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
205 lines
8.7 KiB
YAML
205 lines
8.7 KiB
YAML
name: core.nwb.misc
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id: core.nwb.misc
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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/
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classes:
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AbstractFeatureSeries:
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name: AbstractFeatureSeries
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description: Abstract features, such as quantitative descriptions of sensory stimuli.
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The TimeSeries::data field is a 2D array, storing those features (e.g., for
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visual grating stimulus this might be orientation, spatial frequency and contrast).
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Null stimuli (eg, uniform gray) can be marked as being an independent feature
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(eg, 1.0 for gray, 0.0 for actual stimulus) or by storing NaNs for feature values,
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or through use of the TimeSeries::control fields. A set of features is considered
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to persist until the next set of features is defined. The final set of features
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stored should be the null set. This is useful when storing the raw stimulus
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is impractical.
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is_a: TimeSeries
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attributes:
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data:
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name: data
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description: Values of each feature at each time.
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multivalued: false
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range: AbstractFeatureSeries__data
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required: true
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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: false
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range: AbstractFeatureSeries__feature_units
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required: false
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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: false
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range: AbstractFeatureSeries__features
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required: true
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AnnotationSeries:
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name: AnnotationSeries
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description: Stores user annotations made during an experiment. The data[] field
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stores a text array, and timestamps are stored for each annotation (ie, interval=1).
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This is largely an alias to a standard TimeSeries storing a text array but that
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is identifiable as storing annotations in a machine-readable way.
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is_a: TimeSeries
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attributes:
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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: false
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range: AnnotationSeries__data
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required: true
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IntervalSeries:
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name: IntervalSeries
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description: Stores intervals of data. The timestamps field stores the beginning
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and end of intervals. The data field stores whether the interval just started
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(>0 value) or ended (<0 value). Different interval types can be represented
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in the same series by using multiple key values (eg, 1 for feature A, 2 for
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feature B, 3 for feature C, etc). The field data stores an 8-bit integer. This
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is largely an alias of a standard TimeSeries but that is identifiable as representing
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time intervals in a machine-readable way.
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is_a: TimeSeries
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attributes:
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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: false
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range: IntervalSeries__data
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required: true
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DecompositionSeries:
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name: DecompositionSeries
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description: Spectral analysis of a time series, e.g. of an LFP or a speech signal.
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is_a: TimeSeries
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attributes:
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data:
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name: data
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description: Data decomposed into frequency bands.
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multivalued: false
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range: DecompositionSeries__data
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required: true
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metric:
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name: metric
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description: The metric used, e.g. phase, amplitude, power.
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multivalued: false
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range: text
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required: true
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source_channels:
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name: 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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multivalued: false
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range: DecompositionSeries__source_channels
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required: false
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bands:
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name: bands
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description: Table for describing the bands that this series was generated
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from. There should be one row in this table for each band.
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multivalued: false
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range: DecompositionSeries__bands
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required: true
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Units:
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name: Units
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description: Data about spiking units. Event times of observed units (e.g. cell,
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synapse, etc.) should be concatenated and stored in spike_times.
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is_a: DynamicTable
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attributes:
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spike_times_index:
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name: spike_times_index
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description: Index into the spike_times dataset.
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multivalued: false
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range: Units__spike_times_index
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required: false
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spike_times:
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name: spike_times
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description: Spike times for each unit in seconds.
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multivalued: false
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range: Units__spike_times
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required: false
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obs_intervals_index:
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name: obs_intervals_index
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description: Index into the obs_intervals dataset.
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multivalued: false
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range: Units__obs_intervals_index
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required: false
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obs_intervals:
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name: obs_intervals
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description: Observation intervals for each unit.
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multivalued: false
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range: Units__obs_intervals
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required: false
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electrodes_index:
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name: electrodes_index
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description: Index into electrodes.
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multivalued: false
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range: Units__electrodes_index
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required: false
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electrodes:
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name: electrodes
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description: Electrode that each spike unit came from, specified using a DynamicTableRegion.
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multivalued: false
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range: Units__electrodes
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required: false
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electrode_group:
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name: electrode_group
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description: Electrode group that each spike unit came from.
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multivalued: true
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range: ElectrodeGroup
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waveform_mean:
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name: waveform_mean
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description: Spike waveform mean for each spike unit.
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multivalued: false
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range: Units__waveform_mean
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required: false
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waveform_sd:
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name: waveform_sd
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description: Spike waveform standard deviation for each spike unit.
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multivalued: false
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range: Units__waveform_sd
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required: false
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waveforms:
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name: waveforms
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description: Individual waveforms for each spike on each electrode. This is
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a 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
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waveform was recorded from a different electrode. The 'waveforms_index_index'
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column indexes the 'waveforms_index' column to indicate which spike events
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belong to a given unit. For example, if the 'waveforms_index_index' column
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has values [2, 5, 6], then the first 2 elements of the 'waveforms_index'
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column correspond to the 2 spike events of the first unit, the next 3 elements
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of the 'waveforms_index' column correspond to the 3 spike events of the
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second unit, and the next 1 element of the 'waveforms_index' column corresponds
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to the 1 spike event of the third unit. If the 'waveforms_index' column
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has values [3, 6, 8, 10, 12, 13], then the first 3 elements of the 'waveforms'
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column contain the 3 spike waveforms that were recorded from 3 different
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electrodes for the first spike time of the 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
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is the number of spike events. The number of electrodes for each spike event
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should be the same within a given unit. The 'electrodes' column should be
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used to indicate which electrodes are associated with each unit, and the
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order of the waveforms within a given unit x spike event should be in the
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same order as the electrodes referenced in the 'electrodes' column of this
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table. The number of samples for each waveform must be the same.
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multivalued: false
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range: Units__waveforms
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required: false
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waveforms_index:
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name: 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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multivalued: false
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range: Units__waveforms_index
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required: false
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waveforms_index_index:
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name: 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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multivalued: false
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range: Units__waveforms_index_index
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required: false
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