@niivue/niivue 0.55.0 → 0.57.0

package/README.md

@@ -23,7 +23,7 @@ The command `npm run demo` will minify the project and locally host all of the [
 
 [Click here for the docs web page](https://niivue.github.io/niivue/devdocs/)
 
-# Projects and People using NiiVue
+# NiiVue Users
 
 - Analysis of Functional NeuroImages (AFNI) [Scientific and Statistical Computing Core](https://afni.nimh.nih.gov/) (National Institutes of Health)
 - [BOOSTLET.js](https://boostlet.org/) image processing plugins work with NiiVue.
@@ -35,11 +35,14 @@ The command `npm run demo` will minify the project and locally host all of the [
 - [Digital Brain Bank](https://elifesciences.org/articles/73153) for navigating MRI datasets
 - FMRIB's Software Library (FSL) [Wellcome Centre for Integrative Neuroimaging](https://www.win.ox.ac.uk/) (University of Oxford)
 - FreeSurfer [Laboratories for Computational Neuroimaging](https://lcn.martinos.org/) (Massachusetts General Hospital) uses NiiVue for [FreeBrowse](https://github.com/freesurfer/freebrowse)
+- [lazybids-ui](https://github.com/lazybids/lazybids-ui) is a web-based user interface for interacting with BIDS datasets.
 - [OpenNeuro.org](https://openneuro.org) uses NiiVue to visualize datasets
 - [neurodesk](https://www.neurodesk.org/) uses NiiVue for their [QSMxT Quantitative Susceptibility Mapping toolbox](https://github.com/QSMxT/QSMxT-UI)
+- [neurosift](https://github.com/flatironinstitute/neurosift) provides NWB visualization and DANDI exploration
 - [Neuroinformatics Research and Development Group](http://neuroinformatics.uw.edu/) embeds NiiVue in [tractoscope](https://github.com/nrdg/tractoscope)
-- [nilearn](https://nilearn.github.io/stable/index.html) is extending [ipyniivue](https://github.com/niivue/ipyniivue)
+- [NiiVueReader](https://github.com/BrunoDG/NiiVueReader) by Bruno Dias demonstrates a full stack deployment. 
 - [niivue-vscode](https://github.com/niivue/niivue-vscode) is a VSCode extension for displaying images
+- [nilearn](https://nilearn.github.io/stable/index.html) is extending [ipyniivue](https://github.com/niivue/ipyniivue)
 - [QuantCo](https://www.quantco.com/) is using NiiVue in medical imaging workflows
 - [FSL Clinical](https://fslclinical.com/) is using NiiVue in brain imaging reports
 - [brain2print](https://brain2print.org/) (from the NiiVue team) uses NiiVue for showing both volume data and converted meshes

package/build/index.d.ts

@@ -152,13 +152,13 @@ declare class NVLabel3D {
     style: NVLabel3DStyle;
     points?: number[] | number[][];
     anchor: LabelAnchorPoint;
-    onClick?: (label: NVLabel3D) => void;
+    onClick?: (label: NVLabel3D, e?: MouseEvent) => void;
     /**
      * @param text - The text of the label
      * @param style - The style of the label
      * @param points - An array of points label for label lines
      */
-    constructor(text: string, style: NVLabel3DStyle, points?: number[] | number[][], anchor?: LabelAnchorPoint, onClick?: (label: NVLabel3D) => void);
+    constructor(text: string, style: NVLabel3DStyle, points?: number[] | number[][], anchor?: LabelAnchorPoint, onClick?: (label: NVLabel3D, e?: MouseEvent) => void);
 }
 
