Class NVImage

a NVImage encapsulates some images data and provides methods to query and operate on images

Constructors

constructor

Methods

applyOptionsUpdate calMinMax clone getImageMetadata getValue getVolumeData saveToDisk saveToUint8Array setVolumeData toUint8Array zeroImage createNiftiArray createNiftiHeader loadFromBase64 loadFromFile loadFromUrl zerosLike

Constructors

constructor

  • new NVImage(dataBuffer?, name?, colormap?, opacity?, pairedImgData?, cal_min?, cal_max?, trustCalMinMax?, percentileFrac?, ignoreZeroVoxels?, useQFormNotSForm?, colormapNegative?, frame4D?, imageType?, cal_minNeg?, cal_maxNeg?, colorbarVisible?, colormapLabel?, colormapType?): NVImage

  • Parameters

    • dataBuffer: ArrayBufferLike | ArrayBuffer[] = null

      an array buffer of image data to load (there are also methods that abstract this more. See loadFromUrl, and loadFromFile)

    • name: string = ''

      a name for this image. Default is an empty string

    • colormap: string = 'gray'

      a color map to use. default is gray

    • opacity: number = 1.0

      the opacity for this image. default is 1

    • pairedImgData: ArrayBuffer = null

      Allows loading formats where header and image are separate files (e.g. nifti.hdr, nifti.img)

    • cal_min: number = NaN

      minimum intensity for color brightness/contrast

    • cal_max: number = NaN

      maximum intensity for color brightness/contrast

    • trustCalMinMax: boolean = true

      whether or not to trust cal_min and cal_max from the nifti header (trusting results in faster loading)

    • percentileFrac: number = 0.02

      the percentile to use for setting the robust range of the display values (smart intensity setting for images with large ranges)

    • ignoreZeroVoxels: boolean = false

      whether or not to ignore zero voxels in setting the robust range of display values

    • useQFormNotSForm: boolean = false

      give precedence to QForm (Quaternion) or SForm (Matrix)

    • colormapNegative: string = ''

      a color map to use for symmetrical negative intensities

    • frame4D: number = 0

      volume displayed, 0 indexed, must be less than nFrame4D

      FIXME the following params are documented but not included in the actual constructor

    • imageType: ImageType = NVIMAGE_TYPE.UNKNOWN

      TODO

    • cal_minNeg: number = NaN

      TODO

    • cal_maxNeg: number = NaN

      TODO

    • colorbarVisible: boolean = true

      TODO

    • colormapLabel: LUT = null

      TODO

    • colormapType: number = 0

    Returns NVImage

Methods

applyOptionsUpdate

  • applyOptionsUpdate(options): void

  • Update options for image

    Parameters

    • options: ImageFromUrlOptions

    Returns void

calMinMax

  • calMinMax(vol?, isBorder?): number[]

  • set contrast/brightness to robust range (2%..98%)

    Parameters

    • vol: number = Number.POSITIVE_INFINITY

      volume for estimate (use -1 to use estimate on all loaded volumes; use INFINITY for current volume)

    • isBorder: boolean = true

      if true (default) only center of volume used for estimate

    Returns number[]

    Sets

    volume brightness and returns array [pct2, pct98, mnScale, mxScale]

    See

    live demo usage

clone

  • clone(): NVImage

  • make a clone of a NVImage instance and return a new NVImage

    Returns NVImage

    NVImage instance

    Example

    myImage = NVImage.loadFromFile(SomeFileObject) // files can be from dialogs or drag and drop
    clonedImage = myImage.clone()

getImageMetadata

  • getImageMetadata(): ImageMetadata

  • get nifti specific metadata about the image

    Returns ImageMetadata

getValue

  • getValue(x, y, z, frame4D?, isReadImaginary?): number

  • Returns voxel intensity at specific native coordinates. Delegates to VolumeUtils.getValue.

    Parameters

    • x: number

      Native X coordinate (0-indexed)

    • y: number

      Native Y coordinate (0-indexed)

    • z: number

      Native Z coordinate (0-indexed)

    • frame4D: number = 0

      4D frame index (0-indexed)

    • isReadImaginary: boolean = false

      Flag to read from imaginary data array

    Returns number

    Scaled voxel intensity

getVolumeData

  • getVolumeData(voxStart?, voxEnd?, dataType?): [TypedVoxelArray, number[]]

  • read a 3D slab of voxels from a volume, specified in RAS coordinates. Delegates to VolumeUtils.getVolumeData.

