copper3d 2.2.3 → 3.0.0

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

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

@@ -0,0 +1,97 @@
+/**
+ * Migration Utilities for MaskVolume
+ *
+ * Provides bidirectional conversion between the legacy per-slice
+ * ImageData storage (`IPaintImages`) and the new contiguous 3D
+ * volumetric storage (`MaskVolume`).
+ *
+ * These utilities enable:
+ *  - **Forward migration**: Import existing annotation data into MaskVolume.
+ *  - **Rollback compatibility**: Export MaskVolume back to IPaintImages.
+ *
+ * @example
+ * ```ts
+ * // Forward: legacy → volume
+ * const volume = convertIPaintImagesToVolume(paintImages, { width: 512, height: 512, depth: 100 });
+ *
+ * // Backward: volume → legacy
+ * const legacy = convertVolumeToIPaintImages(volume);
+ * ```
+ */
+import type { Dimensions } from './types';
+import { MaskVolume } from './MaskVolume';
+/**
+ * A single painted slice (legacy format).
+ */
+export interface IPaintImage {
+    index: number;
+    image: ImageData;
+}
+/**
+ * Per-axis collection of painted slices (legacy format).
+ */
+export interface IPaintImages {
+    x: IPaintImage[];
+    y: IPaintImage[];
+    z: IPaintImage[];
+}
+/**
+ * Convert legacy per-slice ImageData storage into a MaskVolume.
+ *
+ * The function iterates over all three axes (`x`, `y`, `z`) and inserts
+ * each slice into the volume using `setSliceFromImageData`.
+ *
+ * **Sparse data handling**: Slices that are absent from the arrays are
+ * left as zero (the MaskVolume default). Duplicate indices are
+ * overwritten in order (last wins).
+ *
+ * @param paintImages Legacy per-axis slice collection.
+ * @param dimensions  Volume dimensions (must match the ImageData sizes).
+ * @param channel     Target channel in the volume (default 0).
+ *
+ * @returns A new MaskVolume populated with the legacy data.
+ *
+ * @throws {Error} If a slice's ImageData dimensions don't match the
+ *                 expected size for its axis.
+ *
+ * @example
+ * ```ts
+ * const volume = convertIPaintImagesToVolume(
+ *   maskData.paintImagesLayer1,
+ *   { width: 512, height: 512, depth: 100 },
+ * );
+ * ```
+ */
+export declare function convertIPaintImagesToVolume(paintImages: IPaintImages, dimensions: Dimensions, channel?: number): MaskVolume;
+/**
+ * Convert a MaskVolume back to legacy per-slice ImageData storage.
+ *
+ * Extracts **all** slices along the Z axis (axial) into an
+ * `IPaintImages` structure. X and Y axes are left as empty arrays
+ * since the legacy system can reconstruct them on demand.
+ *
+ * Only non-empty slices (those containing at least one non-zero pixel)
+ * are included, matching the sparse behaviour of the original storage.
+ *
+ * @param volume  The MaskVolume to export.
+ * @param channel Channel to extract (default 0).
+ * @param options Export options.
+ * @param options.includeAllAxes If true, also export X and Y axis slices
+ *                               (expensive — use only if needed for full
+ *                               backward compatibility). Default: false.
+ * @param options.includeEmpty   If true, include slices that are entirely
+ *                               zero. Default: false.
+ *
+ * @returns A legacy IPaintImages structure.
+ *
+ * @example
+ * ```ts
+ * const legacy = convertVolumeToIPaintImages(volume);
+ * // legacy.z contains non-empty axial slices
+ * // legacy.x and legacy.y are empty by default
+ * ```
+ */
+export declare function convertVolumeToIPaintImages(volume: MaskVolume, channel?: number, options?: {
+    includeAllAxes?: boolean;
+    includeEmpty?: boolean;
+}): IPaintImages;

