copper3d / Modules / Utils/segmentation/NrrdTools / NrrdTools

Class: 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"] });

Constructors

constructor

Properties

Accessors

start

Methods

Constructors

constructor

• new NrrdTools(container, options?)

Parameters

Name	Type
`container`	`HTMLDivElement`
`options?`	`Object`
`options.layers?`	`string`[]

Defined in

src/Utils/segmentation/NrrdTools.ts:113

Properties

_aiAssistActive

• Private _aiAssistActive: boolean = false

Whether AI-assist mode is currently active.

Defined in

src/Utils/segmentation/NrrdTools.ts:1266

_aiPrevVisibility

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

Layer visibility snapshot taken on enter, restored on exit.

Defined in

src/Utils/segmentation/NrrdTools.ts:1268

_calculatorActive

• Private _calculatorActive: boolean = false

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

Defined in

src/Utils/segmentation/NrrdTools.ts:73

_pendingSliceStep

• Private _pendingSliceStep: number = 0

Defined in

src/Utils/segmentation/NrrdTools.ts:70

_sliceRAFId

• Private _sliceRAFId: null | number = null

Defined in

src/Utils/segmentation/NrrdTools.ts:69

container

• container: HTMLDivElement

Defined in

src/Utils/segmentation/NrrdTools.ts:58

dataLoader

• Private dataLoader: DataLoader

Data loading (extracted module)

Defined in

src/Utils/segmentation/NrrdTools.ts:82

dragOperator

• dragOperator: DragOperator

Drag operator for slice navigation.

Defined in

src/Utils/segmentation/NrrdTools.ts:65

drawCore

• Private drawCore: DrawToolCore

Core drawing tool orchestrator.

Defined in

src/Utils/segmentation/NrrdTools.ts:63

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:99

guiParameterSettings

• Private guiParameterSettings: undefined | IGuiParameterSettings

Defined in

src/Utils/segmentation/NrrdTools.ts:68

layerChannelManager

• Private layerChannelManager: LayerChannelManager

Layer/channel management (extracted module)

Defined in

src/Utils/segmentation/NrrdTools.ts:76

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

Name	Type
`message`	`string`
`level`	`"error"` \| `"warning"` \| `"info"`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:89

preTimer

• Private preTimer: any

Defined in

src/Utils/segmentation/NrrdTools.ts:67

sliceRenderPipeline

• Private sliceRenderPipeline: SliceRenderPipeline

Slice rendering pipeline (extracted module)

Defined in

src/Utils/segmentation/NrrdTools.ts:79

state

• Private state: CanvasState

Shared state container.

Defined in

src/Utils/segmentation/NrrdTools.ts:61

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:1584

Methods

addSkip

▸ addSkip(index): void

Parameters

Name	Type
`index`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:890

adjustContrast

▸ adjustContrast(type, delta): void

Parameters

Name	Type
`type`	`"windowLow"` \| `"windowHigh"`
`delta`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:447

aiApplyMask

▸ aiApplyMask(result): void

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

Parameters

Name	Type
`result`	`AiMaskResult`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1352

aiCancelLasso

▸ aiCancelLasso(): void

Abandon the in-progress lasso (Esc).

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1363

aiClearPrompts

▸ aiClearPrompts(): void

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

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1354

aiClearSegment

▸ aiClearSegment(label): void

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

Parameters

Name	Type
`label`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1344

aiCommitRegion

▸ aiCommitRegion(): void

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

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1369

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

Name	Type	Default value
`targetLayer`	`string`	`"layer1"`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1443

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

Name	Type
`targetLayer`	`string`
`mapping`	`Record`<`number`, `number`>

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1398

aiDiscard

▸ aiDiscard(): void

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

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1371

aiFinishLasso

▸ aiFinishLasso(): void

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

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1357

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:1380

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:1375

aiHasData

▸ aiHasData(): boolean

True if the scratch volume holds any predicted voxels.

Returns

boolean

Defined in

src/Utils/segmentation/NrrdTools.ts:1373

aiIsLassoEditing

▸ aiIsLassoEditing(): boolean

True while the user is placing lasso vertices.

Returns

boolean

Defined in

src/Utils/segmentation/NrrdTools.ts:1365

aiLassoRedo

▸ aiLassoRedo(): void

Redo the last undone lasso vertex change.

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1361

aiLassoUndo

▸ aiLassoUndo(): void

Undo the last lasso vertex add/delete.

