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https://github.com/p2p-ld/nwb-linkml.git
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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
359 lines
14 KiB
YAML
359 lines
14 KiB
YAML
name: core.nwb.base
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id: core.nwb.base
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imports:
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- hdmf-common.base
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- hdmf-common.table
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- nwb.language
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default_prefix: core.nwb.base/
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classes:
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NWBData:
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name: NWBData
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description: An abstract data type for a dataset.
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is_a: Data
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TimeSeriesReferenceVectorData:
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name: TimeSeriesReferenceVectorData
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description: Column storing references to a TimeSeries (rows). For each TimeSeries
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this VectorData column stores the start_index and count to indicate the range
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in time to be selected as well as an object reference to the TimeSeries.
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is_a: VectorData
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Image:
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name: Image
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description: An abstract data type for an image. Shape can be 2-D (x, y), or 3-D
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where the third dimension can have three or four elements, e.g. (x, y, (r, g,
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b)) or (x, y, (r, g, b, a)).
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is_a: NWBData
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attributes:
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resolution:
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name: resolution
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description: Pixel resolution of the image, in pixels per centimeter.
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range: float32
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description:
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name: description
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description: Description of the image.
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range: text
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array:
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name: array
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range: Image_Array
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Image_Array:
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name: Image_Array
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is_a: Arraylike
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attributes:
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x:
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name: x
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range: numeric
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required: true
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y:
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name: y
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range: numeric
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required: true
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r, g, b:
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name: r, g, b
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range: numeric
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required: false
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minimum_cardinality: 3
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maximum_cardinality: 3
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r, g, b, a:
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name: r, g, b, a
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range: numeric
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required: false
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minimum_cardinality: 4
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maximum_cardinality: 4
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ImageReferences:
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name: ImageReferences
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description: Ordered dataset of references to Image objects.
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is_a: NWBData
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attributes:
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array:
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name: array
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range: ImageReferences_Array
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ImageReferences_Array:
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name: ImageReferences_Array
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is_a: Arraylike
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attributes:
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num_images:
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name: num_images
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range: Image
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required: true
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NWBContainer:
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name: NWBContainer
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description: An abstract data type for a generic container storing collections
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of data and metadata. Base type for all data and metadata containers.
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is_a: Container
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NWBDataInterface:
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name: NWBDataInterface
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description: An abstract data type for a generic container storing collections
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of data, as opposed to metadata.
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is_a: NWBContainer
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TimeSeries:
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name: TimeSeries
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description: General purpose time series.
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is_a: NWBDataInterface
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attributes:
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description:
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name: description
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description: Description of the time series.
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range: text
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comments:
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name: comments
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description: Human-readable comments about the TimeSeries. This second descriptive
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field can be used to store additional information, or descriptive information
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if the primary description field is populated with a computer-readable string.
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range: text
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data:
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name: data
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description: Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first
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dimension should always represent time. This can also be used to store binary
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data (e.g., image frames). This can also be a link to data stored in an
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external file.
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multivalued: false
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range: TimeSeries_data
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required: true
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starting_time:
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name: starting_time
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description: Timestamp of the first sample in seconds. When timestamps are
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uniformly spaced, the timestamp of the first sample can be specified and
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all subsequent ones calculated from the sampling rate attribute.
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multivalued: false
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range: TimeSeries_starting_time
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required: false
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timestamps:
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name: timestamps
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description: Timestamps for samples stored in data, in seconds, relative to
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the common experiment master-clock stored in NWBFile.timestamps_reference_time.
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multivalued: false
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range: TimeSeries_timestamps
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required: false
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control:
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name: control
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description: Numerical labels that apply to each time point in data for the
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purpose of querying and slicing data by these values. If present, the length
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of this array should be the same size as the first dimension of data.
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multivalued: false
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range: TimeSeries_control
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required: false
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control_description:
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name: control_description
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description: Description of each control value. Must be present if control
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is present. If present, control_description[0] should describe time points
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where control == 0.
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multivalued: false
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range: TimeSeries_control_description
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required: false
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sync:
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name: sync
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description: Lab-specific time and sync information as provided directly from
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hardware devices and that is necessary for aligning all acquired time information
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to a common timebase. The timestamp array stores time in the common timebase.
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This group will usually only be populated in TimeSeries that are stored
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external to the NWB file, in files storing raw data. Once timestamp data
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is calculated, the contents of 'sync' are mostly for archival purposes.
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multivalued: false
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range: TimeSeries_sync
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required: false
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TimeSeries_data:
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name: TimeSeries_data
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description: Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension
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should always represent time. This can also be used to store binary data (e.g.,
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image frames). This can also be a link to data stored in an external file.
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attributes:
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conversion:
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name: conversion
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description: Scalar to multiply each element in data to convert it to the
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specified 'unit'. If the data are stored in acquisition system units or
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other units that require a conversion to be interpretable, multiply the
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data by 'conversion' to convert the data to the specified 'unit'. e.g. if
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the data acquisition system stores values in this object as signed 16-bit
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integers (int16 range -32,768 to 32,767) that correspond to a 5V range (-2.5V
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to 2.5V), and the data acquisition system gain is 8000X, then the 'conversion'
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multiplier to get from raw data acquisition values to recorded volts is
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2.5/32768/8000 = 9.5367e-9.
