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Documentation\n\nhttps://copper3d-visualisation.readthedocs.io/en/latest/\n\n### Previous versions\n\nOld: https://www.npmjs.com/package/copper3d_visualisation\nVery old: https://www.npmjs.com/package/gltfloader-plugin-test\n\n### Examples\n\n[Pick model with Gltfloader](https://linkungao.github.io/loadHumanModel_example/)\n[Copper3d_examples](https://linkungao.github.io/copper3d_examples)\n\n---\n\n### AI coding assistants (MCP)\n\ncopper3d ships a machine-readable index of its own API and guides. Point your AI\nassistant at it through the [`copper3d-mcp`](https://www.npmjs.com/package/copper3d-mcp)\nserver and it can look up real signatures instead of inventing them.\n\nIt reads the index from the copper3d **installed in your project**, so what the\nassistant sees always matches the version you actually depend on.\n\nFour read-only tools: `copper3d_search_api`, `copper3d_get_symbol`,\n`copper3d_list_guides`, `copper3d_get_guide`.\n\nFull guide: [AI Coding Assistants (MCP)](https://linkungao.github.io/copper3d_visualisation/guide/mcp-server).\n\n**Claude Code** — one command, no path needed:\n\n```bash\n# just you, in this project\nclaude mcp add copper3d -- npx -y copper3d-mcp\n\n# commit it to .mcp.json so the whole team gets it on clone\nclaude mcp add --scope project copper3d -- npx -y copper3d-mcp\n\n# all your projects\nclaude mcp add --scope user copper3d -- npx -y copper3d-mcp\n```\n\n**Every other client** needs to be told where the project is, because they start\nthe server with a working directory that is not your project\n([why](https://github.com/anthropics/claude-code/issues/75266)):\n\n| Client | Config file | Root key | Needs `--project` |\n|---|---|---|---|\n| Claude Code | `claude mcp add`, or `.mcp.json` | `mcpServers` | no |\n| Cursor | `.cursor/mcp.json` or `~/.cursor/mcp.json` | `mcpServers` | **yes** |\n| VS Code / Copilot | `.vscode/mcp.json` | **`servers`** | **yes** |\n| Claude Desktop | `%APPDATA%\\Claude\\claude_desktop_config.json`<br>`~/Library/Application Support/Claude/claude_desktop_config.json` | `mcpServers` | **yes** |\n| Windsurf | `~/.codeium/windsurf/mcp_config.json` | `mcpServers` | **yes** |\n\n<details>\n<summary><b>Cursor</b> — <code>.cursor/mcp.json</code></summary>\n\n```json\n{\n  \"mcpServers\": {\n    \"copper3d\": {\n      \"command\": \"npx\",\n      \"args\": [\"-y\", \"copper3d-mcp\", \"--project\", \"/absolute/path/to/your/project\"]\n    }\n  }\n}\n```\n\n</details>\n\n<details>\n<summary><b>VS Code / Copilot</b> — <code>.vscode/mcp.json</code> (note: <code>servers</code>, not <code>mcpServers</code>)</summary>\n\n```json\n{\n  \"servers\": {\n    \"copper3d\": {\n      \"type\": \"stdio\",\n      \"command\": \"npx\",\n      \"args\": [\"-y\", \"copper3d-mcp\", \"--project\", \"${workspaceFolder}\"]\n    }\n  }\n}\n```\n\n</details>\n\n<details>\n<summary><b>Claude Desktop</b> — <code>claude_desktop_config.json</code></summary>\n\nThe absolute path is required here: Claude Desktop has no project, and it ignores\nthe `cwd` field.\n\n```json\n{\n  \"mcpServers\": {\n    \"copper3d\": {\n      \"command\": \"npx\",\n      \"args\": [\"-y\", \"copper3d-mcp\", \"--project\", \"/absolute/path/to/your/project\"]\n    }\n  }\n}\n```\n\n</details>\n\n<details>\n<summary><b>Windsurf</b> — <code>~/.codeium/windsurf/mcp_config.json</code></summary>\n\n```json\n{\n  \"mcpServers\": {\n    \"copper3d\": {\n      \"command\": \"npx\",\n      \"args\": [\"-y\", \"copper3d-mcp\", \"--project\", \"/absolute/path/to/your/project\"]\n    }\n  }\n}\n```\n\n</details>\n\n**If it does not work**\n\n| Symptom | Cause | Fix |\n|---|---|---|\n| Tools never appear in VS Code | Used `mcpServers` in `.vscode/mcp.json` | VS Code calls it `servers` |\n| \"AI index was not found\" | copper3d not installed, or the client lost the project directory | `npm i copper3d`, then add `--project /abs/path` |\n| Assistant still invents APIs | Server not connected | `claude mcp list`, or your client's MCP panel |\n\nYou can also skip discovery entirely by setting `COPPER3D_INDEX_PATH` to the\n`node_modules/copper3d/ai-index` directory.\n\n**What it does not do.** This is documentation lookup only. copper3d is a browser\nWebGL library and the server is a Node process — it cannot render a scene, run your\ncode, or look at a canvas.