mirror of
https://github.com/p2p-ld/nwb-linkml.git
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sneakers-the-rat
be21325123
- split off generated subclasses into "include" files, not sure if that's good, but in any case we have them separable now. - more work on cleanly un-nesting scalar and 1D-vector data into attributes and lists, respectively - brought the pydantic generator in-repo to do a bunch of overrides
277 lines
10 KiB
YAML
277 lines
10 KiB
YAML
name: core.nwb.misc.include
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id: core.nwb.misc.include
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imports:
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- core.nwb.base
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- hdmf-common.table
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- core.nwb.ecephys
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- nwb.language
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- core.nwb.misc.include
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- core.nwb.misc
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default_prefix: core.nwb.misc.include/
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classes:
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AbstractFeatureSeries__data:
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name: AbstractFeatureSeries__data
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description: Values of each feature at each time.
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attributes:
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unit:
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name: unit
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description: Since there can be different units for different features, store
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the units in 'feature_units'. The default value for this attribute is "see
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'feature_units'".
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range: text
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array:
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name: array
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range: AbstractFeatureSeries__data__Array
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AbstractFeatureSeries__data__Array:
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name: AbstractFeatureSeries__data__Array
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is_a: Arraylike
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attributes:
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num_times:
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name: num_times
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range: numeric
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required: true
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num_features:
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name: num_features
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range: numeric
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required: false
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AbstractFeatureSeries__feature_units:
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name: AbstractFeatureSeries__feature_units
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description: Units of each feature.
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attributes:
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feature_units:
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name: feature_units
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description: Units of each feature.
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multivalued: true
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range: text
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required: false
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AbstractFeatureSeries__features:
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name: AbstractFeatureSeries__features
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description: Description of the features represented in TimeSeries::data.
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attributes:
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features:
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name: features
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description: Description of the features represented in TimeSeries::data.
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multivalued: true
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range: text
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required: true
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AnnotationSeries__data:
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name: AnnotationSeries__data
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description: Annotations made during an experiment.
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attributes:
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resolution:
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name: resolution
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description: Smallest meaningful difference between values in data. Annotations
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have no units, so the value is fixed to -1.0.
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range: float32
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unit:
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name: unit
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description: Base unit of measurement for working with the data. Annotations
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have no units, so the value is fixed to 'n/a'.
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range: text
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data:
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name: data
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description: Annotations made during an experiment.
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multivalued: true
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range: text
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required: true
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IntervalSeries__data:
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name: IntervalSeries__data
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description: Use values >0 if interval started, <0 if interval ended.
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attributes:
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resolution:
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name: resolution
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description: Smallest meaningful difference between values in data. Annotations
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have no units, so the value is fixed to -1.0.
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range: float32
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unit:
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name: unit
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description: Base unit of measurement for working with the data. Annotations
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have no units, so the value is fixed to 'n/a'.
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range: text
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data:
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name: data
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description: Use values >0 if interval started, <0 if interval ended.
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multivalued: true
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range: int8
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required: true
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DecompositionSeries__data:
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name: DecompositionSeries__data
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description: Data decomposed into frequency bands.
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attributes:
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unit:
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name: unit
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description: Base unit of measurement for working with the data. Actual stored
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values are not necessarily stored in these units. To access the data in
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these units, multiply 'data' by 'conversion'.
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range: text
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array:
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name: array
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range: DecompositionSeries__data__Array
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DecompositionSeries__data__Array:
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name: DecompositionSeries__data__Array
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is_a: Arraylike
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attributes:
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num_times:
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name: num_times
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range: numeric
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required: false
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num_channels:
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name: num_channels
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range: numeric
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required: false
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num_bands:
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name: num_bands
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range: numeric
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required: false
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DecompositionSeries__source_channels:
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name: DecompositionSeries__source_channels
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description: DynamicTableRegion pointer to the channels that this decomposition
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series was generated from.
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is_a: DynamicTableRegion
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DecompositionSeries__bands:
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name: DecompositionSeries__bands
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description: Table for describing the bands that this series was generated from.
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There should be one row in this table for each band.
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is_a: DynamicTable
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attributes:
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band_name:
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name: band_name
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description: Name of the band, e.g. theta.
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multivalued: true
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range: text
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band_limits:
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name: band_limits
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description: Low and high limit of each band in Hz. If it is a Gaussian filter,
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use 2 SD on either side of the center.
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multivalued: false
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range: DecompositionSeries__bands__band_limits
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required: true
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band_mean:
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name: band_mean
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description: The mean Gaussian filters, in Hz.
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multivalued: false
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range: DecompositionSeries__bands__band_mean
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required: true
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band_stdev:
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name: band_stdev
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description: The standard deviation of Gaussian filters, in Hz.
