copper3d 3.3.2 → 3.4.0

package/dist/Utils/segmentation/core/MarchingSquares.d.ts

@@ -0,0 +1,72 @@
+/**
+ * MarchingSquares — Extract vector contours from a 2D voxel label grid.
+ *
+ * For each label, produces a `Path2D` whose subpaths are small per-cell
+ * polygons. The polygons tile the region occupied by the target label; the
+ * union (via `ctx.fill(path, 'nonzero')`) is the label's silhouette on the
+ * voxel grid.
+ *
+ * Coordinate convention:
+ *   - Voxel (i, j) occupies the unit square [i, i+1] × [j, j+1] in render
+ *     space, with its center at (i+0.5, j+0.5). This matches ITK-SNAP /
+ *     standard imaging viewers and the existing `renderSliceToCanvas`
+ *     `scale(scaledW / W, scaledH / H)` mapping.
+ *   - Marching squares treats voxels as point samples at their centers:
+ *     cell (i, j) has corners at voxel centers (i+0.5, j+0.5),
+ *     (i+1.5, j+0.5), (i+1.5, j+1.5), (i+0.5, j+1.5).
+ *   - This produces 45°-cut contours (diamonds for isolated voxels, rounded
+ *     corners for connected regions) that stay within the voxel-square
+ *     bounds, so the rendered silhouette is a slightly-inset version of the
+ *     ITK-SNAP silhouette with smooth diagonals.
+ *
+ * Saddle cases (5 and 10) use a fixed convention: the two in-corners are
+ * treated as disconnected within the cell (4-connectivity interpretation).
+ */
+export interface ContourBBox {
+    /** Inclusive left voxel (0 ≤ x0 ≤ width). */
+    x0: number;
+    /** Inclusive top voxel (0 ≤ y0 ≤ height). */
+    y0: number;
+    /** Exclusive right voxel (x1 > x0). */
+    x1: number;
+    /** Exclusive bottom voxel (y1 > y0). */
+    y1: number;
+}
+/** A single polygon's vertices in voxel-space coordinates. */
+export type ContourPolygon = ReadonlyArray<readonly [number, number]>;
+/**
+ * Emit all per-cell polygons covering the voxels where `labels === targetLabel`.
+ * Pure geometry function — no Canvas dependency. Consumers can build a Path2D
+ * (see {@link extractLabelContours}) or walk the vertex arrays directly
+ * (tests, export, stroke rendering).
+ */
+export declare function extractLabelPolygons(labels: Uint8Array, width: number, height: number, targetLabel: number, stride?: number, channelOffset?: number, bbox?: ContourBBox): ContourPolygon[];
+/**
+ * Extract a `Path2D` covering all voxels equal to `targetLabel`.
+ *
+ * @param labels      Flat label array. Addressed as
+ *                    `labels[(y * width + x) * stride + channelOffset]`.
+ * @param width       Grid width in voxels.
+ * @param height      Grid height in voxels.
+ * @param targetLabel Label value to extract (1..255; 0 is background).
+ * @param stride      Bytes per voxel (default 1). Use MaskVolume.numChannels
+ *                    when reading interleaved slices.
+ * @param channelOffset Offset within each voxel's channels to sample.
+ *                    Default 0 (first channel = label id).
+ * @param bbox        Optional voxel-space bbox to limit extraction.
+ *                    Cells in a 1-voxel halo around the bbox are still
+ *                    visited so the contour closes correctly at the bbox edges.
+ */
+export declare function extractLabelContours(labels: Uint8Array, width: number, height: number, targetLabel: number, stride?: number, channelOffset?: number, bbox?: ContourBBox): Path2D;
+/**
+ * Detect the distinct non-zero labels present in a slice region.
+ *
+ * @param labels        Flat label array (see {@link extractLabelContours}).
+ * @param width         Grid width.
+ * @param height        Grid height.
+ * @param stride        Bytes per voxel.
+ * @param channelOffset Offset within each voxel.
+ * @param bbox          Optional region to scan (defaults to full grid).
+ * @returns Sorted array of distinct label values (0 omitted).
+ */
+export declare function findLabelsInSlice(labels: Uint8Array, width: number, height: number, stride?: number, channelOffset?: number, bbox?: ContourBBox): number[];

