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https://github.com/p2p-ld/nwb-linkml.git
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sneakers-the-rat
4faaa8efe8
or at least all the semantics are present. it's not pretty by any stretch of the imagination
353 lines
12 KiB
YAML
353 lines
12 KiB
YAML
name: core.nwb.image
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id: core.nwb.image
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imports:
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- core.nwb.base
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- nwb.language
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default_prefix: core.nwb.image/
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classes:
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GrayscaleImage:
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name: GrayscaleImage
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description: A grayscale image.
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is_a: Image
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attributes:
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array:
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name: array
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range: GrayscaleImage_Array
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GrayscaleImage_Array:
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name: GrayscaleImage_Array
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is_a: Arraylike
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attributes:
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x:
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name: x
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range: numeric
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required: false
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y:
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name: y
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range: numeric
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required: false
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RGBImage:
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name: RGBImage
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description: A color image.
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is_a: Image
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attributes:
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array:
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name: array
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range: RGBImage_Array
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RGBImage_Array:
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name: RGBImage_Array
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is_a: Arraylike
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attributes:
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x:
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name: x
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range: numeric
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required: false
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y:
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name: y
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range: numeric
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required: false
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r, g, b:
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name: r, g, b
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range: numeric
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required: false
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minimum_cardinality: 3
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maximum_cardinality: 3
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RGBAImage:
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name: RGBAImage
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description: A color image with transparency.
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is_a: Image
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attributes:
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array:
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name: array
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range: RGBAImage_Array
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RGBAImage_Array:
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name: RGBAImage_Array
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is_a: Arraylike
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attributes:
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x:
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name: x
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range: numeric
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required: false
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y:
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name: y
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range: numeric
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required: false
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r, g, b, a:
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name: r, g, b, a
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range: numeric
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required: false
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minimum_cardinality: 4
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maximum_cardinality: 4
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ImageSeries:
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name: ImageSeries
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description: General image data that is common between acquisition and stimulus
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time series. Sometimes the image data is stored in the file in a raw format
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while other times it will be stored as a series of external image files in the
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host file system. The data field will either be binary data, if the data is
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stored in the NWB file, or empty, if the data is stored in an external image
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stack. [frame][x][y] or [frame][x][y][z].
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is_a: TimeSeries
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attributes:
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data:
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name: data
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description: Binary data representing images across frames. If data are stored
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in an external file, this should be an empty 3D array.
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multivalued: false
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range: ImageSeries_data
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required: true
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dimension:
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name: dimension
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description: Number of pixels on x, y, (and z) axes.
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multivalued: false
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range: ImageSeries_dimension
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required: false
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external_file:
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name: external_file
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description: Paths to one or more external file(s). The field is only present
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if format='external'. This is only relevant if the image series is stored
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in the file system as one or more image file(s). This field should NOT be
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used if the image is stored in another NWB file and that file is linked
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to this file.
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multivalued: false
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range: ImageSeries_external_file
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required: false
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format:
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name: format
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description: Format of image. If this is 'external', then the attribute 'external_file'
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contains the path information to the image files. If this is 'raw', then
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the raw (single-channel) binary data is stored in the 'data' dataset. If
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this attribute is not present, then the default format='raw' case is assumed.
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multivalued: false
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range: ImageSeries_format
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required: false
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ImageSeries_data:
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name: ImageSeries_data
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description: Binary data representing images across frames. If data are stored
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in an external file, this should be an empty 3D array.
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attributes:
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array:
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name: array
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range: ImageSeries_data_Array
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ImageSeries_data_Array:
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name: ImageSeries_data_Array
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is_a: Arraylike
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attributes:
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frame:
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name: frame
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range: numeric
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required: true
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x:
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name: x
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range: numeric
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required: true
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y:
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name: y
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range: numeric
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required: true
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z:
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name: z
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range: numeric
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required: false
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ImageSeries_dimension:
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name: ImageSeries_dimension
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description: Number of pixels on x, y, (and z) axes.
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attributes:
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array:
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name: array
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range: ImageSeries_dimension_Array
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ImageSeries_dimension_Array:
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name: ImageSeries_dimension_Array
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is_a: Arraylike
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attributes:
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rank:
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name: rank
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range: int32
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required: true
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ImageSeries_external_file:
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name: ImageSeries_external_file
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description: Paths to one or more external file(s). The field is only present
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if format='external'. This is only relevant if the image series is stored in
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the file system as one or more image file(s). This field should NOT be used
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if the image is stored in another NWB file and that file is linked to this file.
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attributes:
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starting_frame:
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name: starting_frame
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description: Each external image may contain one or more consecutive frames
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of the full ImageSeries. This attribute serves as an index to indicate which
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frames each file contains, to facilitate random access. The 'starting_frame'
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attribute, hence, contains a list of frame numbers within the full ImageSeries
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of the first frame of each file listed in the parent 'external_file' dataset.
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Zero-based indexing is used (hence, the first element will always be zero).
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For example, if the 'external_file' dataset has three paths to files and
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the first file has 5 frames, the second file has 10 frames, and the third
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file has 20 frames, then this attribute will have values [0, 5, 15]. If
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there is a single external file that holds all of the frames of the ImageSeries
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(and so there is a single element in the 'external_file' dataset), then
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this attribute should have value [0].