\n\n---\n\n### Basic Usage\n\n**Load demo**\n\n```ts\nimport * as Copper from \"copper3d\";\nimport { getCurrentInstance, onMounted } from \"vue\";\n\nlet appRenderer;\nonMounted(() => {\n  const { $refs } = (getCurrentInstance() as any).proxy;\n  const bg: HTMLDivElement = $refs.classfy;\n  appRenderer = new Copper.copperRenderer(bg);\n  appRenderer.getCurrentScene().createDemoMesh();\n  appRenderer.animate();\n});\n```\n\n**Options**\n\n```ts\nappRenderer = new Copper.copperRenderer(bg, { guiOpen: true });\n```\n\n**Multiple scenes with glTF**\n\n```ts\nfunction loadModel(url: string, name: string) {\n  let scene = appRenderer.getSceneByName(name);\n  if (!scene) {\n    scene = appRenderer.createScene(name);\n    appRenderer.setCurrentScene(scene);\n    scene.loadViewUrl(\"/noInfarct_view.json\");\n    scene.loadGltf(url);\n  } else {\n    appRenderer.setCurrentScene(scene);\n  }\n}\n```\n\n**View data structure**\n\n```ts\nCameraViewPoint {\n  nearPlane: number = 0.1;\n  farPlane: number = 2000.0;\n  eyePosition: Array<number> = [0.0, 0.0, 0.0];\n  targetPosition: Array<number> = [0.0, 0.0, 0.0];\n  upVector: Array<number> = [0.0, 1.0, 0.0];\n}\n```\n\n---\n\n### Loading NRRD volumes\n\n`scene.loadNrrd(url, loadingBar, segmentation, callback, opts?)` fetches, gunzips and parses\nthe volume **in a shared Web Worker**; the pixel buffer comes back as a transferable and the\nmain thread only rehydrates a `Volume` around it. Two concurrent loads of the same URL share\none network transfer. The worker is inlined into the bundle, so there is no second asset file\nto serve.\n\n```ts\nconst controller = new AbortController();\n\nscene.loadNrrd(url, loadingBar, false, (volume, meshes, slices) => { /* ... */ }, {\n  openGui: false,\n  axes: [\"z\"],                  // extract only the planes you show\n  knownMinMax: [min, max],      // skip three's whole-volume intensity scan\n  signal: controller.signal,    // cancel a superseded load\n  onProgress: (e) => setProgress(e.total > 0 ? e.loaded / e.total : null),\n  onError: (err) => showFailure(err),\n});\n```\n\n| Option | Type | Description |\n|--------|------|-------------|\n| `openGui` | `boolean` | Show the built-in volume GUI |\n| `container` | `HTMLDivElement` | Host element for that GUI |\n| `axes` | `readonly (\"x\"\\|\"y\"\\|\"z\")[]` | Which slice planes to extract. Default `[\"x\",\"y\",\"z\"]`. Omitted axes are `undefined` on the callback's `meshes` / `slices` |\n| `knownMinMax` | `[number, number]` | Volume intensity range, if already known (e.g. from a backend headers endpoint). Skips `Volume.computeMinMax()`'s full voxel scan |\n| `signal` | `AbortSignal` | Aborts the in-flight fetch. `onError` fires with a `DOMException` whose `name` is `\"AbortError\"` |\n| `onProgress` | `(e: ProgressEvent) => void` | Download progress, in addition to the built-in loading bar |\n| `onError` | `(error: unknown) => void` | Fetch or parse failure |\n\nSkipped a plane and need it later? `ensureAxisExtracted(slices, axis, meshes?)` extracts it on\ndemand, mutating `slices` (and `meshes`) in place. `NrrdTools.setSliceOrientation()` already\ncalls it for you, so an axial-only load can still switch to sagittal or coronal.\n\n---\n\n## NrrdTools Usage Guide\n\n> Copper3D `NrrdTools` — Medical Image Segmentation Annotation Engine\n\n`NrrdTools` manages multi-layer mask volumes, a layered canvas pipeline, drawing tools, undo/redo history, channel color customization, and keyboard shortcuts on top of a Three.js medical image viewer.\n\n> **Internal Architecture**: `NrrdTools` is a **Facade** using **composition** (no inheritance). It composes:\n> - **`CanvasState`** — unified state container (nrrd_states, gui_states, protectedData, callbacks, keyboardSettings)\n> - **`DrawToolCore`** — tool orchestration and event routing\n> - **`RenderingUtils`** — slice extraction and canvas compositing helpers\n> - **`LayerChannelManager`** — layer/channel/sphere-type management and color customization\n> - **`SliceRenderPipeline`** — slice setup, canvas rendering, mask reload, canvas flip\n> - **`DataLoader`** — NRRD slice loading, NIfTI voxel loading\n>\n> The old inheritance chain (`NrrdTools → DrawToolCore → CommToolsData`) has been fully replaced. All modules communicate via `ToolContext` (shared state). The public API below is unchanged.