copper3d 3.4.9 → 3.6.0

package/dist/Utils/segmentation/tools/AiAssistTool.js

@@ -0,0 +1,470 @@
+/**
+ * AiAssistTool — interactive prompt-based segmentation (experimental).
+ *
+ * The clinician left-clicks foreground / background points (or drags a box /
+ * scribbles) on the current slice; a backend model returns a region mask that
+ * is written into an INDEPENDENT scratch MaskVolume (`aiAssistMaskVolume`,
+ * registered as `maskData.volumes['aiScratch']`) — never the validated layers.
+ *
+ * Network lives in the app layer: this tool only (a) maps screen → voxel-slice
+ * coordinates, (b) accumulates the prompt for the current slice, (c) fires
+ * `onPrompt` so the app can call the backend, and (d) applies the returned mask
+ * via `applyMask`. The app's `useAiAssist` composable wires (c)→(d).
+ *
+ * Sandbox: snapshot on enter (`snapshot`), then on exit either `discard`
+ * (restore snapshot) or merge is handled by NrrdTools (clone + pushGroup).
+ *
+ * Coordinate mapping supports all three views (axial/sagittal/coronal); it
+ * inverts the per-axis display transform of RenderingUtils.renderSliceToCanvas
+ * (only coronal 'y' is vertically flipped). Merge captures painted voxels from
+ * any view (the scratch is a full 3D volume).
+ */
+import { BaseTool } from "./BaseTool";
+import { MaskVolume, AI_MASK_CHANNEL_COLORS } from "../core";
+/** Scratch volume key in maskData.volumes — kept OUT of image.layers so
+ *  compositeAllLayers ignores it (we render it ourselves in start()). */
+export const AI_SCRATCH_LAYER = "aiScratch";
+export class AiAssistTool extends BaseTool {
+    constructor(ctx, host) {
+        super(ctx);
+        /** Independent scratch volume (also registered at maskData.volumes['aiScratch']). */
+        this.scratchVol = null;
+        /** Snapshot of the scratch buffer taken on enter (for discard). */
+        this.snapshotData = null;
+        /** Frozen regions ("New region" commits here). Pixels recorded here survive a
+         *  later re-prediction — even on the SAME channel — so multiple separate regions
+         *  can be drawn without the newest prediction wiping the previous ones. Null =
+         *  nothing frozen yet (applySliceRle then behaves as a single live region). */
+        this.committedVol = null;
+        this.promptTool = "point";
+        this.polarity = 1; // 1 = foreground (positive), 0 = background
+        /** Target channel/label (1-8) the AI paints into — the "AI layer" channel. */
+        this.channel = 1;
+        /** Scribble brush radius (px), user-adjustable via slider. */
+        this.scribbleSize = 5;
+        /** Accumulated prompts for the CURRENT slice; reset on slice/axis change. */
+        this.points = [];
+        this.scribble = [];
+        this.activeSlice = -1;
+        // Drag state (box / scribble) — voxel coords for the prompt
+        this.dragging = false;
+        this.dragStart = null;
+        // Screen-space (display px) copies for the LIVE preview drawn each frame.
+        this.dragScreenStart = null;
+        this.dragScreen = null;
+        this.screenScribble = [];
+        // Live cursor position (screen px) for the scribble brush-size preview ring —
+        // updated on every hover move so the ring follows the mouse like the paint brush.
+        this.hoverScreen = null;
+        /** Fired when a prompt gesture completes — app calls backend, then applyMask(). */
+        this.onPrompt = null;
+        this.host = host;
+    }
+    // ── Configuration (driven from the panel via NrrdTools) ────────────────────
+    setPromptTool(tool) {
+        // Switching tool starts a clean gesture — drop any stale points/box/scribble
+        // and drag state so the next click behaves predictably.