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

@@ -0,0 +1,163 @@
+/**
+ * Migration Utilities for MaskVolume
+ *
+ * Provides bidirectional conversion between the legacy per-slice
+ * ImageData storage (`IPaintImages`) and the new contiguous 3D
+ * volumetric storage (`MaskVolume`).
+ *
+ * These utilities enable:
+ *  - **Forward migration**: Import existing annotation data into MaskVolume.
+ *  - **Rollback compatibility**: Export MaskVolume back to IPaintImages.
+ *
+ * @example
+ * ```ts
+ * // Forward: legacy → volume
+ * const volume = convertIPaintImagesToVolume(paintImages, { width: 512, height: 512, depth: 100 });
+ *
+ * // Backward: volume → legacy
+ * const legacy = convertVolumeToIPaintImages(volume);
+ * ```
+ */
+import { MaskVolume } from './MaskVolume';
+// ── Forward migration: IPaintImages → MaskVolume ────────────────────────
+/**
+ * Convert legacy per-slice ImageData storage into a MaskVolume.
+ *
+ * The function iterates over all three axes (`x`, `y`, `z`) and inserts
+ * each slice into the volume using `setSliceFromImageData`.
+ *
+ * **Sparse data handling**: Slices that are absent from the arrays are
+ * left as zero (the MaskVolume default). Duplicate indices are
+ * overwritten in order (last wins).
+ *
+ * @param paintImages Legacy per-axis slice collection.
+ * @param dimensions  Volume dimensions (must match the ImageData sizes).
+ * @param channel     Target channel in the volume (default 0).
+ *
+ * @returns A new MaskVolume populated with the legacy data.
+ *
+ * @throws {Error} If a slice's ImageData dimensions don't match the
+ *                 expected size for its axis.
+ *
+ * @example
+ * ```ts
+ * const volume = convertIPaintImagesToVolume(
+ *   maskData.paintImagesLayer1,
+ *   { width: 512, height: 512, depth: 100 },
+ * );
+ * ```
+ */
+export function convertIPaintImagesToVolume(paintImages, dimensions, channel = 0) {
+    if (!paintImages) {
+        throw new Error('paintImages is null or undefined');
+    }
+    if (dimensions.width < 1 ||
+        dimensions.height < 1 ||
+        dimensions.depth < 1) {
+        throw new RangeError(`Dimensions must be ≥ 1, got (${dimensions.width}, ${dimensions.height}, ${dimensions.depth})`);
+    }
+    const volume = new MaskVolume(dimensions.width, dimensions.height, dimensions.depth);
+    // Process each axis
+    const axes = [
+        { key: 'z', axis: 'z' },
+        { key: 'y', axis: 'y' },
+        { key: 'x', axis: 'x' },
+    ];
+    for (const { key, axis } of axes) {
+        const slices = paintImages[key];
+        if (!slices || !Array.isArray(slices))
+            continue;
+        for (const paintImage of slices) {
+            if (!paintImage || paintImage.image == null)
+                continue;
+            const { index, image } = paintImage;
+            // Validate slice index bounds
+            const maxIndex = axis === 'x' ? dimensions.width :
+                axis === 'y' ? dimensions.height :
+                    dimensions.depth;
+            if (index < 0 || index >= maxIndex) {
+                continue; // Skip out-of-bounds slices silently
+            }
+            volume.setSliceFromImageData(index, image, axis, channel);
+        }
+    }
+    return volume;
+}
+// ── Backward migration: MaskVolume → IPaintImages ───────────────────────
+/**
+ * Convert a MaskVolume back to legacy per-slice ImageData storage.
+ *
+ * Extracts **all** slices along the Z axis (axial) into an
+ * `IPaintImages` structure. X and Y axes are left as empty arrays
+ * since the legacy system can reconstruct them on demand.
+ *
+ * Only non-empty slices (those containing at least one non-zero pixel)
+ * are included, matching the sparse behaviour of the original storage.
+ *
+ * @param volume  The MaskVolume to export.
+ * @param channel Channel to extract (default 0).
+ * @param options Export options.
+ * @param options.includeAllAxes If true, also export X and Y axis slices
+ *                               (expensive — use only if needed for full
+ *                               backward compatibility). Default: false.
+ * @param options.includeEmpty   If true, include slices that are entirely
+ *                               zero. Default: false.
+ *
+ * @returns A legacy IPaintImages structure.
+ *
+ * @example
+ * ```ts
+ * const legacy = convertVolumeToIPaintImages(volume);
+ * // legacy.z contains non-empty axial slices
+ * // legacy.x and legacy.y are empty by default
+ * ```
+ */
+export function convertVolumeToIPaintImages(volume, channel = 0, options = {}) {
+    if (!volume) {
+        throw new Error('volume is null or undefined');
+    }
+    const { includeAllAxes = false, includeEmpty = false } = options;
+    const dims = volume.getDimensions();
+    const result = { x: [], y: [], z: [] };
+    const renderOpts = { channel };
+    // Always export Z axis (axial slices — most commonly used)
+    for (let z = 0; z < dims.depth; z++) {
+        const imageData = volume.getSliceImageData(z, 'z', renderOpts);
+        if (includeEmpty || hasNonZeroPixels(imageData)) {
+            result.z.push({ index: z, image: imageData });
+        }
+    }
+    // Optionally export X and Y axes
+    if (includeAllAxes) {
+        for (let y = 0; y < dims.height; y++) {
+            const imageData = volume.getSliceImageData(y, 'y', renderOpts);
+            if (includeEmpty || hasNonZeroPixels(imageData)) {
+                result.y.push({ index: y, image: imageData });
+            }
+        }
+        for (let x = 0; x < dims.width; x++) {
+            const imageData = volume.getSliceImageData(x, 'x', renderOpts);
+            if (includeEmpty || hasNonZeroPixels(imageData)) {
+                result.x.push({ index: x, image: imageData });
+            }
+        }
+    }
+    return result;
+}
+// ── Helpers ──────────────────────────────────────────────────────────────
+/**
+ * Check whether an ImageData has any non-zero pixel data.
+ *
+ * Only checks the R channel (index 0 of every 4-byte group) since
+ * MaskVolume stores grayscale values in the R channel.
+ */
+function hasNonZeroPixels(imageData) {
+    const data = imageData.data;
+    // Check R channel of each pixel (stride 4)
+    for (let i = 0; i < data.length; i += 4) {
+        if (data[i] !== 0)
+            return true;
+    }
+    return false;
+}
+//# sourceMappingURL=MigrationUtils.js.map

