@niivue/niivue 0.40.0 → 0.41.0

package/build/index.d.ts

@@ -313,7 +313,7 @@ type MGH = AnyNumberArray | {
     colormapLabel: LUT;
 };
 type X3D = {
-    positions: number[];
+    positions: Float32Array;
     indices: Int32Array;
     rgba255: number[];
 };
@@ -346,7 +346,7 @@ type NVMeshLayer = {
     frame4D: number;
     nFrame4D: number;
     values: number[];
-    isOutlineBorder: boolean;
+    outlineBorder?: number;
     isTransparentBelowCalMin?: boolean;
     alphaThreshold: boolean;
     base64?: string;
@@ -550,7 +550,6 @@ type ImageFromUrlOptions = {
     cal_max?: number;
     trustCalMinMax?: boolean;
     percentileFrac?: number;
-    visible?: boolean;
     useQFormNotSForm?: boolean;
     alphaThreshold?: boolean;
     colormapNegative?: string;
@@ -577,7 +576,6 @@ type ImageFromFileOptions = {
     trustCalMinMax?: boolean;
     percentileFrac?: number;
     ignoreZeroVoxels?: boolean;
-    visible?: boolean;
     useQFormNotSForm?: boolean;
     colormapNegative?: string;
     imageType?: ImageType;
@@ -594,7 +592,6 @@ type ImageFromBase64 = {
     trustCalMinMax?: boolean;
     percentileFrac?: number;
     ignoreZeroVoxels?: boolean;
-    visible?: boolean;
 };
 type ImageMetadata = {
     id: string;
@@ -609,7 +606,7 @@ type ImageMetadata = {
     dt: number;
     bpv: number;
 };
-declare const NVImageFromUrlOptions: (url: string, urlImageData?: string, name?: string, colormap?: string, opacity?: number, cal_min?: number, cal_max?: number, trustCalMinMax?: boolean, percentileFrac?: number, ignoreZeroVoxels?: boolean, visible?: boolean, useQFormNotSForm?: boolean, colormapNegative?: string, frame4D?: number, imageType?: ImageType, cal_minNeg?: number, cal_maxNeg?: number, colorbarVisible?: boolean, alphaThreshold?: boolean, colormapLabel?: string[]) => ImageFromUrlOptions;
+declare const NVImageFromUrlOptions: (url: string, urlImageData?: string, name?: string, colormap?: string, opacity?: number, cal_min?: number, cal_max?: number, trustCalMinMax?: boolean, percentileFrac?: number, ignoreZeroVoxels?: boolean, useQFormNotSForm?: boolean, colormapNegative?: string, frame4D?: number, imageType?: ImageType, cal_minNeg?: number, cal_maxNeg?: number, colorbarVisible?: boolean, alphaThreshold?: boolean, colormapLabel?: string[]) => ImageFromUrlOptions;
 
 /**
  * a NVImage encapsulates some images data and provides methods to query and operate on images
@@ -633,7 +630,6 @@ declare class NVImage {
     cal_minNeg: number;
     cal_maxNeg: number;
     colorbarVisible: boolean;
-    visible: boolean;
     modulationImage: number | null;
     modulateAlpha: number;
     series: any;
@@ -708,7 +704,6 @@ declare class NVImage {
      * @param trustCalMinMax - whether or not to trust cal_min and cal_max from the nifti header (trusting results in faster loading)
      * @param percentileFrac - the percentile to use for setting the robust range of the display values (smart intensity setting for images with large ranges)
      * @param ignoreZeroVoxels - whether or not to ignore zero voxels in setting the robust range of display values
-     * @param visible - whether or not this image is to be visible
      * @param useQFormNotSForm - give precedence to QForm (Quaternion) or SForm (Matrix)
      * @param colormapNegative - a color map to use for symmetrical negative intensities
      * @param frame4D - volume displayed, 0 indexed, must be less than nFrame4D
@@ -724,7 +719,7 @@ declare class NVImage {
      * @param colorbarVisible - TODO
      * @param colormapLabel - TODO
      */
