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Merge pull request #482 from NeurodataWithoutBorders/schema-260-release
add schema files and update default version
2 parents 8879f01 + f7fef6a commit 4bb8ef2

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‎generateCore.m‎

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%
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% See also GENERATEEXTENSION
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latestVersion = '2.5.0';
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latestVersion = '2.6.0';
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if nargin == 0 || strcmp(varargin{1}, 'savedir')
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version = latestVersion;

‎nwb-schema/2.6.0/core/nwb.base.yaml‎

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datasets:
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- neurodata_type_def: NWBData
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neurodata_type_inc: Data
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doc: An abstract data type for a dataset.
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- neurodata_type_def: TimeSeriesReferenceVectorData
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neurodata_type_inc: VectorData
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default_name: timeseries
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dtype:
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- name: idx_start
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dtype: int32
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doc: Start index into the TimeSeries 'data' and 'timestamp' datasets of the referenced
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TimeSeries. The first dimension of those arrays is always time.
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- name: count
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dtype: int32
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doc: Number of data samples available in this time series, during this epoch
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- name: timeseries
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dtype:
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target_type: TimeSeries
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reftype: object
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doc: The TimeSeries that this index applies to
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doc: Column storing references to a TimeSeries (rows). For each TimeSeries this
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VectorData column stores the start_index and count to indicate the range in time
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to be selected as well as an object reference to the TimeSeries.
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- neurodata_type_def: Image
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neurodata_type_inc: NWBData
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dtype: numeric
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dims:
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- - x
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- y
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- - x
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- y
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- r, g, b
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- - x
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- y
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- r, g, b, a
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shape:
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- - null
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- null
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- - null
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- null
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- 3
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- - null
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- null
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- 4
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doc: An abstract data type for an image. Shape can be 2-D (x, y), or 3-D where the
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third dimension can have three or four elements, e.g. (x, y, (r, g, b)) or
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(x, y, (r, g, b, a)).
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attributes:
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- name: resolution
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dtype: float32
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doc: Pixel resolution of the image, in pixels per centimeter.
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required: false
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- name: description
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dtype: text
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doc: Description of the image.
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required: false
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- neurodata_type_def: ImageReferences
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neurodata_type_inc: NWBData
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dtype:
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target_type: Image
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reftype: object
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dims:
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- num_images
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shape:
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- null
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doc: Ordered dataset of references to Image objects.
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groups:
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- neurodata_type_def: NWBContainer
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neurodata_type_inc: Container
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doc: An abstract data type for a generic container storing collections of data and
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metadata. Base type for all data and metadata containers.
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- neurodata_type_def: NWBDataInterface
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neurodata_type_inc: NWBContainer
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doc: An abstract data type for a generic container storing collections of data,
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as opposed to metadata.
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- neurodata_type_def: TimeSeries
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neurodata_type_inc: NWBDataInterface
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doc: General purpose time series.
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attributes:
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- name: description
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dtype: text
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default_value: no description
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doc: Description of the time series.
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required: false
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- name: comments
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dtype: text
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default_value: no comments
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doc: Human-readable comments about the TimeSeries. This second descriptive field
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can be used to store additional information, or descriptive information if the
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primary description field is populated with a computer-readable string.
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required: false
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datasets:
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- name: data
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dims:
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- - num_times
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- - num_times
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- num_DIM2
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- - num_times
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- num_DIM2
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- num_DIM3
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- - num_times
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- num_DIM2
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- num_DIM3
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- num_DIM4
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shape:
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- - null
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- - null
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- null
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- - null
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- null
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- null
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- - null
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- null
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- null
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- null
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doc: Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension
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should always represent time. This can also be used to store binary data
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(e.g., image frames). This can also be a link to data stored in an external file.
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attributes:
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- name: conversion
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dtype: float32
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default_value: 1.0
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doc: Scalar to multiply each element in data to convert it to the specified 'unit'.
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If the data are stored in acquisition system units or other units
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that require a conversion to be interpretable, multiply the data by 'conversion'
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to convert the data to the specified 'unit'. e.g. if the data acquisition system
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stores values in this object as signed 16-bit integers (int16 range
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-32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data
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acquisition system gain is 8000X, then the 'conversion' multiplier to get from
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raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9.