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

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

@@ -0,0 +1,47 @@
+/**
+ * UndoManager — Per-Layer Slice-Snapshot Undo/Redo
+ *
+ * Phase 6: Replaces the old HTMLImageElement-based undo system.
+ *
+ * Design:
+ * - Each layer has an independent undo and redo stack.
+ * - Each entry (MaskDelta) stores a full 2D slice snapshot before and after
+ *   the operation (cheaper than full volume, sufficient for single-stroke ops).
+ * - maxStackSize: 50 entries per layer.
+ * - Undo/redo operations also trigger backend sync via getMask callback.
+ */
+export interface MaskDelta {
+    layerId: string;
+    axis: "x" | "y" | "z";
+    sliceIndex: number;
+    /** Full slice data captured before the drawing operation. */
+    oldSlice: Uint8Array;
+    /** Full slice data captured after the drawing operation. */
+    newSlice: Uint8Array;
+}
+export declare class UndoManager {
+    private undoStacks;
+    private redoStacks;
+    private activeLayer;
+    constructor();
+    /** Set the currently active layer (determines which stack undo/redo operates on). */
+    setActiveLayer(layer: string): void;
+    /** Push a delta onto the active layer's undo stack and clear the redo stack. */
+    push(delta: MaskDelta): void;
+    /**
+     * Undo the last operation on the active layer.
+     * @returns The delta that was undone, or undefined if nothing to undo.
+     */
+    undo(): MaskDelta | undefined;
+    /**
+     * Redo the last undone operation on the active layer.
+     * @returns The delta that was redone, or undefined if nothing to redo.
+     */
+    redo(): MaskDelta | undefined;
+    canUndo(): boolean;
+    canRedo(): boolean;
+    /** Clear undo and redo stacks for a specific layer (called on clearStoreImages). */
+    clearLayer(layer: string): void;
+    /** Clear all stacks for all layers (called on full dataset reload). */
+    clearAll(): void;
+}

