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

name: core.nwb.image
id: core.nwb.image
imports:
- core.nwb.base
- nwb.language
default_prefix: core.nwb.image/
classes:
  GrayscaleImage:
    name: GrayscaleImage
    description: A grayscale image.
    is_a: Image
    attributes:
      array:
        name: array
        range: GrayscaleImage_Array
  GrayscaleImage_Array:
    name: GrayscaleImage_Array
    is_a: Arraylike
    attributes:
      x:
        name: x
        range: numeric
        required: false
      y:
        name: y
        range: numeric
        required: false
  RGBImage:
    name: RGBImage
    description: A color image.
    is_a: Image
    attributes:
      array:
        name: array
        range: RGBImage_Array
  RGBImage_Array:
    name: RGBImage_Array
    is_a: Arraylike
    attributes:
      x:
        name: x
        range: numeric
        required: false
      y:
        name: y
        range: numeric
        required: false
      r, g, b:
        name: r, g, b
        range: numeric
        required: false
        minimum_cardinality: 3
        maximum_cardinality: 3
  RGBAImage:
    name: RGBAImage
    description: A color image with transparency.
    is_a: Image
    attributes:
      array:
        name: array
        range: RGBAImage_Array
  RGBAImage_Array:
    name: RGBAImage_Array
    is_a: Arraylike
    attributes:
      x:
        name: x
        range: numeric
        required: false
      y:
        name: y
        range: numeric
        required: false
      r, g, b, a:
        name: r, g, b, a
        range: numeric
        required: false
        minimum_cardinality: 4
        maximum_cardinality: 4
  ImageSeries:
    name: ImageSeries
    description: General image data that is common between acquisition and stimulus
      time series. Sometimes the image data is stored in the file in a raw format
      while other times it will be stored as a series of external image files in the
      host file system. The data field will either be binary data, if the data is
      stored in the NWB file, or empty, if the data is stored in an external image
      stack. [frame][x][y] or [frame][x][y][z].
    is_a: TimeSeries
    attributes:
      data:
        name: data
        description: Binary data representing images across frames. If data are stored
          in an external file, this should be an empty 3D array.
        multivalued: false
        range: ImageSeries_data
        required: true
      dimension:
        name: dimension
        description: Number of pixels on x, y, (and z) axes.
        multivalued: false
        range: ImageSeries_dimension
        required: false
      external_file:
        name: external_file
        description: Paths to one or more external file(s). The field is only present
          if format='external'. This is only relevant if the image series is stored
          in the file system as one or more image file(s). This field should NOT be
          used if the image is stored in another NWB file and that file is linked
          to this file.
        multivalued: false
        range: ImageSeries_external_file
        required: false
      format:
        name: format
        description: Format of image. If this is 'external', then the attribute 'external_file'
          contains the path information to the image files. If this is 'raw', then
          the raw (single-channel) binary data is stored in the 'data' dataset. If
          this attribute is not present, then the default format='raw' case is assumed.
        multivalued: false
        range: ImageSeries_format
        required: false
  ImageSeries_data:
    name: ImageSeries_data
    description: Binary data representing images across frames. If data are stored
      in an external file, this should be an empty 3D array.
    attributes:
      array:
        name: array
        range: ImageSeries_data_Array
  ImageSeries_data_Array:
    name: ImageSeries_data_Array
    is_a: Arraylike
    attributes:
      frame:
        name: frame
        range: numeric
        required: true
      x:
        name: x
        range: numeric
        required: true
      y:
        name: y
        range: numeric
        required: true
      z:
        name: z
        range: numeric
        required: false
  ImageSeries_dimension:
    name: ImageSeries_dimension
    description: Number of pixels on x, y, (and z) axes.
    attributes:
      array:
        name: array
        range: ImageSeries_dimension_Array
  ImageSeries_dimension_Array:
    name: ImageSeries_dimension_Array
    is_a: Arraylike
    attributes:
      rank:
        name: rank
        range: int32
        required: true
  ImageSeries_external_file:
    name: ImageSeries_external_file
    description: Paths to one or more external file(s). The field is only present
      if format='external'. This is only relevant if the image series is stored in
      the file system as one or more image file(s). This field should NOT be used
      if the image is stored in another NWB file and that file is linked to this file.
    attributes:
      starting_frame:
        name: starting_frame
        description: Each external image may contain one or more consecutive frames
          of the full ImageSeries. This attribute serves as an index to indicate which
          frames each file contains, to facilitate random access. The 'starting_frame'
          attribute, hence, contains a list of frame numbers within the full ImageSeries
          of the first frame of each file listed in the parent 'external_file' dataset.
          Zero-based indexing is used (hence, the first element will always be zero).
