@niivue/niivue 0.63.0 → 0.65.0

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package/build/niivue/index.d.ts

@@ -1,5 +1,5 @@
-import { a as TRACT, b as TT, c as TRX, d as TCK, e as TRK, V as VTK, N as NVMesh, f as NVMeshLayer, A as ANNOT, D as DefaultMeshType, M as MZ3, g as MGH, X as X3D, G as GII, L as LUT, h as SyncOpts, i as DRAG_MODE, j as NVImage, I as ImageFromUrlOptions, k as LoadFromUrlParams, S as SLICE_TYPE, l as DragReleaseParams, m as NVDocument, n as NVConfigOptions, o as Scene, C as ColorMap, p as LegacyConnectome, E as ExportDocumentData, F as FreeSurferConnectome, q as NVConnectomeNode, r as Connectome, s as NiftiHeader, t as NiiDataType, u as MouseEventConfig, v as TouchEventConfig, w as NVLabel3D, x as NVLabel3DStyle, y as LabelAnchorPoint } from '../nvdocument-5GNlbB1d.js';
-export { Z as COLORMAP_TYPE, R as CompletedAngle, Q as CompletedMeasurement, a4 as ConnectomeOptions, _ as DEFAULT_OPTIONS, a0 as DocumentData, $ as INITIAL_SCENE_DATA, P as LabelLineTerminator, O as LabelTextAlignment, a5 as LegacyNodes, Y as MULTIPLANAR_TYPE, a3 as NVConnectomeEdge, K as NVImageFromUrlOptions, z as NVMeshFromUrlOptions, B as NVMeshLayerDefaults, a7 as NiiVueLocation, a6 as NiiVueLocationValue, U as PEN_TYPE, a2 as Point, W as SHOW_RENDER, a1 as Volume, J as cmapper, H as colortables } from '../nvdocument-5GNlbB1d.js';
+import { a as TRACT, b as TT, V as ValuesArray, c as TRX, d as TCK, e as TRK, f as VTK, N as NVMesh, g as NVMeshLayer, A as ANNOT, D as DefaultMeshType, M as MZ3, h as MGH, X as X3D, G as GII, L as LUT, i as SyncOpts, j as DRAG_MODE, k as NVImage, I as ImageFromUrlOptions, l as LoadFromUrlParams, S as SLICE_TYPE, m as DragReleaseParams, n as NVDocument, o as NVConfigOptions, p as Scene, C as ColorMap, q as LegacyConnectome, E as ExportDocumentData, F as FreeSurferConnectome, r as NVConnectomeNode, s as Connectome, t as NiftiHeader, u as NiiDataType, v as MouseEventConfig, w as TouchEventConfig, x as NVLabel3D, y as NVLabel3DStyle, z as LabelAnchorPoint } from '../nvdocument-Bma8slLJ.js';
+export { _ as COLORMAP_TYPE, U as CompletedAngle, R as CompletedMeasurement, a5 as ConnectomeOptions, $ as DEFAULT_OPTIONS, a1 as DocumentData, a0 as INITIAL_SCENE_DATA, Q as LabelLineTerminator, P as LabelTextAlignment, a6 as LegacyNodes, Z as MULTIPLANAR_TYPE, a4 as NVConnectomeEdge, O as NVImageFromUrlOptions, B as NVMeshFromUrlOptions, H as NVMeshLayerDefaults, a8 as NiiVueLocation, a7 as NiiVueLocationValue, W as PEN_TYPE, a3 as Point, Y as SHOW_RENDER, a2 as Volume, K as cmapper, J as colortables } from '../nvdocument-Bma8slLJ.js';
 import { mat4, vec3, vec4, vec2 } from 'gl-matrix';
 import 'nifti-reader-js';
 
@@ -126,6 +126,21 @@ declare class NVUtilities {
 declare class NVMeshLoaders {
     static readTRACT(buffer: ArrayBuffer): TRACT;
     static readTT(buffer: ArrayBuffer): Promise<TT>;
+    /**
+     * Assemble dpg from a map-of-groups into a ValuesArray ordered by groups[].
