copper3d 3.4.8 → 3.4.9

package/dist/Loader/copperDicomLoader.d.ts

@@ -1,5 +1,11 @@
-import { copperVolumeType } from "../types/types";
+import { copperVolumeType, planeCorners } from "../types/types";
 export declare function copperDicomLoader(url: string, callback?: (copperVolume: copperVolumeType) => void): void;
+/**
+ * Compute the 4 world-space corners of a DICOM image plane from its geometry tags.
+ * IPP is the CENTER of pixel (0,0), so corners sit half a pixel out. PixelSpacing is
+ * [rowSpacing, colSpacing]; IOP's first vector is the +column-index direction.
+ */
+export declare function computeImagePlaneCorners(ipp: number[], iop: number[], spacing: number[], cols: number, rows: number): planeCorners;
 export declare function getLut(data: Uint16Array, windowWidth: number, windowCenter: number, invert: boolean, voiLUT: any): {
     minPixelValue: number;
     maxPixelValue: number;

package/dist/Loader/copperDicomLoader.js

@@ -51,6 +51,17 @@ export function copperDicomLoader(url, callback) {
             windowCenter = 226;
             windowWidth = 537;
         }
+        // Spatial geometry tags (DS VR, backslash-delimited) used to place the image plane
+        // at its true world pose, plus InstanceNumber as an ordering fallback.
+        const ipp = parseDS(dataSet.string("x00200032")); // ImagePositionPatient
+        const iop = parseDS(dataSet.string("x00200037")); // ImageOrientationPatient
+        const spacing = parseDS(dataSet.string("x00280030")); // PixelSpacing
+        let instanceNumber = parseInt(dataSet.string("x00200013"));
+        if (Number.isNaN(instanceNumber))
+            instanceNumber = undefined;
+        const corners = ipp && iop && spacing
+            ? computeImagePlaneCorners(ipp, iop, spacing, w, h)
+            : undefined;
         let pixelData = dataSet.elements.x7fe00010;
         let uint16 = convertImplicitElement(pixelData, dicomFileAsBuffer);
         let voiLUT;
@@ -69,10 +80,44 @@ export function copperDicomLoader(url, callback) {
             uint16,
             uint8,
             order,
+            instanceNumber,
+            imagePositionPatient: ipp,
+            imageOrientationPatient: iop,
+            pixelSpacing: spacing,
+            corners,
         };
         callback && callback(copperVolume);
     });
 }
+// Parse a DICOM DS/IS multi-value string ("a\\b\\c") into a number[].
+function parseDS(s) {
+    if (!s)
+        return undefined;
+    const a = s.split("\\").map((v) => parseFloat(v));
+    return a.length && !a.some((n) => Number.isNaN(n)) ? a : undefined;
+}
+/**
+ * Compute the 4 world-space corners of a DICOM image plane from its geometry tags.
+ * IPP is the CENTER of pixel (0,0), so corners sit half a pixel out. PixelSpacing is
+ * [rowSpacing, colSpacing]; IOP's first vector is the +column-index direction.
+ */
+export function computeImagePlaneCorners(ipp, iop, spacing, cols, rows) {
+    const row = new THREE.Vector3(iop[0], iop[1], iop[2]); // +column-index dir
+    const col = new THREE.Vector3(iop[3], iop[4], iop[5]); // +row-index dir
+    const sc = spacing[1]; // column spacing (along row)
+    const sr = spacing[0]; // row spacing (along col)
+    const O = new THREE.Vector3(ipp[0], ipp[1], ipp[2]); // center of pixel (0,0)
+    const p = (a, b) => O.clone()
+        .addScaledVector(row, a * sc)
+        .addScaledVector(col, b * sr)
+        .toArray();
+    return {
+        tl: p(-0.5, -0.5),
+        tr: p(cols - 0.5, -0.5),
+        bl: p(-0.5, rows - 0.5),
+        br: p(cols - 0.5, rows - 0.5),
+    };
+}
 function convertImplicitElement(elementData, dicomFileAsBuffer) {
     let w1Buffer = dicomParser.sharedCopy(dicomFileAsBuffer, elementData.dataOffset, elementData.length);
     let unit16 = new Uint16Array(w1Buffer.buffer, w1Buffer.byteOffset, w1Buffer.byteLength / Uint16Array.BYTES_PER_ELEMENT);

package/dist/Loader/copperDicomLoader.js.map

@@ -1 +1 @@
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package/dist/Renderer/copperRenderer.d.ts