+        if (tool !== this.promptTool) {
+            this.resetPrompts();
+            this.dragging = false;
+            this.dragStart = null;
+        }
+        this.promptTool = tool;
+    }
+    setPolarity(label) { this.polarity = label === 0 ? 0 : 1; }
+    setScribbleSize(size) {
+        this.scribbleSize = Math.max(1, Math.min(40, Math.round(size)));
+    }
+    setChannel(channel) {
+        const c = Math.max(1, Math.min(8, Math.round(channel)));
+        // Changing channel starts a NEW region in the new colour — otherwise the
+        // accumulated points would be re-predicted and repainted in the new label,
+        // recolouring the previous channel's region.
+        if (c !== this.channel)
+            this.resetPrompts();
+        this.channel = c;
+    }
+    getChannel() { return this.channel; }
+    getScratchVolume() { return this.scratchVol; }
+    /** Serialize the scratch volume as per-z-slice RLE (only NON-empty slices),
+     *  for persisting to ai_generated_nii_LPS on the backend. Binary (any channel →
+     *  1); RLE is alternating run lengths starting with a 0-run — the exact format
+     *  the backend's rle_decode expects. Uses getSliceUint8 (the same path the
+     *  clinician layer's /api/mask/replace uses) so orientation matches. */
+    getScratchSlices() {
+        if (!this.scratchVol)
+            return null;
+        const { depth } = this.scratchVol.getDimensions();
+        const out = [];
+        let width = 0;
+        let height = 0;
+        for (let z = 0; z < depth; z++) {
+            const { data, width: w, height: h } = this.scratchVol.getSliceUint8(z, "z");
+            width = w;
+            height = h;
+            // RLE-encode (binarized) in one pass; skip fully-empty slices.
+            const runs = [];
+            let value = 0; // always begin with a 0-run (matches backend rle_encode)
+            let count = 0;
+            let any = false;
+            for (let i = 0; i < data.length; i++) {
+                const v = data[i] !== 0 ? 1 : 0;
+                if (v)
+                    any = true;
+                if (v === value) {
+                    count++;
+                }
+                else {
+                    runs.push(count);
+                    value = v;
+                    count = 1;
+                }
+            }
+            runs.push(count);
+            if (any)
+                out.push({ sliceIndex: z, rle: runs });
+        }
+        return { axis: "z", width, height, slices: out };
+    }
+    // ── Sandbox lifecycle ──────────────────────────────────────────────────────
+    /** Create (or reuse) the scratch volume sized to the layer grid and register
+     *  it under maskData.volumes['aiScratch']. Snapshots the empty buffer. */
+    enter() {
+        const volumes = this.ctx.protectedData.maskData.volumes;
+        const baseId = this.ctx.nrrd_states.image.layers[0];
+        const base = volumes[baseId];
+        if (!base)
+            return;
+        const d = base.getDimensions();
+        if (!this.scratchVol ||
+            this.scratchVol.getDimensions().width !== d.width ||
+            this.scratchVol.getDimensions().height !== d.height ||
+            this.scratchVol.getDimensions().depth !== d.depth) {
+            this.scratchVol = new MaskVolume(d.width, d.height, d.depth, 1);
+        }
+        else {
+            this.scratchVol.clear();
+        }
+        volumes[AI_SCRATCH_LAYER] = this.scratchVol;
+        // Paint the AI scratch with the AI-Assist palette (channel 1 = cyan) so the 2D
+        // overlay matches the cyan ai_generated GLB. Scoped to THIS volume only — the
+        // global palette / clinician mask colours are untouched.
