copper3d / Modules / Utils/segmentation/NrrdTools / NrrdTools

Class: NrrdTools ​

Utils/segmentation/NrrdTools.NrrdTools

Core NRRD annotation tool for medical image segmentation.

Acts as a Facade that delegates to composed modules:

• CanvasState — pure state container
• DrawToolCore — tool orchestration, event routing
• LayerChannelManager — layer/channel/sphere-type management
• SliceRenderPipeline — slice rendering, canvas flip, mask reload
• DataLoader — NRRD slice loading, legacy mask loading, NIfTI loading

No longer extends DrawToolCore — uses composition instead.

Example

// Default 3 layers: layer1, layer2, layer3
const tools = new NrrdTools(container);

// Custom layers
const tools = new NrrdTools(container, { layers: ["layer1", "layer2"] });

// Default 3 layers: layer1, layer2, layer3
const tools = new NrrdTools(container);

// Custom layers
const tools = new NrrdTools(container, { layers: ["layer1", "layer2"] });

Table of contents ​

Constructors ​

• constructor

Properties ​

• _aiAssistActive
• _aiPrevVisibility
• _calculatorActive
• _pendingSliceStep
• _sliceRAFId
• container
• dataLoader
• dragOperator
• drawCore
• guiCallbacks
• guiParameterSettings
• layerChannelManager
• notifyUser
• preTimer
• sliceRenderPipeline
• state

Accessors ​

• start

Methods ​

• addSkip
• adjustContrast
• aiApplyMask
• aiCancelLasso
• aiClearPrompts
• aiClearSegment
• aiCommitRegion
• aiCommitToLayer
• aiCommitToLayerMapped
• aiDiscard
• aiFinishLasso
• aiGetScratchSegments
• aiGetScratchSlices
• aiHasData
• aiIsLassoEditing
• aiLassoRedo
• aiLassoUndo
• aiLassoVertCount
• aiNewSegment
• aiOnLassoChange
• aiOnPrompt
• aiSetActiveSegment
• aiSetPolarity
• aiSetPromptTool
• aiSetScribbleSize
• aiSetSegmentColor
• appendLoadingbar
• clearActiveLayer
• clearDictionary
• commitSeriesLoad
• commitSkipsAndContrast
• configMouseSliceWheel
• copyLayerData
• drag
• draw
• drawCalculatorSphereOnEachViews
• enableContrastDragEvents
• enterAiAssistMode
• enterKeyboardConfig
• enterSphereMode
• executeAction
• exitAiAssistMode
• exitKeyboardConfig
• exitSphereMode
• finishWindowAdjustment
• flipDisplayImageByAxis
• getActiveChannel
• getActiveLayer
• getActiveSphereType
• getBrushSize
• getChannelColor
• getChannelCssColor
• getChannelHexColor
• getChannelVisibility
• getContainer
• getCurrentImageDimension
• getCurrentSliceIndex
• getCurrentSlicesNumAndContrastNum
• getDrawingCanvas
• getIsShowContrastState
• getKeyboardSettings
• getLayerOpacity
• getLayerOpacityMap
• getLayerVisibility
• getMaskData
• getMaxSliceNum
• getMode
• getNrrdToolsSettings
• getOpacity
• getPencilColor
• getSliderMeta
• getSpaceOrigin
• getSphereBrushRadius
• getVoxelSpacing
• hasLayerData
• init
• initNrrdToolsModules
• isAiAssistActive
• isAnnotationSuspended
• isCalculatorActive
• isChannelVisible
• isContrastShortcutEnabled
• isLayerVisible
• redo
• redrawDisplayCanvas
• redrawMianPreOnDisplayCanvas
• refreshSphereOverlay
• reloadMasksFromVolume
• removeSkip
• replaceLayerVolume
• reset
• resetChannelColors
• resetLayerCanvas
• resetPaintAreaUIPosition
• resizePaintArea
• setActiveChannel
• setActiveLayer
• setActiveSphereType
• setAllLayersChannelColor
• setAllSlices
• setAnnotationSuspended
• setBaseDrawDisplayCanvasesSize
• setBrushSize
• setCalculateDistanceSphere
• setChannelColor
• setChannelColors
• setChannelVisible
• setContrastIndex
• setContrastShortcutEnabled
• setDisplaySliceIndexPanel
• setEmptyCanvasSize
• setIsDrawFalse
• setKeyboardSettings
• setLayerOpacity
• setLayerVisible
• setMainAreaSize
• setMasksData
• setMasksFromNIfTI
• setMode
• setOpacity
• setPencilColor
• setPencilIconUrls
• setShowInMainArea
• setSkips
• setSliceMoving
• setSliceOrientation
• setSphereBrushRadius
• setSyncsliceNum
• setWindowHigh
• setWindowLow
• setupGUI
• switchAllSlicesArrayData
• switchSlicesPreservingView
• syncGuiParameterSettings
• undo
• updateMouseWheelEvent
• updateOriginAndChangedWH
• wireDrawCoreMethods

