev/null +++ b/nwb_linkml/schema/hdmf-common.table.include.yaml @@ -0,0 +1,48 @@ +name: hdmf-common.table.include +id: hdmf-common.table.include +imports: +- hdmf-common.base +- nwb.language +- hdmf-common.table.include +- hdmf-common.table +default_prefix: hdmf-common.table.include/ +classes: + VectorData__Array: + name: VectorData__Array + is_a: Arraylike + attributes: + dim0: + name: dim0 + range: AnyType + required: true + dim1: + name: dim1 + range: AnyType + required: false + dim2: + name: dim2 + range: AnyType + required: false + dim3: + name: dim3 + range: AnyType + required: false + ElementIdentifiers__Array: + name: ElementIdentifiers__Array + is_a: Arraylike + attributes: + num_elements: + name: num_elements + range: int + required: true + DynamicTable__id: + name: DynamicTable__id + description: Array of unique identifiers for the rows of this dynamic table. + is_a: ElementIdentifiers + attributes: + id: + name: id + description: Array of unique identifiers for the rows of this dynamic table. + multivalued: true + range: int + required: true diff --git a/nwb_linkml/schema/hdmf-common.table.yaml b/nwb_linkml/schema/hdmf-common.table.yaml index ce283e6..0dcb0f8 100644 --- a/nwb_linkml/schema/hdmf-common.table.yaml +++ b/nwb_linkml/schema/hdmf-common.table.yaml @@ -3,6 +3,8 @@ id: hdmf-common.table imports: - hdmf-common.base - nwb.language +- hdmf-common.table.include +- hdmf-common.table default_prefix: hdmf-common.table/ classes: VectorData: @@ -23,27 +25,7 @@ classes: range: text array: name: array - range: VectorData_Array - VectorData_Array: - name: VectorData_Array - is_a: Arraylike - attributes: - dim0: - name: dim0 - range: AnyType - required: true - dim1: - name: dim1 - range: AnyType - required: false - dim2: - name: dim2 - range: AnyType - required: false - dim3: - name: dim3 - range: AnyType - required: false + range: VectorData__Array VectorIndex: name: VectorIndex description: Used with VectorData to encode a ragged array. An array of indices @@ -57,17 +39,6 @@ classes: name: target description: Reference to the target dataset that this index applies to. range: VectorData - array: - name: array - range: VectorIndex_Array - VectorIndex_Array: - name: VectorIndex_Array - is_a: Arraylike - attributes: - num_rows: - name: num_rows - range: uint8 - required: true ElementIdentifiers: name: ElementIdentifiers description: A list of unique identifiers for values within a dataset, e.g. rows @@ -76,15 +47,7 @@ classes: attributes: array: name: array - range: ElementIdentifiers_Array - ElementIdentifiers_Array: - name: ElementIdentifiers_Array - is_a: Arraylike - attributes: - num_elements: - name: num_elements - range: int - required: true + range: ElementIdentifiers__Array DynamicTableRegion: name: DynamicTableRegion description: DynamicTableRegion provides a link from one table to an index or @@ -107,17 +70,6 @@ classes: name: description description: Description of what this table region points to. range: text - array: - name: array - range: DynamicTableRegion_Array - DynamicTableRegion_Array: - name: DynamicTableRegion_Array - is_a: Arraylike - attributes: - num_rows: - name: num_rows - range: int - required: true DynamicTable: name: DynamicTable description: A group containing multiple datasets that are aligned on the first @@ -153,7 +105,7 @@ classes: name: id description: Array of unique identifiers for the rows of this dynamic table. multivalued: false - range: DynamicTable_id + range: DynamicTable__id required: true VectorData: name: VectorData @@ -161,22 +113,6 @@ classes: multivalued: true range: VectorData required: false - DynamicTable_id: - name: DynamicTable_id - description: Array of unique identifiers for the rows of this dynamic table. - is_a: ElementIdentifiers - attributes: - array: - name: array - range: DynamicTable_id_Array - DynamicTable_id_Array: - name: DynamicTable_id_Array - is_a: Arraylike - attributes: - num_rows: - name: num_rows - range: int - required: true AlignedDynamicTable: name: AlignedDynamicTable description: DynamicTable container that supports storing a collection of sub-tables. diff --git a/nwb_linkml/schema/hdmf-experimental.experimental.include.yaml b/nwb_linkml/schema/hdmf-experimental.experimental.include.yaml new file mode 100644 index 0000000..d7fcc65 --- /dev/null +++ b/nwb_linkml/schema/hdmf-experimental.experimental.include.yaml @@ -0,0 +1,8 @@ +name: hdmf-experimental.experimental.include +id: hdmf-experimental.experimental.include +imports: +- hdmf-common.table +- nwb.language +- hdmf-experimental.experimental.include +- hdmf-experimental.experimental +default_prefix: