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
    attributes:
      name:
        name: name
        range: string
        required: true
    tree_root: true
  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
    attributes:
      name:
        name: name
        range: string
        required: true
    tree_root: true
  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:
      name:
        name: name
        range: string
        required: true
      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
    tree_root: true
  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:
      name:
        name: name
        range: string
        required: true
      array:
        name: array
        range: ImageReferences__Array
    tree_root: true
  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
    attributes:
      name:
        name: name
        range: string
        required: true
    tree_root: true
  NWBDataInterface:
    name: NWBDataInterface
    description: An abstract data type for a generic container storing collections
      of data, as opposed to metadata.
    is_a: NWBContainer
    attributes:
      name:
        name: name
        range: string
        required: true
    tree_root: true
  TimeSeries:
    name: TimeSeries
    description: General purpose time series.
    is_a: NWBDataInterface
    attributes:
      name:
        name: name
        range: string
        required: true
      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: true
        range: float64
        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: true
        range: uint8
        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: true
        range: text
        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
    tree_root: true
  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:
      name:
        name: name
        ifabsent: string(data)
        range: string
        required: true
        equals_string: data
      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:
      name:
        name: name
        ifabsent: string(starting_time)
        range: string
        required: true
        equals_string: starting_time
      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
      value:
        name: value
        range: float64
        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.
    attributes:
      name:
        name: name
        ifabsent: string(sync)
        range: string
        required: true
        equals_string: sync
  ProcessingModule:
    name: ProcessingModule
    description: A collection of processed data.
    is_a: NWBContainer
    attributes:
      name:
        name: name
        range: string
        required: true
      description:
        name: description
        description: Description of this collection of processed data.
        range: text
      nwb_data_interface:
        name: nwb_data_interface
        description: Data objects stored in this collection.
        multivalued: true
        range: NWBDataInterface
        required: false
      dynamic_table:
        name: dynamic_table
        description: Tables stored in this collection.
        multivalued: true
        range: DynamicTable
        required: false
    tree_root: true
  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:
      name:
        name: name
        range: string
        required: true
      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
    tree_root: true
  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
    attributes:
      name:
        name: name
        ifabsent: string(order_of_images)
        range: string
        required: true
        equals_string: order_of_images