Constructors ​

constructor ​

• new NrrdTools(container, options?)

Parameters ​

Defined in ​

src/Utils/segmentation/NrrdTools.ts:112

Properties ​

_aiAssistActive ​

• Private _aiAssistActive: boolean = false

Whether AI-assist mode is currently active.

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1177

_aiPrevVisibility ​

• Private _aiPrevVisibility: null | Record<string, boolean> = null

Layer visibility snapshot taken on enter, restored on exit.

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1179

_calculatorActive ​

• Private _calculatorActive: boolean = false

Whether calculator mode is active (not part of gui_states interface)

Defined in ​

src/Utils/segmentation/NrrdTools.ts:72

_pendingSliceStep ​

• Private _pendingSliceStep: number = 0

Defined in ​

src/Utils/segmentation/NrrdTools.ts:69

_sliceRAFId ​

• Private _sliceRAFId: null | number = null

Defined in ​

src/Utils/segmentation/NrrdTools.ts:68

container ​

• container: HTMLDivElement

Defined in ​

src/Utils/segmentation/NrrdTools.ts:57

dataLoader ​

• Private dataLoader: DataLoader

Data loading (extracted module)

Defined in ​

src/Utils/segmentation/NrrdTools.ts:81

dragOperator ​

• dragOperator: DragOperator

Drag operator for slice navigation.

Defined in ​

src/Utils/segmentation/NrrdTools.ts:64

drawCore ​

• Private drawCore: DrawToolCore

Core drawing tool orchestrator.

Defined in ​

src/Utils/segmentation/NrrdTools.ts:62

guiCallbacks ​

• Private guiCallbacks: null | { finishContrastAdjustment: () => void ; updateCalDistance: (val: "tumour" | "skin" | "nipple" | "ribcage") => void ; updateEraserState: () => void ; updatePencilState: () => void ; updateSphereState: () => void ; updateWindowHigh: (value: number) => void ; updateWindowLow: (value: number) => void } = null

Stored closure callbacks from gui.ts setupGui()

Defined in ​

src/Utils/segmentation/NrrdTools.ts:98

guiParameterSettings ​

• Private guiParameterSettings: undefined | IGuiParameterSettings

Defined in ​

src/Utils/segmentation/NrrdTools.ts:67

layerChannelManager ​

• Private layerChannelManager: LayerChannelManager

Layer/channel management (extracted module)

Defined in ​

src/Utils/segmentation/NrrdTools.ts:75

notifyUser ​

• notifyUser: (message: string, level: "error" | "warning" | "info") => void

Type declaration ​

▸ (message, level): void

How a message reaches the reader. Defaults to the console: this package ships without a UI and must not import the host application's, or it cannot be built on its own. A host that has a toast or a banner assigns this after construction.

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:88

preTimer ​

• Private preTimer: any

Defined in ​

src/Utils/segmentation/NrrdTools.ts:66

sliceRenderPipeline ​

• Private sliceRenderPipeline: SliceRenderPipeline

Slice rendering pipeline (extracted module)

Defined in ​

src/Utils/segmentation/NrrdTools.ts:78

state ​

• Private state: CanvasState

Shared state container.

Defined in ​

src/Utils/segmentation/NrrdTools.ts:60

Accessors ​

start ​

• get start(): () => void

Get the DrawToolCore's start() render loop callback. This is called by DragSliceTool's requestAnimationFrame loop.