+     *
+     * @param dpgMap - map from groupId -> ValuesArray (entries for that group)
+     * @param groups - ValuesArray describing groups; groups[i].id defines the ordering
+     * @returns ValuesArray - one entry per tag where vals is the concatenation of each group's vals in groups[] order
+     *
+     * @throws Error when:
+     *  - groups is empty or missing
+     *  - any group in groups is missing from dpgMap
+     *  - any group contains duplicate entries for a tag
+     *  - tag coverage differs between groups (missing tag in any group)
+     *  - any entry has invalid/unconvertible vals
+     */
+    static assembleDpgFromMap(dpgMap: Record<string, ValuesArray>, groups: ValuesArray): ValuesArray;
     static readTRX(buffer: ArrayBuffer): Promise<TRX>;
     static readTXT(buffer: ArrayBuffer, n_count?: number): Float32Array;
     static readTSF(buffer: ArrayBuffer, n_vert?: number): Float32Array;
@@ -156,7 +171,7 @@ declare class NVMeshLoaders {
     static readSTL(buffer: ArrayBuffer): DefaultMeshType;
     static decimateLayerVertices(nVertLayer: number, nVertMesh: number): number;
     static readNII2(buffer: ArrayBuffer, n_vert?: number, anatomicalStructurePrimary?: string): Promise<Int32Array | Float32Array | Int16Array | Uint8Array>;
-    static readNII(buffer: ArrayBuffer, n_vert?: number, anatomicalStructurePrimary?: string): Promise<Float32Array | Uint8Array | Int32Array | Int16Array>;
+    static readNII(buffer: ArrayBuffer, pts: Float32Array, anatomicalStructurePrimary?: string): Promise<Float32Array | Uint8Array | Int32Array | Int16Array>;
     static readMGH(buffer: ArrayBuffer, n_vert?: number, isReadColortables?: boolean): Promise<MGH>;
     static readX3D(buffer: ArrayBuffer): X3D;
     static readGII(buffer: ArrayBuffer, n_vert?: number): Promise<GII>;
@@ -284,6 +299,7 @@ type UIData = {
     activeDragButton: number | null;
     angleFirstLine: number[];
     angleState: 'none' | 'drawing_first_line' | 'drawing_second_line' | 'complete';
+    activeClipPlaneIndex: number;
 };
 type SaveImageOptions = {
     filename: string;
@@ -943,6 +959,12 @@ declare class Niivue {
      * @internal
      */
     handlePinchZoom(e: TouchEvent): void;
+    /**
+     * Cycles active clip plane
+     * @internal
+     * @returns active clip plane index
+     */
+    cycleActiveClipPlane(): number;
     /**
      * Handles keyboard shortcuts for toggling clip planes and slice view modes with debounce logic.
      * @internal
@@ -1512,8 +1534,25 @@ declare class Niivue {
      * @example
      * niivue = new Niivue()
      * xyz = niivue.sph2cartDeg(42, 42)
+     * @internal
      */
     sph2cartDeg(azimuth: number, elevation: number): number[];
+    /**
+     * Set multiple clip planes from their depth/azimuth/elevation definitions.
+     *
+     *  depth: distance of clip plane from center of volume, range 0..~1.73
+     *         (e.g. 2.0 for no clip plane)
+     *  azimuth: camera position in degrees around object, typically 0..360
+     *           (or -180..+180)
+     *  elevation: camera height in degrees, range -90..90
+     *
+     * This replaces the entire `clipPlanes` and `clipPlaneDepthAziElevs` arrays,
+     * ensuring they always have the same length.
+     *
+     * @param depthAziElevs - array of `[depth, azimuthDeg, elevationDeg]` values
+     * @see {@link https://niivue.com/demos/features/clipplanesmulti.html | live demo usage}
+     */
+    setClipPlanes(depthAziElevs: number[][]): void;
     /**
      * Update the clip plane orientation in 3D view mode.
      * @param depthAzimuthElevation - a 3-component array:
@@ -1616,30 +1655,31 @@ declare class Niivue {
      */
     setScale(scale: number): void;
     /**
-     * set the color of the 3D clip plane
-     * @param color - the new color. expects an array of RGBA values. values can range from 0 to 1
+     * Set the color of the 3D clip plane.
+     * @param {number[]} color - An array of RGBA values.
+     *   - **R**, **G**, **B** components range from `0.0` to `1.0`.
+     *   - **A** (alpha) component ranges from `-1.0` to `1.0`, where:
+     *       - `0.0–1.0` → controls background translucency.
+     *       - `-1.0–0.0` → applies translucent shading to the volume instead of the background.
+     *
      * @example
-     * niivue.setClipPlaneColor([1, 1, 1, 0.5]) // white, transparent
-     * @see {@link https://niivue.com/demos/features/clipplanes.html | live demo usage}
+     * niivue.setClipPlaneColor([1, 1, 1, 0.5]);   // white, translucent background
+     * niivue.setClipPlaneColor([1, 1, 1, -0.5]);  // white, translucent shading
+     * @see {@link https://niivue.com/demos/features/clipplanes.html | Live demo usage}
      */
     setClipPlaneColor(color: number[]): void;
     /**
-     * adjust thickness of the 3D clip plane
-     * @param thick - thickness of slab. Value 0..1.73 (cube opposite corner length is sqrt(3)).
-     * @example
-     * niivue.setClipPlaneThick(0.3) // thin slab
-     * @see {@link https://niivue.com/demos/features/clipplanes.html | live demo usage}
+     * @deprecated This method has been removed.