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required: false
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- name: offset
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dtype: float32
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default_value: 0.0
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doc: Scalar to add to the data after scaling by 'conversion' to finalize its coercion
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to the specified 'unit'. Two common examples of this include (a) data stored in an
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unsigned type that requires a shift after scaling to re-center the data,
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and (b) specialized recording devices that naturally cause a scalar offset with
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respect to the true units.
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required: false
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- name: resolution
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dtype: float32
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default_value: -1.0
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doc: Smallest meaningful difference between values in data, stored in the specified
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by unit, e.g., the change in value of the least significant bit, or a larger
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number if signal noise is known to be present. If unknown, use -1.0.
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required: false
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- name: unit
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dtype: text
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doc: Base unit of measurement for working with the data. Actual stored values are
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not necessarily stored in these units. To access the data in these units,
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multiply 'data' by 'conversion' and add 'offset'.
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- name: continuity
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dtype: text
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doc: Optionally describe the continuity of the data. Can be "continuous", "instantaneous", or
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"step". For example, a voltage trace would be "continuous", because samples
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are recorded from a continuous process. An array of lick times would be "instantaneous",
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because the data represents distinct moments in time. Times of image presentations would be
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"step" because the picture remains the same until the next timepoint. This field is optional,
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but is useful in providing information about the underlying data. It may inform the way this
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data is interpreted, the way it is visualized, and what analysis methods are applicable.
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required: false
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- name: starting_time
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dtype: float64
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doc: Timestamp of the first sample in seconds. When timestamps are uniformly
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spaced, the timestamp of the first sample can be specified and all subsequent
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ones calculated from the sampling rate attribute.
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quantity: '?'
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attributes:
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- name: rate
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dtype: float32
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doc: Sampling rate, in Hz.
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- name: unit
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dtype: text
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value: seconds
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doc: Unit of measurement for time, which is fixed to 'seconds'.
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- name: timestamps
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dtype: float64
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dims:
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- num_times
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shape:
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- null
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doc: Timestamps for samples stored in data, in seconds, relative to the
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common experiment master-clock stored in NWBFile.timestamps_reference_time.
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quantity: '?'
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attributes:
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- name: interval
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dtype: int32
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value: 1
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doc: Value is '1'
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- name: unit
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dtype: text
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value: seconds
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doc: Unit of measurement for timestamps, which is fixed to 'seconds'.
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- name: control
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dtype: uint8
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dims:
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- num_times
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shape:
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- null
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doc: Numerical labels that apply to each time point in data for the purpose of
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querying and slicing data by these values. If present, the length of this
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array should be the same size as the first dimension of data.
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quantity: '?'
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- name: control_description
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dtype: text
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dims:
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- num_control_values
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shape:
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- null
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doc: Description of each control value. Must be present if control is present.
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If present, control_description[0] should describe time points where control == 0.
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quantity: '?'
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groups:
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- name: sync
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doc: Lab-specific time and sync information as provided directly from hardware
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devices and that is necessary for aligning all acquired time information to
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a common timebase. The timestamp array stores time in the common timebase.
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This group will usually only be populated in TimeSeries that are
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stored external to the NWB file, in files storing raw data. Once timestamp
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data is calculated, the contents of 'sync' are mostly for archival purposes.
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quantity: '?'
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- neurodata_type_def: ProcessingModule
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neurodata_type_inc: NWBContainer
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doc: A collection of processed data.
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attributes:
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- name: description
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dtype: text
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doc: Description of this collection of processed data.
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groups:
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- neurodata_type_inc: NWBDataInterface
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doc: Data objects stored in this collection.
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quantity: '*'
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- neurodata_type_inc: DynamicTable
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doc: Tables stored in this collection.
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quantity: '*'
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- neurodata_type_def: Images
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neurodata_type_inc: NWBDataInterface
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default_name: Images
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doc: A collection of images with an optional way to specify the order of the images
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using the "order_of_images" dataset. An order must be specified if the images are
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referenced by index, e.g., from an IndexSeries.
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attributes:
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- name: description
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dtype: text
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doc: Description of this collection of images.
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datasets:
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- neurodata_type_inc: Image
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doc: Images stored in this collection.
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quantity: '+'
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- name: order_of_images
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neurodata_type_inc: ImageReferences
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doc: Ordered dataset of references to Image objects stored in the parent group.
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Each Image object in the Images group should be stored once and only once, so
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the dataset should have the same length as the number of images.
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quantity: '?'

