Class SegmentationUserLayer

Hierarchy

Base
- SegmentationUserLayer

Index

Constructors

Accessors

isReady localCoordinateSpace localCoordinateSpaceCombiner localPosition manager type volumeOptions

Methods

activateDataSubsources addAnnotationLayerState addCategoryText addCoordinateSpace addDataSource addLocalAnnotations addRef addRenderLayer addStaticAnnotations addText bindSegmentListWidth canAddDataSource captureSelectionState copySelectionState displayAnnotationState displaySegmentationSelection displaySelectionState dispose disposed filterBySegmentLabel filterSegments getDataSourceSpecifications getLegacyDataSourceSpecifications getValueAt handleAction initializationDone initializeAnnotationLayerViewTab initializeSelectionState markLoading moveToSegment refCountReachedZero registerCancellable registerDisposer registerEventListener removeRenderLayer resetSelectionState restoreState selectAnnotation selectSegment selectedValueFromJson selectedValueToJson selectionStateFromJson selectionStateToJson setAnnotationColorPicker setLayerPosition toJSON transformPickedValue unregisterDisposer updateDataSubsourceActivations

Constructors

constructor

new SegmentationUserLayer(managedLayer: ManagedUserLayer): SegmentationUserLayer
Parameters
- managedLayer: ManagedUserLayer
Returns SegmentationUserLayer
Overrides Base.constructor
- Defined in src/neuroglancer/segmentation_user_layer.ts:372

Properties

anchorSegment

anchorSegment: TrackableValue<undefined | Uint64> = ...

annotationColorPicker

annotationColorPicker: undefined | AnnotationColorWidget = undefined

annotationCrossSectionRenderScaleHistogram

annotationCrossSectionRenderScaleHistogram: RenderScaleHistogram = ...

annotationCrossSectionRenderScaleTarget

annotationCrossSectionRenderScaleTarget: TrackableValue<number> = ...

annotationDisplayState

annotationDisplayState: AnnotationDisplayState = ...

annotationProjectionRenderScaleHistogram

annotationProjectionRenderScaleHistogram: RenderScaleHistogram = ...

annotationProjectionRenderScaleTarget

annotationProjectionRenderScaleTarget: TrackableValue<number> = ...

annotationStates

annotationStates: MergedAnnotationStates = ...

dataSources

dataSources: LayerDataSource[] = []

dataSourcesChanged

dataSourcesChanged: NullarySignal = ...

displayState

displayState: SegmentationUserLayerDisplayState = ...

disposedStacks

disposedStacks: any

`Readonly` hasSkeletonsLayer

hasSkeletonsLayer: CachedLazyDerivedWatchableValue<boolean> = ...

layersChanged

layersChanged: NullarySignal = ...

managedLayer

managedLayer: ManagedUserLayer

panels

panels: UserLayerSidePanelsState = ...

pick

pick: TrackableBoolean = ...

readyStateChanged

readyStateChanged: NullarySignal = ...

refCount

refCount: number = 1

renderLayers

renderLayers: RenderLayer[] = ...

segmentQueryFocusTime

segmentQueryFocusTime: WatchableValue<number> = ...

selectionState

selectionState: UserLayerSelectionState

sliceViewRenderScaleHistogram

sliceViewRenderScaleHistogram: RenderScaleHistogram = ...

sliceViewRenderScaleTarget

sliceViewRenderScaleTarget: TrackableValue<number> = ...

specificationChanged

specificationChanged: NullarySignal = ...

tabs

tabs: TabSpecification = ...

tool

tool: SelectedLegacyTool = ...

toolBinder

toolBinder: LayerToolBinder = ...

wasDisposed

wasDisposed: undefined | boolean

`Static` supportsPickOption

supportsPickOption: boolean = true

`Static` type

type: string = 'segmentation'

`Static` typeAbbreviation

typeAbbreviation: string = 'seg'