-    constructor(dataBuffer?: ArrayBuffer | ArrayBuffer[] | null, name?: string, colormap?: string, opacity?: number, pairedImgData?: ArrayBuffer | null, cal_min?: number, cal_max?: number, trustCalMinMax?: boolean, percentileFrac?: number, ignoreZeroVoxels?: boolean, visible?: boolean, useQFormNotSForm?: boolean, colormapNegative?: string, frame4D?: number, imageType?: ImageType, cal_minNeg?: number, cal_maxNeg?: number, colorbarVisible?: boolean, colormapLabel?: LUT | null);
+    constructor(dataBuffer?: ArrayBuffer | ArrayBuffer[] | null, name?: string, colormap?: string, opacity?: number, pairedImgData?: ArrayBuffer | null, cal_min?: number, cal_max?: number, trustCalMinMax?: boolean, percentileFrac?: number, ignoreZeroVoxels?: boolean, useQFormNotSForm?: boolean, colormapNegative?: string, frame4D?: number, imageType?: ImageType, cal_minNeg?: number, cal_maxNeg?: number, colorbarVisible?: boolean, colormapLabel?: LUT | null);
     computeObliqueAngle(mtx44: mat4): number;
     calculateOblique(): void;
     THD_daxes_to_NIFTI(xyzDelta: number[], xyzOrigin: number[], orientSpecific: number[]): void;
@@ -763,7 +758,7 @@ declare class NVImage {
      * factory function to load and return a new NVImage instance from a given URL
      * @returns  NVImage instance
      */
-    static loadFromUrl({ url, urlImgData, headers, name, colormap, opacity, cal_min, cal_max, trustCalMinMax, percentileFrac, ignoreZeroVoxels, visible, useQFormNotSForm, colormapNegative, frame4D, isManifest, limitFrames4D, imageType, colorbarVisible }?: Partial<Omit<ImageFromUrlOptions, 'url'>> & {
+    static loadFromUrl({ url, urlImgData, headers, name, colormap, opacity, cal_min, cal_max, trustCalMinMax, percentileFrac, ignoreZeroVoxels, useQFormNotSForm, colormapNegative, frame4D, isManifest, limitFrames4D, imageType, colorbarVisible }?: Partial<Omit<ImageFromUrlOptions, 'url'>> & {
         url?: string | Uint8Array | ArrayBuffer;
     }): Promise<NVImage>;
     static readFileAsync(file: File, bytesToLoad?: number): Promise<ArrayBuffer>;
@@ -771,7 +766,7 @@ declare class NVImage {
      * factory function to load and return a new NVImage instance from a file in the browser
      */
     static loadFromFile({ file, // file can be an array of file objects or a single file object
-    name, colormap, opacity, urlImgData, cal_min, cal_max, trustCalMinMax, percentileFrac, ignoreZeroVoxels, visible, useQFormNotSForm, colormapNegative, frame4D, limitFrames4D, imageType }: ImageFromFileOptions): Promise<NVImage>;
+    name, colormap, opacity, urlImgData, cal_min, cal_max, trustCalMinMax, percentileFrac, ignoreZeroVoxels, useQFormNotSForm, colormapNegative, frame4D, limitFrames4D, imageType }: ImageFromFileOptions): Promise<NVImage>;
     /**
      * factory function to load and return a new NVImage instance from a base64 encoded string
      *
@@ -779,7 +774,7 @@ declare class NVImage {
      * @example
      * myImage = NVImage.loadFromBase64('SomeBase64String')
      */
-    static loadFromBase64({ base64, name, colormap, opacity, cal_min, cal_max, trustCalMinMax, percentileFrac, ignoreZeroVoxels, visible }: ImageFromBase64): NVImage;
+    static loadFromBase64({ base64, name, colormap, opacity, cal_min, cal_max, trustCalMinMax, percentileFrac, ignoreZeroVoxels }: ImageFromBase64): NVImage;
     /**
      * make a clone of a NVImage instance and return a new NVImage
      * @returns NVImage instance
@@ -918,7 +913,7 @@ type NVConfigOptions = {
     longTouchTimeout: number;
     keyDebounceTime: number;
     isNearestInterpolation: boolean;
-    isAtlasOutline: boolean;
+    atlasOutline: number;
     isRuler: boolean;
     isColorbar: boolean;
     isOrientCube: boolean;
@@ -1358,7 +1353,7 @@ declare class NVMeshLoaders {
     static readTCK(buffer: ArrayBuffer): TCK;
     static readTRK(buffer: ArrayBuffer): TRK;
     static readTxtVTK(buffer: ArrayBuffer): VTK;
