Class NVImage

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

Constructors

constructor

Methods

applyOptionsUpdate calMinMax clone getImageMetadata getVolumeData setVolumeData toNiivueObject3D toUint8Array zeroImage createNiftiArray 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?): NVImage

  • Parameters

    • dataBuffer: ArrayBuffer | 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

    Returns NVImage

Methods

applyOptionsUpdate

  • applyOptionsUpdate(options): void

  • Update options for image

    Parameters

    • options: ImageFromUrlOptions

    Returns void

calMinMax

  • calMinMax(vol?): 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)

    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

getVolumeData

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

  • read a 3D slab of voxels from a volume

    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

    See

    live demo usage

setVolumeData

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

  • write a 3D slab of voxels from a volume

    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)

    Returns void

    See

    live demo usage

toNiivueObject3D

  • toNiivueObject3D(id, gl): NiivueObject3D

  • Parameters

    • id: number

      id of 3D Object (is this the base volume or an overlay?)

    • gl: WebGL2RenderingContext

      WebGL rendering context

    Returns NiivueObject3D

    new 3D object in model space

toUint8Array

  • toUint8Array(drawingBytes?): Uint8Array

  • Converts NVImage to NIfTI compliant byte array

    Parameters

    • drawingBytes: Uint8Array = null

    Returns 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

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

    Parameters

    • dims: number[] = ...
    • pixDims: number[] = ...
    • affine: number[] = ...
    • datatypeCode: number = 2
    • img: Uint8Array = ...

    Returns Uint8Array

    NVImage instance

    Example

    myImage = NVImage.loadFromBase64('SomeBase64String')

StaticloadFromBase64

  • loadFromBase64(__namedParameters): NVImage

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

    Parameters

    • __namedParameters: ImageFromBase64

    Returns 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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