package/dist/Utils/segmentation/core/MarchingSquares.js

@@ -0,0 +1,169 @@
+/**
+ * MarchingSquares — Extract vector contours from a 2D voxel label grid.
+ *
+ * For each label, produces a `Path2D` whose subpaths are small per-cell
+ * polygons. The polygons tile the region occupied by the target label; the
+ * union (via `ctx.fill(path, 'nonzero')`) is the label's silhouette on the
+ * voxel grid.
+ *
+ * Coordinate convention:
+ *   - Voxel (i, j) occupies the unit square [i, i+1] × [j, j+1] in render
+ *     space, with its center at (i+0.5, j+0.5). This matches ITK-SNAP /
+ *     standard imaging viewers and the existing `renderSliceToCanvas`
+ *     `scale(scaledW / W, scaledH / H)` mapping.
+ *   - Marching squares treats voxels as point samples at their centers:
+ *     cell (i, j) has corners at voxel centers (i+0.5, j+0.5),
+ *     (i+1.5, j+0.5), (i+1.5, j+1.5), (i+0.5, j+1.5).
+ *   - This produces 45°-cut contours (diamonds for isolated voxels, rounded
+ *     corners for connected regions) that stay within the voxel-square
+ *     bounds, so the rendered silhouette is a slightly-inset version of the
+ *     ITK-SNAP silhouette with smooth diagonals.
+ *
+ * Saddle cases (5 and 10) use a fixed convention: the two in-corners are
+ * treated as disconnected within the cell (4-connectivity interpretation).
+ */
+/**
+ * Per-cell polygon lookup for the 16 marching-squares cases.
+ *
+ * Corner bit layout:  TL=8, TR=4, BR=2, BL=1
+ *
+ * Coordinates are within the unit cell, 0 ≤ x ≤ 1, 0 ≤ y ≤ 1,
+ * where (0, 0) is the TL corner of the cell. Add (i, j) to get absolute.
+ *
+ * Each case may emit 0, 1, or 2 polygons (saddles → 2).
+ * Polygon vertices are listed in a CCW order in screen space (y-down),
+ * which corresponds to CW in math coords. Path2D `fill(nonzero)` handles
+ * this consistently.
+ */
+const CELL_POLYGONS = [
+    /* 0  (empty) */ [],
+    /* 1  (BL)    */ [[[0, 0.5], [0.5, 1], [0, 1]]],
+    /* 2  (BR)    */ [[[0.5, 1], [1, 0.5], [1, 1]]],
+    /* 3  (BR+BL) */ [[[0, 0.5], [1, 0.5], [1, 1], [0, 1]]],
+    /* 4  (TR)    */ [[[0.5, 0], [1, 0], [1, 0.5]]],
+    /* 5  (TR+BL saddle) */ [
+        [[0.5, 0], [1, 0], [1, 0.5]],
+        [[0, 0.5], [0.5, 1], [0, 1]],
+    ],
+    /* 6  (TR+BR) */ [[[0.5, 0], [1, 0], [1, 1], [0.5, 1]]],
+    /* 7  (TR+BR+BL, !TL) */ [[[0.5, 0], [1, 0], [1, 1], [0, 1], [0, 0.5]]],
+    /* 8  (TL)    */ [[[0, 0], [0.5, 0], [0, 0.5]]],
+    /* 9  (TL+BL) */ [[[0, 0], [0.5, 0], [0.5, 1], [0, 1]]],
+    /* 10 (TL+BR saddle) */ [
+        [[0, 0], [0.5, 0], [0, 0.5]],
+        [[0.5, 1], [1, 0.5], [1, 1]],
+    ],
+    /* 11 (TL+BR+BL, !TR) */ [[[0, 0], [0.5, 0], [1, 0.5], [1, 1], [0, 1]]],
+    /* 12 (TL+TR) */ [[[0, 0], [1, 0], [1, 0.5], [0, 0.5]]],