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1359

aiLassoVertCount

▸ aiLassoVertCount(): number

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

Returns

number

Defined in

src/Utils/segmentation/NrrdTools.ts:1367

aiNewSegment

▸ aiNewSegment(label): void

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

Parameters

Name	Type
`label`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1342

aiOnLassoChange

▸ aiOnLassoChange(cb): void

Parameters

Name	Type
`cb`	(`count`: `number`, `editing`: `boolean`) => `void`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1350

aiOnPrompt

▸ aiOnPrompt(cb): void

Parameters

Name	Type
`cb`	(`payload`: `AiPromptPayload`) => `void`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1348

aiSetActiveSegment

▸ aiSetActiveSegment(label): void

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

Parameters

Name	Type
`label`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1336

aiSetPolarity

▸ aiSetPolarity(label): void

Parameters

Name	Type
`label`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1334

aiSetPromptTool

▸ aiSetPromptTool(tool): void

Parameters

Name	Type
`tool`	`AiPromptTool`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1333

aiSetScribbleSize

▸ aiSetScribbleSize(size): void

Set the scribble brush radius (px).

Parameters

Name	Type
`size`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1346

aiSetSegmentColor

▸ aiSetSegmentColor(label, color): void

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

Parameters

Name	Type
`label`	`number`
`color`	`Object`
`color.a`	`number`
`color.b`	`number`
`color.g`	`number`
`color.r`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1338

appendLoadingbar

▸ appendLoadingbar(loadingbar): void

Parameters

Name	Type
`loadingbar`	`HTMLDivElement`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1049

clearActiveLayer

▸ clearActiveLayer(): void

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1454

clearChannel

▸ clearChannel(layerId, channel): void

Erase one channel's mask on one layer, undoably.

The missing third of the clear family that executeAction exposes: clearActiveSliceMask takes one slice, clearActiveLayerMask takes a whole layer, and neither can take a single label. Deleting one annotation needs exactly that — its mask is one label inside a volume shared with every other annotation on the layer.

Not folded into executeAction: that signature is an action name plus an options bag, and this needs two required arguments.

Deltas go onto the engine's own undo stack, so a mistaken clear is recoverable for as long as the case stays open. That is the whole reason this lives here rather than in the app: writing zeros from outside and forcing a repaint by stepping the slice would bypass the stack, and an accidental clear would be permanent.

Only slices that actually carry the label are touched, so a small annotation in a deep volume costs a scan and a handful of callbacks rather than one per slice.

Parameters

Name	Type	Description
`layerId`	`string`	Layer whose mask to edit.
`channel`	`number`	Label to erase, 1-255.

Returns

void

Throws

If layerId names no layer. Deliberately NOT routed through getVolumeForLayer, which warns and falls back to the first layer — for a destructive call that would quietly erase a different layer's annotation.

Throws

If channel is outside [1, 255] (from MaskVolume).

Defined in

src/Utils/segmentation/NrrdTools.ts:624

clearDictionary

▸ Private clearDictionary(dic): void

Parameters

Name	Type
`dic`	`ISkipSlicesDictType`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1574

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

Name	Type
`allSlices`	`nrrdSliceType`[]
`skipEntries`	{ `index`: `number` ; `skip`: `boolean` }[]
`contrastIndex`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1029

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

Name	Type
`skipEntries`	{ `index`: `number` ; `skip`: `boolean` }[]
`contrastIndex`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1005

configMouseSliceWheel

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

Returns

fn

▸ (e): void

Parameters

Name	Type
`e`	`WheelEvent`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1514

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

Name	Type	Description
`sourceLayerId`	`string`	Layer to copy from (e.g. "layer2").
`targetLayerId`	`string`	Layer to copy into (e.g. "layer3").

Returns

void

Example

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

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

Defined in

src/Utils/segmentation/NrrdTools.ts:1613

drag

▸ drag(opts?): void

Parameters

Name	Type
`opts?`	`IDragOpts`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:716

draw

▸ draw(opts?): void

Core drawing entry point.

Parameters

Name	Type
`opts?`	`any`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:723

drawCalculatorSphereOnEachViews

▸ drawCalculatorSphereOnEachViews(axis): void

Expose drawCalculatorSphereOnEachViews for external use.

Parameters

Name	Type
`axis`	`"x"` \| `"y"` \| `"z"`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1591

enableContrastDragEvents

▸ enableContrastDragEvents(callback): void

Parameters

Name	Type
`callback`	(`step`: `number`, `towards`: `"horizental"` \| `"vertical"`) => `void`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:744

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:1296

enterKeyboardConfig

▸ enterKeyboardConfig(): void

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:680

enterSphereMode

▸ enterSphereMode(): void

Enter sphere mode.