+        for (let ch = 1; ch <= 8; ch++) {
+            const c = AI_MASK_CHANNEL_COLORS[ch];
+            if (c)
+                this.scratchVol.setChannelColor(ch, { r: c.r, g: c.g, b: c.b, a: c.a });
+        }
+        this.snapshotData = this.scratchVol.getRawData().slice();
+        this.committedVol = null; // nothing frozen at session start
+        this.resetPrompts();
+    }
+    /** Remove the scratch volume from the registry and drop references. */
+    exit() {
+        const volumes = this.ctx.protectedData.maskData.volumes;
+        delete volumes[AI_SCRATCH_LAYER];
+        this.scratchVol = null;
+        this.snapshotData = null;
+        this.committedVol = null;
+        this.resetPrompts();
+        this.dragging = false;
+        this.dragStart = null;
+    }
+    /** Discard everything painted since enter() — restore the snapshot. */
+    discard() {
+        if (this.scratchVol && this.snapshotData) {
+            this.scratchVol.setRawData(this.snapshotData.slice());
+        }
+        this.committedVol = null; // discard wipes frozen regions too
+        this.resetPrompts();
+    }
+    /** "New region": freeze every voxel painted so far so it survives later
+     *  re-predictions (even on the same channel), then start a fresh prompt set.
+     *  This is what makes drawing multiple separate regions actually work — without
+     *  it the next prediction's same-channel cleanup erases the previous region. */
+    commitRegion() {
+        if (this.scratchVol) {
+            const d = this.scratchVol.getDimensions();
+            if (!this.committedVol ||
+                this.committedVol.getDimensions().width !== d.width ||
+                this.committedVol.getDimensions().height !== d.height ||
+                this.committedVol.getDimensions().depth !== d.depth) {
+                this.committedVol = new MaskVolume(d.width, d.height, d.depth, 1);
+            }
+            this.committedVol.setRawData(this.scratchVol.getRawData().slice());
+        }
+        this.resetPrompts();
+    }
+    /** Clear the in-progress prompt set (e.g. slice/axis change). Does NOT freeze —
+     *  use commitRegion() for the "New region" action. */
+    resetPrompts() {
+        this.points = [];
+        this.scribble = [];
+        this.box = undefined;
+        this.dragScreenStart = null;
+        this.dragScreen = null;
+        this.screenScribble = [];
+    }
+    // ── Coordinate mapping (all three views) ───────────────────────────────────
+    //
+    // Mapping must INVERT exactly what RenderingUtils.renderSliceToCanvas does to
+    // display the overlay (it is the renderer used by renderOverlay):
+    //   - axial (z) / sagittal (x): no flip
+    //   - coronal (y): vertical flip (scale(1,-1))
+    // Slice voxel dims & canvas mm extents per axis (matches MaskVolume
+    // getSliceDimensions + SphereTool.setSphereCanvasSize):
+    //   z → (W=width,  H=height) over (x_mm, y_mm)
+    //   y → (W=width,  H=depth ) over (x_mm, z_mm)   [vertical flip]
+    //   x → (W=depth,  H=height) over (z_mm, y_mm)
+    /** Voxel-slice (width,height) for the current axis. */
+    sliceDims() {
+        if (!this.scratchVol)
+            return null;
+        const d = this.scratchVol.getDimensions();
+        switch (this.ctx.protectedData.axis) {
+            case "z": return { w: d.width, h: d.height };
+            case "y": return { w: d.width, h: d.depth };
+            case "x": return { w: d.depth, h: d.height };
+            default: return null;
+        }
+    }
+    /** Screen offset → voxel-slice (vx,vy) for the current axis. */
+    toVoxel(e) {
+        const sd = this.sliceDims();
+        if (!sd || !this.scratchVol)
+            return null;
+        const nrrd = this.ctx.nrrd_states;
+        const img = nrrd.image;
+        const mx = e.offsetX / nrrd.view.sizeFactor;
+        const my = e.offsetY / nrrd.view.sizeFactor;
+        let hMM, vMM, flipV;
+        switch (this.ctx.protectedData.axis) {
+            case "z":