\n\n---\n\n### 1. Quick Start\n\n```typescript\nimport * as Copper from 'copper3d';\n\nconst container = document.getElementById('viewer') as HTMLDivElement;\nconst nrrdTools = new Copper.NrrdTools(container);\n\nnrrdTools.reset();\nnrrdTools.setAllSlices(allSlices); // allSlices from Copper scene loader\n\nnrrdTools.drag({ getSliceNum: (index) => console.log('Slice:', index) });\n\nnrrdTools.draw({\n  getMaskData: (sliceData, layerId, channelId, sliceIndex, axis, width, height, clearFlag) => {\n    // Called after every stroke, undo, redo — sync to backend here\n  }\n});\n\nscene.addPreRenderCallbackFunction(nrrdTools.start);\n```\n\n---\n\n### 2. Constructor & Initialization\n\n```typescript\nnew Copper.NrrdTools(container: HTMLDivElement, options?: { layers?: string[] })\n```\n\n| Parameter | Type | Default | Description |\n|-----------|------|---------|-------------|\n| `container` | `HTMLDivElement` | required | Host DOM element for all annotation canvases |\n| `options.layers` | `string[]` | `[\"layer1\",\"layer2\",\"layer3\"]` | Named layers to create |\n\n```typescript\n// Custom layer set — any names, not just layerN\nconst nrrdTools = new Copper.NrrdTools(container, {\n  layers: ['tumour', 'edema', 'necrosis', 'vessel']\n});\n\n// Read-only reference viewer — shows the image, nothing to annotate into.\n// Scrub / zoom / pan / window-level / crosshair all still work.\nconst reference = new Copper.NrrdTools(container, { layers: [] });\n\n// Optional: show current slice index in a panel\nnrrdTools.setDisplaySliceIndexPanel(document.getElementById('slice-panel') as HTMLDivElement);\n\n// Optional: connect dat.GUI / lil-gui\nimport GUI from 'lil-gui';\nnrrdTools.setupGUI(new GUI() as any);\n```\n\n---\n\n### 3. Data Loading\n\n```typescript\n// Reset state then load new slices\nnrrdTools.reset();\nnrrdTools.setAllSlices(allSlices);\n```\n\n**Loading existing NIfTI mask data**\n\nEach buffer must have its own NIfTI voxel grid registered first. A buffer whose grid does not\nmatch the loaded image — or that was never registered — is **refused**, not truncated or\nzero-padded, because a wrong-grid mask would otherwise render silently offset onto the wrong\nvoxels. Other layers in the same map still load.\n\n```typescript\nimport { registerNiftiMaskGrid } from 'copper3d';\n\nregisterNiftiMaskGrid(layer1Uint8Array, layer1Dims); // dims = NIfTI header [x, y, z]\nregisterNiftiMaskGrid(layer2Uint8Array, layer2Dims);\n\nconst layerVoxels = new Map<string, Uint8Array>([\n  ['layer1', layer1Uint8Array],\n  ['layer2', layer2Uint8Array],\n]);\nnrrdTools.setMasksFromNIfTI(layerVoxels);\n\n// With loading progress bar\nconst loadingBar = { value: 0 };\nnrrdTools.setMasksFromNIfTI(layerVoxels, loadingBar);\n```\n\nA refused layer is logged and reported through `notifyUser`, which defaults to a console\nwrite — the package ships without a UI and does not reach into yours. Point it at your own:\n\n```typescript\nnrrdTools.notifyUser = (message, level) => toast[level](message); // 'error' | 'warning' | 'info'\n```\n\n**Previewing one slice before the volume loads**\n\n```typescript\n// Put one plane on screen immediately, positioned as slice `index` of the full stack\nnrrdTools.showPreviewSlice(header, slice, index, async (target) => {\n  const next = await fetchSinglePlane(caseId, target);   // `target` is already clamped\n  nrrdTools.showPreviewSlice(header, next, target, onSliceMove);\n});\n\n// Later, when the real volume arrives — keeps the previewed index\nnrrdTools.switchSlicesPreservingView(allSlices);\n```\n\nWhile previewing, wheel/keys/drag do **not** move the display — the shown slice has depth 1,\nso the target index is handed to your callback to fetch instead. `header` is the full volume's\ngeometry, not the plane's. Axial only. `isPreviewing()` reports the state; it ends on\n`switchSlicesPreservingView`, `setAllSlices` or `reset`.