@@ -8,7 +8,9 @@ export declare class copperRenderer extends baseRenderer {
     private delta;
     private interval;
     preRenderCallbackFunctions: Array<Function>;
+    private running;
     constructor(container: HTMLDivElement, options?: ICopperRenderOpt);
+    stop(): void;
     getSceneByName(name: string): copperScene | import("../Scene/baseScene").baseScene | import("..").copperMScene;
     setFPS(fps: number): void;
     setCurrentScene(sceneIn: copperScene): void;

package/dist/Renderer/copperRenderer.js

@@ -10,8 +10,11 @@ export class copperRenderer extends baseRenderer {
         this.delta = 0;
         this.interval = 1 / this.fps;
         this.preRenderCallbackFunctions = [];
+        this.running = true;
         this.animate = (time) => {
             var _a, _b, _c;
+            if (!this.running)
+                return;
             switch ((_a = this.options) === null || _a === void 0 ? void 0 : _a.fpsMode) {
                 case "1":
                     // fpsControl one: 30fps
@@ -38,6 +41,10 @@ export class copperRenderer extends baseRenderer {
             }
         };
     }
+    // Stop the render loop (call on teardown to release the RAF and let GC reclaim).
+    stop() {
+        this.running = false;
+    }
     getSceneByName(name) {
         return this.sceneMap[name];
     }

package/dist/Renderer/copperRenderer.js.map

@@ -1 +1 @@
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package/dist/Scene/copperScene.d.ts

@@ -5,7 +5,7 @@ import { OrbitControls } from "three/examples/jsm/controls/OrbitControls";
 import { baseScene } from "./baseScene";
 import { vtkModels } from "../types/types";
 import { TrackballControls } from "three/examples/jsm/controls/TrackballControls";
-import { ICopperSceneOpts } from "../types/types";
+import { ICopperSceneOpts, aligned4DOptsType, Aligned4DController } from "../types/types";
 export declare class copperScene extends baseScene {
     clock: THREE.Clock;
     controls: Copper3dTrackballControls | OrbitControls | TrackballControls;
@@ -13,7 +13,6 @@ export declare class copperScene extends baseScene {
     private playRate;
     private modelReady;
     private clipAction;
-    private texture2dMesh;
     constructor(container: HTMLDivElement, renderer: THREE.WebGLRenderer, opt?: ICopperSceneOpts);
     loadGltf(url: string, callback?: (content: THREE.Group) => void): void;
     loadPureGLB(url: string, callback?: (mesh: THREE.Group) => void, opts?: {
@@ -22,7 +21,13 @@ export declare class copperScene extends baseScene {
     }): void;
     loadVtk(url: string): void;
     loadVtks(models: Array<vtkModels>): void;
-    texture2d(url: string): void;
+    /**
+     * Load an aligned 4D scene: a cine MRI (one slice, N cardiac phases) rendered as a
+     * world-placed plane, plus 0..N deforming surface sequences (e.g. LV endo/epi). MRI
+     * and surfaces stay in their shared patient coordinate frame (no center/scale), and
+     * advance together off ONE shared frame clock. Returns a controller (play/pause/...).
+     */
+    loadAligned4D(opts: aligned4DOptsType, callback?: (ctrl: Aligned4DController) => void): void;
     getPlayRate(): number;
     setPlayRate(playRate: number): void;
     setModelPosition(model: THREE.Group | THREE.Mesh, position: {