Accessors

isReady

get isReady(): boolean
Returns boolean
Inherited from Base.isReady
- Defined in src/neuroglancer/layer.ts:228

localCoordinateSpace

get localCoordinateSpace(): TrackableCoordinateSpace
Returns TrackableCoordinateSpace
Inherited from Base.localCoordinateSpace
- Defined in src/neuroglancer/layer.ts:95

localCoordinateSpaceCombiner

get localCoordinateSpaceCombiner(): CoordinateSpaceCombiner
Returns CoordinateSpaceCombiner
Inherited from Base.localCoordinateSpaceCombiner
- Defined in src/neuroglancer/layer.ts:91

localPosition

get localPosition(): Position
Returns Position
Inherited from Base.localPosition
- Defined in src/neuroglancer/layer.ts:87

manager

get manager(): LayerListSpecification
Returns LayerListSpecification
Inherited from Base.manager
- Defined in src/neuroglancer/layer.ts:240

type

get type(): string
Returns string
Inherited from Base.type
- Defined in src/neuroglancer/layer.ts:102

volumeOptions

get volumeOptions(): {
volumeType: VolumeType;
}
Returns {
volumeType: VolumeType;
}
- volumeType: VolumeType
- Defined in src/neuroglancer/segmentation_user_layer.ts:405

Methods

activateDataSubsources

activateDataSubsources(subsources: Iterable<LoadedDataSubsource>): void
Parameters
- subsources: Iterable<LoadedDataSubsource>
Returns void
Overrides Base.activateDataSubsources
- Defined in src/neuroglancer/segmentation_user_layer.ts:425

addAnnotationLayerState

addAnnotationLayerState(state: AnnotationLayerState, loadedSubsource: LoadedDataSubsource): void
Parameters
- state: AnnotationLayerState
- loadedSubsource: LoadedDataSubsource
Returns void
Inherited from Base.addAnnotationLayerState
- Defined in src/neuroglancer/ui/annotations.ts:3645

addCategoryText

addCategoryText(parent: HTMLElement, select: HTMLSelectElement, annotationLayer: AnnotationLayerState, reference: AnnotationReference, annotation: Annotation): Promise<void>
Adds the category text to the annotation on selecting a new category.

Returns
void
Parameters
- parent: HTMLElement
  
  parent HTML Element
- select: HTMLSelectElement
  
  select dropdown
- annotationLayer: AnnotationLayerState
  
  annotation layer in which annotation is present
- reference: AnnotationReference
  
  annotation reference
- annotation: Annotation
  
  annotation value
Returns Promise<void>
Inherited from Base.addCategoryText
- Defined in src/neuroglancer/ui/annotations.ts:3268

addCoordinateSpace

addCoordinateSpace(coordinateSpace: WatchableValueInterface<CoordinateSpace>): (() => void)
Parameters
- coordinateSpace: WatchableValueInterface<CoordinateSpace>
Returns (() => void)
- - (): void
  - Returns void
Inherited from Base.addCoordinateSpace
- Defined in src/neuroglancer/layer.ts:322

addDataSource

addDataSource(spec: undefined | DataSourceSpecification): LayerDataSource
Parameters
- spec: undefined | DataSourceSpecification
Returns LayerDataSource
Inherited from Base.addDataSource
- Defined in src/neuroglancer/layer.ts:267

addLocalAnnotations

addLocalAnnotations(loadedSubsource: LoadedDataSubsource, source: AnnotationSource, role: RenderLayerRole): void
Parameters
- loadedSubsource: LoadedDataSubsource
- source: AnnotationSource
- role: RenderLayerRole
Returns void
Inherited from Base.addLocalAnnotations
- Defined in src/neuroglancer/ui/annotations.ts:3618

addRef

addRef(): SegmentationUserLayer
Returns SegmentationUserLayer
Inherited from Base.addRef
- Defined in src/neuroglancer/util/disposable.ts:48

addRenderLayer

addRenderLayer(layer: RenderLayer): (() => void)
Parameters
- layer: RenderLayer
Returns (() => void)
- - (): void
  - Returns void
Inherited from Base.addRenderLayer
- Defined in src/neuroglancer/layer.ts:384

addStaticAnnotations

addStaticAnnotations(loadedSubsource: LoadedDataSubsource): boolean
Parameters
- loadedSubsource: LoadedDataSubsource
Returns boolean
Inherited from Base.addStaticAnnotations
- Defined in src/neuroglancer/ui/annotations.ts:3634