-    static readLayer(name: string | undefined, buffer: ArrayBuffer, nvmesh: NVMesh, opacity?: number, colormap?: string, colormapNegative?: string, useNegativeCmap?: boolean, cal_min?: number | null, cal_max?: number | null, isOutlineBorder?: boolean): void;
+    static readLayer(name: string | undefined, buffer: ArrayBuffer, nvmesh: NVMesh, opacity?: number, colormap?: string, colormapNegative?: string, useNegativeCmap?: boolean, cal_min?: number | null, cal_max?: number | null, outlineBorder?: number): void;
     static readSMP(buffer: ArrayBuffer, n_vert: number): Float32Array;
     static readSTC(buffer: ArrayBuffer, n_vert: number): Float32Array;
     static readCURV(buffer: ArrayBuffer, n_vert: number): Float32Array;
@@ -1372,6 +1367,7 @@ declare class NVMeshLoaders {
     static readICO(buffer: ArrayBuffer): DefaultMeshType;
     static readGEO(buffer: ArrayBuffer, isFlipWinding?: boolean): DefaultMeshType;
     static readOFF(buffer: ArrayBuffer): DefaultMeshType;
+    static readOBJMNI(buffer: ArrayBuffer): DefaultMeshType;
     static readOBJ(buffer: ArrayBuffer): DefaultMeshType;
     static readFreeSurfer(buffer: ArrayBuffer): DefaultMeshType;
     static readSRF(buffer: ArrayBuffer): DefaultMeshType;
@@ -1484,7 +1480,7 @@ type NiiVueOptions = {
     loadingText?: string;
     dragAndDropEnabled?: boolean;
     isNearestInterpolation?: boolean;
-    isAtlasOutline?: boolean;
+    atlasOutline?: number;
     isRuler?: boolean;
     isColorbar?: boolean;
     isOrientCube?: boolean;
@@ -1614,6 +1610,7 @@ declare class Niivue {
     position?: vec3;
     extentsMin?: vec3;
     extentsMax?: vec3;
+    private resizeObserver;
     syncOpts: Record<string, unknown>;
     readyForSync: boolean;
     uiData: UIData;
@@ -1845,7 +1842,7 @@ declare class Niivue {
         longTouchTimeout: number;
         keyDebounceTime: number;
         isNearestInterpolation: boolean;
-        isAtlasOutline: boolean;
+        atlasOutline: number;
         isRuler: boolean;
         isColorbar: boolean;
         isOrientCube: boolean;
@@ -2245,6 +2242,17 @@ declare class Niivue {
      * @see {@link https://niivue.github.io/niivue/features/meshes.html|live demo usage}
      */
     setMeshProperty(id: number, key: keyof NVMesh, val: number): void;
+    /**
+     * returns the index of the mesh vertex that is closest to the provided coordinates
+     * @param id - identity of mesh to change
+     * @param Xmm - location in left/right dimension
+     * @param Ymm - location in posterior/anterior dimension
+     * @param Zmm - location in foot/head dimension
+     * @returns the an array where ret[0] is the mesh index and ret[1] is distance from vertex to coordinates
+     * @example niivue.indexNearestXYZmm(niivue.meshes[0].id, -22, 42, 13)
+     * @see {@link https://niivue.github.io/niivue/features/clipplanes.html | live demo usage}
+     */
+    indexNearestXYZmm(mesh: number, Xmm: number, Ymm: number, Zmm: number): number[];
     /**
      * reverse triangle winding of mesh (swap front and back faces)
      * @param id - identity of mesh to change
@@ -2862,7 +2870,7 @@ declare class Niivue {
     drawTextBetween(startXYendXY: number[], str: string, scale?: number, color?: number[] | null): void;
     drawTextBelow(xy: number[], str: string, scale?: number, color?: number[] | null): void;
     updateInterpolation(layer: number, isForceLinear?: boolean): void;
-    setAtlasOutline(isOutline: boolean): void;
+    setAtlasOutline(isOutline: number): void;
     /**
      * select between nearest and linear interpolation for voxel based images
      * @param isNearest - whether nearest neighbor interpolation is used, else linear interpolation