          For example, if the 'external_file' dataset has three paths to files and
          the first file has 5 frames, the second file has 10 frames, and the third
          file has 20 frames, then this attribute will have values [0, 5, 15]. If
          there is a single external file that holds all of the frames of the ImageSeries
          (and so there is a single element in the 'external_file' dataset), then
          this attribute should have value [0].
        range: int32
      array:
        name: array
        range: ImageSeries_external_file_Array
  ImageSeries_external_file_Array:
    name: ImageSeries_external_file_Array
    is_a: Arraylike
    attributes:
      num_files:
        name: num_files
        range: text
        required: true
  ImageSeries_format:
    name: ImageSeries_format
    description: Format of image. If this is 'external', then the attribute 'external_file'
      contains the path information to the image files. If this is 'raw', then the
      raw (single-channel) binary data is stored in the 'data' dataset. If this attribute
      is not present, then the default format='raw' case is assumed.
  ImageMaskSeries:
    name: ImageMaskSeries
    description: An alpha mask that is applied to a presented visual stimulus. The
      'data' array contains an array of mask values that are applied to the displayed
      image. Mask values are stored as RGBA. Mask can vary with time. The timestamps
      array indicates the starting time of a mask, and that mask pattern continues
      until it's explicitly changed.
    is_a: ImageSeries
  OpticalSeries:
    name: OpticalSeries
    description: Image data that is presented or recorded. A stimulus template movie
      will be stored only as an image. When the image is presented as stimulus, additional
      data is required, such as field of view (e.g., how much of the visual field
      the image covers, or how what is the area of the target being imaged). If the
      OpticalSeries represents acquired imaging data, orientation is also important.
    is_a: ImageSeries
    attributes:
      distance:
        name: distance
        description: Distance from camera/monitor to target/eye.
        multivalued: false
        range: OpticalSeries_distance
        required: false
      field_of_view:
        name: field_of_view
        description: Width, height and depth of image, or imaged area, in meters.
        multivalued: false
        range: OpticalSeries_field_of_view
        required: false
      data:
        name: data
        description: Images presented to subject, either grayscale or RGB
        multivalued: false
        range: OpticalSeries_data
        required: true
      orientation:
        name: orientation
        description: Description of image relative to some reference frame (e.g.,
          which way is up). Must also specify frame of reference.
        multivalued: false
        range: OpticalSeries_orientation
        required: false
  OpticalSeries_distance:
    name: OpticalSeries_distance
    description: Distance from camera/monitor to target/eye.
  OpticalSeries_field_of_view:
    name: OpticalSeries_field_of_view
    description: Width, height and depth of image, or imaged area, in meters.
    attributes:
      array:
        name: array
        range: OpticalSeries_field_of_view_Array
  OpticalSeries_field_of_view_Array:
    name: OpticalSeries_field_of_view_Array
    is_a: Arraylike
    attributes:
      width, height:
        name: width, height
        range: float32
        required: false
        minimum_cardinality: 2
        maximum_cardinality: 2
      width, height, depth:
        name: width, height, depth
        range: float32
        required: false
        minimum_cardinality: 3
        maximum_cardinality: 3
  OpticalSeries_data:
    name: OpticalSeries_data
    description: Images presented to subject, either grayscale or RGB
    attributes:
      array:
        name: array
        range: OpticalSeries_data_Array
  OpticalSeries_data_Array:
    name: OpticalSeries_data_Array
    is_a: Arraylike
    attributes:
      frame:
        name: frame
        range: numeric
        required: true
      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
  OpticalSeries_orientation:
    name: OpticalSeries_orientation
    description: Description of image relative to some reference frame (e.g., which
      way is up). Must also specify frame of reference.
  IndexSeries:
    name: IndexSeries
    description: Stores indices to image frames stored in an ImageSeries. The purpose
      of the IndexSeries is to allow a static image stack to be stored in an Images
      object, and the images in the stack to be referenced out-of-order. This can
      be for the display of individual images, or of movie segments (as a movie is
      simply a series of images). The data field stores the index of the frame in
      the referenced Images object, and the timestamps array indicates when that image
      was displayed.
    is_a: TimeSeries
    attributes:
      data:
        name: data
        description: Index of the image (using zero-indexing) in the linked Images
          object.
        multivalued: false
        range: IndexSeries_data
        required: true
  IndexSeries_data:
    name: IndexSeries_data
    description: Index of the image (using zero-indexing) in the linked Images object.
    attributes:
      conversion:
        name: conversion
        description: This field is unused by IndexSeries.
        range: float32
      resolution:
        name: resolution
        description: This field is unused by IndexSeries.
        range: float32
      offset:
        name: offset
        description: This field is unused by IndexSeries.
        range: float32
      unit:
        name: unit
        description: This field is unused by IndexSeries and has the value N/A.
        range: text
      array:
        name: array
        range: IndexSeries_data_Array
  IndexSeries_data_Array:
    name: IndexSeries_data_Array
    is_a: Arraylike
    attributes:
      num_times:
        name: num_times
        range: uint32
        required: true