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

name: core.nwb.image
id: core.nwb.image
imports:
- core.nwb.base
- core.nwb.device
- nwb.language
default_prefix: core.nwb.image/
classes:
  GrayscaleImage:
    name: GrayscaleImage
    description: A grayscale image.
    is_a: Image
    attributes:
      name:
        name: name
        range: string
        required: true
      array:
        name: array
        range: GrayscaleImage__Array
    tree_root: true
  GrayscaleImage__Array:
    name: GrayscaleImage__Array
    is_a: Arraylike
    attributes:
      x:
        name: x
        range: numeric
        required: true
      y:
        name: y
        range: numeric
        required: true
  RGBImage:
    name: RGBImage
    description: A color image.
    is_a: Image
    attributes:
      name:
        name: name
        range: string
        required: true
      array:
        name: array
        range: RGBImage__Array
    tree_root: true
  RGBImage__Array:
    name: RGBImage__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: true
        minimum_cardinality: 3
        maximum_cardinality: 3
  RGBAImage:
    name: RGBAImage
    description: A color image with transparency.
    is_a: Image
    attributes:
      name:
        name: name
        range: string
        required: true
      array:
        name: array
        range: RGBAImage__Array
    tree_root: true
  RGBAImage__Array:
    name: RGBAImage__Array
    is_a: Arraylike
    attributes:
      x:
        name: x
        range: numeric
        required: true
      y:
        name: y
        range: numeric
        required: true
      r, g, b, a:
        name: r, g, b, a
        range: numeric
        required: true
        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:
      name:
        name: name
        range: string
        required: true
      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: true
        range: int32
        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: true
        range: text
        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: text
        required: false
    tree_root: true
  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:
      name:
        name: name
        ifabsent: string(data)
        range: string
        required: true
        equals_string: data
      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
  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
    attributes:
      name:
        name: name
        range: string
        required: true
    tree_root: true
  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:
      name:
        name: name
        range: string
        required: true
      distance:
        name: distance
        description: Distance from camera/monitor to target/eye.
        multivalued: false
        range: float32
        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: text
        required: false
    tree_root: true
  OpticalSeries__field_of_view:
    name: OpticalSeries__field_of_view
    description: Width, height and depth of image, or imaged area, in meters.
    attributes:
      name:
        name: name
        ifabsent: string(field_of_view)
        range: string
        required: true
        equals_string: field_of_view
      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:
      name:
        name: name
        ifabsent: string(data)
        range: string
        required: true
        equals_string: data
      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
  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:
      name:
        name: name
        range: string
        required: true
      data:
        name: data
        description: Index of the image (using zero-indexing) in the linked Images
          object.
        multivalued: true
        range: uint32
        required: true
    tree_root: true