package/dist/Scene/copperScene.js

@@ -3,10 +3,13 @@ import { Copper3dTrackballControls } from "../Controls/Copper3dTrackballControls
 import { copperGltfLoader } from "../Loader/copperGltfLoader";
 import { OrbitControls } from "three/examples/jsm/controls/OrbitControls";
 import { copperVtkLoader, copperMultipleVtk } from "../Loader/copperVtkLoader";
-import { createTexture2D_Zip } from "../Utils/texture2d";
+import { createTexture2D_Array } from "../Utils/texture2d";
+import { copperDicomLoader } from "../Loader/copperDicomLoader";
+import { VTKLoader } from "three/examples/jsm/loaders/VTKLoader.js";
 import { baseScene } from "./baseScene";
 import { TrackballControls } from "three/examples/jsm/controls/TrackballControls";
 export class copperScene extends baseScene {
+    // rayster pick
     constructor(container, renderer, opt) {
         super(container, renderer, opt);
         this.clock = new THREE.Clock();
@@ -14,9 +17,6 @@ export class copperScene extends baseScene {
         this.mixer = null;
         this.playRate = 1.0;
         this.modelReady = false;
-        // rayster pick
-        // texture2d
-        this.texture2dMesh = null;
         if ((opt === null || opt === void 0 ? void 0 : opt.controls) === "trackball") {
             this.controls = new TrackballControls(this.camera, this.renderer.domElement);
         }
@@ -222,38 +222,177 @@ export class copperScene extends baseScene {
             this.exportContent.animations.push(clip);
         };
     }
-    // texture2d
-    texture2d(url) {
-        createTexture2D_Zip(url, this.scene);
-        const textureInterval = setInterval(() => {
-            var _a;
-            this.scene.children.forEach((child) => {
-                if (child.isMesh) {
-                    if (child.name === "texture2d_mesh_zip") {
-                        this.texture2dMesh = child;
-                        const render_texture2d = () => {
-                            if (this.texture2dMesh) {
-                                let value = this.texture2dMesh.material.uniforms["depth"].value;
-                                value += this.depthStep;
-                                if (value > 109.0 || value < 0.0) {
-                                    if (value > 1.0)
-                                        value = 109.0 * 2.0 - value;
-                                    if (value < 0.0)
-                                        value = -value;
-                                    this.depthStep = -this.depthStep;
-                                }
-                                this.texture2dMesh.material.uniforms["depth"].value =
-                                    value;
-                            }
-                        };
-                        this.addPreRenderCallbackFunction(render_texture2d);
-                    }
-                }
+    /**
+     * Load an aligned 4D scene: a cine MRI (one slice, N cardiac phases) rendered as a
+     * world-placed plane, plus 0..N deforming surface sequences (e.g. LV endo/epi). MRI
+     * and surfaces stay in their shared patient coordinate frame (no center/scale), and
+     * advance together off ONE shared frame clock. Returns a controller (play/pause/...).
+     */
+    loadAligned4D(opts, callback) {
+        var _a;
+        const dicomDepth = opts.dicomUrls.length;
+        const loadDicomStack = () => new Promise((resolve) => {
+            const volumes = [];
+            opts.dicomUrls.forEach((url) => {
+                copperDicomLoader(url, (volume) => {
+                    volumes.push(volume);
+                    if (volumes.length !== dicomDepth)
+                        return;
+                    // order frames by cardiac phase (TriggerTime / SliceLocation)
+                    volumes.sort((a, b) => a.order - b.order);
+                    const frameSize = volumes[0].width * volumes[0].height;
+                    const uint8 = new Uint8ClampedArray(frameSize * dicomDepth);
+                    const uint16 = new Uint16Array(uint8.length);
+                    volumes.forEach((v, index) => {
+                        uint8.set(v.uint8, index * frameSize);
+                        uint16.set(v.uint16, index * frameSize);
+                    });
+                    const stacked = Object.assign(Object.assign({}, volumes[0]), { uint8,
+                        uint16 });
+                    resolve(stacked);
+                });
+            });
+        });
+        const loadSurfaceSequence = (urls) => new Promise((resolve) => {
+            const loader = new VTKLoader();
+            const geometries = new Array(urls.length);
+            let done = 0;
+            urls.forEach((url, index) => {
+                loader.load(url, (geometry) => {
+                    // keep world coordinates — no center()/scale()
+                    geometry.computeVertexNormals();
+                    geometries[index] = geometry;
+                    if (++done === urls.length)
+                        resolve(geometries);
+                });
             });
-            if (((_a = this.texture2dMesh) === null || _a === void 0 ? void 0 : _a.name) === "texture2d_mesh_zip") {
-                clearInterval(textureInterval);
+        });
+        const surfaceDefs = (_a = opts.surfaces) !== null && _a !== void 0 ? _a : [];
+        Promise.all([
