copper3d 3.2.0 → 3.3.0

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

@@ -0,0 +1,55 @@
+/**
+ * GaussianSmoother — 3D Gaussian smoothing for segmentation masks.
+ *
+ * Applies a separable 3D Gaussian blur to a single label channel within a
+ * MaskVolume, then thresholds the result back to a binary mask. This smooths
+ * jagged edges and fills small holes in segmentation annotations.
+ *
+ * Pure, stateless utility — no DOM/Canvas/GUI dependencies.
+ *
+ * Performance: uses direct typed-array access (bypassing getVoxel/setVoxel
+ * boundary checks) and branch-free convolution for the interior region.
+ */
+import type { MaskVolume } from './MaskVolume';
+export declare class GaussianSmoother {
+    /**
+     * Smooth a single label channel in-place using separable 3D Gaussian blur.
+     *
+     * Steps:
+     *  1. Extract — create a Float32Array with 1.0 where voxel === channel, 0.0 elsewhere.
+     *  2. Blur — apply separable Gaussian (X → Y → Z) on the float buffer.
+     *  3. Threshold — binarize at 0.5.
+     *  4. Write back — overwrite/erase voxels according to the thresholded result.
+     *
+     * @param volume  The MaskVolume to operate on (modified in-place).
+     * @param channel The label value to smooth (must be > 0).
+     * @param sigma   Base Gaussian sigma in voxel units (default 1.0).
+     * @param spacing Optional voxel spacing [sx, sy, sz]. When provided, per-axis
+     *                sigma is computed as `sigma / spacing[axis]` so that the
+     *                physical smoothing radius is isotropic.
+     */
+    static gaussianSmooth3D(volume: MaskVolume, channel: number, sigma?: number, spacing?: [number, number, number]): void;
+    /**
+     * Generate a normalized 1D Gaussian kernel truncated at ±3σ.
+     *
+     * @param sigma Standard deviation (in voxels). Must be > 0.
+     * @returns Normalized Float32Array of odd length.
+     */
+    static generateKernel1D(sigma: number): Float32Array;
+    /**
+     * In-place single-axis convolution with zero-padding at boundaries.
+     *
+     * Uses a 3-segment approach: left boundary (with bounds check),
+     * middle interior (branch-free, ~95% of work), right boundary
+     * (with bounds check). This eliminates per-element branching
+     * in the hot inner loop.
+     *
+     * @param data   Flat float buffer (width × height × depth).
+     * @param width  X dimension.
+     * @param height Y dimension.
+     * @param depth  Z dimension.
+     * @param axis   0 = X, 1 = Y, 2 = Z.
+     * @param kernel 1D convolution kernel (odd length).
+     */
+    private static convolve1D;
+}