Returns ​

fn

▸ (): void

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1495

Methods ​

addSkip ​

▸ addSkip(index): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:818

adjustContrast ​

▸ adjustContrast(type, delta): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:446

aiApplyMask ​

▸ aiApplyMask(result): void

Apply a backend mask result into the scratch volume (overlay repaints next frame).

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1263

aiCancelLasso ​

▸ aiCancelLasso(): void

Abandon the in-progress lasso (Esc).

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1274

aiClearPrompts ​

▸ aiClearPrompts(): void

Clear the in-progress prompt set (e.g. slice change).

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1265

aiClearSegment ​

▸ aiClearSegment(label): void

Delete a Segmentation: erase all its label's voxels from scratch + committed.

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1255

aiCommitRegion ​

▸ aiCommitRegion(): void

"New region": freeze current regions (they persist) + start a fresh prompt set.

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1280

aiCommitToLayer ​

▸ aiCommitToLayer(targetLayer?): void

Back-compat shim: merge with an IDENTITY mapping (each AI label → the same channel number) via the mapped path above. Newer callers should use aiCommitToLayerMapped with an explicit per-segmentation mapping.

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1354

aiCommitToLayerMapped ​

▸ aiCommitToLayerMapped(targetLayer, mapping): void

Merge the AI scratch into a target layer with an explicit per-segmentation mapping, as a single undoable group (sandbox merge — non-destructive + one Ctrl+Z). mapping is { AI scratch label -> target channel(1-8) }; any label absent from the mapping (or mapped to 0) is DISCARDED (not merged). Several AI labels MAY map to the SAME channel — after merge the channel is the identity (CLAUDE.md decision M2), so the merged voxels take that channel's fixed colour.

UNION semantics (M4): an AI voxel only fills a target voxel that is currently EMPTY (0) — existing manual annotation is NEVER erased. Where two AI labels map to different channels and overlap the same voxel, the first one written wins (iteration order), an accepted edge case for a single-value-per-voxel mask. Scans all z-slices, so voxels painted from any view are caught.

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1309

aiDiscard ​

▸ aiDiscard(): void

Discard all AI scratch painting since enter (sandbox discard).

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1282

aiFinishLasso ​

▸ aiFinishLasso(): void

Close + send the in-progress lasso to the backend (needs ≥3 vertices).

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1268

aiGetScratchSegments ​

▸ aiGetScratchSegments(): null | { axis: "z" ; height: number ; segments: { label: number ; slices: { rle: number[] ; sliceIndex: number }[] }[] ; width: number }

Per-segmentation serialization (one binary RLE per label per z-slice) for the multi-label / per-colour 3D build.

Returns ​

null | { axis: "z" ; height: number ; segments: { label: number ; slices: { rle: number[] ; sliceIndex: number }[] }[] ; width: number }

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1291

aiGetScratchSlices ​

▸ aiGetScratchSlices(): null | { axis: "z" ; height: number ; slices: { rle: number[] ; sliceIndex: number }[] ; width: number }

Serialize the AI scratch as per-slice RLE for persisting to ai_generated_nii_LPS.

Returns ​

null | { axis: "z" ; height: number ; slices: { rle: number[] ; sliceIndex: number }[] ; width: number }

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1286

aiHasData ​

▸ aiHasData(): boolean

True if the scratch volume holds any predicted voxels.

Returns ​

boolean

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1284

aiIsLassoEditing ​

▸ aiIsLassoEditing(): boolean

True while the user is placing lasso vertices.

Returns ​

boolean

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1276

aiLassoRedo ​

▸ aiLassoRedo(): void

Redo the last undone lasso vertex change.

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1272

aiLassoUndo ​

▸ aiLassoUndo(): void

Undo the last lasso vertex add/delete.

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1270

aiLassoVertCount ​

▸ aiLassoVertCount(): number

Number of placed lasso vertices (drives the Finish button).

Returns ​

number

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1278

aiNewSegment ​

▸ aiNewSegment(label): void

"New segmentation": freeze current regions + switch to a new label.

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1253

aiOnLassoChange ​

▸ aiOnLassoChange(cb): void

Register the callback fired when the lasso vertex set changes (drives the Finish button).