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1229

executeAction

▸ executeAction(action, opts?): void

Parameters

Name	Type
`action`	`"undo"` \| `"redo"` \| `"resetZoom"` \| `"downloadCurrentMask"` \| `"clearActiveSliceMask"` \| `"clearActiveLayerMask"` \| `"gaussianSmooth"`
`opts?`	`Object`
`opts.sigma?`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:506

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:1316

exitKeyboardConfig

▸ exitKeyboardConfig(): void

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:684

exitSphereMode

▸ exitSphereMode(): void

Exit sphere mode.

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1248

finishWindowAdjustment

▸ finishWindowAdjustment(): void

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:443

flipDisplayImageByAxis

▸ flipDisplayImageByAxis(): void

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1175

getActiveChannel

▸ getActiveChannel(): number

Returns

number

Defined in

src/Utils/segmentation/NrrdTools.ts:1123

getActiveLayer

▸ getActiveLayer(): string

Returns

string

Defined in

src/Utils/segmentation/NrrdTools.ts:1121

getActiveSphereType

▸ getActiveSphereType(): SphereType

Returns

SphereType

Defined in

src/Utils/segmentation/NrrdTools.ts:1125

getBrushSize

▸ getBrushSize(): number

Returns

number

Defined in

src/Utils/segmentation/NrrdTools.ts:421

getChannelColor

▸ getChannelColor(layerId, channel): RGBAColor

Parameters

Name	Type
`layerId`	`string`
`channel`	`number`

Returns

RGBAColor

Defined in

src/Utils/segmentation/NrrdTools.ts:1136

getChannelCssColor

▸ getChannelCssColor(layerId, channel): string

Parameters

Name	Type
`layerId`	`string`
`channel`	`number`

Returns

string

Defined in

src/Utils/segmentation/NrrdTools.ts:1138

getChannelHexColor

▸ getChannelHexColor(layerId, channel): string

Parameters

Name	Type
`layerId`	`string`
`channel`	`number`

Returns

string

Defined in

src/Utils/segmentation/NrrdTools.ts:1137

getChannelVisibility

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

Returns

Record<string, Record<number, boolean>>

Defined in

src/Utils/segmentation/NrrdTools.ts:1132

getContainer

▸ getContainer(): HTMLElement

Returns

HTMLElement

Defined in

src/Utils/segmentation/NrrdTools.ts:1073

getCurrentImageDimension

▸ getCurrentImageDimension(): number[]

Returns

number[]

Defined in

src/Utils/segmentation/NrrdTools.ts:1057

getCurrentSliceIndex

▸ getCurrentSliceIndex(): number

Returns

number

Defined in

src/Utils/segmentation/NrrdTools.ts:1103

getCurrentSlicesNumAndContrastNum

▸ getCurrentSlicesNumAndContrastNum(): Object

Returns

Object

Name	Type
`contrastIndex`	`number`
`currentSliceIndex`	`number`

Defined in

src/Utils/segmentation/NrrdTools.ts:1096

getDrawingCanvas

▸ getDrawingCanvas(): HTMLCanvasElement

Returns

HTMLCanvasElement

Defined in

src/Utils/segmentation/NrrdTools.ts:1077

getIsShowContrastState

▸ getIsShowContrastState(): boolean

Returns

boolean

Defined in

src/Utils/segmentation/NrrdTools.ts:1109

getKeyboardSettings

▸ getKeyboardSettings(): IKeyBoardSettings

Returns

IKeyBoardSettings

Defined in

src/Utils/segmentation/NrrdTools.ts:708

getLayerOpacity

▸ getLayerOpacity(layerId): number

Parameters

Name	Type
`layerId`	`string`

Returns

number

Defined in

src/Utils/segmentation/NrrdTools.ts:1145

getLayerOpacityMap

▸ getLayerOpacityMap(): Record<string, number>

Returns

Record<string, number>

Defined in

src/Utils/segmentation/NrrdTools.ts:1146

getLayerVisibility

▸ getLayerVisibility(): Record<string, boolean>

Returns

Record<string, boolean>

Defined in

src/Utils/segmentation/NrrdTools.ts:1131

getMaskData

▸ getMaskData(): IMaskData

Returns

IMaskData

Defined in

src/Utils/segmentation/NrrdTools.ts:1069

getMaskRenderMode

▸ getMaskRenderMode(): MaskRenderMode

Returns

MaskRenderMode

Defined in

src/Utils/segmentation/NrrdTools.ts:1163

getMaxSliceNum

▸ getMaxSliceNum(): number[]