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

@@ -0,0 +1,210 @@
+/**
+ * GaussianSmoother — 3D Gaussian smoothing for segmentation masks.
+ *
+ * Applies a separable 3D Gaussian blur to a single label channel within a
+ * MaskVolume, then thresholds the result back to a binary mask. This smooths
+ * jagged edges and fills small holes in segmentation annotations.
+ *
+ * Pure, stateless utility — no DOM/Canvas/GUI dependencies.
+ *
+ * Performance: uses direct typed-array access (bypassing getVoxel/setVoxel
+ * boundary checks) and branch-free convolution for the interior region.
+ */
+export class GaussianSmoother {
+    /**
+     * Smooth a single label channel in-place using separable 3D Gaussian blur.
+     *
+     * Steps:
+     *  1. Extract — create a Float32Array with 1.0 where voxel === channel, 0.0 elsewhere.
+     *  2. Blur — apply separable Gaussian (X → Y → Z) on the float buffer.
+     *  3. Threshold — binarize at 0.5.
+     *  4. Write back — overwrite/erase voxels according to the thresholded result.
+     *
+     * @param volume  The MaskVolume to operate on (modified in-place).
+     * @param channel The label value to smooth (must be > 0).
+     * @param sigma   Base Gaussian sigma in voxel units (default 1.0).
+     * @param spacing Optional voxel spacing [sx, sy, sz]. When provided, per-axis
+     *                sigma is computed as `sigma / spacing[axis]` so that the
+     *                physical smoothing radius is isotropic.
+     */
+    static gaussianSmooth3D(volume, channel, sigma = 1.0, spacing) {
+        const dims = volume.getDimensions();
+        const { width, height, depth } = dims;
+        const totalVoxels = width * height * depth;
+        // Direct access to underlying buffer — bypasses getVoxel/setVoxel
+        // boundary checks for ~10x speedup in hot loops.
+        const rawData = volume.getRawData();
+        const channels = volume.getChannels();
+        const bytesPerSlice = volume.getBytesPerSlice();
+        const rowStride = width * channels;
+        // Compute per-axis sigma (normalized to voxel units)
+        const sigmaX = spacing ? sigma / spacing[0] : sigma;
+        const sigmaY = spacing ? sigma / spacing[1] : sigma;
+        const sigmaZ = spacing ? sigma / spacing[2] : sigma;
+        // 1. Extract binary float buffer — direct array access
+        const buffer = new Float32Array(totalVoxels);
+        for (let z = 0; z < depth; z++) {
+            const zOffset = z * bytesPerSlice;
+            for (let y = 0; y < height; y++) {
+                const zyOffset = zOffset + y * rowStride;
+                for (let x = 0; x < width; x++) {
+                    const bufIdx = z * height * width + y * width + x;
+                    buffer[bufIdx] = rawData[zyOffset + x * channels] === channel ? 1.0 : 0.0;
+                }
+            }
+        }
+        // 2. Separable Gaussian blur: X → Y → Z
+        const kernelX = GaussianSmoother.generateKernel1D(sigmaX);
+        const kernelY = GaussianSmoother.generateKernel1D(sigmaY);
+        const kernelZ = GaussianSmoother.generateKernel1D(sigmaZ);
+        GaussianSmoother.convolve1D(buffer, width, height, depth, 0, kernelX); // X axis
+        GaussianSmoother.convolve1D(buffer, width, height, depth, 1, kernelY); // Y axis
+        GaussianSmoother.convolve1D(buffer, width, height, depth, 2, kernelZ); // Z axis
+        // 3 & 4. Threshold and write back — direct array access
+        for (let z = 0; z < depth; z++) {
+            const zOffset = z * bytesPerSlice;
+            for (let y = 0; y < height; y++) {
+                const zyOffset = zOffset + y * rowStride;
+                for (let x = 0; x < width; x++) {
+                    const bufIdx = z * height * width + y * width + x;
+                    const smoothed = buffer[bufIdx] >= 0.5 ? 1 : 0;
+                    const rawIdx = zyOffset + x * channels;
+                    const original = rawData[rawIdx];
+                    if (smoothed === 1 && original !== channel) {
+                        // Smoothed region expands into this voxel — overwrite
+                        rawData[rawIdx] = channel;
+                    }
+                    else if (smoothed === 0 && original === channel) {
+                        // Smoothed region retreats — erase
+                        rawData[rawIdx] = 0;
+                    }
+                    // Otherwise leave unchanged
+                }
+            }
+        }
+    }
+    /**
+     * Generate a normalized 1D Gaussian kernel truncated at ±3σ.
+     *
+     * @param sigma Standard deviation (in voxels). Must be > 0.
+     * @returns Normalized Float32Array of odd length.
+     */
+    static generateKernel1D(sigma) {
+        if (sigma <= 0) {
+            return new Float32Array([1.0]);
+        }
+        const radius = Math.ceil(sigma * 3);
+        const size = 2 * radius + 1;
+        const kernel = new Float32Array(size);
+        const twoSigmaSq = 2 * sigma * sigma;
+        let sum = 0;
+        for (let i = 0; i < size; i++) {
+            const x = i - radius;
+            kernel[i] = Math.exp(-(x * x) / twoSigmaSq);
+            sum += kernel[i];
+        }
+        // Normalize
+        for (let i = 0; i < size; i++) {
+            kernel[i] /= sum;
+        }
+        return kernel;
+    }
+    /**
+     * In-place single-axis convolution with zero-padding at boundaries.
+     *
+     * Uses a 3-segment approach: left boundary (with bounds check),
+     * middle interior (branch-free, ~95% of work), right boundary
+     * (with bounds check). This eliminates per-element branching
+     * in the hot inner loop.
+     *
+     * @param data   Flat float buffer (width × height × depth).
+     * @param width  X dimension.
+     * @param height Y dimension.
+     * @param depth  Z dimension.
+     * @param axis   0 = X, 1 = Y, 2 = Z.
+     * @param kernel 1D convolution kernel (odd length).
+     */
+    static convolve1D(data, width, height, depth, axis, kernel) {
+        const kLen = kernel.length;
+        const radius = (kLen - 1) / 2;
+        // Determine the dimension length along the convolution axis
+        // and the stride between consecutive elements along that axis
+        let axisLen;
+        let stride;
+        let outerCount;
+        if (axis === 0) {
+            // X axis: stride = 1, iterate over all (y, z) lines
+            axisLen = width;
+            stride = 1;
+            outerCount = height * depth;
+        }
+        else if (axis === 1) {
+            // Y axis: stride = width, iterate over all (x, z) lines
+            axisLen = height;
+            stride = width;
+            outerCount = width * depth;
+        }
+        else {
+            // Z axis: stride = width * height, iterate over all (x, y) lines
+            axisLen = depth;
+            stride = width * height;
+            outerCount = width * height;
+        }
+        // Precompute middle segment bounds
+        const midStart = radius;
+        const midEnd = axisLen - radius;
+        // Temporary line buffer to avoid read-after-write issues
+        const line = new Float32Array(axisLen);
+        for (let outer = 0; outer < outerCount; outer++) {
+            // Compute the starting index for this line
+            let lineStart;
+            if (axis === 0) {
+                lineStart = outer * width;
+            }
+            else if (axis === 1) {
+                const z = Math.floor(outer / width);
+                const x = outer % width;
+                lineStart = z * width * height + x;
+            }
+            else {
+                lineStart = outer;
+            }
+            // Read the line
+            for (let i = 0; i < axisLen; i++) {
+                line[i] = data[lineStart + i * stride];
+            }
+            // Left boundary segment (i = 0 .. radius-1): lower bound check
+            for (let i = 0; i < midStart; i++) {
+                let sum = 0;
+                for (let k = 0; k < kLen; k++) {
+                    const j = i + k - radius;
+                    if (j >= 0) {
+                        sum += line[j] * kernel[k];
+                    }
+                }
+                data[lineStart + i * stride] = sum;
+            }
+            // Middle segment (i = radius .. axisLen-radius-1): NO bounds check
+            for (let i = midStart; i < midEnd; i++) {
+                let sum = 0;
+                const lineOffset = i - radius;
+                for (let k = 0; k < kLen; k++) {
+                    sum += line[lineOffset + k] * kernel[k];
+                }
+                data[lineStart + i * stride] = sum;
+            }
+            // Right boundary segment (i = axisLen-radius .. axisLen-1): upper bound check
+            for (let i = midEnd; i < axisLen; i++) {
+                let sum = 0;
+                for (let k = 0; k < kLen; k++) {
+                    const j = i + k - radius;
+                    if (j < axisLen) {
+                        sum += line[j] * kernel[k];
+                    }
+                }
+                data[lineStart + i * stride] = sum;
+            }
+        }
+    }
+}
+//# sourceMappingURL=GaussianSmoother.js.map

