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

name: core.nwb.misc
id: core.nwb.misc
imports:
- core.nwb.base
- hdmf-common.table
- core.nwb.ecephys
- nwb.language
default_prefix: core.nwb.misc/
classes:
  AbstractFeatureSeries:
    name: AbstractFeatureSeries
    description: Abstract features, such as quantitative descriptions of sensory stimuli.
      The TimeSeries::data field is a 2D array, storing those features (e.g., for
      visual grating stimulus this might be orientation, spatial frequency and contrast).
      Null stimuli (eg, uniform gray) can be marked as being an independent feature
      (eg, 1.0 for gray, 0.0 for actual stimulus) or by storing NaNs for feature values,
      or through use of the TimeSeries::control fields. A set of features is considered
      to persist until the next set of features is defined. The final set of features
      stored should be the null set. This is useful when storing the raw stimulus
      is impractical.
    is_a: TimeSeries
    attributes:
      name:
        name: name
        range: string
        required: true
      data:
        name: data
        description: Values of each feature at each time.
        multivalued: false
        range: AbstractFeatureSeries__data
        required: true
      feature_units:
        name: feature_units
        description: Units of each feature.
        multivalued: true
        range: text
        required: false
      features:
        name: features
        description: Description of the features represented in TimeSeries::data.
        multivalued: true
        range: text
        required: true
    tree_root: true
  AbstractFeatureSeries__data:
    name: AbstractFeatureSeries__data
    description: Values of each feature at each time.
    attributes:
      name:
        name: name
        ifabsent: string(data)
        range: string
        required: true
        equals_string: data
      unit:
        name: unit
        description: Since there can be different units for different features, store
          the units in 'feature_units'. The default value for this attribute is "see
          'feature_units'".
        range: text
      array:
        name: array
        range: AbstractFeatureSeries__data__Array
  AbstractFeatureSeries__data__Array:
    name: AbstractFeatureSeries__data__Array
    is_a: Arraylike
    attributes:
      num_times:
        name: num_times
        range: numeric
        required: true
      num_features:
        name: num_features
        range: numeric
        required: false
  AnnotationSeries:
    name: AnnotationSeries
    description: Stores user annotations made during an experiment. The data[] field
      stores a text array, and timestamps are stored for each annotation (ie, interval=1).
      This is largely an alias to a standard TimeSeries storing a text array but that
      is identifiable as storing annotations in a machine-readable way.
    is_a: TimeSeries
    attributes:
      name:
        name: name
        range: string
        required: true
      data:
        name: data
        description: Annotations made during an experiment.
        multivalued: true
        range: text
        required: true
    tree_root: true
  IntervalSeries:
    name: IntervalSeries
    description: Stores intervals of data. The timestamps field stores the beginning
      and end of intervals. The data field stores whether the interval just started
      (>0 value) or ended (<0 value). Different interval types can be represented
      in the same series by using multiple key values (eg, 1 for feature A, 2 for
      feature B, 3 for feature C, etc). The field data stores an 8-bit integer. This
      is largely an alias of a standard TimeSeries but that is identifiable as representing
      time intervals in a machine-readable way.
    is_a: TimeSeries
    attributes:
      name:
        name: name
        range: string
        required: true
      data:
        name: data
        description: Use values >0 if interval started, <0 if interval ended.
        multivalued: true
        range: int8
        required: true
    tree_root: true
  DecompositionSeries:
    name: DecompositionSeries
    description: Spectral analysis of a time series, e.g. of an LFP or a speech signal.
    is_a: TimeSeries
    attributes:
      name:
        name: name
        range: string
        required: true
      data:
        name: data
        description: Data decomposed into frequency bands.
        multivalued: false
        range: DecompositionSeries__data
        required: true
      metric:
        name: metric
        description: The metric used, e.g. phase, amplitude, power.
        multivalued: false
        range: text
        required: true
      source_channels:
        name: source_channels
        description: DynamicTableRegion pointer to the channels that this decomposition
          series was generated from.
        multivalued: false
        range: DecompositionSeries__source_channels
        required: false
      bands:
        name: bands
        description: Table for describing the bands that this series was generated
          from. There should be one row in this table for each band.
        multivalued: false
        range: DynamicTable
        required: true
    tree_root: true
  DecompositionSeries__data:
    name: DecompositionSeries__data
    description: Data decomposed into frequency bands.
    attributes:
      name:
        name: name
        ifabsent: string(data)
        range: string
        required: true
        equals_string: data
      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'.
        range: text
      array:
        name: array
        range: DecompositionSeries__data__Array
  DecompositionSeries__data__Array:
    name: DecompositionSeries__data__Array
    is_a: Arraylike
    attributes:
      num_times:
        name: num_times
        range: numeric
        required: true
      num_channels:
        name: num_channels
        range: numeric
        required: true
      num_bands:
        name: num_bands
        range: numeric
        required: true
  DecompositionSeries__source_channels:
    name: DecompositionSeries__source_channels
    description: DynamicTableRegion pointer to the channels that this decomposition
      series was generated from.