+    /* 13 (TL+TR+BL, !BR) */ [[[0, 0], [1, 0], [1, 0.5], [0.5, 1], [0, 1]]],
+    /* 14 (TL+TR+BR, !BL) */ [[[0, 0], [1, 0], [1, 1], [0.5, 1], [0, 0.5]]],
+    /* 15 (full)  */ [[[0, 0], [1, 0], [1, 1], [0, 1]]],
+];
+/**
+ * Emit all per-cell polygons covering the voxels where `labels === targetLabel`.
+ * Pure geometry function — no Canvas dependency. Consumers can build a Path2D
+ * (see {@link extractLabelContours}) or walk the vertex arrays directly
+ * (tests, export, stroke rendering).
+ */
+export function extractLabelPolygons(labels, width, height, targetLabel, stride = 1, channelOffset = 0, bbox) {
+    var _a, _b, _c, _d;
+    const out = [];
+    const cx0 = ((_a = bbox === null || bbox === void 0 ? void 0 : bbox.x0) !== null && _a !== void 0 ? _a : 0) - 1;
+    const cy0 = ((_b = bbox === null || bbox === void 0 ? void 0 : bbox.y0) !== null && _b !== void 0 ? _b : 0) - 1;
+    const cx1 = (_c = bbox === null || bbox === void 0 ? void 0 : bbox.x1) !== null && _c !== void 0 ? _c : width;
+    const cy1 = (_d = bbox === null || bbox === void 0 ? void 0 : bbox.y1) !== null && _d !== void 0 ? _d : height;
+    const i0 = Math.max(-1, cx0);
+    const j0 = Math.max(-1, cy0);
+    const i1 = Math.min(width, cx1);
+    const j1 = Math.min(height, cy1);
+    const sample = (x, y) => {
+        if (x < 0 || x >= width || y < 0 || y >= height)
+            return false;
+        return labels[(y * width + x) * stride + channelOffset] === targetLabel;
+    };
+    // Shift output by +0.5 so that marching-squares samples (voxel positions)
+    // map to voxel-square CENTERS in render space. Voxel (i, j) occupies
+    // render square [i, i+1] × [j, j+1]; its center is (i+0.5, j+0.5).
+    const SHIFT = 0.5;
+    for (let j = j0; j < j1; j++) {
+        for (let i = i0; i < i1; i++) {
+            const tl = sample(i, j);
+            const tr = sample(i + 1, j);
+            const br = sample(i + 1, j + 1);
+            const bl = sample(i, j + 1);
+            const code = (tl ? 8 : 0) |
+                (tr ? 4 : 0) |
+                (br ? 2 : 0) |
+                (bl ? 1 : 0);
+            if (code === 0)
+                continue;
+            const polygons = CELL_POLYGONS[code];
+            for (let p = 0; p < polygons.length; p++) {
+                const poly = polygons[p];
+                const abs = new Array(poly.length);
+                for (let k = 0; k < poly.length; k++) {
+                    abs[k] = [i + poly[k][0] + SHIFT, j + poly[k][1] + SHIFT];
+                }
+                out.push(abs);
+            }
+        }
+    }
+    return out;
+}
+/**
+ * Extract a `Path2D` covering all voxels equal to `targetLabel`.
+ *