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1261

aiOnPrompt ​

▸ aiOnPrompt(cb): void

Register the callback invoked when a prompt gesture completes (app → backend).

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1259

aiSetActiveSegment ​

▸ aiSetActiveSegment(label): void

Select the active Segmentation by its label value (the AI paints into it).

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1247

aiSetPolarity ​

▸ aiSetPolarity(label): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1245

aiSetPromptTool ​

▸ aiSetPromptTool(tool): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1244

aiSetScribbleSize ​

▸ aiSetScribbleSize(size): void

Set the scribble brush radius (px).

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1257

aiSetSegmentColor ​

▸ aiSetSegmentColor(label, color): void

Set a Segmentation's colour (its label's colorMap entry; 2D overlay repaints).

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1249

appendLoadingbar ​

▸ appendLoadingbar(loadingbar): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:977

clearActiveLayer ​

▸ clearActiveLayer(): void

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1365

clearDictionary ​

▸ Private clearDictionary(dic): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1485

commitSeriesLoad ​

▸ commitSeriesLoad(allSlices, skipEntries, contrastIndex): void

Case-load completion, fully batched: swap in the acquisition-ordered slice array, reconcile skip state, and land on the target contrast -- one resetDisplaySlicesStatus() instead of three (switchAllSlicesArrayData + setSkips + setContrastIndex used to each pay their own full refresh here; see commitSkipsAndContrast above for why only the batched form's single refresh is needed).

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:957

commitSkipsAndContrast ​

▸ commitSkipsAndContrast(skipEntries, contrastIndex): void

Batched form of setSkips + setContrastIndex for a load that ends by reconciling skip state and landing on a phase in the same turn (see useCaseManagement.handleAllImagesLoaded). Calling them separately is correct but wasteful: each pays resetDisplaySlicesStatus()'s full display/canvas/mask refresh, and with nothing reading the display in between, only the second call's paint was ever visible -- measured at two ~300ms refreshes back-to-back once setSkips had already absorbed the earlier per-phase addSkip/removeSkip loop cost.

contrastIndex is set before the single resetDisplaySlicesStatus() call, not after: the resulting displaySlices length/order depends only on skipSlicesDic, which is already written by the time it runs, so the callbacks inside that one refresh (repraintCurrentContrastSlice etc.) paint the target contrast directly. The clamp below still runs after, against the freshly rebuilt displaySlices, for parity with setContrastIndex's own bounds check.

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:933

configMouseSliceWheel ​

▸ configMouseSliceWheel(): (e: WheelEvent) => void

Returns ​

fn

▸ (e): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1425

copyLayerData ​

▸ copyLayerData(sourceLayerId, targetLayerId): void

Copy all voxel data from one layer's MaskVolume to another.

After the copy the target layer's display is refreshed so the UI shows the updated data immediately. The target layer's color map is preserved — only the raw voxel buffer is overwritten.

Use case: when editing layer2 cascades to layer3 on the backend, call this to keep the frontend in sync without a network round-trip.

Parameters ​

Returns ​

void

Example

nrrdTools.copyLayerData("layer2", "layer3");

nrrdTools.copyLayerData("layer2", "layer3");

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1524

drag ​

▸ drag(opts?): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:644

draw ​

▸ draw(opts?): void

Core drawing entry point.

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:651

drawCalculatorSphereOnEachViews ​

▸ drawCalculatorSphereOnEachViews(axis): void

Expose drawCalculatorSphereOnEachViews for external use.

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1502

enableContrastDragEvents ​

▸ enableContrastDragEvents(callback): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:672

enterAiAssistMode ​

▸ enterAiAssistMode(): void

Enter AI-assist mode (sandbox): hides the existing layer masks so ONLY the AI overlay is shown, takes canvas ownership (left-click = prompt), and creates the scratch volume. Right-drag still pans; wheel/slider still scrub slices. The hidden masks are restored on exit (merge writes into them first if asked).

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1207

enterKeyboardConfig ​

▸ enterKeyboardConfig(): void

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:608

enterSphereMode ​

▸ enterSphereMode(): void

Enter sphere mode.