+                hMM = img.nrrd_x_mm;
+                vMM = img.nrrd_y_mm;
+                flipV = false;
+                break;
+            case "y":
+                hMM = img.nrrd_x_mm;
+                vMM = img.nrrd_z_mm;
+                flipV = true;
+                break;
+            case "x":
+                hMM = img.nrrd_z_mm;
+                vMM = img.nrrd_y_mm;
+                flipV = false;
+                break;
+            default: return null;
+        }
+        const vx = Math.round(mx * sd.w / hMM);
+        let vy = Math.round(my * sd.h / vMM);
+        if (flipV)
+            vy = sd.h - 1 - vy;
+        if (vx < 0 || vx >= sd.w || vy < 0 || vy >= sd.h)
+            return null;
+        return { vx, vy, w: sd.w, h: sd.h };
+    }
+    // ── Pointer handlers (left button; right stays pan in EventRouter) ──────────
+    onPointerDown(e) {
+        const hit = this.toVoxel(e);
+        if (!hit)
+            return;
+        this.syncSlice();
+        if (this.promptTool === "point") {
+            this.points.push({ x: hit.vx, y: hit.vy, label: this.polarity });
+            this.emit();
+        }
+        else {
+            // box / scribble: begin a drag
+            this.dragging = true;
+            this.dragStart = { x: hit.vx, y: hit.vy };
+            this.dragScreenStart = { x: e.offsetX, y: e.offsetY };
+            this.dragScreen = { x: e.offsetX, y: e.offsetY };
+            this.screenScribble = [];
+            if (this.promptTool === "scribble") {
+                this.scribble.push({ x: hit.vx, y: hit.vy, label: this.polarity });
+                this.screenScribble.push({ x: e.offsetX, y: e.offsetY });
+            }
+        }
+    }
+    onPointerMove(e) {
+        // Track hover for the scribble preview ring even when not drawing.
+        this.hoverScreen = { x: e.offsetX, y: e.offsetY };
+        if (!this.dragging)
+            return;
+        // Track screen pos first so the live preview follows even slightly out of bounds.
+        this.dragScreen = { x: e.offsetX, y: e.offsetY };
+        const hit = this.toVoxel(e);
+        if (!hit)
+            return;
+        if (this.promptTool === "scribble") {
+            this.scribble.push({ x: hit.vx, y: hit.vy, label: this.polarity });
+            this.screenScribble.push({ x: e.offsetX, y: e.offsetY });
+        }
+        else if (this.promptTool === "box" && this.dragStart) {
+            this.box = {
+                x0: this.dragStart.x, y0: this.dragStart.y,
+                x1: hit.vx, y1: hit.vy,
+                label: this.polarity, // foreground box grows within; background box excludes
+            };
+        }
+    }
+    onPointerUp(_e) {
+        if (!this.dragging)
+            return;
+        this.dragging = false;
+        this.emit();
+        this.dragStart = null;
+        this.dragScreenStart = null;
+        this.dragScreen = null;
+        this.screenScribble = [];
+    }
+    /** Reset the accumulated prompt set when the user scrubs to a new slice. */
+    syncSlice() {
+        const slice = this.ctx.nrrd_states.view.currentSliceIndex;
+        if (slice !== this.activeSlice) {
+            this.activeSlice = slice;
+            this.resetPrompts();
+        }
+    }
+    emit() {
+        if (!this.onPrompt)
+            return;
+        const sd = this.sliceDims();
+        if (!sd)
+            return;
+        this.onPrompt({
+            axis: this.ctx.protectedData.axis,
+            sliceIndex: this.ctx.nrrd_states.view.currentSliceIndex,
+            width: sd.w,
+            height: sd.h,
+            points: [...this.points],
+            box: this.box,
+            scribble: this.scribble.length ? [...this.scribble] : undefined,
+            scribbleRadius: this.scribbleSize,
+        });
+    }
+    // ── Apply backend result → scratch volume ──────────────────────────────────
+    applyMask(result) {
+        if (!this.scratchVol)
+            return;
+        // 3D result (engine B): write each slice across the covered span.
