nwb.base.yaml

datasets:
- neurodata_type_def: NWBData
  neurodata_type_inc: Data
  doc: An abstract data type for a dataset.

- neurodata_type_def: TimeSeriesReferenceVectorData
  neurodata_type_inc: VectorData
  default_name: timeseries
  dtype:
  - name: idx_start
    dtype: int32
    doc: Start index into the TimeSeries 'data' and 'timestamp' datasets of the referenced
      TimeSeries. The first dimension of those arrays is always time.
  - name: count
    dtype: int32
    doc: Number of data samples available in this time series, during this epoch
  - name: timeseries
    dtype:
      target_type: TimeSeries
      reftype: object
    doc: The TimeSeries that this index applies to
  doc: Column storing references to a TimeSeries (rows). For each TimeSeries this
    VectorData column stores the start_index and count to indicate the range in time
    to be selected as well as an object reference to the TimeSeries.

- neurodata_type_def: Image
  neurodata_type_inc: NWBData
  dtype: numeric
  dims:
  - - x
    - y
  - - x
    - y
    - r, g, b
  - - x
    - y
    - r, g, b, a
  shape:
  - - null
    - null
  - - null
    - null
    - 3
  - - null
    - null
    - 4
  doc: An abstract data type for an image. Shape can be 2-D (x, y), or 3-D where the
    third dimension can have three or four elements, e.g. (x, y, (r, g, b)) or
    (x, y, (r, g, b, a)).
  attributes:
  - name: resolution
    dtype: float32
    doc: Pixel resolution of the image, in pixels per centimeter.
    required: false
  - name: description
    dtype: text
    doc: Description of the image.
    required: false

- neurodata_type_def: ImageReferences
  neurodata_type_inc: NWBData
  dtype:
    target_type: Image
    reftype: object
  dims:
  - num_images
  shape:
  - null
  doc: Ordered dataset of references to Image objects.

groups:
- neurodata_type_def: NWBContainer
  neurodata_type_inc: Container
  doc: An abstract data type for a generic container storing collections of data and
    metadata. Base type for all data and metadata containers.

- neurodata_type_def: NWBDataInterface
  neurodata_type_inc: NWBContainer
  doc: An abstract data type for a generic container storing collections of data,
    as opposed to metadata.