    Parameters

    • voxStart: number[] = ...

      first row, column and slice (RAS order) for selection

    • voxEnd: number[] = ...

      final row, column and slice (RAS order) for selection

    • dataType: string = 'same'

      array data type. Options: 'same' (default), 'uint8', 'float32', 'scaled', 'normalized', 'windowed'

    Returns [TypedVoxelArray, number[]]

    the an array where ret[0] is the voxel values and ret[1] is dimension of selection

saveToDisk

  • saveToDisk(fnm?, drawing8?): Promise<Uint8Array>

  • save image as NIfTI volume and trigger download. Delegates to ImageWriter.saveToDisk.

    Parameters

    • fnm: string = ''

      Filename for download. If empty, returns data without download.

    • drawing8: Uint8Array = null

      Optional Uint8Array drawing overlay

    Returns Promise<Uint8Array>

    Promise

saveToUint8Array

  • saveToUint8Array(fnm, drawing8?): Promise<Uint8Array>

  • Converts NVImage to NIfTI compliant byte array, potentially compressed. Delegates to ImageWriter.saveToUint8Array.

    Parameters

    • fnm: string

      Filename (determines if compression is needed via .gz suffix)

    • drawing8: Uint8Array = null

      Optional Uint8Array drawing overlay

    Returns Promise<Uint8Array>

    Promise

setVolumeData

  • setVolumeData(voxStart?, voxEnd?, img?): void

  • write a 3D slab of voxels from a volume, specified in RAS coordinates. Delegates to VolumeUtils.setVolumeData. Input slabData is assumed to be in the correct raw data type for the target image.

    Parameters

    • voxStart: number[] = ...

      first row, column and slice (RAS order) for selection

    • voxEnd: number[] = ...

      final row, column and slice (RAS order) for selection

    • img: TypedVoxelArray = ...

      array of voxel values to insert (RAS order, raw data type)

    Returns void

toUint8Array

  • toUint8Array(drawingBytes?): Uint8Array

  • Converts NVImage to NIfTI compliant byte array. Handles potential re-orientation of drawing data. Delegates to ImageWriter.toUint8Array.

    Parameters

    • drawingBytes: Uint8Array = null

      Optional Uint8Array drawing overlay

    Returns Uint8Array

    Uint8Array

zeroImage

  • zeroImage(): void

  • fill a NVImage instance with zeros for the image data

    Returns void

    Example

    myImage = NVImage.loadFromFile(SomeFileObject) // files can be from dialogs or drag and drop
    clonedImageWithZeros = myImage.clone().zeroImage()

StaticcreateNiftiArray

  • createNiftiArray(dims?, pixDims?, affine?, datatypeCode?, img?): Uint8Array

  • Creates a Uint8Array representing a NIFTI file (header + optional image data). Delegates to ImageWriter.createNiftiArray.

    Parameters

    • dims: number[] = ...
    • pixDims: number[] = ...
    • affine: number[] = ...
    • datatypeCode: NiiDataType = NiiDataType.DT_UINT8
    • img: TypedVoxelArray = ...

    Returns Uint8Array

StaticcreateNiftiHeader

  • createNiftiHeader(dims?, pixDims?, affine?, datatypeCode?): NIFTI1

  • Creates a NIFTI1 header object with basic properties. Delegates to ImageWriter.createNiftiHeader.

    Parameters

    • dims: number[] = ...
    • pixDims: number[] = ...
    • affine: number[] = ...
    • datatypeCode: NiiDataType = NiiDataType.DT_UINT8

    Returns NIFTI1

StaticloadFromBase64

  • loadFromBase64(__namedParameters): Promise<NVImage>

  • factory function to load and return a new NVImage instance from a base64 encoded string

    Parameters

    • __namedParameters: ImageFromBase64

    Returns Promise<NVImage>

    NVImage instance

    Example

    myImage = NVImage.loadFromBase64('SomeBase64String')

StaticloadFromFile

  • loadFromFile(__namedParameters): Promise<NVImage>

  • factory function to load and return a new NVImage instance from a file in the browser

    Parameters

    • __namedParameters: ImageFromFileOptions

    Returns Promise<NVImage>

StaticloadFromUrl

  • loadFromUrl(__namedParameters?): Promise<NVImage>

  • factory function to load and return a new NVImage instance from a given URL

    Parameters

    • __namedParameters: Partial<Omit<ImageFromUrlOptions, "url">> & {
          url?: string | ArrayBuffer | Uint8Array;
      } = {}

    Returns Promise<NVImage>

    NVImage instance

StaticzerosLike

  • zerosLike(nvImage, dataType?): NVImage

  • a factory function to make a zero filled image given a NVImage as a reference

    Parameters

    • nvImage: NVImage

      an existing NVImage as a reference

    • dataType: string = 'same'

      the output data type. Options: 'same', 'uint8'

    Returns NVImage

    new NVImage filled with zeros for the image data

    Example

    myImage = NVImage.loadFromFile(SomeFileObject) // files can be from dialogs or drag and drop
    newZeroImage = NVImage.zerosLike(myImage)

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