\n\n**Contrast series**\n\nA case is a series of contrasts. `addSkip` / `removeSkip` index the **full** contrast list;\n`setContrastIndex` indexes `displaySlices`, the displayed subset. Each of those ends in a full\ndisplay refresh, so use the batched forms when changing several at once:\n\n```typescript\nnrrdTools.setSkips([{ index: 1, skip: true }, { index: 2, skip: true }]);\nnrrdTools.commitSkipsAndContrast(skipEntries, 0);        // skips + contrast, one refresh\nnrrdTools.commitSeriesLoad(allSlices, skipEntries, 0);   // whole case load, one refresh\n```\n\n**Read-only preview while loading**\n\n`setAnnotationSuspended(true)` blocks every input that can write into a mask, while slice\nscrubbing, zoom, pan and the crosshair stay live:\n\n```typescript\nnrrdTools.setAnnotationSuspended(true);\nawait loadAllContrasts(caseId);\nnrrdTools.commitSeriesLoad(allSlices, skipEntries, 0);\nnrrdTools.setAnnotationSuspended(false);\n```\n\nDisabling your own toolbar is not equivalent: a tool selected before the load began stays\narmed on the canvas, and a stroke made during loading cannot be undone — `afterLoadSlice`\nclears the undo stack each time a slice arrives.\n\n---\n\n### 4. Render Loop Integration\n\n```typescript\n// Register once after initialization\nconst callbackId = scene.addPreRenderCallbackFunction(nrrdTools.start);\n\n// Unregister on teardown, then release the instance\nscene.removePreRenderCallbackFunction(callbackId);\nnrrdTools.dispose();\n```\n\n`dispose()` releases what the instance holds outside its own DOM subtree — the event router's\nlisteners (its window `blur` listener pins the whole engine graph), a pending slice step, and\nthe drawing-flag timer. Without it, an app that builds a viewer per case leaks one engine graph\nper case. The instance must not be used afterwards; calling it twice is safe.\n\n---\n\n### 5. Drawing Setup\n\n#### `drag()` — Slice navigation\n\n```typescript\nnrrdTools.drag({\n  showNumber: true,\n  getSliceNum: (sliceIndex, contrastIndex) => updateUI(sliceIndex),\n});\n```\n\n#### `draw()` — Annotation callbacks\n\n```typescript\nnrrdTools.draw({\n  getMaskData: (sliceData, layerId, channelId, sliceIndex, axis, width, height, clearFlag?) => {\n    sendSliceToBackend({ sliceData, layerId, channelId, sliceIndex, axis, width, height, clearFlag });\n  },\n  onClearLayerVolume: (layerId) => notifyBackendLayerCleared(layerId),\n  getSphereData: (sphereOrigin, sphereRadius) => sendSphereToBackend({ sphereOrigin, sphereRadius }),\n  getCalculateSpherePositionsData: (tumour, skin, rib, nipple, axis) => {\n    if (tumour && skin && rib && nipple) aiBackend.runSegmentation({ tumour, skin, rib, nipple, axis });\n  },\n});\n```\n\n#### `enableContrastDragEvents()` — Window/Level\n\n```typescript\nnrrdTools.enableContrastDragEvents((step, towards) => {\n  console.log(`Contrast: ${towards} ${step}`);\n});\n```\n\n#### SphereTool — Sphere Types & Channel Mapping\n\n| Sphere Type | Channel | Default Color | `activeSphereType` value |\n|-------------|---------|---------------|--------------------------|\n| tumour      | 1       | `#10b981`     | `\"tumour\"` (default)     |\n| nipple      | 2       | `#f43f5e`     | `\"nipple\"`               |\n| ribcage     | 3       | `#3b82f6`     | `\"ribcage\"`              |\n| skin        | 4       | `#fbbf24`     | `\"skin\"`                 |\n\n```typescript\nnrrdTools.setActiveSphereType('nipple');  // also updates brush/fill color\nconst type = nrrdTools.getActiveSphereType(); // → 'tumour' | 'skin' | 'nipple' | 'ribcage'\n```\n\n**Programmatic sphere placement (backend → frontend):**\n\n```typescript\n// Replicates full click flow internally — no user interaction needed\nnrrdTools.setCalculateDistanceSphere(120, 95, 42, 'tumour');\n// Coordinates are in unscaled image space; sizeFactor is applied internally\n```\n\n---\n\n### 6. Layer & Channel Management\n\n```typescript\n// Active layer / channel\nnrrdTools.setActiveLayer('layer2');\nnrrdTools.setActiveChannel(3);\nconst layer   = nrrdTools.getActiveLayer();\nconst channel = nrrdTools.getActiveChannel();\n\n// Layer visibility\nnrrdTools.setLayerVisible('layer2', false);\nconst visible = nrrdTools.isLayerVisible('layer2');\nconst visMap  = nrrdTools.getLayerVisibility(); // { layer1: true, layer2: false, ... }\n\n// Channel visibility (per layer)\nnrrdTools.setChannelVisible('layer1', 2, false);\nconst allChannelVis = nrrdTools.getChannelVisibility();\n\n// Check if a layer has annotations\nif (nrrdTools.hasLayerData('layer1')) await saveLayer('layer1');\n```\n\n**Reading and replacing a whole layer volume**\n\n```typescript\n// Move a mask from layer2 to layer3, undoably\nconst voxels = nrrdTools.getLayerVolume('layer2');   // a COPY, or null\nif (voxels) nrrdTools.replaceLayerVolume('layer3', voxels, { undoable: true });\n```\n\n`copyLayerData(src, dst)` also copies between layers and is faster, but it writes the target\nbuffer directly and leaves nothing for Ctrl+Z. Use it only to mirror a backend cascade; if a\nperson triggered the change, go through the pair above.