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

@@ -0,0 +1,86 @@
+/**
+ * UndoManager — Per-Layer Slice-Snapshot Undo/Redo
+ *
+ * Phase 6: Replaces the old HTMLImageElement-based undo system.
+ *
+ * Design:
+ * - Each layer has an independent undo and redo stack.
+ * - Each entry (MaskDelta) stores a full 2D slice snapshot before and after
+ *   the operation (cheaper than full volume, sufficient for single-stroke ops).
+ * - maxStackSize: 50 entries per layer.
+ * - Undo/redo operations also trigger backend sync via getMask callback.
+ */
+const MAX_STACK_SIZE = 50;
+const LAYER_IDS = ["layer1", "layer2", "layer3"];
+export class UndoManager {
+    constructor() {
+        this.activeLayer = "layer1";
+        this.undoStacks = new Map(LAYER_IDS.map((id) => [id, []]));
+        this.redoStacks = new Map(LAYER_IDS.map((id) => [id, []]));
+    }
+    /** Set the currently active layer (determines which stack undo/redo operates on). */
+    setActiveLayer(layer) {
+        this.activeLayer = layer;
+    }
+    /** Push a delta onto the active layer's undo stack and clear the redo stack. */
+    push(delta) {
+        var _a, _b;
+        const stack = (_a = this.undoStacks.get(delta.layerId)) !== null && _a !== void 0 ? _a : this.undoStacks.get("layer1");
+        stack.push(delta);
+        if (stack.length > MAX_STACK_SIZE) {
+            stack.shift();
+        }
+        // Any new operation invalidates the redo history for that layer
+        const redoStack = (_b = this.redoStacks.get(delta.layerId)) !== null && _b !== void 0 ? _b : this.redoStacks.get("layer1");
+        redoStack.length = 0;
+    }
+    /**
+     * Undo the last operation on the active layer.
+     * @returns The delta that was undone, or undefined if nothing to undo.
+     */
+    undo() {
+        const stack = this.undoStacks.get(this.activeLayer);
+        const delta = stack.pop();
+        if (delta) {
+            this.redoStacks.get(this.activeLayer).push(delta);
+        }
+        return delta;
+    }
+    /**
+     * Redo the last undone operation on the active layer.
+     * @returns The delta that was redone, or undefined if nothing to redo.
+     */
+    redo() {
+        const stack = this.redoStacks.get(this.activeLayer);
+        const delta = stack.pop();
+        if (delta) {
+            this.undoStacks.get(this.activeLayer).push(delta);
+        }
+        return delta;
+    }
+    canUndo() {
+        var _a, _b;
+        return ((_b = (_a = this.undoStacks.get(this.activeLayer)) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0;
+    }
+    canRedo() {
+        var _a, _b;
+        return ((_b = (_a = this.redoStacks.get(this.activeLayer)) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0;
+    }
+    /** Clear undo and redo stacks for a specific layer (called on clearStoreImages). */
+    clearLayer(layer) {
+        const undo = this.undoStacks.get(layer);
+        const redo = this.redoStacks.get(layer);
+        if (undo)
+            undo.length = 0;
+        if (redo)
+            redo.length = 0;
+    }
+    /** Clear all stacks for all layers (called on full dataset reload). */
+    clearAll() {
+        for (const id of LAYER_IDS) {
+            this.undoStacks.get(id).length = 0;
+            this.redoStacks.get(id).length = 0;
+        }
+    }
+}
+//# sourceMappingURL=UndoManager.js.map

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

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

@@ -0,0 +1,76 @@
+/**
+ * @module segmentation/core
+ *
+ * Core 3D Volumetric Mask Storage System
+ *
+ * This module provides a memory-efficient 3D mask storage solution for medical
+ * image annotation, replacing the legacy per-slice ImageData approach with a
+ * single contiguous {@link MaskVolume} backed by a `Uint8Array`.
+ *
+ * ## Architecture
+ *
+ * ```
+ * core/
+ * ├── types.ts          — Shared type definitions (Dimensions, RenderMode, colors)
+ * ├── MaskVolume.ts     — Core volume class (storage, access, rendering)
+ * ├── MigrationUtils.ts — Legacy ↔ Volume bidirectional conversion
+ * └── index.ts          — Public API barrel export (this file)
+ * ```
+ *
+ * ## Memory Layout
+ *
+ * The backing buffer uses **slice-major** order: `[z][y][x][channel]`.
+ *
+ * ```
+ * index = z * (width × height × channels)
+ *       + y * (width × channels)
+ *       + x * channels
+ *       + channel
+ * ```
+ *
+ * For a 512×512×100 single-channel volume this allocates ~25 MB,
+ * compared to ~100 MB for ImageData-per-slice (Z only) or ~524 MB
+ * for all three axes.
+ *
+ * ## Quick Start
+ *
+ * ```ts
+ * import { MaskVolume, RenderMode } from './core';
+ *
+ * // Create a volume matching the NRRD dimensions
+ * const vol = new MaskVolume(512, 512, 100);
+ *
+ * // Paint a voxel
+ * vol.setVoxel(256, 256, 50, 255);
+ *
+ * // Extract a slice for Canvas rendering
+ * const slice = vol.getSliceImageData(50, 'z');
+ * ctx.putImageData(slice, 0, 0);
+ *
+ * // Colored rendering
+ * const colored = vol.getSliceImageData(50, 'z', {
+ *   mode: RenderMode.COLORED_SINGLE,
+ *   channel: 0,
+ *   opacity: 0.6,
+ * });
+ * ```
+ *
+ * ## Migration from Legacy Storage
+ *
+ * ```ts
+ * import { convertIPaintImagesToVolume, convertVolumeToIPaintImages } from './core';
+ *
+ * // Forward: legacy IPaintImages → MaskVolume
+ * const volume = convertIPaintImagesToVolume(paintImages, { width: 512, height: 512, depth: 100 });
+ *
+ * // Backward: MaskVolume → legacy IPaintImages (for rollback)
+ * const legacy = convertVolumeToIPaintImages(volume);
+ * ```
+ */
+export type { Dimensions, RGBAColor, ChannelColorMap, SliceRenderOptions, LayerId, ChannelValue, } from './types';
+export { RenderMode, MASK_CHANNEL_COLORS, MASK_CHANNEL_CSS_COLORS, CHANNEL_COLORS, CHANNEL_HEX_COLORS, rgbaToHex, rgbaToCss, } from './types';
+export { MaskVolume } from './MaskVolume';
+export type { IPaintImage, IPaintImages } from './MigrationUtils';
+export { convertIPaintImagesToVolume, convertVolumeToIPaintImages, } from './MigrationUtils';
+export type { MaskDelta } from './UndoManager';
+export { UndoManager } from './UndoManager';