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1140

executeAction ​

▸ executeAction(action, opts?): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:505

exitAiAssistMode ​

▸ exitAiAssistMode(): void

Exit AI-assist mode: drop the scratch volume, restore normal tooling AND the layer-mask visibility hidden on enter. If the caller merged first, the merged result is now part of the layer volume and reappears with the restored masks.

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1227

exitKeyboardConfig ​

▸ exitKeyboardConfig(): void

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:612

exitSphereMode ​

▸ exitSphereMode(): void

Exit sphere mode.

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1159

finishWindowAdjustment ​

▸ finishWindowAdjustment(): void

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:442

flipDisplayImageByAxis ​

▸ flipDisplayImageByAxis(): void

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1086

getActiveChannel ​

▸ getActiveChannel(): number

Returns ​

number

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1051

getActiveLayer ​

▸ getActiveLayer(): string

Returns ​

string

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1049

getActiveSphereType ​

▸ getActiveSphereType(): SphereType

Returns ​

SphereType

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1053

getBrushSize ​

▸ getBrushSize(): number

Returns ​

number

Defined in ​

src/Utils/segmentation/NrrdTools.ts:420

getChannelColor ​

▸ getChannelColor(layerId, channel): RGBAColor

Parameters ​

Returns ​

RGBAColor

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1064

getChannelCssColor ​

▸ getChannelCssColor(layerId, channel): string

Parameters ​

Returns ​

string

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1066

getChannelHexColor ​

▸ getChannelHexColor(layerId, channel): string

Parameters ​

Returns ​

string

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1065

getChannelVisibility ​

▸ getChannelVisibility(): Record<string, Record<number, boolean>>

Returns ​

Record<string, Record<number, boolean>>

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1060

getContainer ​

▸ getContainer(): HTMLElement

Returns ​

HTMLElement

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1001

getCurrentImageDimension ​

▸ getCurrentImageDimension(): number[]

Returns ​

number[]

Defined in ​

src/Utils/segmentation/NrrdTools.ts:985

getCurrentSliceIndex ​

▸ getCurrentSliceIndex(): number

Returns ​

number

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1031

getCurrentSlicesNumAndContrastNum ​

▸ getCurrentSlicesNumAndContrastNum(): Object

Returns ​

Object

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1024

getDrawingCanvas ​

▸ getDrawingCanvas(): HTMLCanvasElement

Returns ​

HTMLCanvasElement

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1005

getIsShowContrastState ​

▸ getIsShowContrastState(): boolean

Returns ​

boolean

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1037

getKeyboardSettings ​

▸ getKeyboardSettings(): IKeyBoardSettings

Returns ​

IKeyBoardSettings

Defined in ​

src/Utils/segmentation/NrrdTools.ts:636

getLayerOpacity ​

▸ getLayerOpacity(layerId): number

Parameters ​

Returns ​

number

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1073

getLayerOpacityMap ​

▸ getLayerOpacityMap(): Record<string, number>

Returns ​

Record<string, number>

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1074

getLayerVisibility ​

▸ getLayerVisibility(): Record<string, boolean>

Returns ​

Record<string, boolean>

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1059

getMaskData ​

▸ getMaskData(): IMaskData

Returns ​

IMaskData

Defined in ​

src/Utils/segmentation/NrrdTools.ts:997

getMaxSliceNum ​

▸ getMaxSliceNum(): number[]

Returns ​

number[]

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1013

getMode ​

▸ getMode(): ToolMode

Returns ​

ToolMode

Defined in ​

src/Utils/segmentation/NrrdTools.ts:392

getNrrdToolsSettings ​

▸ getNrrdToolsSettings(): NrrdState

Returns ​

NrrdState

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1009

getOpacity ​

▸ getOpacity(): number

Returns ​

number

Defined in ​

src/Utils/segmentation/NrrdTools.ts:410

getPencilColor ​

▸ getPencilColor(): string

Returns ​

string

Defined in ​

src/Utils/segmentation/NrrdTools.ts:501

getSliderMeta ​

▸ getSliderMeta(key): null | IGuiMeta

Parameters ​

Returns ​

null | IGuiMeta

Defined in ​

src/Utils/segmentation/NrrdTools.ts:463

getSpaceOrigin ​

▸ getSpaceOrigin(): number[]

