nwb-linkml/nwb_linkml/models/core_nwb_base.py

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,
    Container
)

from .hdmf_common_table import (
    DynamicTable,
    VectorData
)


metamodel_version = "None"
version = "None"

class ConfiguredBaseModel(BaseModel,
                validate_assignment = True,
                validate_default = True,
                extra = 'forbid',
                arbitrary_types_allowed = True,
                use_enum_values = True):
    pass


class NWBData(Data):
    """
    An abstract data type for a dataset.
    """
    name:str= Field(...)
    

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.
    """
    name:str= Field(...)
    description:Optional[str]= Field(None, description="""Description of what these vectors represent.""")
    array:Optional[Union[
        NDArray[Shape["* dim0"], Any],
        NDArray[Shape["* dim0, * dim1"], Any],
        NDArray[Shape["* dim0, * dim1, * dim2"], Any],
        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)).
    """
    name:str= Field(...)
    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[Union[
        NDArray[Shape["* x, * y"], Number],
        NDArray[Shape["* x, * y, 3 r_g_b"], Number],
        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.
    """
    name:str= Field(...)
    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.
    """
    name:str= Field(...)
    

class NWBDataInterface(NWBContainer):
    """
    An abstract data type for a generic container storing collections of data, as opposed to metadata.
    """
    name:str= Field(...)
    

class TimeSeries(NWBDataInterface):
    """
    General purpose time series.
    """
    name:str= Field(...)
    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[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.""")
    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.""")
    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.""")
    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.
    """
    name:Literal["data"]= Field("data")
    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[Union[
        NDArray[Shape["* num_times"], Any],
        NDArray[Shape["* num_times, * num_DIM2"], Any],
        NDArray[Shape["* num_times, * num_DIM2, * num_DIM3"], Any],
        NDArray[Shape["* num_times, * num_DIM2, * num_DIM3, * num_DIM4"], 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.
    """
    name:Literal["starting_time"]= Field("starting_time")
    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'.""")
    value:float= 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.
    """
    name:Literal["sync"]= Field("sync")
    

class ProcessingModule(NWBContainer):
    """
    A collection of processed data.
    """
    name:str= Field(...)
    description:Optional[str]= Field(None, description="""Description of this collection of processed data.""")
    nwb_data_interface:Optional[List[NWBDataInterface]]= Field(default_factory=list, description="""Data objects stored in this collection.""")
    dynamic_table: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.
    """
    name:str= Field(...)
    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.
    """
    name:Literal["order_of_images"]= Field("order_of_images")
    array:Optional[List[Image] | Image]= Field(None)
    


# Model rebuild
# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model
NWBData.model_rebuild()
TimeSeriesReferenceVectorData.model_rebuild()
Image.model_rebuild()
ImageReferences.model_rebuild()
NWBContainer.model_rebuild()
NWBDataInterface.model_rebuild()
TimeSeries.model_rebuild()
TimeSeriesData.model_rebuild()
TimeSeriesStartingTime.model_rebuild()
TimeSeriesSync.model_rebuild()
ProcessingModule.model_rebuild()
Images.model_rebuild()
ImagesOrderOfImages.model_rebuild()