- neurodata_type_def: TimeSeries
  neurodata_type_inc: NWBDataInterface
  doc: General purpose time series.
  attributes:
  - name: description
    dtype: text
    default_value: no description
    doc: Description of the time series.
    required: false
  - name: comments
    dtype: text
    default_value: no comments
    doc: Human-readable comments about the TimeSeries. This second descriptive field
      can be used to store additional information, or descriptive information if the
      primary description field is populated with a computer-readable string.
    required: false
  datasets:
  - name: data
    dims:
    - - num_times
    - - num_times
      - num_DIM2
    - - num_times
      - num_DIM2
      - num_DIM3
    - - num_times
      - num_DIM2
      - num_DIM3
      - num_DIM4
    shape:
    - - null
    - - null
      - null
    - - null
      - null
      - null
    - - null
      - null
      - null
      - null
    doc: Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension
      should always represent time. This can also be used to store binary data
      (e.g., image frames). This can also be a link to data stored in an external file.
    attributes:
    - name: conversion
      dtype: float32
      default_value: 1.0
      doc: Scalar to multiply each element in data to convert it to the specified 'unit'.
        If the data are stored in acquisition system units or other units
        that require a conversion to be interpretable, multiply the data by 'conversion'
        to convert the data to the specified 'unit'. e.g. if the data acquisition system
        stores values in this object as signed 16-bit integers (int16 range
        -32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data
        acquisition system gain is 8000X, then the 'conversion' multiplier to get from
        raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9.
      required: false
    - name: offset
      dtype: float32
      default_value: 0.0
      doc: Scalar to add to the data after scaling by 'conversion' to finalize its coercion
        to the specified 'unit'. Two common examples of this include (a) data stored in an
        unsigned type that requires a shift after scaling to re-center the data,
        and (b) specialized recording devices that naturally cause a scalar offset with
        respect to the true units.
      required: false
    - name: resolution
      dtype: float32
      default_value: -1.0
      doc: Smallest meaningful difference between values in data, stored in the specified
        by unit, e.g., the change in value of the least significant bit, or a larger
        number if signal noise is known to be present. If unknown, use -1.0.
      required: false
    - name: unit
      dtype: text
      doc: 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' and add 'offset'.
    - name: continuity
      dtype: text
      doc: Optionally describe the continuity of the data. Can be "continuous", "instantaneous", or
        "step". For example, a voltage trace would be "continuous", because samples
        are recorded from a continuous process. An array of lick times would be "instantaneous",
        because the data represents distinct moments in time. Times of image presentations would be
        "step" because the picture remains the same until the next timepoint. This field is optional,
        but is useful in providing information about the underlying data. It may inform the way this
        data is interpreted, the way it is visualized, and what analysis methods are applicable.
      required: false
  - name: starting_time
    dtype: float64
    doc: Timestamp of the first sample in seconds. When timestamps are uniformly
      spaced, the timestamp of the first sample can be specified and all subsequent
      ones calculated from the sampling rate attribute.
    quantity: '?'
    attributes:
    - name: rate
      dtype: float32
      doc: Sampling rate, in Hz.
    - name: unit
      dtype: text
      value: seconds
      doc: Unit of measurement for time, which is fixed to 'seconds'.
  - name: timestamps
    dtype: float64
    dims:
    - num_times
    shape:
    - null
    doc: Timestamps for samples stored in data, in seconds, relative to the
      common experiment master-clock stored in NWBFile.timestamps_reference_time.
    quantity: '?'
    attributes:
    - name: interval
      dtype: int32
      value: 1
      doc: Value is '1'
    - name: unit
      dtype: text
      value: seconds
      doc: Unit of measurement for timestamps, which is fixed to 'seconds'.
  - name: control
    dtype: uint8
    dims:
    - num_times
    shape:
    - null
    doc: Numerical labels that apply to each time point in data for the purpose of
      querying and slicing data by these values. If present, the length of this
      array should be the same size as the first dimension of data.
    quantity: '?'
  - name: control_description
    dtype: text
    dims:
    - num_control_values
    shape:
    - null
    doc: Description of each control value. Must be present if control is present.
      If present, control_description[0] should describe time points where control == 0.
    quantity: '?'
  groups:
  - name: sync
    doc: Lab-specific time and sync information as provided directly from hardware
      devices and that is necessary for aligning all acquired time information to
      a common timebase. The timestamp array stores time in the common timebase.
      This group will usually only be populated in TimeSeries that are
      stored external to the NWB file, in files storing raw data. Once timestamp
      data is calculated, the contents of 'sync' are mostly for archival purposes.
    quantity: '?'

- neurodata_type_def: ProcessingModule
  neurodata_type_inc: NWBContainer
  doc: A collection of processed data.
  attributes:
  - name: description
    dtype: text
    doc: Description of this collection of processed data.
  groups:
  - neurodata_type_inc: NWBDataInterface
    doc: Data objects stored in this collection.
    quantity: '*'
  - neurodata_type_inc: DynamicTable
    doc: Tables stored in this collection.
    quantity: '*'

- neurodata_type_def: Images
  neurodata_type_inc: NWBDataInterface
  default_name: Images
  doc: A collection of images with an optional way to specify the order of the images
    using the "order_of_images" dataset. An order must be specified if the images are
    referenced by index, e.g., from an IndexSeries.
  attributes:
  - name: description
    dtype: text
    doc: Description of this collection of images.
  datasets:
  - neurodata_type_inc: Image
    doc: Images stored in this collection.
    quantity: '+'
  - name: order_of_images
    neurodata_type_inc: ImageReferences
    doc: Ordered dataset of references to Image objects stored in the parent group.
      Each Image object in the Images group should be stored once and only once, so
      the dataset should have the same length as the number of images.
    quantity: '?'