\n\n---\n\n### Mask render mode — fill or outline\n\n```typescript\nnrrdTools.setMaskRenderMode('outline');  // stroke only the boundary\nnrrdTools.setMaskRenderMode('fill');     // paint the silhouette (default)\n```\n\n`\"outline\"` leaves each mask's interior clear so the tissue underneath stays readable. It is a\ndisplay decision only — what is stored, uploaded, exported and undone is the complete mask\neither way — and it applies to every layer and channel at once, repainting immediately. The\npencil and eraser render the layer filled for the duration of a stroke, so you do not need to\nleave outline mode to annotate.\n\n---\n\n### Mask mirroring — show one viewer's masks on another\n\n```typescript\n// `reference` draws `primary`'s masks over its own image\nreference.setMaskMirror(primary);\n\n// with a row-major 4×4 mapping reference's voxel (x, y, z, 1) → primary's voxel\nreference.setMaskMirror(primary, mirrorToSource);\n\nreference.setMaskMirror(null);   // detach\n```\n\nEverything is read live from the source — volumes, channel colours, layer and channel\nvisibility, per-layer opacity, fill/outline mode — so changing any of them on the source\nupdates the mirror on the next frame. It is display only: nothing is written to either\nviewer's masks, and the mirror holds no mask data of its own.\n\nA mirroring viewer needs no layers, so `{ layers: [] }` pairs naturally with this. `dispose()`\nbreaks the link from both ends.\n\n---\n\n### Zoom range — showing below 1:1\n\nThe zoom factor used to bottom out at `1`. Lower the floor and a large volume can be fitted\ninto a small panel:\n\n```typescript\nnrrdTools.setMinSizeFactor(0.5);   // clamped to [0.05, 1]; default 1\nnrrdTools.setMainAreaSize(0.6);    // now valid\n```\n\n`setMainAreaSize`, wheel zoom and the `\"mainAreaSize\"` GUI slider all follow it; the upper\nbound stays `8`. If the current factor is below the new floor it is raised and repainted.\n\nThe engine never recomputes the floor — the right value depends on the image and axis\ndimensions *and* your panel size — so re-apply it after each case load, axis switch and panel\nresize.\n\n---\n\n### 7. Channel Color Customization\n\n**Default colors:**\n\n| Channel | Color | Hex |\n|---------|-------|-----|\n| 1 | Emerald | `#10b981` |\n| 2 | Rose | `#f43f5e` |\n| 3 | Blue | `#3b82f6` |\n| 4 | Amber | `#fbbf24` |\n| 5 | Fuchsia | `#d946ef` |\n| 6 | Cyan | `#06b6d4` |\n| 7 | Orange | `#f97316` |\n| 8 | Violet | `#8b5cf6` |\n\nChannels **9–255** are generated from a golden-angle hue walk (137.508° per step) at fixed\nsaturation and lightness — only hue varies, because a mask that changes brightness between\nchannels reads as a difference in the greyscale image rather than in the annotation. The eight\nseeds above are kept verbatim, so cases annotated before this keep the colours they were\nsigned off with. `Copper.MAX_ENGINE_CHANNEL` is the ceiling (`255` — one byte per voxel, and\nthe value *is* the label).\n\n> Distinct is not the same as distinguishable: past roughly twenty channels, neighbouring hues\n> stop being tellable apart by eye on a greyscale background. All 255 are addressable; how many\n> your product should offer at once is a separate question.\n\n```typescript\n// Set one channel color (RGBAColor: { r, g, b, a } — 0-255)\nnrrdTools.setChannelColor('layer1', 3, { r: 255, g: 128, b: 0, a: 255 });\n\n// Batch-set (one reloadMasksFromVolume call — better performance)\nnrrdTools.setChannelColors('layer1', {\n  1: { r: 255, g: 80, b: 80, a: 255 },\n  2: { r: 80, g: 180, b: 255, a: 255 },\n});\n\n// Apply same channel color across all layers\nnrrdTools.setAllLayersChannelColor(1, { r: 0, g: 220, b: 100, a: 255 });\n\n// Read colors\nconst rgba = nrrdTools.getChannelColor('layer1', 3);\nconst hex  = nrrdTools.getChannelHexColor('layer1', 3);  // → \"#ff8000\"\nconst css  = nrrdTools.getChannelCssColor('layer1', 3);  // → \"rgba(255,128,0,1.00)\"\n\n// Reset\nnrrdTools.resetChannelColors('layer1', 3); // one channel\nnrrdTools.resetChannelColors('layer1');    // all channels in layer\nnrrdTools.resetChannelColors();            // everything\n```\n\n---\n\n### 8. Undo / Redo\n\nPer-layer undo stack (max 50 entries). Every completed stroke pushes a delta snapshot.