    is_a: DynamicTableRegion
    attributes:
      name:
        name: name
        ifabsent: string(source_channels)
        range: string
        required: true
        equals_string: source_channels
  Units:
    name: Units
    description: Data about spiking units. Event times of observed units (e.g. cell,
      synapse, etc.) should be concatenated and stored in spike_times.
    is_a: DynamicTable
    attributes:
      name:
        name: name
        range: string
        required: true
      spike_times_index:
        name: spike_times_index
        description: Index into the spike_times dataset.
        multivalued: false
        range: Units__spike_times_index
        required: false
      spike_times:
        name: spike_times
        description: Spike times for each unit in seconds.
        multivalued: false
        range: Units__spike_times
        required: false
      obs_intervals_index:
        name: obs_intervals_index
        description: Index into the obs_intervals dataset.
        multivalued: false
        range: Units__obs_intervals_index
        required: false
      obs_intervals:
        name: obs_intervals
        description: Observation intervals for each unit.
        multivalued: false
        range: Units__obs_intervals
        required: false
      electrodes_index:
        name: electrodes_index
        description: Index into electrodes.
        multivalued: false
        range: Units__electrodes_index
        required: false
      electrodes:
        name: electrodes
        description: Electrode that each spike unit came from, specified using a DynamicTableRegion.
        multivalued: false
        range: Units__electrodes
        required: false
      electrode_group:
        name: electrode_group
        description: Electrode group that each spike unit came from.
        multivalued: true
        range: ElectrodeGroup
      waveform_mean:
        name: waveform_mean
        description: Spike waveform mean for each spike unit.
        multivalued: false
        range: Units__waveform_mean
        required: false
      waveform_sd:
        name: waveform_sd
        description: Spike waveform standard deviation for each spike unit.
        multivalued: false
        range: Units__waveform_sd
        required: false
      waveforms:
        name: waveforms
        description: Individual waveforms for each spike on each electrode. This is
          a doubly indexed column. The 'waveforms_index' column indexes which waveforms
          in this column belong to the same spike event for a given unit, where each
          waveform was recorded from a different electrode. The 'waveforms_index_index'
          column indexes the 'waveforms_index' column to indicate which spike events
          belong to a given unit. For example, if the 'waveforms_index_index' column
          has values [2, 5, 6], then the first 2 elements of the 'waveforms_index'
          column correspond to the 2 spike events of the first unit, the next 3 elements
          of the 'waveforms_index' column correspond to the 3 spike events of the
          second unit, and the next 1 element of the 'waveforms_index' column corresponds
          to the 1 spike event of the third unit. If the 'waveforms_index' column
          has values [3, 6, 8, 10, 12, 13], then the first 3 elements of the 'waveforms'
          column contain the 3 spike waveforms that were recorded from 3 different
          electrodes for the first spike time of the first unit. See https://nwb-schema.readthedocs.io/en/stable/format_description.html#doubly-ragged-arrays
          for a graphical representation of this example. When there is only one electrode
          for each unit (i.e., each spike time is associated with a single waveform),
          then the 'waveforms_index' column will have values 1, 2, ..., N, where N
          is the number of spike events. The number of electrodes for each spike event
          should be the same within a given unit. The 'electrodes' column should be
          used to indicate which electrodes are associated with each unit, and the
          order of the waveforms within a given unit x spike event should be in the
          same order as the electrodes referenced in the 'electrodes' column of this
          table. The number of samples for each waveform must be the same.
        multivalued: false
        range: Units__waveforms
        required: false
      waveforms_index:
        name: waveforms_index
        description: Index into the waveforms dataset. One value for every spike event.
          See 'waveforms' for more detail.
        multivalued: false
        range: Units__waveforms_index
        required: false
      waveforms_index_index:
        name: waveforms_index_index
        description: Index into the waveforms_index dataset. One value for every unit
          (row in the table). See 'waveforms' for more detail.
        multivalued: false
        range: Units__waveforms_index_index
        required: false
    tree_root: true
  Units__spike_times_index:
    name: Units__spike_times_index
    description: Index into the spike_times dataset.
    is_a: VectorIndex
    attributes:
      name:
        name: name
        ifabsent: string(spike_times_index)
        range: string
        required: true
        equals_string: spike_times_index
  Units__spike_times:
    name: Units__spike_times
    description: Spike times for each unit in seconds.
    is_a: VectorData
    attributes:
      name:
        name: name
        ifabsent: string(spike_times)
        range: string
        required: true
        equals_string: spike_times
      resolution:
        name: resolution
        description: The smallest possible difference between two spike times. Usually
          1 divided by the acquisition sampling rate from which spike times were extracted,
          but could be larger if the acquisition time series was downsampled or smaller
          if the acquisition time series was smoothed/interpolated and it is possible
          for the spike time to be between samples.