+ * @param labels      Flat label array. Addressed as
+ *                    `labels[(y * width + x) * stride + channelOffset]`.
+ * @param width       Grid width in voxels.
+ * @param height      Grid height in voxels.
+ * @param targetLabel Label value to extract (1..255; 0 is background).
+ * @param stride      Bytes per voxel (default 1). Use MaskVolume.numChannels
+ *                    when reading interleaved slices.
+ * @param channelOffset Offset within each voxel's channels to sample.
+ *                    Default 0 (first channel = label id).
+ * @param bbox        Optional voxel-space bbox to limit extraction.
+ *                    Cells in a 1-voxel halo around the bbox are still
+ *                    visited so the contour closes correctly at the bbox edges.
+ */
+export function extractLabelContours(labels, width, height, targetLabel, stride = 1, channelOffset = 0, bbox) {
+    const polygons = extractLabelPolygons(labels, width, height, targetLabel, stride, channelOffset, bbox);
+    const path = new Path2D();
+    for (let p = 0; p < polygons.length; p++) {
+        const poly = polygons[p];
+        path.moveTo(poly[0][0], poly[0][1]);
+        for (let k = 1; k < poly.length; k++) {
+            path.lineTo(poly[k][0], poly[k][1]);
+        }
+        path.closePath();
+    }
+    return path;
+}
+/**
+ * Detect the distinct non-zero labels present in a slice region.
+ *
+ * @param labels        Flat label array (see {@link extractLabelContours}).
+ * @param width         Grid width.
+ * @param height        Grid height.
+ * @param stride        Bytes per voxel.
+ * @param channelOffset Offset within each voxel.
+ * @param bbox          Optional region to scan (defaults to full grid).
+ * @returns Sorted array of distinct label values (0 omitted).
+ */
+export function findLabelsInSlice(labels, width, height, stride = 1, channelOffset = 0, bbox) {
+    var _a, _b, _c, _d;
+    const x0 = (_a = bbox === null || bbox === void 0 ? void 0 : bbox.x0) !== null && _a !== void 0 ? _a : 0;
+    const y0 = (_b = bbox === null || bbox === void 0 ? void 0 : bbox.y0) !== null && _b !== void 0 ? _b : 0;
+    const x1 = (_c = bbox === null || bbox === void 0 ? void 0 : bbox.x1) !== null && _c !== void 0 ? _c : width;
+    const y1 = (_d = bbox === null || bbox === void 0 ? void 0 : bbox.y1) !== null && _d !== void 0 ? _d : height;
+    const seen = new Set();
+    for (let y = y0; y < y1; y++) {
+        for (let x = x0; x < x1; x++) {
+            const v = labels[(y * width + x) * stride + channelOffset];
+            if (v !== 0)
+                seen.add(v);
+        }
+    }
+    return Array.from(seen).sort((a, b) => a - b);
+}
+//# sourceMappingURL=MarchingSquares.js.map