 /**
@@ -390,7 +390,7 @@ declare class NVImage {
      */
     constructor(dataBuffer?: ArrayBuffer | ArrayBuffer[] | ArrayBufferLike | 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, colormapType?: number);
     init(dataBuffer?: ArrayBuffer | ArrayBuffer[] | ArrayBufferLike | 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, colormapType?: number, imgRaw?: ArrayBuffer | ArrayBufferLike | null): void;
-    static new(dataBuffer?: ArrayBuffer | ArrayBuffer[] | ArrayBufferLike | 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, colormapType?: number): Promise<NVImage>;
+    static new(dataBuffer: ArrayBuffer | ArrayBuffer[] | ArrayBufferLike | 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, colormapType: number, zarrData: null | unknown): Promise<NVImage>;
     computeObliqueAngle(mtx44: mat4): number;
     float32V1asRGBA(inImg: Float32Array): Uint8Array;
     loadImgV1(isFlipX?: boolean, isFlipY?: boolean, isFlipZ?: boolean): boolean;
@@ -403,6 +403,7 @@ declare class NVImage {
     readNPZ(buffer: ArrayBuffer): Promise<ArrayBuffer>;
     imageDataFromArrayBuffer(buffer: ArrayBuffer): Promise<ImageData>;
     readBMP(buffer: ArrayBuffer): Promise<ArrayBuffer>;
+    readZARR(buffer: ArrayBuffer, zarrData: unknown): Promise<Uint8Array>;
     readVMR(buffer: ArrayBuffer): ArrayBuffer;
     readFIB(buffer: ArrayBuffer): Promise<[ArrayBuffer, Float32Array]>;
     readSRC(buffer: ArrayBuffer): Promise<ArrayBuffer>;
@@ -775,8 +776,10 @@ type NVConfigOptions = {
     isAlphaClipDark: boolean;
     gradientOrder: number;
     gradientOpacity: number;
+    renderSilhouette: number;
     gradientAmount: number;
     invertScrollDirection: boolean;
+    is2DSliceShader: boolean;
 };
 declare const DEFAULT_OPTIONS: NVConfigOptions;
 type SceneData = {
@@ -1204,6 +1207,9 @@ type NVMeshLayer = {
     colormapType?: number;
     base64?: string;
     colorbarVisible?: boolean;
+    showLegend?: boolean;
+    labels?: NVLabel3D[];
+    atlasValues?: AnyNumberArray;
 };
 declare const NVMeshLayerDefaults: {
     colormap: string;
@@ -1217,6 +1223,8 @@ declare const NVMeshLayerDefaults: {
     cal_maxNeg: number;
     colormapType: COLORMAP_TYPE;
     values: number[];
+    useNegativeCmap: boolean;
+    showLegend: boolean;
 };
 declare class NVMeshFromUrlOptions {
     url: string;
@@ -1330,6 +1338,7 @@ declare class NVMesh {
     updateFibers(gl: WebGL2RenderingContext): void;
     indexNearestXYZmm(Xmm: number, Ymm: number, Zmm: number): number[];
     unloadMesh(gl: WebGL2RenderingContext): void;
+    scalars2RGBA(rgba: Uint8ClampedArray, layer: NVMeshLayer, scalars: AnyNumberArray, isNegativeCmap?: boolean): Uint8ClampedArray;
     blendColormap(u8: Uint8Array, additiveRGBA: Uint8Array, layer: NVMeshLayer, mn: number, mx: number, lut: Uint8ClampedArray, invert?: boolean): void;
     updateMesh(gl: WebGL2RenderingContext): void;
     reverseFaces(gl: WebGL2RenderingContext): void;
@@ -1498,6 +1507,7 @@ type Graph = {
     lineColor?: number[];
     textColor?: number[];
     lineThickness?: number;
+    gridLineThickness?: number;
     lineAlpha?: number;
     lines?: number[][];
     selectedColumn?: number;
@@ -1565,6 +1575,8 @@ type UIData = {
     lastTwoTouchDistance: number;
     multiTouchGesture: boolean;
     dpr?: number;
+    max2D?: number;
+    max3D?: number;
     windowX: number;
     windowY: number;
 };
@@ -1617,6 +1629,7 @@ declare class Niivue {
     overlayTexture: WebGLTexture | null;
     overlayTextureID: WebGLTexture | null;
     sliceMMShader?: Shader;
+    slice2DShader?: Shader;
     sliceV1Shader?: Shader;
     orientCubeShader?: Shader;
     orientCubeShaderVAO: WebGLVertexArrayObject | null;
@@ -1702,6 +1715,11 @@ declare class Niivue {
     VOLUME_ID: number;
     DISTANCE_FROM_CAMERA: number;
     graph: Graph;
+    customLayout: Array<{
+        sliceType: SLICE_TYPE;
+        position: [number, number, number, number];
+        sliceMM?: number;
+    }>;
     meshShaders: Array<{
         Name: string;
         Frag: string;