+        if (result.slices && result.sliceRange) {
+            const [lo] = result.sliceRange;
+            for (let k = 0; k < result.slices.length; k++) {
+                this.applySliceRle(result.slices[k], result.axis, lo + k, result.width, result.height);
+            }
+            return;
+        }
+        // 2D result (engines mock / regiongrow / medsam2d): single slice.
+        this.applySliceRle(result.rle, result.axis, result.sliceIndex, result.width, result.height);
+    }
+    /** Merge one RLE-encoded predicted slice into the scratch volume at sliceIndex.
+     *  Predicted pixels → current channel; stale current-channel pixels cleared
+     *  UNLESS they belong to a frozen (committed) region; OTHER channels preserved. */
+    applySliceRle(rle, axis, sliceIndex, width, height) {
+        if (!this.scratchVol)
+            return;
+        const predicted = new Uint8Array(width * height);
+        let pos = 0;
+        let value = 0;
+        for (const run of rle) {
+            if (value === 1 && run > 0) {
+                const end = Math.min(pos + run, predicted.length);
+                for (let i = pos; i < end; i++)
+                    predicted[i] = 1;
+            }
+            pos += run;
+            value ^= 1;
+        }
+        const ch = this.channel;
+        try {
+            const out = this.scratchVol.getSliceUint8(sliceIndex, axis).data; // copy
+            // Frozen same-channel pixels for this slice (if any region was committed).
+            let frozen = null;
+            if (this.committedVol) {
+                try {
+                    frozen = this.committedVol.getSliceUint8(sliceIndex, axis).data;
+                }
+                catch (_a) {
+                    frozen = null;
+                }
+            }
+            const n = Math.min(out.length, predicted.length);
+            for (let i = 0; i < n; i++) {
+                if (predicted[i])
+                    out[i] = ch;
+                // Clear stale LIVE same-channel pixels (refinement), but never erase a
+                // frozen region committed via "New region".
+                else if (out[i] === ch && !(frozen && frozen[i] === ch))
+                    out[i] = 0;
+            }
+            this.scratchVol.setSliceUint8(sliceIndex, out, axis);
+        }
+        catch (_b) {
+            // slice out of bounds / dims changed — ignore
+        }
+    }
+    // ── Overlay render (called from DrawToolCore.start() while in aiAssist) ──────
+    renderOverlay(targetCtx) {
+        if (!this.scratchVol)
+            return;
+        const axis = this.ctx.protectedData.axis;
+        const slice = this.ctx.nrrd_states.view.currentSliceIndex;
+        const buffer = this.host.getOrCreateSliceBuffer(axis);
+        if (!buffer)
+            return;
+        try {
+            this.host.renderSliceToCanvas(AI_SCRATCH_LAYER, axis, slice, buffer, targetCtx, this.ctx.nrrd_states.view.changedWidth, this.ctx.nrrd_states.view.changedHeight);
+        }
+        catch (_a) {
+            // volume not ready / slice out of bounds
+        }
+        // Live drag preview (screen space) — rubber-band box / scribble stroke so the
+        // user sees the gesture before the prediction lands on pointer-up.
+        if (this.dragging && this.dragScreenStart && this.dragScreen) {
+            targetCtx.save();
+            // Green-ish for foreground (include), red-ish for background (exclude).
+            const color = this.polarity === 1 ? "rgba(120,255,180,0.95)" : "rgba(255,120,120,0.95)";
+            targetCtx.strokeStyle = color;
+            if (this.promptTool === "box") {
+                targetCtx.setLineDash([5, 4]);
+                targetCtx.lineWidth = 1.5;
+                const x = Math.min(this.dragScreenStart.x, this.dragScreen.x);
+                const y = Math.min(this.dragScreenStart.y, this.dragScreen.y);
+                const w = Math.abs(this.dragScreen.x - this.dragScreenStart.x);
+                const h = Math.abs(this.dragScreen.y - this.dragScreenStart.y);
+                targetCtx.strokeRect(x, y, w, h);
+            }
+            else if (this.promptTool === "scribble" && this.screenScribble.length > 1) {
+                targetCtx.lineCap = "round";
+                targetCtx.lineJoin = "round";
+                // Stroke thickness reflects the scribble brush size (diameter ≈ 2·radius).