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

@@ -0,0 +1,75 @@
+/**
+ * @module segmentation/core
+ *
+ * Core 3D Volumetric Mask Storage System
+ *
+ * This module provides a memory-efficient 3D mask storage solution for medical
+ * image annotation, replacing the legacy per-slice ImageData approach with a
+ * single contiguous {@link MaskVolume} backed by a `Uint8Array`.
+ *
+ * ## Architecture
+ *
+ * ```
+ * core/
+ * ├── types.ts          — Shared type definitions (Dimensions, RenderMode, colors)
+ * ├── MaskVolume.ts     — Core volume class (storage, access, rendering)
+ * ├── MigrationUtils.ts — Legacy ↔ Volume bidirectional conversion
+ * └── index.ts          — Public API barrel export (this file)
+ * ```
+ *
+ * ## Memory Layout
+ *
+ * The backing buffer uses **slice-major** order: `[z][y][x][channel]`.
+ *
+ * ```
+ * index = z * (width × height × channels)
+ *       + y * (width × channels)
+ *       + x * channels
+ *       + channel
+ * ```
+ *
+ * For a 512×512×100 single-channel volume this allocates ~25 MB,
+ * compared to ~100 MB for ImageData-per-slice (Z only) or ~524 MB
+ * for all three axes.
+ *
+ * ## Quick Start
+ *
+ * ```ts
+ * import { MaskVolume, RenderMode } from './core';
+ *
+ * // Create a volume matching the NRRD dimensions
+ * const vol = new MaskVolume(512, 512, 100);
+ *
+ * // Paint a voxel
+ * vol.setVoxel(256, 256, 50, 255);
+ *
+ * // Extract a slice for Canvas rendering
+ * const slice = vol.getSliceImageData(50, 'z');
+ * ctx.putImageData(slice, 0, 0);
+ *
+ * // Colored rendering
+ * const colored = vol.getSliceImageData(50, 'z', {
+ *   mode: RenderMode.COLORED_SINGLE,
+ *   channel: 0,
+ *   opacity: 0.6,
+ * });
+ * ```
+ *
+ * ## Migration from Legacy Storage
+ *
+ * ```ts
+ * import { convertIPaintImagesToVolume, convertVolumeToIPaintImages } from './core';
+ *
+ * // Forward: legacy IPaintImages → MaskVolume
+ * const volume = convertIPaintImagesToVolume(paintImages, { width: 512, height: 512, depth: 100 });
+ *
+ * // Backward: MaskVolume → legacy IPaintImages (for rollback)
+ * const legacy = convertVolumeToIPaintImages(volume);
+ * ```
+ */
+export { RenderMode, MASK_CHANNEL_COLORS, MASK_CHANNEL_CSS_COLORS, CHANNEL_COLORS, CHANNEL_HEX_COLORS, rgbaToHex, rgbaToCss, } from './types';
+// ── Core volume ────────────────────────────────────────────────────────────
+export { MaskVolume } from './MaskVolume';
+export { convertIPaintImagesToVolume, convertVolumeToIPaintImages, } from './MigrationUtils';
+export { UndoManager } from './UndoManager';
+//# sourceMappingURL=index.js.map

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

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