nwb-linkml/nwb_linkml/schema/core.nwb.base.yaml

380 lines
13 KiB
YAML

name: core.nwb.base
id: core.nwb.base
imports:
- hdmf-common.base
- hdmf-common.table
- nwb.language
default_prefix: core.nwb.base/
classes:
NWBData:
name: NWBData
description: An abstract data type for a dataset.
is_a: Data
attributes:
name:
name: name
range: string
required: true
tree_root: true
TimeSeriesReferenceVectorData:
name: TimeSeriesReferenceVectorData
description: 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.
is_a: VectorData
attributes:
name:
name: name
range: string
required: true
tree_root: true
Image:
name: Image
description: 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)).
is_a: NWBData
attributes:
name:
name: name
range: string
required: true
resolution:
name: resolution
description: Pixel resolution of the image, in pixels per centimeter.
range: float32
description:
name: description
description: Description of the image.
range: text
array:
name: array
range: Image__Array
tree_root: true
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:
name: ImageReferences
description: Ordered dataset of references to Image objects.
is_a: NWBData
attributes:
name:
name: name
range: string
required: true
array:
name: array
range: ImageReferences__Array
tree_root: true
ImageReferences__Array:
name: ImageReferences__Array
is_a: Arraylike
attributes:
num_images:
name: num_images
range: Image
required: true
NWBContainer:
name: NWBContainer
description: An abstract data type for a generic container storing collections
of data and metadata. Base type for all data and metadata containers.
is_a: Container
attributes:
name:
name: name
range: string
required: true
tree_root: true
NWBDataInterface:
name: NWBDataInterface
description: An abstract data type for a generic container storing collections
of data, as opposed to metadata.
is_a: NWBContainer
attributes:
name:
name: name
range: string
required: true
tree_root: true
TimeSeries:
name: TimeSeries
description: General purpose time series.
is_a: NWBDataInterface
attributes:
name:
name: name
range: string
required: true
description:
name: description
description: Description of the time series.
range: text
comments:
name: comments
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.
range: text
data:
name: 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.
multivalued: false
range: TimeSeries__data
required: true
starting_time:
name: 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.
multivalued: false
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: true
range: float64
required: false
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
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
sync:
name: 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.
multivalued: false
range: TimeSeries__sync
required: false
tree_root: 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:
name:
name: name
ifabsent: string(data)
range: string
required: true
equals_string: data
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:
name:
name: name
ifabsent: string(starting_time)
range: string
required: true
equals_string: starting_time
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
value:
name: value
range: float64
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.
attributes:
name:
name: name
ifabsent: string(sync)
range: string
required: true
equals_string: sync
ProcessingModule:
name: ProcessingModule
description: A collection of processed data.
is_a: NWBContainer
attributes:
name:
name: name
range: string
required: true
description:
name: description
description: Description of this collection of processed data.
range: text
nwb_data_interface:
name: nwb_data_interface
description: Data objects stored in this collection.
multivalued: true
range: NWBDataInterface
required: false
dynamic_table:
name: dynamic_table
description: Tables stored in this collection.
multivalued: true
range: DynamicTable
required: false
tree_root: true
Images:
name: Images
description: 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.
is_a: NWBDataInterface
attributes:
name:
name: name
range: string
required: true
description:
name: description
description: Description of this collection of images.
range: text
Image:
name: Image
description: Images stored in this collection.
multivalued: true
range: Image
required: true
order_of_images:
name: 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.
multivalued: false
range: Images__order_of_images
required: false
tree_root: true
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
attributes:
name:
name: name
ifabsent: string(order_of_images)
range: string
required: true
equals_string: order_of_images