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sneakers-the-rat
4faaa8efe8
or at least all the semantics are present. it's not pretty by any stretch of the imagination
614 lines
22 KiB
YAML
614 lines
22 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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- nwb.language
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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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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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array:
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name: array
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range: AbstractFeatureSeries_feature_units_Array
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AbstractFeatureSeries_feature_units_Array:
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name: AbstractFeatureSeries_feature_units_Array
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is_a: Arraylike
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attributes:
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num_features:
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name: num_features
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range: text
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required: true
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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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array:
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name: array
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range: AbstractFeatureSeries_features_Array
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AbstractFeatureSeries_features_Array:
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name: AbstractFeatureSeries_features_Array
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is_a: Arraylike
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attributes:
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num_features:
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name: num_features
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range: text
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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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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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array:
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name: array
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range: AnnotationSeries_data_Array
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AnnotationSeries_data_Array:
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name: AnnotationSeries_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: text
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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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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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array:
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name: array
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range: IntervalSeries_data_Array
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IntervalSeries_data_Array:
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name: IntervalSeries_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: int8
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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: DecompositionSeries_metric
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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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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_metric:
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name: DecompositionSeries_metric
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description: The metric used, e.g. phase, amplitude, power.
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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: false
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range: DecompositionSeries_bands_band_name
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required: true
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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_name:
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name: DecompositionSeries_bands_band_name
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description: Name of the band, e.g. theta.
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is_a: VectorData
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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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attributes:
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array:
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name: array
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range: DecompositionSeries_bands_band_limits_Array
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DecompositionSeries_bands_band_limits_Array:
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name: DecompositionSeries_bands_band_limits_Array
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is_a: Arraylike
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attributes:
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num_bands:
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name: num_bands
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range: float32
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required: false
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low, high:
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name: low, high
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range: float32
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required: false
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minimum_cardinality: 2
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maximum_cardinality: 2
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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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attributes:
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array:
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name: array
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range: DecompositionSeries_bands_band_mean_Array
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DecompositionSeries_bands_band_mean_Array:
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name: DecompositionSeries_bands_band_mean_Array
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is_a: Arraylike
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attributes:
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num_bands:
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name: num_bands
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range: float32
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required: true
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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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attributes:
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array:
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name: array
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range: DecompositionSeries_bands_band_stdev_Array
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DecompositionSeries_bands_band_stdev_Array:
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name: DecompositionSeries_bands_band_stdev_Array
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is_a: Arraylike
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attributes:
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num_bands:
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name: num_bands
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range: float32
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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: false
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range: Units_electrode_group
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required: false
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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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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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attributes:
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array:
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name: array
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range: Units_obs_intervals_Array
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Units_obs_intervals_Array:
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name: Units_obs_intervals_Array
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is_a: Arraylike
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attributes:
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num_intervals:
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name: num_intervals
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range: float64
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required: false
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start|end:
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name: start|end
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range: float64
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required: false
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minimum_cardinality: 2
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maximum_cardinality: 2
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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_electrode_group:
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name: Units_electrode_group
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description: Electrode group that each spike unit came from.
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is_a: VectorData
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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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array:
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name: array
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range: Units_waveform_mean_Array
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Units_waveform_mean_Array:
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name: Units_waveform_mean_Array
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is_a: Arraylike
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attributes:
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num_units:
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name: num_units
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range: float32
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required: true
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num_samples:
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name: num_samples
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range: float32
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required: true
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num_electrodes:
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name: num_electrodes
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range: float32
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required: false
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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:
|
|
name: unit
|
|
description: Unit of measurement. This value is fixed to 'volts'.
|
|
range: text
|
|
array:
|
|
name: array
|
|
range: Units_waveform_sd_Array
|
|
Units_waveform_sd_Array:
|
|
name: Units_waveform_sd_Array
|
|
is_a: Arraylike
|
|
attributes:
|
|
num_units:
|
|
name: num_units
|
|
range: float32
|
|
required: true
|
|
num_samples:
|
|
name: num_samples
|
|
range: float32
|
|
required: true
|
|
num_electrodes:
|
|
name: num_electrodes
|
|
range: float32
|
|
required: false
|
|
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:
|
|
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
|
|
array:
|
|
name: array
|
|
range: Units_waveforms_Array
|
|
Units_waveforms_Array:
|
|
name: Units_waveforms_Array
|
|
is_a: Arraylike
|
|
attributes:
|
|
num_waveforms:
|
|
name: num_waveforms
|
|
range: numeric
|
|
required: false
|
|
num_samples:
|
|
name: num_samples
|
|
range: numeric
|
|
required: false
|
|
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
|
|
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
|