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

name: core.nwb.base
id: core.nwb.base
imports:
- hdmf-common.base
- hdmf-common.table
- nwb.language
default_prefix: core.nwb.base/
classes:
  NWBData:
    name: NWBData
    description: An abstract data type for a dataset.
    is_a: Data
  TimeSeriesReferenceVectorData:
    name: TimeSeriesReferenceVectorData
    description: 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.
    is_a: VectorData
  Image:
    name: Image
    description: 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)).
    is_a: NWBData
    attributes:
      resolution:
        name: resolution
        description: Pixel resolution of the image, in pixels per centimeter.
        range: float32
      description:
        name: description
        description: Description of the image.
        range: text
      array:
        name: array
        range: Image_Array
  Image_Array:
    name: Image_Array
    is_a: Arraylike
    attributes:
      x:
        name: x
        range: numeric
        required: true
      y:
        name: y
        range: numeric
        required: true
      r, g, b:
        name: r, g, b
        range: numeric
        required: false
        minimum_cardinality: 3
        maximum_cardinality: 3
      r, g, b, a:
        name: r, g, b, a
        range: numeric
        required: false
        minimum_cardinality: 4
        maximum_cardinality: 4
  ImageReferences:
    name: ImageReferences
    description: Ordered dataset of references to Image objects.
    is_a: NWBData
    attributes:
      array:
        name: array
        range: ImageReferences_Array
  ImageReferences_Array:
    name: ImageReferences_Array
    is_a: Arraylike
    attributes:
      num_images:
        name: num_images
        range: Image
        required: true
  NWBContainer:
    name: NWBContainer
    description: An abstract data type for a generic container storing collections
      of data and metadata. Base type for all data and metadata containers.
    is_a: Container
  NWBDataInterface:
    name: NWBDataInterface
    description: An abstract data type for a generic container storing collections
      of data, as opposed to metadata.
    is_a: NWBContainer
  TimeSeries:
    name: TimeSeries
    description: General purpose time series.
    is_a: NWBDataInterface
    attributes:
      description:
        name: description
        description: Description of the time series.
        range: text
      comments:
        name: comments
        description: 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.
        range: text
      data:
        name: data
        description: 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.
        multivalued: false
        range: TimeSeries_data
        required: true
      starting_time:
        name: starting_time
        description: 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.
        multivalued: false
        range: TimeSeries_starting_time
        required: false
      timestamps:
        name: timestamps
        description: Timestamps for samples stored in data, in seconds, relative to
          the common experiment master-clock stored in NWBFile.timestamps_reference_time.
        multivalued: false
        range: TimeSeries_timestamps
        required: false
      control:
        name: control
        description: 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.
        multivalued: false
        range: TimeSeries_control
        required: false
      control_description:
        name: control_description
        description: Description of each control value. Must be present if control
          is present. If present, control_description[0] should describe time points
          where control == 0.
        multivalued: false
        range: TimeSeries_control_description
        required: false
      sync:
        name: sync
        description: 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.
        multivalued: false
        range: TimeSeries_sync
        required: false
  TimeSeries_data:
    name: TimeSeries_data
    description: 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:
      conversion:
        name: conversion
        description: 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.
        range: float32
      offset:
        name: offset
        description: 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.
        range: float32
      resolution:
        name: resolution
        description: 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.
        range: float32
      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' and add 'offset'.
        range: text
      continuity:
        name: continuity
        description: 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.
        range: text
      array:
        name: array
        range: TimeSeries_data_Array
  TimeSeries_data_Array:
    name: TimeSeries_data_Array
    is_a: Arraylike
    attributes:
      num_times:
        name: num_times
        range: AnyType
        required: true
      num_DIM2:
        name: num_DIM2
        range: AnyType
        required: false
      num_DIM3:
        name: num_DIM3
        range: AnyType
        required: false
      num_DIM4:
        name: num_DIM4
        range: AnyType
        required: false
  TimeSeries_starting_time:
    name: TimeSeries_starting_time
    description: 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.
    attributes:
      rate:
        name: rate
        description: Sampling rate, in Hz.
        range: float32
      unit:
        name: unit
        description: Unit of measurement for time, which is fixed to 'seconds'.
        range: text
  TimeSeries_timestamps:
    name: TimeSeries_timestamps
    description: Timestamps for samples stored in data, in seconds, relative to the
      common experiment master-clock stored in NWBFile.timestamps_reference_time.
    attributes:
      interval:
        name: interval
        description: Value is '1'
        range: int32
      unit:
        name: unit
        description: Unit of measurement for timestamps, which is fixed to 'seconds'.
        range: text
      array:
        name: array
        range: TimeSeries_timestamps_Array
  TimeSeries_timestamps_Array:
    name: TimeSeries_timestamps_Array
    is_a: Arraylike
    attributes:
      num_times:
        name: num_times
        range: float64
        required: true
  TimeSeries_control:
    name: TimeSeries_control
    description: 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.
    attributes:
      array:
        name: array
        range: TimeSeries_control_Array
  TimeSeries_control_Array:
    name: TimeSeries_control_Array
    is_a: Arraylike
    attributes:
      num_times:
        name: num_times
        range: uint8
        required: true
  TimeSeries_control_description:
    name: TimeSeries_control_description
    description: Description of each control value. Must be present if control is
      present. If present, control_description[0] should describe time points where
      control == 0.
    attributes:
      array:
        name: array
        range: TimeSeries_control_description_Array
  TimeSeries_control_description_Array:
    name: TimeSeries_control_description_Array
    is_a: Arraylike
    attributes:
      num_control_values:
        name: num_control_values
        range: text
        required: true
  TimeSeries_sync:
    name: TimeSeries_sync
    description: 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.
  ProcessingModule:
    name: ProcessingModule
    description: A collection of processed data.
    is_a: NWBContainer
    attributes:
      description:
        name: description
        description: Description of this collection of processed data.
        range: text
      NWBDataInterface:
        name: NWBDataInterface
        description: Data objects stored in this collection.
        multivalued: true
        range: NWBDataInterface
        required: false
      DynamicTable:
        name: DynamicTable
        description: Tables stored in this collection.
        multivalued: true
        range: DynamicTable
        required: false
  Images:
    name: Images
    description: 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.
    is_a: NWBDataInterface
    attributes:
      description:
        name: description
        description: Description of this collection of images.
        range: text
      Image:
        name: Image
        description: Images stored in this collection.
        multivalued: true
        range: Image
        required: true
      order_of_images:
        name: order_of_images
        description: 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.
        multivalued: false
        range: Images_order_of_images
        required: false
  Images_order_of_images:
    name: Images_order_of_images
    description: 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.
    is_a: ImageReferences