+            loadDicomStack(),
+            ...surfaceDefs.map((s) => loadSurfaceSequence(s.urls)),
+        ]).then(([stacked, ...surfaceGeoms]) => {
+            var _a;
+            if (opts.window) {
+                stacked.windowCenter = opts.window.center;
+                stacked.windowWidth = opts.window.width;
             }
-        }, 500);
+            const tex = createTexture2D_Array(stacked, dicomDepth, this.scene, undefined, true);
+            tex.setFrame(0);
+            if (opts.window)
+                tex.setWindow(opts.window.center, opts.window.width);
+            const surfaceMeshes = {};
+            const seqs = [];
+            surfaceDefs.forEach((def, i) => {
+                var _a;
+                const geometries = surfaceGeoms[i];
+                const { vtkmaterial } = copperMultipleVtk(def.opts);
+                const mesh = new THREE.Mesh(geometries[0], vtkmaterial);
+                mesh.name = def.name;
+                this.scene.add(mesh);
+                surfaceMeshes[def.name] = mesh;
+                seqs.push({ mesh, geometries, offset: (_a = def.offset) !== null && _a !== void 0 ? _a : 0 });
+            });
+            const frameCount = dicomDepth;
+            // Default one cardiac cycle ≈ 1012ms (32 phases × ~31.6ms) unless overridden.
+            const cycleMs = (_a = opts.cycleMs) !== null && _a !== void 0 ? _a : 1012;
+            let frameIndex = 0;
+            let speed = 1;
+            let playing = true;
+            let disposed = false;
+            let lastStep = performance.now();
+            const dtBase = cycleMs / frameCount;
+            const applyFrame = () => {
+                tex.setFrame(frameIndex);
+                for (const s of seqs) {
+                    const i = (frameIndex + s.offset + s.geometries.length) % s.geometries.length;
+                    s.mesh.geometry = s.geometries[i];
+                }
+            };
+            const tick = () => {
+                if (disposed || !playing)
+                    return;
+                const now = performance.now();
+                if (now - lastStep >= dtBase / speed) {
+                    lastStep = now;
+                    frameIndex = (frameIndex + 1) % frameCount;
+                    applyFrame();
+                }
+            };
+            this.addPreRenderCallbackFunction(tick);
+            const clockId = tick.id;
+            const ctrl = {
+                plane: tex.mesh,
+                surfaceMeshes,
+                frameCount,
+                play: () => {
+                    playing = true;
+                    lastStep = performance.now();
+                },
+                pause: () => {
+                    playing = false;
+                },
+                toggle: () => {
+                    playing = !playing;
+                    lastStep = performance.now();
+                },
+                setSpeed: (x) => {
+                    speed = Math.max(0.01, x);
+                },
+                setFrame: (i) => {
+                    frameIndex = ((i % frameCount) + frameCount) % frameCount;
+                    applyFrame();
+                },
+                setFrameOffset: (name, n) => {
+                    const s = seqs.find((q) => q.mesh.name === name);
+                    if (s) {
+                        s.offset = n;
+                        applyFrame();
+                    }
+                },
+                setWindow: (center, width) => {
+                    tex.setWindow(center, width);
+                },
+                setPlaneOpacity: (v) => {
+                    const m = tex.mesh.material;
+                    m.transparent = v < 1;
+                    m.uniforms.uOpacity.value = v;
+                    m.needsUpdate = true;
+                },
+                setSurfaceOpacity: (name, v) => {
+                    const mesh = surfaceMeshes[name];
+                    if (!mesh)
+                        return;
+                    const m = mesh.material;
+                    m.transparent = v < 1;
+                    m.opacity = v;
+                    m.needsUpdate = true;
+                },
+                setSurfaceVisible: (name, visible) => {
+                    const mesh = surfaceMeshes[name];
+                    if (mesh)
+                        mesh.visible = visible;
+                },
+                dispose: () => {
+                    var _a, _b;
+                    disposed = true;
+                    this.removePreRenderCallbackFunction(clockId);
+                    // plane
+                    this.scene.remove(tex.mesh);
+                    tex.mesh.geometry.dispose();
+                    const pm = tex.mesh.material;
+                    (_b = (_a = pm.uniforms.diffuse.value) === null || _a === void 0 ? void 0 : _a.dispose) === null || _b === void 0 ? void 0 : _b.call(_a);
+                    pm.dispose();
+                    // surfaces
+                    for (const s of seqs) {
+                        this.scene.remove(s.mesh);
+                        s.geometries.forEach((g) => g.dispose());
+                        s.mesh.material.dispose();
+                    }
+                },
+            };
+            callback && callback(ctrl);
+        });
     }
     getPlayRate() {
         return this.playRate;