@@ -2127,6 +2145,50 @@ declare class Niivue {
      * @see {@link https://niivue.github.io/niivue/features/layout.html | live demo usage}
      */
     setHeroImage(fraction: number): void;
+    /**
+     * Set a custom slice layout. This overrides the built-in layouts.
+     * @param layout - Array of layout specifications for each slice view
+     * @example
+     * niivue.setCustomLayout([
+     *     // Left 50% - Sag
+     *     {sliceType: 2, position: [0, 0, 0.5, 1.0]},
+     *     // Top right - Cor
+     *     {sliceType: 1, position: [0.5, 0, 0.5, 0.5]},
+     *     // Bottom right - Ax
+     *     {sliceType: 0, position: [0.5, 0.5, 0.5, 0.5]}
+     *   ])
+     *
+     * produces:
+     * +----------------+----------------+
+     * |                |                |
+     * |                |     coronal    |
+     * |                |                |
+     * |                |                |
+     * |   sagittal     +----------------+
+     * |                |                |
+     * |                |     axial      |
+     * |                |                |
+     * |                |                |
+     * +----------------+----------------+
+     */
+    setCustomLayout(layout: Array<{
+        sliceType: SLICE_TYPE;
+        position: [number, number, number, number];
+        sliceMM?: number;
+    }>): void;
+    /**
+     * Clear custom layout and rely on built-in layouts
+     */
+    clearCustomLayout(): void;
+    /**
+     * Get the current custom layout if set
+     * @returns The current custom layout or null if using built-in layouts
+     */
+    getCustomLayout(): Array<{
+        sliceType: SLICE_TYPE;
+        position: [number, number, number, number];
+        sliceMM?: number;
+    }> | null;
     /**
      * control whether 2D slices use radiological or neurological convention.
      * @param isRadiologicalConvention - new display convention
@@ -2525,11 +2587,12 @@ declare class Niivue {
     /**
      * set volume rendering opacity influence of the gradient magnitude
      * @param gradientOpacity - amount of gradient magnitude influence on opacity (0..1), default 0 (no-influence)
+     * @param renderSilhouette - make core transparent to enhance rims (0..1), default 0 (no-influence)
      * @example
      * niivue.setGradientOpacity(0.6);
      * @see {@link https://niivue.github.io/niivue/features/gradient.opacity.html | live demo usage}
      */
-    setGradientOpacity(gradientOpacity?: number): Promise<void>;
+    setGradientOpacity(gradientOpacity?: number, renderSilhouette?: number): Promise<void>;
     overlayRGBA(volume: NVImage): Uint8ClampedArray;
     vox2mm(XYZ: number[], mtx: mat4): vec3;
     /**
@@ -2695,7 +2758,9 @@ declare class Niivue {
      * @see {@link https://niivue.github.io/niivue/features/cactus.html | live demo usage}
      */
     refreshDrawing(isForceRedraw?: boolean, useClickToSegmentBitmap?: boolean): void;
+    r8Tex2D(texID: WebGLTexture | null, activeID: number, dims: number[], isInit?: boolean): WebGLTexture | null;
     r8Tex(texID: WebGLTexture | null, activeID: number, dims: number[], isInit?: boolean): WebGLTexture | null;
+    rgbaTex2D(texID: WebGLTexture | null, activeID: number, dims: number[], data?: Uint8Array | null, isFlipVertical?: boolean): WebGLTexture | null;
     rgbaTex(texID: WebGLTexture | null, activeID: number, dims: number[], isInit?: boolean): WebGLTexture | null;
     rgba16Tex(texID: WebGLTexture | null, activeID: number, dims: number[], isInit?: boolean): WebGLTexture | null;
     requestCORSIfNotSameOrigin(img: HTMLImageElement, url: string): void;
@@ -3069,6 +3134,7 @@ declare class Niivue {
      * @see {@link https://niivue.github.io/niivue/features/mosaics.html | live demo usage}
      */
     drawMosaic(mosaicStr: string): void;
+    calculateWidthHeight(sliceType: number, volScale: number[], containerWidth: number, containerHeight: number): [number, number];
     drawSceneCore(): string | void;
     drawScene(): string | void;
     get gl(): WebGL2RenderingContext;