Returns

number[]

Defined in

src/Utils/segmentation/NrrdTools.ts:1085

getMode

▸ getMode(): ToolMode

Returns

ToolMode

Defined in

src/Utils/segmentation/NrrdTools.ts:393

getNrrdToolsSettings

▸ getNrrdToolsSettings(): NrrdState

Returns

NrrdState

Defined in

src/Utils/segmentation/NrrdTools.ts:1081

getOpacity

▸ getOpacity(): number

Returns

number

Defined in

src/Utils/segmentation/NrrdTools.ts:411

getPencilColor

▸ getPencilColor(): string

Returns

string

Defined in

src/Utils/segmentation/NrrdTools.ts:502

getSliderMeta

▸ getSliderMeta(key): null | IGuiMeta

Parameters

Name	Type
`key`	`string`

Returns

null | IGuiMeta

Defined in

src/Utils/segmentation/NrrdTools.ts:464

getSpaceOrigin

▸ getSpaceOrigin(): number[]

Returns

number[]

Defined in

src/Utils/segmentation/NrrdTools.ts:1065

getSphereBrushRadius

▸ getSphereBrushRadius(): number

Returns

number

Defined in

src/Utils/segmentation/NrrdTools.ts:429

getVoxelSpacing

▸ getVoxelSpacing(): number[]

Returns

number[]

Defined in

src/Utils/segmentation/NrrdTools.ts:1061

hasLayerData

▸ hasLayerData(layerId): boolean

Parameters

Name	Type
`layerId`	`string`

Returns

boolean

Defined in

src/Utils/segmentation/NrrdTools.ts:1133

init

▸ Private init(): void

A initialise function for nrrd_tools

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:181

initNrrdToolsModules

▸ Private initNrrdToolsModules(): void

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:191

isAiAssistActive

▸ isAiAssistActive(): boolean

Returns

boolean

Defined in

src/Utils/segmentation/NrrdTools.ts:1270

isAnnotationSuspended

▸ isAnnotationSuspended(): boolean

Returns

boolean

Defined in

src/Utils/segmentation/NrrdTools.ts:1286

isCalculatorActive

▸ isCalculatorActive(): boolean

Returns

boolean

Defined in

src/Utils/segmentation/NrrdTools.ts:403

isChannelVisible

▸ isChannelVisible(layerId, channel): boolean

Parameters

Name	Type
`layerId`	`string`
`channel`	`number`

Returns

boolean

Defined in

src/Utils/segmentation/NrrdTools.ts:1130

isContrastShortcutEnabled

▸ isContrastShortcutEnabled(): boolean

Returns

boolean

Defined in

src/Utils/segmentation/NrrdTools.ts:692

isLayerVisible

▸ isLayerVisible(layerId): boolean

Parameters

Name	Type
`layerId`	`string`

Returns

boolean

Defined in

src/Utils/segmentation/NrrdTools.ts:1128

redo

▸ redo(): void

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:676

redrawDisplayCanvas

▸ redrawDisplayCanvas(): void

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1177

redrawMianPreOnDisplayCanvas

▸ redrawMianPreOnDisplayCanvas(): void

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1173

refreshSphereOverlay

▸ Private refreshSphereOverlay(): void

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

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1222

reloadMasksFromVolume

▸ Private reloadMasksFromVolume(): void

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1178

removeSkip

▸ removeSkip(index): void

Parameters

Name	Type
`index`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:902

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

Name	Type	Description
`layerId`	`string`	Layer to overwrite.
`data`	`Uint8Array`	Voxels, exactly the layer volume's length.
`opts`	`Object`	`undoable: true` records one Ctrl+Z step for the whole volume.
`opts.undoable?`	`boolean`	-