package/dist/Scene/copperScene.js.map

@@ -1 +1 @@
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package/dist/Utils/texture2d.d.ts

@@ -1,10 +1,12 @@
 import * as THREE from "three";
 import { copperVolumeType } from "../types/types";
 import { GUI } from "dat.gui";
-export declare function createTexture2D_Zip(url: string, scene: THREE.Scene): void;
-export declare function createTexture2D_NRRD(data: Uint8Array, width: number, height: number, depth: number, callback: (mesh: THREE.Mesh) => void): void;
-export declare function createTexture2D_Array(copperVolume: copperVolumeType, depth: number, scene: THREE.Scene, gui?: GUI): {
-    mesh: THREE.Mesh<THREE.PlaneGeometry, THREE.ShaderMaterial, THREE.Object3DEventMap>;
+export interface texture2dResult {
+    mesh: THREE.Mesh;
     copperVolume: copperVolumeType;
-    updateTexture: (copperVolumeUp: copperVolumeType) => void;
-};
+    updateTexture: (copperVolume: copperVolumeType) => void;
+    setFrame: (i: number) => void;
+    setWindow: (center: number, width: number) => void;
+}
+export declare function createTexture2D_NRRD(data: Uint8Array, width: number, height: number, depth: number, callback: (mesh: THREE.Mesh) => void): void;
+export declare function createTexture2D_Array(copperVolume: copperVolumeType, depth: number, scene: THREE.Scene, gui?: GUI, aligned?: boolean): texture2dResult;