package/dist/Utils/segmentation/core/MarchingSquares.js.map

@@ -0,0 +1 @@
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package/dist/Utils/segmentation/core/index.d.ts

@@ -72,3 +72,5 @@ export { RenderMode, MASK_CHANNEL_COLORS, MASK_CHANNEL_CSS_COLORS, CHANNEL_COLOR
 export { MaskVolume } from './MaskVolume';
 export type { MaskDelta, UndoEntry } from './UndoManager';
 export { UndoManager } from './UndoManager';
+export type { ContourBBox, ContourPolygon } from './MarchingSquares';
+export { extractLabelContours, extractLabelPolygons, findLabelsInSlice, } from './MarchingSquares';

package/dist/Utils/segmentation/core/index.js

@@ -71,4 +71,5 @@ export { RenderMode, MASK_CHANNEL_COLORS, MASK_CHANNEL_CSS_COLORS, CHANNEL_COLOR
 // ── Core volume ────────────────────────────────────────────────────────────
 export { MaskVolume } from './MaskVolume';
 export { UndoManager } from './UndoManager';
+export { extractLabelContours, extractLabelPolygons, findLabelsInSlice, } from './MarchingSquares';
 //# sourceMappingURL=index.js.map

package/dist/Utils/segmentation/core/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/Utils/segmentation/core/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAoEG;AA8CH,OAAO,EACL,UAAU,EACV,mBAAmB,EACnB,uBAAuB,EACvB,cAAc,EACd,kBAAkB,EAClB,SAAS,EACT,SAAS,GACV,MAAM,SAAS,CAAC;AAEjB,8EAA8E;AAC9E,OAAO,EAAE,UAAU,EAAE,MAAM,cAAc,CAAC;AAI1C,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/Utils/segmentation/core/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAoEG;AA8CH,OAAO,EACL,UAAU,EACV,mBAAmB,EACnB,uBAAuB,EACvB,cAAc,EACd,kBAAkB,EAClB,SAAS,EACT,SAAS,GACV,MAAM,SAAS,CAAC;AAEjB,8EAA8E;AAC9E,OAAO,EAAE,UAAU,EAAE,MAAM,cAAc,CAAC;AAI1C,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAI5C,OAAO,EACL,oBAAoB,EACpB,oBAAoB,EACpB,iBAAiB,GAClB,MAAM,mBAAmB,CAAC"}

package/dist/Utils/segmentation/eventRouter/EventRouter.js

@@ -26,6 +26,11 @@ const DEFAULT_KEYBOARD_SETTINGS = {
  * Drawing tools that can be used with Shift+drag
  */
 const DRAWING_TOOLS = new Set(['pencil', 'brush', 'eraser']);
+/**
+ * Sphere-family tools (single-placement sphere + brush/eraser variants).
+ * All three participate in the same crosshair / contrast mutual-exclusion rules.
+ */
+const SPHERE_TOOLS = new Set(['sphere', 'sphereBrush', 'sphereEraser']);
 export class EventRouter {
     constructor(config) {
         // === State ===
@@ -156,8 +161,8 @@ export class EventRouter {
      */
     setGuiTool(tool) {
         this.guiTool = tool;
-        // When entering sphere mode, keep crosshair if active, otherwise idle
-        if (tool === 'sphere') {
+        // When entering any sphere-family tool, keep crosshair if active, otherwise idle
+        if (SPHERE_TOOLS.has(tool)) {
             if (!this.state.crosshairEnabled) {
                 this.setMode('idle');
             }
@@ -169,10 +174,12 @@ export class EventRouter {
      * Blocked when draw or contrast mode is active, or left button is held (mutual exclusion).
      */
     toggleCrosshair() {
-        // Allow crosshair in drawing tools and sphere mode
-        if (!DRAWING_TOOLS.has(this.guiTool) && this.guiTool !== 'sphere')
+        // Allow crosshair in drawing tools and all sphere-family tools (sphere / sphereBrush / sphereEraser)
+        if (!DRAWING_TOOLS.has(this.guiTool) && !SPHERE_TOOLS.has(this.guiTool))
             return;
-        // Block crosshair activation during draw, contrast, or while left button held
+        // Block crosshair activation during draw, contrast, or while left button held.
+        // The leftButtonDown guard also enforces "once a sphere preview is on screen,
+        // S is ignored until mouseup" for sphereBrush/sphereEraser.
         if (this.state.shiftHeld || this.state.leftButtonDown || this.mode === 'draw' || this.mode === 'contrast')
             return;
         this.state.crosshairEnabled = !this.state.crosshairEnabled;
@@ -299,9 +306,9 @@ export class EventRouter {
             }
         }
         if (this.contrastEnabled && this.keyboardSettings.contrast.includes(ev.key)) {
-            // Block contrast state when crosshair, draw, or sphere is active (mutual exclusion)
+            // Block contrast state when crosshair, draw, or any sphere-family tool is active (mutual exclusion)
             if (!this.state.crosshairEnabled && this.mode !== 'draw'
-                && this.guiTool !== 'sphere') {
+                && !SPHERE_TOOLS.has(this.guiTool)) {
                 this.state.ctrlHeld = true;
             }
         }

package/dist/Utils/segmentation/eventRouter/EventRouter.js.map

@@ -1 +1 @@
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package/dist/Utils/segmentation/tools/DrawingTool.d.ts