+                targetCtx.lineWidth = Math.max(2, this.scribbleSize * 2);
+                targetCtx.beginPath();
+                targetCtx.moveTo(this.screenScribble[0].x, this.screenScribble[0].y);
+                for (let i = 1; i < this.screenScribble.length; i++) {
+                    targetCtx.lineTo(this.screenScribble[i].x, this.screenScribble[i].y);
+                }
+                targetCtx.stroke();
+            }
+            targetCtx.restore();
+        }
+        // Scribble brush-size preview ring (when NOT dragging) — a circle centred on
+        // the cursor whose radius = scribbleSize, so the user sees the brush size and
+        // how the slider changes it (mirrors the paint brush's preview ring). Drawn
+        // every frame from the live hover position by copper3d's render loop.
+        if (this.promptTool === "scribble" && !this.dragging && this.hoverScreen) {
+            targetCtx.save();
+            const fg = this.polarity === 1;
+            targetCtx.strokeStyle = fg ? "rgba(120,255,180,0.9)" : "rgba(255,120,120,0.9)";
+            targetCtx.lineWidth = 1.5;
+            if (!fg)
+                targetCtx.setLineDash([4, 4]); // dashed for background (exclude), like the eraser
+            targetCtx.beginPath();
+            targetCtx.arc(this.hoverScreen.x, this.hoverScreen.y, Math.max(2, this.scribbleSize), 0, Math.PI * 2);
+            targetCtx.stroke();
+            targetCtx.restore();
+        }
+    }
+}
+//# sourceMappingURL=AiAssistTool.js.map

package/dist/Utils/segmentation/tools/AiAssistTool.js.map

@@ -0,0 +1 @@
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package/dist/Utils/surfaceAnnotation/MeshGraph.d.ts

@@ -0,0 +1,40 @@
+import * as THREE from "three";
+/**
+ * 从 BufferGeometry 的索引构建顶点邻接图,用于模式 B(测地线)的最短路径。
+ * 顶点坐标按 local 存;传入的查询点需先转为 local(mesh.worldToLocal)。
+ *
+ * 说明:几何须为已索引(indexed)。modelLoader 用 mergeVertices 焊接重复顶点,
+ * 保证同一表面位置共享顶点,邻接图才连通。
+ *
+ * 性能:O(V²) Dijkstra + O(V) 最近顶点查找。对几万顶点单次点击可接受;
+ * 若过大可后续换二叉堆 + 空间网格加速(留作升级)。
+ */
+export declare class MeshGraph {
+    private positions;
+    private normals;
+    private adj;
+    readonly vertexCount: number;
+    constructor(geometry: THREE.BufferGeometry);
+    private px;
+    private py;
+    private pz;
+    /** 最近顶点(传入 local 坐标)。 */
+    nearestVertex(localPoint: THREE.Vector3): number;
+    /**
+     * 两顶点间最短路径(含端点的顶点索引序列)。二叉堆 Dijkstra,O(E log V)。
+     * 不连通时返回 [start,end] 兜底。
+     */
+    shortestPath(startV: number, endV: number): number[];
+    vertexWorld(i: number, matrixWorld: THREE.Matrix4): THREE.Vector3;
+    vertexNormalWorld(i: number, mesh: THREE.Mesh): THREE.Vector3;
+    /** 顶点的 local 坐标 + local 法线(图几何即 local 空间)。 */
+    vertexLocal(i: number): {
+        x: number;
+        y: number;
+        z: number;
+        nx: number;
+        ny: number;
+        nz: number;
+        faceIndex: number;
+    };
+}