‎nwb-schema/2.6.0/core/nwb.behavior.yaml‎

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groups:
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- neurodata_type_def: SpatialSeries
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neurodata_type_inc: TimeSeries
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doc: "Direction, e.g., of gaze or travel, or position. The TimeSeries::data field\
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\ is a 2D array storing position or direction relative to some reference frame.\
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\ Array structure: [num measurements] [num dimensions]. Each SpatialSeries has\
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\ a text dataset reference_frame that indicates the zero-position, or the zero-axes\
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\ for direction. For example, if representing gaze direction, 'straight-ahead'\
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\ might be a specific pixel on the monitor, or some other point in space. For\
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\ position data, the 0,0 point might be the top-left corner of an enclosure, as\
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\ viewed from the tracking camera. The unit of data will indicate how to interpret\
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\ SpatialSeries values."
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datasets:
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- name: data
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dtype: numeric
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dims:
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- - num_times
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- - num_times
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- x
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- - num_times
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- x,y
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- - num_times
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- x,y,z
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shape:
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- - null
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- - null
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- 1
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- - null
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- 2
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- - null
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- 3
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doc: 1-D or 2-D array storing position or direction relative to some reference frame.
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attributes:
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- name: unit
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dtype: text
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default_value: meters
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doc: Base unit of measurement for working with the data. The default value
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is 'meters'. Actual stored values are not necessarily stored in these units.
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To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.
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required: false
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- name: reference_frame
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dtype: text
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doc: Description defining what exactly 'straight-ahead' means.
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quantity: '?'
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- neurodata_type_def: BehavioralEpochs
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neurodata_type_inc: NWBDataInterface
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default_name: BehavioralEpochs
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doc: TimeSeries for storing behavioral epochs. The objective of this and the other
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two Behavioral interfaces (e.g. BehavioralEvents and BehavioralTimeSeries) is
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to provide generic hooks for software tools/scripts. This allows a tool/script
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to take the output one specific interface (e.g., UnitTimes) and plot that data
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relative to another data modality (e.g., behavioral events) without having to
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define all possible modalities in advance. Declaring one of these interfaces means
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that one or more TimeSeries of the specified type is published. These TimeSeries
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should reside in a group having the same name as the interface. For example, if
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a BehavioralTimeSeries interface is declared, the module will have one or more
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TimeSeries defined in the module sub-group 'BehavioralTimeSeries'. BehavioralEpochs
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should use IntervalSeries. BehavioralEvents is used for irregular events. BehavioralTimeSeries
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is for continuous data.
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groups:
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- neurodata_type_inc: IntervalSeries
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doc: IntervalSeries object containing start and stop times of epochs.
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quantity: '*'
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- neurodata_type_def: BehavioralEvents
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neurodata_type_inc: NWBDataInterface
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default_name: BehavioralEvents
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doc: TimeSeries for storing behavioral events. See description of <a href="#BehavioralEpochs">BehavioralEpochs</a>
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for more details.
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groups:
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- neurodata_type_inc: TimeSeries
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doc: TimeSeries object containing behavioral events.
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quantity: '*'
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- neurodata_type_def: BehavioralTimeSeries
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neurodata_type_inc: NWBDataInterface
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default_name: BehavioralTimeSeries
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doc: TimeSeries for storing Behavoioral time series data. See description of <a href="#BehavioralEpochs">BehavioralEpochs</a>
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for more details.
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groups:
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- neurodata_type_inc: TimeSeries
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doc: TimeSeries object containing continuous behavioral data.
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quantity: '*'
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- neurodata_type_def: PupilTracking
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neurodata_type_inc: NWBDataInterface
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default_name: PupilTracking
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doc: Eye-tracking data, representing pupil size.
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groups:
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- neurodata_type_inc: TimeSeries
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doc: TimeSeries object containing time series data on pupil size.
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quantity: '+'
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- neurodata_type_def: EyeTracking
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neurodata_type_inc: NWBDataInterface
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default_name: EyeTracking
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doc: Eye-tracking data, representing direction of gaze.
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groups:
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- neurodata_type_inc: SpatialSeries
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doc: SpatialSeries object containing data measuring direction of gaze.
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quantity: '*'
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- neurodata_type_def: CompassDirection
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neurodata_type_inc: NWBDataInterface
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default_name: CompassDirection
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doc: With a CompassDirection interface, a module publishes a SpatialSeries object
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representing a floating point value for theta. The SpatialSeries::reference_frame
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field should indicate what direction corresponds to 0 and which is the direction
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of rotation (this should be clockwise). The si_unit for the SpatialSeries should
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be radians or degrees.
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groups:
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- neurodata_type_inc: SpatialSeries
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doc: SpatialSeries object containing direction of gaze travel.
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quantity: '*'
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- neurodata_type_def: Position
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neurodata_type_inc: NWBDataInterface
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default_name: Position
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doc: Position data, whether along the x, x/y or x/y/z axis.
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groups:
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- neurodata_type_inc: SpatialSeries
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doc: SpatialSeries object containing position data.
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quantity: '+'

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