+     * Use {@link setClipPlanes} instead, which generalizes clip plane configuration
+     * @see {@link https://niivue.com/demos/features/clipplanesmulti.html | Multiple clip plane demo}
      */
-    setClipPlaneThick(thick: number): void;
+    setClipPlaneThick(_thick: number): void;
     /**
-     * set the clipping region for volume rendering
-     * @param low - 3-component array specifying the lower bound of the clipping region along the X, Y, and Z axes. Values range from 0 (start) to 1 (end of volume).
-     * @param high - 3-component array specifying the upper bound of the clipping region along the X, Y, and Z axes. Values range from 0 to 1.
-     * @example
-     * niivue.setClipPlaneColor([0.0, 0.0, 0.2], [1.0, 1.0, 0.7]) // remove inferior 20% and superior 30%
-     * @see {@link https://niivue.com/demos/features/clipplanes.html | live demo usage}
+     * @deprecated This method has been removed.
+     * Use {@link setClipPlanes} instead, which generalizes clip plane configuration
+     * @see {@link https://niivue.com/demos/features/clipplanesmulti.html | Multiple clip plane demo}
      */
-    setClipVolume(low: number[], high: number[]): void;
+    setClipVolume(_low: number[], _high: number[]): void;
     /**
      * set proportion of volume rendering influenced by selected matcap.
      * @param gradientAmount - amount of matcap (NaN or 0..1), default 0 (matte, surface normal does not influence color). NaN renders the gradients.
@@ -2417,11 +2457,6 @@ declare class Niivue {
      * @internal
      */
     sliceScroll3D(posChange?: number): void;
-    /**
-     * Deletes loaded thumbnail texture and frees memory.
-     * @internal
-     */
-    deleteThumbnail(): void;
     /**
      * Checks if (x,y) is within the visible graph plotting area.
      * @internal
@@ -2754,7 +2789,7 @@ declare class Niivue {
      * Configures viewport and accounts for radiological orientation, depth clipping, and camera rotation.
      * @internal
      */
-    calculateMvpMatrix2D(leftTopWidthHeight: number[], mn: vec3, mx: vec3, clipTolerance: number, clipDepth: number, azimuth: number, elevation: number, isRadiolgical: boolean): MvpMatrix2D;
+    calculateMvpMatrix2D(leftTopWidthHeight: number[], mn: vec3, mx: vec3, clipTolerance?: number, clipDepth?: number, azimuth?: number, elevation?: number, isRadiolgical?: boolean): MvpMatrix2D;
     /**
      * Reorders the components of a 3D vector based on the slice orientation (axial, coronal, or sagittal).
      * @internal
@@ -2802,13 +2837,14 @@ declare class Niivue {
     draw2D(leftTopWidthHeight: number[], axCorSag: SLICE_TYPE, customMM?: number, imageWidthHeight?: number[]): void;
     /**
      * Build MVP, Model, and Normal matrices for rendering.
-     * @param _unused - reserved
-     * @param leftTopWidthHeight - viewport rectangle [x, y, w, h] in device pixels
-     * @param azimuth - azimuth rotation in degrees
-     * @param elevation - elevation rotation in degrees
-     * @param flipX - whether to mirror the X axis (default true for radiological convention)
+     * Note: 3D MVP is identical for radiological and neurological conventions.
+     * @param _unused - Reserved for future use.
+     * @param leftTopWidthHeight - Viewport rectangle [x, y, w, h] in device pixels.
+     * @param azimuth - Azimuth rotation in degrees.
+     * @param elevation - Elevation rotation in degrees.
+     * @internal
      */
-    calculateMvpMatrix(_unused: unknown, leftTopWidthHeight: number[], azimuth: number, elevation: number, flipX?: boolean): mat4[];
+    calculateMvpMatrix(_unused: unknown, leftTopWidthHeight: number[], azimuth: number, elevation: number): mat4[];
     /**
      * Computes the model transformation matrix for the given azimuth and elevation.
      * Applies optional oblique RAS rotation if available.
@@ -2818,6 +2854,7 @@ declare class Niivue {
     /**
      * Returns the normalized near-to-far ray direction for the given view angles.
      * Ensures components are nonzero to avoid divide-by-zero errors.
+     * n.b. volumes can have shear (see shear.html), so invert instead of transpose
      * @internal
      */
     calculateRayDirection(azimuth: number, elevation: number): vec3;
@@ -2921,7 +2958,7 @@ declare class Niivue {
      * Render all visible 3D meshes with proper blending, depth, and shader settings.
      * @internal
      */
-    drawMesh3D(isDepthTest?: boolean, alpha?: number, m?: mat4, modelMtx?: mat4, normMtx?: mat4): void;
+    drawMesh3D(isDepthTest?: boolean, alpha?: number, m?: mat4, modelMtx?: mat4, normMtx?: mat4, is2D?: boolean): void;
     /**
      * Render 3D crosshairs at the current crosshair position with optional depth testing and transparency.
      * @internal