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range: float32
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offset:
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name: offset
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description: Scalar to add to the data after scaling by 'conversion' to finalize
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its coercion to the specified 'unit'. Two common examples of this include
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(a) data stored in an unsigned type that requires a shift after scaling
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to re-center the data, and (b) specialized recording devices that naturally
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cause a scalar offset with respect to the true units.
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range: float32
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resolution:
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name: resolution
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description: Smallest meaningful difference between values in data, stored
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in the specified by unit, e.g., the change in value of the least significant
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bit, or a larger number if signal noise is known to be present. If unknown,
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use -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. 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' and add 'offset'.
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range: text
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continuity:
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name: continuity
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description: Optionally describe the continuity of the data. Can be "continuous",
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"instantaneous", or "step". For example, a voltage trace would be "continuous",
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because samples are recorded from a continuous process. An array of lick
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times would be "instantaneous", because the data represents distinct moments
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in time. Times of image presentations would be "step" because the picture
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remains the same until the next timepoint. This field is optional, but is
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useful in providing information about the underlying data. It may inform
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the way this data is interpreted, the way it is visualized, and what analysis
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methods are applicable.
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range: text
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array:
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name: array
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range: TimeSeries_data_Array
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TimeSeries_data_Array:
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name: TimeSeries_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: AnyType
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required: true
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num_DIM2:
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name: num_DIM2
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range: AnyType
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required: false
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num_DIM3:
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name: num_DIM3
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range: AnyType
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required: false
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num_DIM4:
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name: num_DIM4
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range: AnyType
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required: false
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TimeSeries_starting_time:
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name: TimeSeries_starting_time
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description: Timestamp of the first sample in seconds. When timestamps are uniformly
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spaced, the timestamp of the first sample can be specified and all subsequent
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ones calculated from the sampling rate attribute.
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attributes:
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rate:
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name: rate
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description: Sampling rate, in Hz.
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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 for time, which is fixed to 'seconds'.
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range: text
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TimeSeries_timestamps:
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name: TimeSeries_timestamps
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description: Timestamps for samples stored in data, in seconds, relative to the
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common experiment master-clock stored in NWBFile.timestamps_reference_time.
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attributes:
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interval:
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name: interval
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description: Value is '1'
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range: int32
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unit:
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name: unit
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description: Unit of measurement for timestamps, which is fixed to 'seconds'.
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range: text
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array:
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name: array
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range: TimeSeries_timestamps_Array
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TimeSeries_timestamps_Array:
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name: TimeSeries_timestamps_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: float64
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required: true
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TimeSeries_control:
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name: TimeSeries_control
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description: Numerical labels that apply to each time point in data for the purpose
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of querying and slicing data by these values. If present, the length of this
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array should be the same size as the first dimension of data.
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attributes:
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array:
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name: array
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range: TimeSeries_control_Array
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TimeSeries_control_Array:
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name: TimeSeries_control_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: uint8
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required: true
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TimeSeries_control_description:
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name: TimeSeries_control_description
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description: Description of each control value. Must be present if control is
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present. If present, control_description[0] should describe time points where
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control == 0.
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attributes:
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array:
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name: array
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range: TimeSeries_control_description_Array
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TimeSeries_control_description_Array:
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name: TimeSeries_control_description_Array
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is_a: Arraylike
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attributes:
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num_control_values:
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name: num_control_values
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range: text
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required: true
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TimeSeries_sync:
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name: TimeSeries_sync
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description: Lab-specific time and sync information as provided directly from
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hardware devices and that is necessary for aligning all acquired time information
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to a common timebase. The timestamp array stores time in the common timebase.
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This group will usually only be populated in TimeSeries that are stored external
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to the NWB file, in files storing raw data. Once timestamp data is calculated,
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the contents of 'sync' are mostly for archival purposes.
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ProcessingModule:
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name: ProcessingModule
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description: A collection of processed data.
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is_a: NWBContainer
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attributes:
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description:
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name: description
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description: Description of this collection of processed data.
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range: text
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NWBDataInterface:
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name: NWBDataInterface
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description: Data objects stored in this collection.
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multivalued: true
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range: NWBDataInterface
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required: false
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DynamicTable:
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name: DynamicTable
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description: Tables stored in this collection.
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multivalued: true
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range: DynamicTable
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required: false
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Images:
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name: Images
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description: A collection of images with an optional way to specify the order
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of the images using the "order_of_images" dataset. An order must be specified
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if the images are referenced by index, e.g., from an IndexSeries.
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is_a: NWBDataInterface
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attributes:
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description:
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name: description
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description: Description of this collection of images.
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range: text
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Image:
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name: Image
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description: Images stored in this collection.
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multivalued: true
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range: Image
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required: true
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order_of_images:
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name: order_of_images
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description: Ordered dataset of references to Image objects stored in the
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parent group. Each Image object in the Images group should be stored once
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and only once, so the dataset should have the same length as the number
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of images.
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multivalued: false
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range: Images_order_of_images
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required: false
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Images_order_of_images:
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name: Images_order_of_images
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description: Ordered dataset of references to Image objects stored in the parent
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group. Each Image object in the Images group should be stored once and only
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once, so the dataset should have the same length as the number of images.
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is_a: ImageReferences
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