@@ -4,6 +4,10 @@
  * Extracted from DrawToolCore.paintOnCanvas() closure (Phase 3).
  * Handles left-click drawing operations: pencil stroke + fill, brush strokes,
  * eraser, and undo snapshot capture/push.
+ *
+ * Phase B: Brush mode now writes voxels directly during mousemove and
+ * re-renders via marching squares, eliminating the visual "snap" between
+ * the smooth canvas stroke and the voxel-based post-release render.
  */
 import { BaseTool } from "./BaseTool";
 import type { ToolContext } from "./BaseTool";
@@ -21,6 +25,8 @@ export declare class DrawingTool extends BaseTool {
     private preDrawSlice;
     private preDrawAxis;
     private preDrawSliceIndex;
+    /** Previous voxel-space position for Bresenham interpolation (brush mode) */
+    private prevVoxel;
     private callbacks;
     constructor(ctx: ToolContext, callbacks: DrawingHostDeps);
     /** Whether a draw operation is currently active */
@@ -56,30 +62,49 @@ export declare class DrawingTool extends BaseTool {
     /**
      * Create a self-managing mouseover/mouseout/mousemove handler
      * that tracks brush hover position for the preview circle.
-     *
-     * The returned function should be registered on drawingCanvas for
-     * "mouseover" and "mouseout" events.  It adds/removes a "mousemove"
-     * listener on itself to keep mouseOverX/Y up-to-date while the
-     * cursor is inside the canvas.
      */
     createBrushTrackingHandler(): (e: MouseEvent) => void;
     /**
      * Render brush circle preview on the drawing context.
-     * Called from the start() render loop when in draw mode and not
-     * actively painting.  Skipped in pencil/eraser mode.
      */
     renderBrushPreview(ctx: CanvasRenderingContext2D, width: number, height: number): void;
+    /**
+     * Convert display (zoomed) coordinates to 3D voxel coordinates.
+     * Same logic as SphereBrushTool.canvasToVoxelCenter.
+     */
+    private canvasToVoxel3D;
+    /**
+     * Get voxel-space brush radius for visible axes.
+     * Converts display-pixel brush size to voxel units.
+     */
+    private getVoxelBrushRadius;
+    /**
+     * Paint a 2D ellipse of voxels on the current slice.
+     * Only the two visible axes are iterated; the slice-direction axis is fixed.
+     */
+    private paintVoxelEllipse;
+    /**
+     * Brush mode mousemove: write voxels along stroke segment, then re-render.
+     * Uses linear interpolation between prev and current positions to ensure
+     * no gaps when the mouse moves fast.
+     */
+    private paintBrushVoxelMove;
+    /**
+     * Re-render the active layer's canvas from MaskVolume via marching squares,
+     * then composite all layers to master.
+     */
+    private refreshLayerFromVolume;
     /** Capture pre-draw slice snapshot for undo */
     private capturePreDrawSnapshot;
     /** Push delta to UndoManager after drawing completes */
     private pushUndoDelta;
     /**
      * Redraws persisted layer data onto ctx before new pencil fill.
-     * Extracted from DrawToolCore.
+     * Delegates to the host's vector renderSliceToCanvas for consistency.
      */
     private redrawPreviousImageToLayerCtx;
-    /** Draw a line segment on a layer canvas */
+    /** Draw a line segment on a layer canvas (pencil mode only) */
     private drawLinesOnLayer;
-    /** Paint a segment on the current layer canvas and composite to master */
+    /** Paint a segment on the current layer canvas and composite to master (pencil mode) */
     private paintOnCanvasLayer;
 }