\n\n```typescript\nnrrdTools.undo();\nnrrdTools.redo();\n\n// Or via keyboard\nwindow.addEventListener('keydown', (e) => {\n  if (e.ctrlKey && e.key === 'z') nrrdTools.undo();\n  if (e.ctrlKey && e.key === 'y') nrrdTools.redo();\n});\n```\n\n---\n\n### 9. Keyboard Shortcuts\n\n| Action | Default Key |\n|--------|-------------|\n| Draw mode | `Shift` (hold) |\n| Undo | `z` |\n| Redo | `y` |\n| Contrast adjust | `Ctrl` / `Meta` (hold) |\n| Crosshair | `s` |\n| Mouse wheel | Zoom |\n\n> **Breaking:** sphere mode no longer has a shortcut. `sphere: \"q\"` is gone and `sphere` has\n> been removed from `IKeyBoardSettings` — it toggled the mode behind the host's back, clearing\n> the masks from the view while the host's UI still showed its own tool as selected. Enter it\n> with `setMode('sphere')` and bind your own key if you want one.\n\n```typescript\nnrrdTools.setKeyboardSettings({ undo: 'u', mouseWheel: 'Scroll:Slice' });\nconst settings = nrrdTools.getKeyboardSettings();\n\n// Suppress shortcuts while a form input is focused\ninputEl.addEventListener('focus', () => nrrdTools.enterKeyboardConfig());\ninputEl.addEventListener('blur',  () => nrrdTools.exitKeyboardConfig());\n```\n\n---\n\n### 10. Clearing Annotations\n\n```typescript\nnrrdTools.reset();            // Reset ALL layers, volumes, undo histories, canvases (use when switching cases)\nnrrdTools.clearActiveLayer(); // Clear active layer's entire 3D volume + undo history, fire onClearLayerVolume\nnrrdTools.clearActiveSlice(); // Clear only the currently viewed 2D slice (undoable)\nnrrdTools.clearChannel('layer1', 3); // Erase ONE channel across the whole layer (undoable)\n```\n\n`clearChannel` is the only one of these that can delete a single annotation: a finding's mask\nis one label inside a volume it shares with every other annotation on the layer, so anything\ncoarser takes the neighbours with it. Its deltas go on the undo stack, so `undo()` brings the\nchannel back — which is why you should use it rather than writing zeros into the volume\nyourself. It throws on an unknown layer, or a channel outside `[1, 255]`.\n\n---\n\n### 11. API Summary\n\n| Category | Method | Description |\n|----------|--------|-------------|\n| **Constructor** | `new NrrdTools(container, { layers })` | Create instance with optional layer config |\n| **Setup** | `drag(opts?)` | Enable slice-drag navigation |\n| | `draw(opts?)` | Bind annotation callbacks |\n| | `setupGUI(gui)` | Connect dat.GUI / lil-gui panel |\n| | `enableContrastDragEvents(cb)` | Enable Ctrl+drag windowing |\n| | `setDisplaySliceIndexPanel(el)` | Show slice index in a panel |\n| | `setBaseDrawDisplayCanvasesSize(n)` | Set canvas resolution multiplier (1–8) |\n| **Data** | `reset()` | Reset all volumes, undo histories, canvases, sphere data |\n| | `clearActiveLayer()` | Clear active layer volume + undo history |\n| | `clearActiveSlice()` | Clear current slice (undoable) |\n| | `clearChannel(id, ch)` | Erase one channel across a whole layer (undoable); throws on unknown layer or channel outside [1, 255] |\n| | `setAllSlices(slices)` | Load NRRD slices, init MaskVolumes |\n| | `setMasksFromNIfTI(map, bar?)` | Load saved NIfTI voxel data (grids must be registered first) |\n| | `registerNiftiMaskGrid(data, dims)` | *(module export)* Record a mask buffer's NIfTI grid for validation |\n| | `notifyUser` | *(assignable property)* How engine messages reach the reader; defaults to a console write |\n| **Contrast Series** | `addSkip(i)` / `removeSkip(i)` | Hide / show one contrast (full-list index) |\n| | `setSkips(entries)` | Batched skip changes — one display refresh |\n| | `setContrastIndex(i)` | Move to a contrast within `displaySlices` |\n| | `commitSkipsAndContrast(entries, i)` | Batched skips + contrast — one refresh |\n| | `commitSeriesLoad(slices, entries, i)` | Case-load completion — one refresh |\n| | `switchAllSlicesArrayData(slices)` | Swap