addText

addText(parent: HTMLElement, select: HTMLSelectElement, annotationLayer: AnnotationLayerState, reference: AnnotationReference, annotation: Annotation): Promise<void>
Parameters
- parent: HTMLElement
- select: HTMLSelectElement
- annotationLayer: AnnotationLayerState
- reference: AnnotationReference
- annotation: Annotation
Returns Promise<void>
Inherited from Base.addText
- Defined in src/neuroglancer/ui/annotations.ts:3234

bindSegmentListWidth

bindSegmentListWidth(element: HTMLElement): (() => void)
Parameters
- element: HTMLElement
Returns (() => void)
- - (): void
  - Returns void
- Defined in src/neuroglancer/segmentation_user_layer.ts:340

canAddDataSource

canAddDataSource(): boolean
Returns boolean
Inherited from Base.canAddDataSource
- Defined in src/neuroglancer/layer.ts:263

captureSelectionState

captureSelectionState(state: UserLayerSelectionState, mouseState: MouseSelectionState): void
Parameters
- state: UserLayerSelectionState
- mouseState: MouseSelectionState
Returns void
Inherited from Base.captureSelectionState
- Defined in src/neuroglancer/ui/annotations.ts:3217

copySelectionState

copySelectionState(dest: UserLayerSelectionState, source: UserLayerSelectionState): void
Parameters
- dest: UserLayerSelectionState
- source: UserLayerSelectionState
Returns void
Inherited from Base.copySelectionState
- Defined in src/neuroglancer/layer.ts:203

displayAnnotationState

displayAnnotationState(state: UserLayerSelectionState, parent: HTMLElement, context: RefCounted): boolean
Parameters
- state: UserLayerSelectionState
- parent: HTMLElement
- context: RefCounted
Returns boolean
Inherited from Base.displayAnnotationState
- Defined in src/neuroglancer/ui/annotations.ts:3294

`Private` displaySegmentationSelection

displaySegmentationSelection(state: UserLayerSelectionState, parent: HTMLElement, context: DependentViewContext): boolean
Parameters
- state: UserLayerSelectionState
- parent: HTMLElement
- context: DependentViewContext
Returns boolean
- Defined in src/neuroglancer/segmentation_user_layer.ts:697

displaySelectionState

displaySelectionState(state: UserLayerSelectionState, parent: HTMLElement, context: DependentViewContext): boolean
Parameters
- state: UserLayerSelectionState
- parent: HTMLElement
- context: DependentViewContext
Returns boolean
Overrides Base.displaySelectionState
- Defined in src/neuroglancer/segmentation_user_layer.ts:765

dispose

dispose(): void
Returns void
Inherited from Base.dispose
- Defined in src/neuroglancer/util/disposable.ts:53

disposed

disposed(): void
Returns void
Inherited from Base.disposed
- Defined in src/neuroglancer/layer.ts:406

filterBySegmentLabel

filterBySegmentLabel(id: Uint64): void
Parameters
- id: Uint64
Returns void
- Defined in src/neuroglancer/segmentation_user_layer.ts:353

filterSegments

filterSegments(query: string): void
Parameters
- query: string
Returns void
- Defined in src/neuroglancer/segmentation_user_layer.ts:360

getDataSourceSpecifications

getDataSourceSpecifications(layerSpec: any): DataSourceSpecification[]
Parameters
- layerSpec: any
Returns DataSourceSpecification[]
Inherited from Base.getDataSourceSpecifications
- Defined in src/neuroglancer/layer.ts:347

getLegacyDataSourceSpecifications

getLegacyDataSourceSpecifications(sourceSpec: any, layerSpec: any, legacyTransform: undefined | CoordinateTransformSpecification, explicitSpecs: DataSourceSpecification[]): DataSourceSpecification[]
Parameters
- sourceSpec: any
- layerSpec: any
- legacyTransform: undefined | CoordinateTransformSpecification
- explicitSpecs: DataSourceSpecification[]
Returns DataSourceSpecification[]
Overrides Base.getLegacyDataSourceSpecifications
- Defined in src/neuroglancer/segmentation_user_layer.ts:517