Returns ​

number[]

Defined in ​

src/Utils/segmentation/NrrdTools.ts:993

getSphereBrushRadius ​

▸ getSphereBrushRadius(): number

Returns ​

number

Defined in ​

src/Utils/segmentation/NrrdTools.ts:428

getVoxelSpacing ​

▸ getVoxelSpacing(): number[]

Returns ​

number[]

Defined in ​

src/Utils/segmentation/NrrdTools.ts:989

hasLayerData ​

▸ hasLayerData(layerId): boolean

Parameters ​

Returns ​

boolean

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1061

init ​

▸ Private init(): void

A initialise function for nrrd_tools

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:180

initNrrdToolsModules ​

▸ Private initNrrdToolsModules(): void

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:190

isAiAssistActive ​

▸ isAiAssistActive(): boolean

Returns ​

boolean

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1181

isAnnotationSuspended ​

▸ isAnnotationSuspended(): boolean

Returns ​

boolean

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1197

isCalculatorActive ​

▸ isCalculatorActive(): boolean

Returns ​

boolean

Defined in ​

src/Utils/segmentation/NrrdTools.ts:402

isChannelVisible ​

▸ isChannelVisible(layerId, channel): boolean

Parameters ​

Returns ​

boolean

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1058

isContrastShortcutEnabled ​

▸ isContrastShortcutEnabled(): boolean

Returns ​

boolean

Defined in ​

src/Utils/segmentation/NrrdTools.ts:620

isLayerVisible ​

▸ isLayerVisible(layerId): boolean

Parameters ​

Returns ​

boolean

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1056

redo ​

▸ redo(): void

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:604

redrawDisplayCanvas ​

▸ redrawDisplayCanvas(): void

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1088

redrawMianPreOnDisplayCanvas ​

▸ redrawMianPreOnDisplayCanvas(): void

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1084

refreshSphereOverlay ​

▸ Private refreshSphereOverlay(): void

Refresh sphere canvas from sphereMaskVolume for the current slice/axis.

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1133

reloadMasksFromVolume ​

▸ Private reloadMasksFromVolume(): void

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1089

removeSkip ​

▸ removeSkip(index): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:830

replaceLayerVolume ​

▸ replaceLayerVolume(layerId, data, opts?): void

Replace a layer's entire voxel buffer.

This call itself does NOT fire onLayerVolumeReplaced - callers (e.g. the mask upload flow) must persist the new volume themselves. The callback fires only later, if the clinician undoes or redoes this replacement, because at that point the backend still holds the newer volume and needs to be told to fall back to the old one.

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1564

reset ​

▸ reset(): void

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1379

resetChannelColors ​

▸ resetChannelColors(layerId?, channel?): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1069

resetLayerCanvas ​

▸ resetLayerCanvas(): void

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1083

resetPaintAreaUIPosition ​

▸ resetPaintAreaUIPosition(l?, t?): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1082

resizePaintArea ​

▸ resizePaintArea(factor): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1085

setActiveChannel ​

▸ setActiveChannel(channel): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1050

setActiveLayer ​

▸ setActiveLayer(layerId): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1045

setActiveSphereType ​

▸ setActiveSphereType(type): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1052

setAllLayersChannelColor ​

▸ setAllLayersChannelColor(channel, color): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1068

setAllSlices ​

▸ setAllSlices(allSlices): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1095

setAnnotationSuspended ​

▸ setAnnotationSuspended(suspended): void

Suspend or resume annotation input.

While suspended the reader may still scrub slices, zoom, pan and place the crosshair, but no input can write into a mask. This is the enforcement behind "during loading you may preview, not annotate": greying the Operation panel's buttons does not achieve it, because a tool selected before the load began stays armed on the canvas -- and a stroke made then cannot even be undone, since afterLoadSlice clears the undo stack each time a slice arrives.