the series (resets view state) |\n| | `switchSlicesPreservingView(slices)` | Swap the series, keep slice index / zoom / pan |\n| **Preview** | `showPreviewSlice(header, slice, i, cb)` | Show one depth-1 slice as slice `i` of the not-yet-loaded stack; slice moves go to `cb` instead of moving the display. Axial only |\n| | `isPreviewing()` | Whether a preview slice is shown |\n| **Render** | `start` | Frame callback — pass to render loop |\n| **Lifecycle** | `dispose()` | Release the event router's listeners, a pending slice step, the drawing-flag timer and any mask-mirror link (from both ends). Instance unusable afterwards; safe to call twice |\n| **Layer** | `setActiveLayer(id)` | Switch drawing target layer |\n| | `getActiveLayer()` | Read current layer |\n| | `setLayerVisible(id, bool)` | Toggle layer in composite view |\n| | `isLayerVisible(id)` | Query layer visibility |\n| | `getLayerVisibility()` | All layer visibility map |\n| | `hasLayerData(id)` | Check if layer has non-zero voxels |\n| | `getLayerVolume(id)` | A **copy** of the layer's voxel buffer, or `null` |\n| | `replaceLayerVolume(id, data, opts?)` | Replace the whole buffer; `{ undoable: true }` records one Ctrl+Z step |\n| | `copyLayerData(src, dst)` | Copy voxels between layers — **not** undoable; keeps the target's colour map |\n| | `setLayerOpacity(id, opacity)` | Set per-layer opacity (0.1–1.0), triggers re-render |\n| | `getLayerOpacity(id)` | Read one layer's opacity |\n| | `getLayerOpacityMap()` | All per-layer opacity values |\n| **Mirror** | `setMaskMirror(src, m?)` | Draw another viewer's masks, read live. `m` = row-major 4×4 voxel→voxel; `null` detaches. Display only |\n| | `getMaskMirrorSource()` | The viewer being mirrored, or `null` |\n| **Sphere** | `setActiveSphereType(type)` | Set active sphere type, updates brush color |\n| | `getActiveSphereType()` | Read current sphere type |\n| | `setCalculateDistanceSphere(x, y, slice, type)` | Programmatically place a calculator sphere |\n| **Channel** | `setActiveChannel(ch)` | Switch drawing target channel |\n| | `getActiveChannel()` | Read current channel |\n| | `setChannelVisible(id, ch, bool)` | Toggle channel visibility in a layer |\n| | `isChannelVisible(id, ch)` | Query channel visibility |\n| | `getChannelVisibility()` | All channel visibility map |\n| **Color** | `setChannelColor(id, ch, rgba)` | Set one channel color in one layer |\n| | `setChannelColors(id, map)` | Batch-set colors in one layer |\n| | `setAllLayersChannelColor(ch, rgba)` | Set one channel color across all layers |\n| | `getChannelColor(id, ch)` | Read RGBA |\n| | `getChannelHexColor(id, ch)` | Read Hex string |\n| | `getChannelCssColor(id, ch)` | Read CSS rgba() string |\n| | `resetChannelColors(id?, ch?)` | Reset to defaults |\n| | `MAX_ENGINE_CHANNEL` | *(module export)* Highest storable label, `255` |\n| **Tool Mode** | `setMode(mode)` | Switch tool: `\"pencil\"` / `\"brush\"` / `\"eraser\"` / `\"sphere\"` / `\"calculator\"` / `\"sphereBrush\"` / `\"sphereEraser\"` |\n| | `getMode()` | Read current tool mode |\n| | `isCalculatorActive()` | Check if calculator (distance) mode is active |\n| | `setAnnotationSuspended(bool)` | Block all mask-writing input; scrubbing, zoom, pan and crosshair stay live |\n| | `isAnnotationSuspended()` | Query the suspension state |\n| **Sphere Brush** | `setSphereBrushRadius(radius)` | Set sphere brush/eraser radius [1, 50] |\n| | `getSphereBrushRadius()` | Read current sphere brush/eraser radius |\n| **Drawing** | `setOpacity(value)` | Set mask overlay opacity [0.1, 1] |\n| | `getOpacity()` | Read current opacity |\n| | `setBrushSize(size)` | Set brush/eraser size [5, 50] |\n| | `getBrushSize()` | Read current brush size |\n| | `setPencilColor(hex)` | Set pencil stroke color (hex string) |\n| | `getPencilColor()` | Read current pencil color |\n| | `setMaskRenderMode(mode)` | `\"fill\"` or `\"outline\"` for every layer/channel; repaints immediately. Display only — the stored mask is unchanged |\n| | `getMaskRenderMode()` | Read the current render mode |\n| **Contrast** | `setWindowHigh(value)` | Set window high |\n| | `setWindowLow(value)` | Set window low |\n| | `finishWindowAdjustment()` | Repaint all contrast slices after drag ends |\n| | `adjustContrast(type, delta)` | Nudge `\"windowHigh\"` / `\"windowLow\"` by a delta |\n| | `getSliderMeta(key)` | Slider min/max/step/value for UI config (`\"globalAlpha\"`, `\"layerAlpha\"`, `\"brushAndEraserSize\"`, …) |\n| **Actions** | `executeAction(action, opts?)