getValueAt

getValueAt(position: Float32Array, pickState: PickState): any
Parameters
- position: Float32Array
- pickState: PickState
Returns any
Inherited from Base.getValueAt
- Defined in src/neuroglancer/layer.ts:417

handleAction

handleAction(action: string, context: SegmentationActionContext): void
Parameters
- action: string
- context: SegmentationActionContext
Returns void
Overrides Base.handleAction
- Defined in src/neuroglancer/segmentation_user_layer.ts:636

initializationDone

initializationDone(): void
Returns void
Inherited from Base.initializationDone
- Defined in src/neuroglancer/layer.ts:331

initializeAnnotationLayerViewTab

initializeAnnotationLayerViewTab(tab: AnnotationLayerView): void
Parameters
- tab: AnnotationLayerView
Returns void
Inherited from Base.initializeAnnotationLayerViewTab
- Defined in src/neuroglancer/ui/annotations.ts:3208

initializeSelectionState

initializeSelectionState(state: UserLayerSelectionState): void
Parameters
- state: UserLayerSelectionState
Returns void
Inherited from Base.initializeSelectionState
- Defined in src/neuroglancer/layer.ts:112

markLoading

markLoading(): (() => void)
Returns (() => void)
- - (): void
  - Returns void
Inherited from Base.markLoading
- Defined in src/neuroglancer/layer.ts:308

moveToSegment

moveToSegment(id: Uint64): void
Parameters
- id: Uint64
Returns void
- Defined in src/neuroglancer/segmentation_user_layer.ts:772

`Protected` refCountReachedZero

refCountReachedZero(): void
Returns void
Inherited from Base.refCountReachedZero
- Defined in src/neuroglancer/util/disposable.ts:66

registerCancellable

registerCancellable<T>(cancellable: T): T
Type Parameters
- T extends {
  cancel: (() => void);
  }
Parameters
- cancellable: T
Returns T
Inherited from Base.registerCancellable
- Defined in src/neuroglancer/util/disposable.ts:100

registerDisposer

registerDisposer<T>(f: T): T
Type Parameters
- T extends Disposer
Parameters
- f: T
Returns T
Inherited from Base.registerDisposer
- Defined in src/neuroglancer/util/disposable.ts:76

registerEventListener

registerEventListener(target: EventTarget, type: string, listener: EventListenerOrEventListenerObject, options?: boolean | AddEventListenerOptions): void
Parameters
- target: EventTarget
- type: string
- listener: EventListenerOrEventListenerObject
- Optional options: boolean | AddEventListenerOptions
Returns void
Inherited from Base.registerEventListener
- Defined in src/neuroglancer/util/disposable.ts:95

removeRenderLayer

removeRenderLayer(layer: RenderLayer): void
Parameters
- layer: RenderLayer
Returns void
Inherited from Base.removeRenderLayer
- Defined in src/neuroglancer/layer.ts:393

resetSelectionState

resetSelectionState(state: UserLayerSelectionState): void
Parameters
- state: UserLayerSelectionState
Returns void
Inherited from Base.resetSelectionState
- Defined in src/neuroglancer/layer.ts:126

restoreState

restoreState(specification: any): void
Parameters
- specification: any
Returns void
Overrides Base.restoreState
- Defined in src/neuroglancer/segmentation_user_layer.ts:561

selectAnnotation

selectAnnotation(annotationLayer: AnnotationLayerState, id: string, pin: boolean | "toggle"): void
Parameters
- annotationLayer: AnnotationLayerState
- id: string
- pin: boolean | "toggle"
Returns void
Inherited from Base.selectAnnotation
- Defined in src/neuroglancer/ui/annotations.ts:3687

selectSegment

selectSegment(id: Uint64, pin: boolean | "toggle"): void
Parameters
- id: Uint64
- pin: boolean | "toggle"
Returns void
- Defined in src/neuroglancer/segmentation_user_layer.ts:346

selectedValueFromJson

selectedValueFromJson(json: any): any
Parameters
- json: any
Returns any
Inherited from Base.selectedValueFromJson
- Defined in src/neuroglancer/layer.ts:459