        range: float64
  Units__obs_intervals_index:
    name: Units__obs_intervals_index
    description: Index into the obs_intervals dataset.
    is_a: VectorIndex
    attributes:
      name:
        name: name
        ifabsent: string(obs_intervals_index)
        range: string
        required: true
        equals_string: obs_intervals_index
  Units__obs_intervals:
    name: Units__obs_intervals
    description: Observation intervals for each unit.
    is_a: VectorData
    attributes:
      name:
        name: name
        ifabsent: string(obs_intervals)
        range: string
        required: true
        equals_string: obs_intervals
  Units__electrodes_index:
    name: Units__electrodes_index
    description: Index into electrodes.
    is_a: VectorIndex
    attributes:
      name:
        name: name
        ifabsent: string(electrodes_index)
        range: string
        required: true
        equals_string: electrodes_index
  Units__electrodes:
    name: Units__electrodes
    description: Electrode that each spike unit came from, specified using a DynamicTableRegion.
    is_a: DynamicTableRegion
    attributes:
      name:
        name: name
        ifabsent: string(electrodes)
        range: string
        required: true
        equals_string: electrodes
  Units__waveform_mean:
    name: Units__waveform_mean
    description: Spike waveform mean for each spike unit.
    is_a: VectorData
    attributes:
      name:
        name: name
        ifabsent: string(waveform_mean)
        range: string
        required: true
        equals_string: waveform_mean
      sampling_rate:
        name: sampling_rate
        description: Sampling rate, in hertz.
        range: float32
      unit:
        name: unit
        description: Unit of measurement. This value is fixed to 'volts'.
        range: text
  Units__waveform_sd:
    name: Units__waveform_sd
    description: Spike waveform standard deviation for each spike unit.
    is_a: VectorData
    attributes:
      name:
        name: name
        ifabsent: string(waveform_sd)
        range: string
        required: true
        equals_string: waveform_sd
      sampling_rate:
        name: sampling_rate
        description: Sampling rate, in hertz.
        range: float32
      unit:
        name: unit
        description: Unit of measurement. This value is fixed to 'volts'.
        range: text
  Units__waveforms:
    name: Units__waveforms
    description: Individual waveforms for each spike on each electrode. This is a
      doubly indexed column. The 'waveforms_index' column indexes which waveforms
      in this column belong to the same spike event for a given unit, where each waveform
      was recorded from a different electrode. The 'waveforms_index_index' column
      indexes the 'waveforms_index' column to indicate which spike events belong to
      a given unit. For example, if the 'waveforms_index_index' column has values
      [2, 5, 6], then the first 2 elements of the 'waveforms_index' column correspond
      to the 2 spike events of the first unit, the next 3 elements of the 'waveforms_index'
      column correspond to the 3 spike events of the second unit, and the next 1 element
      of the 'waveforms_index' column corresponds to the 1 spike event of the third
      unit. If the 'waveforms_index' column has values [3, 6, 8, 10, 12, 13], then
      the first 3 elements of the 'waveforms' column contain the 3 spike waveforms
      that were recorded from 3 different electrodes for the first spike time of the
      first unit. See https://nwb-schema.readthedocs.io/en/stable/format_description.html#doubly-ragged-arrays
      for a graphical representation of this example. When there is only one electrode
      for each unit (i.e., each spike time is associated with a single waveform),
      then the 'waveforms_index' column will have values 1, 2, ..., N, where N is
      the number of spike events. The number of electrodes for each spike event should
      be the same within a given unit. The 'electrodes' column should be used to indicate
      which electrodes are associated with each unit, and the order of the waveforms
      within a given unit x spike event should be in the same order as the electrodes
      referenced in the 'electrodes' column of this table. The number of samples for
      each waveform must be the same.
    is_a: VectorData
    attributes:
      name:
        name: name
        ifabsent: string(waveforms)
        range: string
        required: true
        equals_string: waveforms
      sampling_rate:
        name: sampling_rate
        description: Sampling rate, in hertz.
        range: float32
      unit:
        name: unit
        description: Unit of measurement. This value is fixed to 'volts'.
        range: text
  Units__waveforms_index:
    name: Units__waveforms_index
    description: Index into the waveforms dataset. One value for every spike event.
      See 'waveforms' for more detail.
    is_a: VectorIndex
    attributes:
      name:
        name: name
        ifabsent: string(waveforms_index)
        range: string
        required: true
        equals_string: waveforms_index
  Units__waveforms_index_index:
    name: Units__waveforms_index_index
    description: Index into the waveforms_index dataset. One value for every unit
      (row in the table). See 'waveforms' for more detail.
    is_a: VectorIndex
    attributes:
      name:
        name: name
        ifabsent: string(waveforms_index_index)
        range: string
        required: true
        equals_string: waveforms_index_index