` | Run: `\"undo\"` / `\"redo\"` / `\"clearActiveSliceMask\"` / `\"clearActiveLayerMask\"` / `\"resetZoom\"` / `\"downloadCurrentMask\"` / `\"gaussianSmooth\"` (takes `{ sigma? }`) |\n| **Navigation** | `setSliceOrientation(axis)` | Switch viewing axis `\"x\"` / `\"y\"` / `\"z\"`; extracts the plane on demand if the load skipped it |\n| | `setSliceMoving(step)` | Step the current slice (coalesced per animation frame) |\n| | `setMainAreaSize(factor)` | Set the main-area zoom factor `[minSizeFactor, 8]` |\n| | `setMinSizeFactor(f)` | Lower the zoom floor below 1:1. Clamped to `[0.05, 1]`; default `1`. Re-apply after case loads, axis switches and panel resizes |\n| | `getMinSizeFactor()` | Read the current zoom floor |\n| **History** | `undo()` / `redo()` | Undo / redo last stroke |\n| **Keyboard** | `setKeyboardSettings(partial)` | Remap shortcuts |\n| | `getKeyboardSettings()` | Read current bindings |\n| | `enterKeyboardConfig()` / `exitKeyboardConfig()` | Suppress / restore shortcuts |\n| | `setContrastShortcutEnabled(bool)` | Enable/disable contrast key |\n| **Inspect** | `getCurrentImageDimension()` | `[w, h, d]` voxel dims |\n| | `getVoxelSpacing()` | Physical mm spacing |\n| | `getSpaceOrigin()` | World-space origin |\n| | `getMaxSliceNum()` | Max slice index per axis |\n| | `getCurrentSlicesNumAndContrastNum()` | Current slice & contrast index |\n| | `getMaskData()` | Raw `IMaskData` object |\n| | `getNrrdToolsSettings()` | Full `NrrdState` snapshot |\n| | `getContainer()` | Host `HTMLElement` |\n| | `getDrawingCanvas()` | Top-layer `HTMLCanvasElement` |\n\n---\n\n### 12. Type Reference\n\n```typescript\ninterface RGBAColor { r: number; g: number; b: number; a: number; } // 0-255\n\ntype ChannelColorMap = Record<number, RGBAColor>; // key = channel number, 1-255\n\ninterface IDrawOpts {\n  getMaskData?: (\n    sliceData: Uint8Array, layerId: string, channelId: number,\n    sliceIndex: number, axis: 'x' | 'y' | 'z',\n    width: number, height: number, clearFlag?: boolean\n  ) => void;\n  onClearLayerVolume?: (layerId: string) => void;\n  getSphereData?: (sphereOrigin: number[], sphereRadius: number) => void;\n  getCalculateSpherePositionsData?: (\n    tumourOrigin: ICommXYZ | null, skinOrigin: ICommXYZ | null,\n    ribOrigin: ICommXYZ | null, nippleOrigin: ICommXYZ | null,\n    axis: 'x' | 'y' | 'z'\n  ) => void;\n}\n\ninterface IDragOpts {\n  showNumber?: boolean;\n  getSliceNum?: (sliceIndex: number, contrastIndex: number) => void;\n}\n\ninterface IKeyBoardSettings {\n  draw: string;\n  undo: string;\n  redo: string;\n  contrast: string[];\n  crosshair: string;\n  mouseWheel: 'Scroll:Zoom' | 'Scroll:Slice';\n}\n\ninterface ICommXYZ { x: number; y: number; z: number; }\n\ntype LayerId        = 'layer1' | 'layer2' | 'layer3' | 'layer4'; // or any string\ntype ChannelValue   = number; // 0 = empty/erased, 1..MAX_ENGINE_CHANNEL (255)\ntype MaskRenderMode = 'fill' | 'outline';\n```\n\n---\n\n## Acknowledgements\n\nSpecial thanks to [Duke University dataset](https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=70226903) for providing the MRI data.\n\n---\n\n[ci]: https://github.com/LinkunGao/copper3d_visualisation/actions/workflows/ci.yml/badge.svg?branch=main\n[ci-url]: https://github.com/LinkunGao/copper3d_visualisation/actions/workflows/ci.yml\n[npm]: https://img.shields.io/npm/v/copper3d\n[npm-url]: https://www.npmjs.com/package/copper3d\n[readthedocs]: https://img.shields.io/readthedocs/copper3d_visualisation\n[readthedocs-url]: https://copper3d-visualisation.readthedocs.io/en/latest/\n[examples]: https://img.shields.io/badge/copper3d__visualisation-examples-orange\n[examples-url]: https://linkungao.github.io/copper3d_examples\n[nrrd_example]: https://img.shields.io/badge/Nrrd__Segmentation__tool-example-orange\n[nrrd_example-url]: https://abi-web-apps.github.io/NRRD_Segmentation_Tool/\n[heart_example-url]: https://uoa-heart-mechanics-research.github.io/medtech-heart/model-heart\n[heart_example]: https://img.shields.io/badge/Medtech%20Heart-example-brightgreen\n","readmeFilename":"README.md"}