selectedValueToJson

selectedValueToJson(value: any): any
Parameters
- value: any
Returns any
Inherited from Base.selectedValueToJson
- Defined in src/neuroglancer/layer.ts:455

selectionStateFromJson

selectionStateFromJson(state: UserLayerSelectionState, json: any): void
Parameters
- state: UserLayerSelectionState
- json: any
Returns void
Overrides Base.selectionStateFromJson
- Defined in src/neuroglancer/segmentation_user_layer.ts:667

selectionStateToJson

selectionStateToJson(state: UserLayerSelectionState, forPython: boolean): any
Parameters
- state: UserLayerSelectionState
- forPython: boolean
Returns any
Overrides Base.selectionStateToJson
- Defined in src/neuroglancer/segmentation_user_layer.ts:678

setAnnotationColorPicker

setAnnotationColorPicker(): void
Sets the annotation picker color based on the annotation property value.

Returns void
Inherited from Base.setAnnotationColorPicker
- Defined in src/neuroglancer/ui/annotations.ts:3194

setLayerPosition

setLayerPosition(modelTransform: RenderLayerTransform, layerPosition: Float32Array): void
Parameters
- modelTransform: RenderLayerTransform
- layerPosition: Float32Array
Returns void
Inherited from Base.setLayerPosition
- Defined in src/neuroglancer/layer.ts:463

toJSON

toJSON(): any
Returns any
Overrides Base.toJSON
- Defined in src/neuroglancer/segmentation_user_layer.ts:599

transformPickedValue

transformPickedValue(value: any): any
Parameters
- value: any
Returns any
Overrides Base.transformPickedValue
- Defined in src/neuroglancer/segmentation_user_layer.ts:628

unregisterDisposer

unregisterDisposer<T>(f: T): T
Type Parameters
- T extends Disposer
Parameters
- f: T
Returns T
Inherited from Base.unregisterDisposer
- Defined in src/neuroglancer/util/disposable.ts:85

updateDataSubsourceActivations

updateDataSubsourceActivations(): void
Returns void
Inherited from Base.updateDataSubsourceActivations
- Defined in src/neuroglancer/layer.ts:279

Class SegmentationUserLayer

Hierarchy

Index

Constructors

Properties

Accessors

Methods

Constructors

constructor

Parameters

managedLayer: ManagedUserLayer

Returns SegmentationUserLayer

Properties

anchorSegment

annotationColorPicker

annotationCrossSectionRenderScaleHistogram

annotationCrossSectionRenderScaleTarget

annotationDisplayState

annotationProjectionRenderScaleHistogram

annotationProjectionRenderScaleTarget

annotationStates

dataSources

dataSourcesChanged

displayState

disposedStacks

graphConnection

Readonly has2dLayer

Readonly has3dLayer

Readonly hasSkeletonsLayer

layersChanged

managedLayer

panels

pick

readyStateChanged

refCount

renderLayers

segmentQueryFocusTime

selectionState

sliceViewRenderScaleHistogram

sliceViewRenderScaleTarget

specificationChanged

tabs

tool

toolBinder

wasDisposed

Static supportsPickOption

Static type

Static typeAbbreviation

Accessors

isReady

Returns boolean

localCoordinateSpace

Returns TrackableCoordinateSpace

localCoordinateSpaceCombiner

Returns CoordinateSpaceCombiner

localPosition

Returns Position

manager

Returns LayerListSpecification

type

Returns string

volumeOptions

Returns { volumeType: VolumeType; }

volumeType: VolumeType

Methods

activateDataSubsources

Parameters

subsources: Iterable<LoadedDataSubsource>

Returns void

addAnnotationLayerState

Parameters

state: AnnotationLayerState

loadedSubsource: LoadedDataSubsource

Returns void

addCategoryText

Returns

Parameters

parent: HTMLElement

select: HTMLSelectElement

annotationLayer: AnnotationLayerState

`Readonly` has2dLayer

`Readonly` has3dLayer

`Readonly` hasSkeletonsLayer

`Static` supportsPickOption

`Static` type

`Static` typeAbbreviation

Returns {
volumeType: VolumeType;
}

`Private` displaySegmentationSelection