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

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

@@ -250,6 +250,15 @@ export declare class MaskVolume {
      * @returns Channel count (≥ 1).
      */
     getChannels(): number;
+    /**
+     * Return the number of bytes in one complete z-slice.
+     *
+     * Equal to `width × height × channels`. Useful for direct buffer
+     * index arithmetic in performance-critical code paths.
+     *
+     * @returns Bytes per z-slice.
+     */
+    getBytesPerSlice(): number;
     /**
      * Return total memory used by the backing buffer, in bytes.
      *

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

@@ -592,6 +592,17 @@ export class MaskVolume {
     getChannels() {
         return this.numChannels;
     }
+    /**
+     * Return the number of bytes in one complete z-slice.
+     *
+     * Equal to `width × height × channels`. Useful for direct buffer
+     * index arithmetic in performance-critical code paths.
+     *
+     * @returns Bytes per z-slice.
+     */
+    getBytesPerSlice() {
+        return this.bytesPerSlice;
+    }
     /**
      * Return total memory used by the backing buffer, in bytes.
      *

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

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

@@ -26,10 +26,6 @@ export declare class DragSliceTool extends BaseTool {
     setShowDragNumberDiv(div: HTMLDivElement): void;
     updateIndex(move: number): void;
     private drawDragSlice;
-    /**
-     * Composite all visible layer canvases to the master display canvas.
-     */
-    private compositeAllLayers;
     private cleanCanvases;
     updateShowNumDiv(contrastNum: number): void;
     updateCurrentContrastSlice(): any;