hdmf-experimental.experimental.include/ diff --git a/nwb_linkml/schema/hdmf-experimental.experimental.yaml b/nwb_linkml/schema/hdmf-experimental.experimental.yaml index d9052ca..a6bd6b7 100644 --- a/nwb_linkml/schema/hdmf-experimental.experimental.yaml +++ b/nwb_linkml/schema/hdmf-experimental.experimental.yaml @@ -3,6 +3,8 @@ id: hdmf-experimental.experimental imports: - hdmf-common.table - nwb.language +- hdmf-experimental.experimental.include +- hdmf-experimental.experimental default_prefix: hdmf-experimental.experimental/ classes: EnumData: diff --git a/nwb_linkml/schema/hdmf-experimental.resources.include.yaml b/nwb_linkml/schema/hdmf-experimental.resources.include.yaml new file mode 100644 index 0000000..9613105 --- /dev/null +++ b/nwb_linkml/schema/hdmf-experimental.resources.include.yaml @@ -0,0 +1,79 @@ +name: hdmf-experimental.resources.include +id: hdmf-experimental.resources.include +imports: +- hdmf-common.base +- nwb.language +- hdmf-experimental.resources.include +- hdmf-experimental.resources +default_prefix: hdmf-experimental.resources.include/ +classes: + HERD__keys: + name: HERD__keys + description: A table for storing user terms that are used to refer to external + resources. + is_a: Data + attributes: + keys: + name: keys + description: A table for storing user terms that are used to refer to external + resources. + multivalued: true + range: AnyType + required: true + HERD__files: + name: HERD__files + description: A table for storing object ids of files used in external resources. + is_a: Data + attributes: + files: + name: files + description: A table for storing object ids of files used in external resources. + multivalued: true + range: AnyType + required: true + HERD__entities: + name: HERD__entities + description: A table for mapping user terms (i.e., keys) to resource entities. + is_a: Data + attributes: + entities: + name: entities + description: A table for mapping user terms (i.e., keys) to resource entities. + multivalued: true + range: AnyType + required: true + HERD__objects: + name: HERD__objects + description: A table for identifying which objects in a file contain references + to external resources. + is_a: Data + attributes: + objects: + name: objects + description: A table for identifying which objects in a file contain references + to external resources. + multivalued: true + range: AnyType + required: true + HERD__object_keys: + name: HERD__object_keys + description: A table for identifying which objects use which keys. + is_a: Data + attributes: + object_keys: + name: object_keys + description: A table for identifying which objects use which keys. + multivalued: true + range: AnyType + required: true + HERD__entity_keys: + name: HERD__entity_keys + description: A table for identifying which keys use which entity. + is_a: Data + attributes: + entity_keys: + name: entity_keys + description: A table for identifying which keys use which entity. + multivalued: true + range: AnyType + required: true diff --git a/nwb_linkml/schema/hdmf-experimental.resources.yaml b/nwb_linkml/schema/hdmf-experimental.resources.yaml index b57caae..104d212 100644 --- a/nwb_linkml/schema/hdmf-experimental.resources.yaml +++ b/nwb_linkml/schema/hdmf-experimental.resources.yaml @@ -3,6 +3,8 @@ id: hdmf-experimental.resources imports: - hdmf-common.base - nwb.language +- hdmf-experimental.resources.include +- hdmf-experimental.resources default_prefix: hdmf-experimental.resources/ classes: HERD: @@ -16,134 +18,36 @@ classes: description: A table for storing user terms that are used to refer to external resources. multivalued: false - range: HERD_keys + range: HERD__keys required: true files: name: files description: A table for storing object ids of files used in external resources. multivalued: false - range: HERD_files + range: HERD__files required: true entities: name: entities description: A table for mapping user terms (i.e., keys) to resource entities. multivalued: false - range: HERD_entities + range: HERD__entities required: true objects: name: objects description: A table for identifying which objects in a file contain references to external resources. multivalued: false - range: HERD_objects + range: HERD__objects required: true object_keys: name: object_keys description: A table for identifying which objects use which keys. multivalued: false - range: HERD_object_keys + range: HERD__object_keys required: true entity_keys: name: entity_keys description: A table for identifying which keys use which entity. multivalued: false - range: HERD_entity_keys - required: true - HERD_keys: - name: HERD_keys - description: A table for