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1193

setBaseDrawDisplayCanvasesSize ​

▸ setBaseDrawDisplayCanvasesSize(size): void

Set the Draw Display Canvas base size

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:658

setBrushSize ​

▸ setBrushSize(size): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:414

setCalculateDistanceSphere ​

▸ setCalculateDistanceSphere(x, y, sliceIndex, cal_position): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1103

setChannelColor ​

▸ setChannelColor(layerId, channel, color): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1063

setChannelColors ​

▸ setChannelColors(layerId, colorMap): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1067

setChannelVisible ​

▸ setChannelVisible(layerId, channel, visible): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1057

setContrastIndex ​

▸ setContrastIndex(index): void

Move to a specific contrast without moving the slice.

index addresses displaySlices — the SELECTED subset — not the full contrast list. With three of five phases selected, valid values are 0..2. Callers that think in phase names must convert first.

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:873

setContrastShortcutEnabled ​

▸ setContrastShortcutEnabled(enabled): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:616

setDisplaySliceIndexPanel ​

▸ setDisplaySliceIndexPanel(panel): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:668

setEmptyCanvasSize ​

▸ setEmptyCanvasSize(axis?): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1087

setIsDrawFalse ​

▸ setIsDrawFalse(target): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1471

setKeyboardSettings ​

▸ setKeyboardSettings(settings): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:624

setLayerOpacity ​

▸ setLayerOpacity(layerId, opacity): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1072

setLayerVisible ​

▸ setLayerVisible(layerId, visible): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1055

setMainAreaSize ​

▸ setMainAreaSize(factor): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:899

setMasksData ​

▸ setMasksData(masksData, loadingBar?): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1096

setMasksFromNIfTI ​

▸ setMasksFromNIfTI(layerVoxels, loadingBar?): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1097

setMode ​

▸ setMode(mode): void

Set the current tool mode.

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:313

setOpacity ​

▸ setOpacity(value): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:406

setPencilColor ​

▸ setPencilColor(hex): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:497

setPencilIconUrls ​

▸ setPencilIconUrls(urls): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:676

setShowInMainArea ​

▸ Private setShowInMainArea(): void

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1481

setSkips ​

▸ setSkips(entries): void

Batched form of addSkip/removeSkip for reconciling many positions at once (e.g. a case load's initial phase selection, see useCaseManagement.reconcileSkips) without paying resetDisplaySlicesStatus()'s full display/canvas/mask refresh once per position.

Calling addSkip/removeSkip in a loop is correct but wasteful here: every entry but the last is immediately superseded (this always runs synchronously, with nothing reading the display in between, and the caller's own follow-up -- landOn's setContrastIndex -- overwrites contrastNum again right after). Measured at over 1 second of main-thread time for a 5-phase series once per-volume extraction stopped dominating the case-load block (narrower axes, see copperNrrdLoader) -- this was always there, just smaller than the cost it used to sit next to.

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:849

setSliceMoving ​

▸ setSliceMoving(step): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:880

setSliceOrientation ​

▸ setSliceOrientation(axisTo): void

Switch all contrast slices' orientation

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:683

setSphereBrushRadius ​

▸ setSphereBrushRadius(radius): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:424

setSyncsliceNum ​

▸ setSyncsliceNum(): void

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1081

setWindowHigh ​

▸ setWindowHigh(value): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:432

setWindowLow ​

▸ setWindowLow(value): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:437

setupGUI ​

▸ setupGUI(gui): void

Set up GUI for drawing panel

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:237

switchAllSlicesArrayData ​

▸ switchAllSlicesArrayData(allSlices): void

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:911

switchSlicesPreservingView ​

▸ switchSlicesPreservingView(allSlices): void

Swap slice data while preserving current slice index, zoom, and pan position. Used for register/origin image switching where the view state should persist.

Parameters ​

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:971

syncGuiParameterSettings ​

▸ Private syncGuiParameterSettings(): void

Sync guiParameterSettings with current volume metadata.

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:298

undo ​

▸ undo(): void

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:600

updateMouseWheelEvent ​

▸ updateMouseWheelEvent(): void

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1445

updateOriginAndChangedWH ​

▸ updateOriginAndChangedWH(): void

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:1080

wireDrawCoreMethods ​

▸ Private wireDrawCoreMethods(): void

Wire DrawToolCore's overridable methods to NrrdTools implementations. This replaces the old inheritance approach.

Returns ​

void

Defined in ​

src/Utils/segmentation/NrrdTools.ts:160