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1653

reset

▸ reset(): void

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1468

resetChannelColors

▸ resetChannelColors(layerId?, channel?): void

Parameters

Name	Type
`layerId?`	`string`
`channel?`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1141

resetLayerCanvas

▸ resetLayerCanvas(): void

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1172

resetPaintAreaUIPosition

▸ resetPaintAreaUIPosition(l?, t?): void

Parameters

Name	Type
`l?`	`number`
`t?`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1171

resizePaintArea

▸ resizePaintArea(factor): void

Parameters

Name	Type
`factor`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1174

setActiveChannel

▸ setActiveChannel(channel): void

Parameters

Name	Type
`channel`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1122

setActiveLayer

▸ setActiveLayer(layerId): void

Parameters

Name	Type
`layerId`	`string`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1117

setActiveSphereType

▸ setActiveSphereType(type): void

Parameters

Name	Type
`type`	`SphereType`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1124

setAllLayersChannelColor

▸ setAllLayersChannelColor(channel, color): void

Parameters

Name	Type
`channel`	`number`
`color`	`RGBAColor`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1140

setAllSlices

▸ setAllSlices(allSlices): void

Parameters

Name	Type
`allSlices`	`nrrdSliceType`[]

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1184

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

Name	Type
`suspended`	`boolean`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1282

setBaseDrawDisplayCanvasesSize

▸ setBaseDrawDisplayCanvasesSize(size): void

Set the Draw Display Canvas base size

Parameters

Name	Type
`size`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:730

setBrushSize

▸ setBrushSize(size): void

Parameters

Name	Type
`size`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:415

setCalculateDistanceSphere

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

Parameters

Name	Type
`x`	`number`
`y`	`number`
`sliceIndex`	`number`
`cal_position`	`"tumour"` \| `"skin"` \| `"nipple"` \| `"ribcage"`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1192

setChannelColor

▸ setChannelColor(layerId, channel, color): void

Parameters

Name	Type
`layerId`	`string`
`channel`	`number`
`color`	`RGBAColor`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1135

setChannelColors

▸ setChannelColors(layerId, colorMap): void

Parameters

Name	Type
`layerId`	`string`
`colorMap`	`Partial`<`ChannelColorMap`>

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1139

setChannelVisible

▸ setChannelVisible(layerId, channel, visible): void

Parameters

Name	Type
`layerId`	`string`
`channel`	`number`
`visible`	`boolean`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1129

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

Name	Type
`index`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:945

setContrastShortcutEnabled

▸ setContrastShortcutEnabled(enabled): void

Parameters

Name	Type
`enabled`	`boolean`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:688

setDisplaySliceIndexPanel

▸ setDisplaySliceIndexPanel(panel): void

Parameters

Name	Type
`panel`	`HTMLDivElement`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:740

setEmptyCanvasSize

▸ setEmptyCanvasSize(axis?): void

Parameters

Name	Type
`axis?`	`"x"` \| `"y"` \| `"z"`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1176

setIsDrawFalse

▸ setIsDrawFalse(target): void

Parameters

Name	Type
`target`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1560

setKeyboardSettings

▸ setKeyboardSettings(settings): void

Parameters

Name	Type
`settings`	`Partial`<`IKeyBoardSettings`>

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:696

setLayerOpacity

▸ setLayerOpacity(layerId, opacity): void

Parameters

Name	Type
`layerId`	`string`
`opacity`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1144

setLayerVisible

▸ setLayerVisible(layerId, visible): void

Parameters

Name	Type
`layerId`	`string`
`visible`	`boolean`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1127

setMainAreaSize

▸ setMainAreaSize(factor): void

Parameters

Name	Type
`factor`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:971

setMaskRenderMode

▸ setMaskRenderMode(mode): void

Fill every mask, or stroke only its boundary — for every layer and channel at once.

A display decision, and nothing but: MaskVolume is not read differently and not written at all, so what is stored, uploaded, exported and undone is the complete mask either way.

Repaints immediately, the same way setChannelVisible does, because there is no other event that would bring the change to the screen — a clinician who switched the mode and then had to scrub a slice to see it would reasonably call that broken.

Parameters

Name	Type
`mode`	`MaskRenderMode`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1158

setMasksData

▸ setMasksData(masksData, loadingBar?): void

Parameters

Name	Type
`masksData`	`storeExportPaintImageType`
`loadingBar?`	`loadingBarType`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1185

setMasksFromNIfTI

▸ setMasksFromNIfTI(layerVoxels, loadingBar?): void

Parameters

Name	Type
`layerVoxels`	`Map`<`string`, `Uint8Array`>
`loadingBar?`	`loadingBarType`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1186

setMode

▸ setMode(mode): void

Set the current tool mode.