storing user terms that are used to refer to external - resources. - is_a: Data - attributes: - array: - name: array - range: HERD_keys_Array - HERD_keys_Array: - name: HERD_keys_Array - is_a: Arraylike - attributes: - num_rows: - name: num_rows - range: AnyType - required: true - HERD_files: - name: HERD_files - description: A table for storing object ids of files used in external resources. - is_a: Data - attributes: - array: - name: array - range: HERD_files_Array - HERD_files_Array: - name: HERD_files_Array - is_a: Arraylike - attributes: - num_rows: - name: num_rows - range: AnyType - required: true - HERD_entities: - name: HERD_entities - description: A table for mapping user terms (i.e., keys) to resource entities. - is_a: Data - attributes: - array: - name: array - range: HERD_entities_Array - HERD_entities_Array: - name: HERD_entities_Array - is_a: Arraylike - attributes: - num_rows: - name: num_rows - range: AnyType - required: true - HERD_objects: - name: HERD_objects - description: A table for identifying which objects in a file contain references - to external resources. - is_a: Data - attributes: - array: - name: array - range: HERD_objects_Array - HERD_objects_Array: - name: HERD_objects_Array - is_a: Arraylike - attributes: - num_rows: - name: num_rows - range: AnyType - required: true - HERD_object_keys: - name: HERD_object_keys - description: A table for identifying which objects use which keys. - is_a: Data - attributes: - array: - name: array - range: HERD_object_keys_Array - HERD_object_keys_Array: - name: HERD_object_keys_Array - is_a: Arraylike - attributes: - num_rows: - name: num_rows - range: AnyType - required: 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version="^7.4.0", optional=true} pytest-depends = {version="^1.0.1", optional=true} dash = {version="^2.12.1", optional=true} dash-cytoscape = {version="^0.3.0", optional=true} +nptyping = "^2.5.0" [tool.poetry.extras] dev = ["nwb_schema_language"] diff --git a/scripts/generate_core.py b/scripts/generate_core.py index 161cba8..9ba8d8c 100644 --- a/scripts/generate_core.py +++ b/scripts/generate_core.py @@ -1,7 +1,7 @@ from argparse import ArgumentParser from pathlib import Path from linkml_runtime.dumpers import yaml_dumper -from linkml.generators import PydanticGenerator +from nwb_linkml.generators.pydantic import NWBPydanticGenerator from nwb_linkml import io @@ -14,9 +14,10 @@ def generate_core_yaml(output_path:Path): def generate_core_pydantic(yaml_path:Path, output_path:Path): for schema in yaml_path.glob('*.yaml'): - pydantic_file = (output_path / schema.name).with_suffix('.py') + python_name = schema.stem.replace('.', '_').replace('-', '_') + pydantic_file = (output_path / python_name).with_suffix('.py') - generator = PydanticGenerator( + generator = NWBPydanticGenerator( str(schema), pydantic_version='1', emit_metadata=True, diff --git a/tests/test_generate.py b/tests/test_generate.py index 3924fd5..98cf466 100644 --- a/tests/test_generate.py +++ b/tests/test_generate.py @@ -6,6 +6,7 @@ import warnings from .fixtures import nwb_core_fixture, tmp_output_dir from linkml_runtime.dumpers import yaml_dumper from linkml.generators import PydanticGenerator +from nwb_linkml.generators.pydantic import NWBPydanticGenerator from nwb_linkml.lang_elements import NwbLangSchema @@ -15,8 +16,11 @@ def test_generate_nwblang(tmp_output_dir): def test_generate_core(nwb_core_fixture, tmp_output_dir): schemas = nwb_core_fixture.build().schemas + + (tmp_output_dir / 'schema').mkdir(exist_ok=True) + for schema in schemas: - output_file = tmp_output_dir / (schema.name + '.yaml') + output_file = tmp_output_dir / 'schema' / (schema.name + '.yaml') yaml_dumper.dump(schema, output_file) @pytest.mark.depends(on=['test_generate_core']) @@ -26,10 +30,15 @@ def test_generate_pydantic(tmp_output_dir): # core_file = tmp_output_dir / 'core.yaml' # pydantic_file = tmp_output_dir / 'core.py' - for schema in tmp_output_dir.glob('*.yaml'): - pydantic_file = (schema.parent / schema.name).with_suffix('.py') + (tmp_output_dir / 'models').mkdir(exist_ok=True) - generator = PydanticGenerator( + for schema in (tmp_output_dir / 'schema').glob('*.yaml'): + # python friendly name + python_name = schema.stem.replace('.', '_').replace('-','_') + + pydantic_file = (schema.parent.parent / 'models' / python_name).with_suffix('.py') + + generator = NWBPydanticGenerator( str(schema), pydantic_version='1', emit_metadata=True, @@ -37,5 +46,7 @@ def test_generate_pydantic(tmp_output_dir): gen_slots=True ) gen_pydantic = generator.serialize() + + with open(pydantic_file, 'w') as pfile: pfile.write(gen_pydantic)