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range: int32
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array:
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name: array
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range: ImageSeries_external_file_Array
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ImageSeries_external_file_Array:
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name: ImageSeries_external_file_Array
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is_a: Arraylike
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attributes:
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num_files:
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name: num_files
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range: text
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required: true
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ImageSeries_format:
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name: ImageSeries_format
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description: Format of image. If this is 'external', then the attribute 'external_file'
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contains the path information to the image files. If this is 'raw', then the
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raw (single-channel) binary data is stored in the 'data' dataset. If this attribute
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is not present, then the default format='raw' case is assumed.
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ImageMaskSeries:
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name: ImageMaskSeries
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description: An alpha mask that is applied to a presented visual stimulus. The
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'data' array contains an array of mask values that are applied to the displayed
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image. Mask values are stored as RGBA. Mask can vary with time. The timestamps
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array indicates the starting time of a mask, and that mask pattern continues
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until it's explicitly changed.
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is_a: ImageSeries
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OpticalSeries:
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name: OpticalSeries
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description: Image data that is presented or recorded. A stimulus template movie
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will be stored only as an image. When the image is presented as stimulus, additional
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data is required, such as field of view (e.g., how much of the visual field
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the image covers, or how what is the area of the target being imaged). If the
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OpticalSeries represents acquired imaging data, orientation is also important.
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is_a: ImageSeries
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attributes:
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distance:
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name: distance
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description: Distance from camera/monitor to target/eye.
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multivalued: false
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range: OpticalSeries_distance
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required: false
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field_of_view:
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name: field_of_view
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description: Width, height and depth of image, or imaged area, in meters.
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multivalued: false
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range: OpticalSeries_field_of_view
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required: false
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data:
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name: data
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description: Images presented to subject, either grayscale or RGB
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multivalued: false
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range: OpticalSeries_data
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required: true
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orientation:
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name: orientation
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description: Description of image relative to some reference frame (e.g.,
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which way is up). Must also specify frame of reference.
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multivalued: false
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range: OpticalSeries_orientation
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required: false
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OpticalSeries_distance:
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name: OpticalSeries_distance
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description: Distance from camera/monitor to target/eye.
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OpticalSeries_field_of_view:
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name: OpticalSeries_field_of_view
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description: Width, height and depth of image, or imaged area, in meters.
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attributes:
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array:
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name: array
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range: OpticalSeries_field_of_view_Array
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OpticalSeries_field_of_view_Array:
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name: OpticalSeries_field_of_view_Array
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is_a: Arraylike
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attributes:
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width, height:
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name: width, height
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range: float32
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required: false
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minimum_cardinality: 2
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maximum_cardinality: 2
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width, height, depth:
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name: width, height, depth
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range: float32
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required: false
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minimum_cardinality: 3
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maximum_cardinality: 3
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OpticalSeries_data:
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name: OpticalSeries_data
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description: Images presented to subject, either grayscale or RGB
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attributes:
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array:
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name: array
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range: OpticalSeries_data_Array
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OpticalSeries_data_Array:
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name: OpticalSeries_data_Array
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is_a: Arraylike
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attributes:
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frame:
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name: frame
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range: numeric
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required: true
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x:
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name: x
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range: numeric
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required: true
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y:
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name: y
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range: numeric
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required: true
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r, g, b:
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name: r, g, b
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range: numeric
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required: false
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minimum_cardinality: 3
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maximum_cardinality: 3
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OpticalSeries_orientation:
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name: OpticalSeries_orientation
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description: Description of image relative to some reference frame (e.g., which
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way is up). Must also specify frame of reference.
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IndexSeries:
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name: IndexSeries
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description: Stores indices to image frames stored in an ImageSeries. The purpose
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of the IndexSeries is to allow a static image stack to be stored in an Images
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object, and the images in the stack to be referenced out-of-order. This can
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be for the display of individual images, or of movie segments (as a movie is
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simply a series of images). The data field stores the index of the frame in
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the referenced Images object, and the timestamps array indicates when that image
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was displayed.
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is_a: TimeSeries
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attributes:
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data:
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name: data
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description: Index of the image (using zero-indexing) in the linked Images
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object.
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multivalued: false
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range: IndexSeries_data
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required: true
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IndexSeries_data:
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name: IndexSeries_data
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description: Index of the image (using zero-indexing) in the linked Images object.
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attributes:
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conversion:
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name: conversion
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description: This field is unused by IndexSeries.
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range: float32
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resolution:
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name: resolution
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description: This field is unused by IndexSeries.
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range: float32
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offset:
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name: offset
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description: This field is unused by IndexSeries.
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range: float32
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unit:
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name: unit
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description: This field is unused by IndexSeries and has the value N/A.
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range: text
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array:
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name: array
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range: IndexSeries_data_Array
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IndexSeries_data_Array:
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name: IndexSeries_data_Array
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is_a: Arraylike
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attributes:
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num_times:
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name: num_times
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range: uint32
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required: true
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