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

@@ -111,8 +111,8 @@ export class DragSliceTool extends BaseTool {
                         }
                     }
                 }
-                // Composite all layers to master canvas
-                this.compositeAllLayers();
+                // Composite all layers to master canvas (uses per-layer alpha)
+                this.callbacks.compositeAllLayers();
             }
             // Refresh sphere overlay from volume for the new slice
             if (this.ctx.gui_states.mode.sphere) {
@@ -121,23 +121,6 @@ export class DragSliceTool extends BaseTool {
             view.switchSliceFlag = false;
         }
     }
-    /**
-     * Composite all visible layer canvases to the master display canvas.
-     */
-    compositeAllLayers() {
-        const masterCtx = this.ctx.protectedData.ctxes.drawingLayerMasterCtx;
-        const width = this.ctx.nrrd_states.view.changedWidth;
-        const height = this.ctx.nrrd_states.view.changedHeight;
-        masterCtx.clearRect(0, 0, width, height);
-        // Master stores full-alpha composite; globalAlpha applied in start() render loop.
-        for (const layerId of this.ctx.nrrd_states.image.layers) {
-            if (!this.ctx.gui_states.layerChannel.layerVisibility[layerId])
-                continue;
-            const target = this.ctx.protectedData.layerTargets.get(layerId);
-            if (target)
-                masterCtx.drawImage(target.canvas, 0, 0, width, height);
-        }
-    }
     // ===== Canvas Cleanup =====
     cleanCanvases(flag) {
         if (flag) {

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

@@ -1 +1 @@
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package/dist/Utils/segmentation/tools/SliceRenderPipeline.js

@@ -330,6 +330,8 @@ export class SliceRenderPipeline extends BaseTool {
      * Then update the changedWidth and changedHeight based on the sizeFactor.
      */
     updateOriginAndChangedWH() {
+        const prevW = this.ctx.nrrd_states.image.originWidth;
+        const prevH = this.ctx.nrrd_states.image.originHeight;
         this.ctx.nrrd_states.image.originWidth =
             this.ctx.protectedData.canvases.originCanvas.width;
         this.ctx.nrrd_states.image.originHeight =
@@ -338,7 +340,12 @@ export class SliceRenderPipeline extends BaseTool {
         // Setting them here would defeat the sizeChanged detection in resizePaintArea,
         // causing canvas elements to keep stale dimensions after axis switches.
         this.resizePaintArea(this.ctx.nrrd_states.view.sizeFactor);
-        this.resetPaintAreaUIPosition();
+        // Only re-center when origin dimensions changed (e.g. axis switch).
+        // Contrast toggle doesn't change origin size, so skip to preserve user's pan/zoom.
+        if (prevW !== this.ctx.nrrd_states.image.originWidth ||
+            prevH !== this.ctx.nrrd_states.image.originHeight) {
+            this.resetPaintAreaUIPosition();
+        }
     }
     /**
      * Keep all contrast slice index to same.

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

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

@@ -66,7 +66,7 @@ export type SphereHostDeps = Pick<ToolHost, 'setEmptyCanvasSize' | 'drawImageOnE
 /** DrawingTool host dependencies */
 export type DrawingHostDeps = Pick<ToolHost, 'setCurrentLayer' | 'compositeAllLayers' | 'syncLayerSliceData' | 'filterDrawedImage' | 'getVolumeForLayer' | 'pushUndoDelta' | 'getEraserUrls'>;
 /** DragSliceTool host dependencies */
-export type DragSliceHostDeps = Pick<ToolHost, 'setSyncsliceNum' | 'setIsDrawFalse' | 'flipDisplayImageByAxis' | 'setEmptyCanvasSize' | 'getOrCreateSliceBuffer' | 'renderSliceToCanvas' | 'refreshSphereOverlay'>;
+export type DragSliceHostDeps = Pick<ToolHost, 'setSyncsliceNum' | 'setIsDrawFalse' | 'flipDisplayImageByAxis' | 'setEmptyCanvasSize' | 'getOrCreateSliceBuffer' | 'renderSliceToCanvas' | 'refreshSphereOverlay' | 'compositeAllLayers'>;
 /** LayerChannelManager host dependencies */
 export type LayerChannelHostDeps = Pick<ToolHost, 'reloadMasksFromVolume' | 'getVolumeForLayer' | 'onChannelColorChanged'>;
 /** SliceRenderPipeline host dependencies */