package/dist/Utils/texture2d.js

@@ -1,35 +1,20 @@
 import * as THREE from "three";
-import { unzipSync } from "fflate";
 import { getLut } from "../Loader/copperDicomLoader";
 import vert_2d from "../lib/shader/texture2d_vertex.glsl";
 import frag_2d from "../lib/shader/texture2d_frag.glsl";
 let planeWidth = 80;
 let planeHeight = 80;
-export function createTexture2D_Zip(url, scene) {
-    new THREE.FileLoader()
-        .setResponseType("arraybuffer")
-        .load(url, function (data) {
-        const zip = unzipSync(new Uint8Array(data));
-        const array = new Uint8Array(zip["head256x256x109"].buffer);
-        const texture = new THREE.DataArrayTexture(array, 256, 256, 109);
-        texture.format = THREE.RedFormat;
-        texture.needsUpdate = true;
-        const material = new THREE.ShaderMaterial({
-            uniforms: {
-                diffuse: { value: texture },
-                depth: { value: 1 },
-                size: { value: new THREE.Vector2(planeWidth, planeHeight) },
-            },
-            vertexShader: vert_2d,
-            fragmentShader: frag_2d,
-            glslVersion: THREE.GLSL3,
-            side: THREE.DoubleSide,
-        });
-        const geometry = new THREE.PlaneGeometry(planeWidth, planeHeight);
-        const mesh = new THREE.Mesh(geometry, material);
-        mesh.name = "texture2d_mesh_zip";
-        scene.add(mesh);
-    });
+// Build a quad from the 4 world-space image-plane corners (preserves real pose).
+function buildAlignedQuad(c) {
+    const g = new THREE.BufferGeometry();
+    // two triangles: tl,bl,tr / tr,bl,br
+    g.setAttribute("position", new THREE.BufferAttribute(new Float32Array([...c.tl, ...c.bl, ...c.tr, ...c.tr, ...c.bl, ...c.br]), 3));
+    // vertex order is tl, bl, tr, tr, bl, br. The fragment shader flips v (vUv.y = 1-uv.y)
+    // and DataArrayTexture has no flipY, so the image-top (data row 0) must map to the
+    // top world corner: tl/tr get uv.y = 1.
+    g.setAttribute("uv", new THREE.BufferAttribute(new Float32Array([0, 1, 0, 0, 1, 1, 1, 1, 0, 0, 1, 0]), 2));
+    g.computeVertexNormals();
+    return g;
 }
 export function createTexture2D_NRRD(data, width, height, depth, callback) {
     const texture = new THREE.DataArrayTexture(data, width, height, depth);
@@ -39,7 +24,7 @@ export function createTexture2D_NRRD(data, width, height, depth, callback) {
         uniforms: {
             diffuse: { value: texture },
             depth: { value: 1 },
-            size: { value: new THREE.Vector2(planeWidth, planeHeight) },
+            uOpacity: { value: 1 },
         },
         vertexShader: vert_2d,
         fragmentShader: frag_2d,
@@ -51,13 +36,9 @@ export function createTexture2D_NRRD(data, width, height, depth, callback) {
     mesh.name = "texture2d_mesh_zip";
     callback(mesh);
 }
-export function createTexture2D_Array(copperVolume, depth, scene, gui) {
+export function createTexture2D_Array(copperVolume, depth, scene, gui, aligned = false) {
     planeWidth = copperVolume.width / 2;
     planeHeight = copperVolume.height / 2;
-    const state = {
-        windowWidth: copperVolume.windowWidth,
-        windowCenter: copperVolume.windowCenter,
-    };
     const texture = new THREE.DataArrayTexture(copperVolume.uint8, copperVolume.width, copperVolume.height, depth);
     texture.format = THREE.RedFormat;
     texture.needsUpdate = true;
@@ -84,18 +65,22 @@ export function createTexture2D_Array(copperVolume, depth, scene, gui) {
     const material = new THREE.ShaderMaterial({
         uniforms: {
             diffuse: { value: texture },
-            depth: { value: 1 },
-            size: { value: new THREE.Vector2(planeWidth, planeHeight) },
+            depth: { value: 0 },
+            uOpacity: { value: 1 },
         },
         vertexShader: vert_2d,
         fragmentShader: frag_2d,
         glslVersion: THREE.GLSL3,
         side: THREE.DoubleSide,
     });
-    const geometry = new THREE.PlaneGeometry(planeWidth, planeHeight);
+    // Aligned world-space quad only when explicitly requested and geometry tags exist;
+    // otherwise the legacy centred plane (keeps existing loadDicom behaviour unchanged).
+    const geometry = aligned && copperVolume.corners
+        ? buildAlignedQuad(copperVolume.corners)
+        : new THREE.PlaneGeometry(planeWidth, planeHeight);
     const mesh = new THREE.Mesh(geometry, material);
-    scene.add(mesh);
     mesh.name = "texture2d_mesh_array";
+    scene.add(mesh);
     function updateTexture(copperVolumeUp) {
         if (!!copperVolumeUp) {
             let voiLUT;
@@ -106,6 +91,14 @@ export function createTexture2D_Array(copperVolume, depth, scene, gui) {
             texture.needsUpdate = true;
         }
     }
-    return { mesh, copperVolume, updateTexture };
+    function setFrame(i) {
+        material.uniforms.depth.value = i;
+    }
+    function setWindow(center, width) {
+        copperVolume.windowCenter = center;
+        copperVolume.windowWidth = width;
+        updateTexture(copperVolume);
+    }
+    return { mesh, copperVolume, updateTexture, setFrame, setWindow };
 }
 //# sourceMappingURL=texture2d.js.map