Parameters

Name	Type
`mode`	`ToolMode`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:314

setOpacity

▸ setOpacity(value): void

Parameters

Name	Type
`value`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:407

setPencilColor

▸ setPencilColor(hex): void

Parameters

Name	Type
`hex`	`string`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:498

setPencilIconUrls

▸ setPencilIconUrls(urls): void

Parameters

Name	Type
`urls`	`string`[]

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:748

setShowInMainArea

▸ Private setShowInMainArea(): void

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1570

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

Name	Type
`entries`	{ `index`: `number` ; `skip`: `boolean` }[]

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:921

setSliceMoving

▸ setSliceMoving(step): void

Parameters

Name	Type
`step`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:952

setSliceOrientation

▸ setSliceOrientation(axisTo): void

Switch all contrast slices' orientation

Parameters

Name	Type
`axisTo`	`"x"` \| `"y"` \| `"z"`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:755

setSphereBrushRadius

▸ setSphereBrushRadius(radius): void

Parameters

Name	Type
`radius`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:425

setSyncsliceNum

▸ setSyncsliceNum(): void

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1170

setWindowHigh

▸ setWindowHigh(value): void

Parameters

Name	Type
`value`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:433

setWindowLow

▸ setWindowLow(value): void

Parameters

Name	Type
`value`	`number`

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:438

setupGUI

▸ setupGUI(gui): void

Set up GUI for drawing panel

Parameters

Name	Type	Description
`gui`	`GUI`	GUI

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:238

switchAllSlicesArrayData

▸ switchAllSlicesArrayData(allSlices): void

Parameters

Name	Type
`allSlices`	`nrrdSliceType`[]

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:983

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

Name	Type
`allSlices`	`nrrdSliceType`[]

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1043

syncGuiParameterSettings

▸ Private syncGuiParameterSettings(): void

Sync guiParameterSettings with current volume metadata.

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:299

undo

▸ undo(): void

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:672

updateMouseWheelEvent

▸ updateMouseWheelEvent(): void

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1534

updateOriginAndChangedWH

▸ updateOriginAndChangedWH(): void

Returns

void

Defined in

src/Utils/segmentation/NrrdTools.ts:1169

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:161

Class: NrrdTools ​

Table of contents ​

Constructors ​

Properties ​

Accessors ​

Methods ​

Constructors ​

constructor ​

Parameters ​

Defined in ​

Properties ​

_aiAssistActive ​

Defined in ​

_aiPrevVisibility ​

Defined in ​

_calculatorActive ​

Defined in ​

_pendingSliceStep ​

Defined in ​

_sliceRAFId ​

Defined in ​

container ​

Defined in ​

dataLoader ​

Defined in ​

dragOperator ​

Defined in ​

drawCore ​

Defined in ​

guiCallbacks ​

Defined in ​

guiParameterSettings ​

Defined in ​

layerChannelManager ​

Defined in ​

notifyUser ​

Type declaration ​

Parameters ​

Returns ​

Defined in ​

preTimer ​

Defined in ​

sliceRenderPipeline ​

Defined in ​

state ​

Defined in ​

Accessors ​

start ​

Returns ​

Returns ​

Defined in ​

Methods ​

addSkip ​

Parameters ​

Returns ​

Defined in ​

adjustContrast ​

Parameters ​

Returns ​

Defined in ​

aiApplyMask ​

Parameters ​

Returns ​

Defined in ​

aiCancelLasso ​

Returns ​

Defined in ​

aiClearPrompts ​

Returns ​

Defined in ​

aiClearSegment ​

Parameters ​

Returns ​

Defined in ​

aiCommitRegion ​

Returns ​

Defined in ​

aiCommitToLayer ​

Parameters ​

Returns ​

Class: NrrdTools

Table of contents

Constructors

Properties

Accessors

Methods

Constructors

constructor

Parameters

Defined in

Properties

_aiAssistActive

Defined in

_aiPrevVisibility

Defined in

_calculatorActive

Defined in

_pendingSliceStep

Defined in

_sliceRAFId

Defined in

container

Defined in

dataLoader

Defined in

dragOperator

Defined in

drawCore

Defined in

guiCallbacks

Defined in

guiParameterSettings

Defined in

layerChannelManager

Defined in

notifyUser

Type declaration

Parameters

Returns

Defined in

preTimer

Defined in

sliceRenderPipeline

Defined in

state

Defined in

Accessors

start

Returns

Returns

Defined in

Methods

addSkip

Parameters

Returns

Defined in

adjustContrast

Parameters

Returns

Defined in

aiApplyMask

Parameters

Returns

Defined in

aiCancelLasso

Returns

Defined in

aiClearPrompts

Returns

Defined in

aiClearSegment

Parameters

Returns

Defined in

aiCommitRegion

Returns

Defined in

aiCommitToLayer

Parameters

Returns