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multivalued: false
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range: DecompositionSeries__bands__band_stdev
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required: true
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DecompositionSeries__bands__band_limits:
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name: DecompositionSeries__bands__band_limits
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description: Low and high limit of each band in Hz. If it is a Gaussian filter,
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use 2 SD on either side of the center.
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is_a: VectorData
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DecompositionSeries__bands__band_mean:
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name: DecompositionSeries__bands__band_mean
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description: The mean Gaussian filters, in Hz.
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is_a: VectorData
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DecompositionSeries__bands__band_stdev:
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name: DecompositionSeries__bands__band_stdev
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description: The standard deviation of Gaussian filters, in Hz.
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is_a: VectorData
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Units__spike_times_index:
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name: Units__spike_times_index
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description: Index into the spike_times dataset.
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is_a: VectorIndex
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Units__spike_times:
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name: Units__spike_times
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description: Spike times for each unit in seconds.
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is_a: VectorData
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attributes:
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resolution:
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name: resolution
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description: The smallest possible difference between two spike times. Usually
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1 divided by the acquisition sampling rate from which spike times were extracted,
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but could be larger if the acquisition time series was downsampled or smaller
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if the acquisition time series was smoothed/interpolated and it is possible
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for the spike time to be between samples.
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range: float64
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Units__obs_intervals_index:
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name: Units__obs_intervals_index
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description: Index into the obs_intervals dataset.
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is_a: VectorIndex
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Units__obs_intervals:
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name: Units__obs_intervals
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description: Observation intervals for each unit.
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is_a: VectorData
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Units__electrodes_index:
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name: Units__electrodes_index
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description: Index into electrodes.
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is_a: VectorIndex
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Units__electrodes:
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name: Units__electrodes
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description: Electrode that each spike unit came from, specified using a DynamicTableRegion.
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is_a: DynamicTableRegion
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Units__waveform_mean:
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name: Units__waveform_mean
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description: Spike waveform mean for each spike unit.
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is_a: VectorData
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attributes:
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sampling_rate:
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name: sampling_rate
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description: Sampling rate, in hertz.
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range: float32
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unit:
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name: unit
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description: Unit of measurement. This value is fixed to 'volts'.
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range: text
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Units__waveform_sd:
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name: Units__waveform_sd
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description: Spike waveform standard deviation for each spike unit.
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is_a: VectorData
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attributes:
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sampling_rate:
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name: sampling_rate
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description: Sampling rate, in hertz.
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range: float32
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unit:
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name: unit
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description: Unit of measurement. This value is fixed to 'volts'.
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range: text
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Units__waveforms:
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name: Units__waveforms
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description: Individual waveforms for each spike on each electrode. This is a
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doubly indexed column. The 'waveforms_index' column indexes which waveforms
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in this column belong to the same spike event for a given unit, where each waveform
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was recorded from a different electrode. The 'waveforms_index_index' column
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indexes the 'waveforms_index' column to indicate which spike events belong to
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a given unit. For example, if the 'waveforms_index_index' column has values
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[2, 5, 6], then the first 2 elements of the 'waveforms_index' column correspond
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to the 2 spike events of the first unit, the next 3 elements of the 'waveforms_index'
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column correspond to the 3 spike events of the second unit, and the next 1 element
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of the 'waveforms_index' column corresponds to the 1 spike event of the third
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unit. If the 'waveforms_index' column has values [3, 6, 8, 10, 12, 13], then
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the first 3 elements of the 'waveforms' column contain the 3 spike waveforms
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that were recorded from 3 different electrodes for the first spike time of the
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first unit. See https://nwb-schema.readthedocs.io/en/stable/format_description.html#doubly-ragged-arrays
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for a graphical representation of this example. When there is only one electrode
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for each unit (i.e., each spike time is associated with a single waveform),
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then the 'waveforms_index' column will have values 1, 2, ..., N, where N is
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the number of spike events. The number of electrodes for each spike event should
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be the same within a given unit. The 'electrodes' column should be used to indicate
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which electrodes are associated with each unit, and the order of the waveforms
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within a given unit x spike event should be in the same order as the electrodes
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referenced in the 'electrodes' column of this table. The number of samples for
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each waveform must be the same.
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is_a: VectorData
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attributes:
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sampling_rate:
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name: sampling_rate
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description: Sampling rate, in hertz.
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range: float32
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unit:
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name: unit
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description: Unit of measurement. This value is fixed to 'volts'.
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range: text
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Units__waveforms_index:
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name: Units__waveforms_index
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description: Index into the waveforms dataset. One value for every spike event.
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See 'waveforms' for more detail.
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is_a: VectorIndex
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Units__waveforms_index_index:
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name: Units__waveforms_index_index
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description: Index into the waveforms_index dataset. One value for every unit
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(row in the table). See 'waveforms' for more detail.
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is_a: VectorIndex
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