Introduction

This guide covers the key concepts of segmentation mask management in Larvitar, utilizing the segmentation module of Cornerstone Tools. In this context, different volumetric data are represented as labelmaps, and each labelmap can contain multiple segments. A labelmap can support up to 2^16 segments.

The values within a labelmap correspond to specific labels, which determine the color from the LUT (Look-Up Table) used for visualization. These labels are assigned distinct colors and can be individually shown or hidden. Each labelmap can be associated with a different colormap and has an active/inactive property that influences the rendering style.

Key Terminology

• Segmentation Mask (or Mask): A set of pixels representing a specific structure within a volume.
• Volume: A buffer that stores one or more segmentations.
• Label: A numerical identifier within a volume, corresponding to a specific segmentation.

Useful setters

• toggleSegmentVisibility:

  setters.toggleSegmentVisibility(htmlelement, segmentvalue, labelmapid);
  

• colorForSegmentIndexOfColorLUT:

  setters.colorForSegmentIndexOfColorLUT(
    colorLutIndex,
    segmentValue,
    colorRGBAarray
  );
  

API Reference

initSegmentationModule

A function to group all settings to load before masks

Syntax

initSegmentationModule(customConfig: SegmentationConfig)

Parameters

Parameter	Type	Description
customConfig	SegmentationConfig	Object containing override values for segmentation module config

Returns

void - sets segmentation module configuration

enableBrushTool

To enable brush tools, user can call directly the setToolEnabled api. Otherwise, Larvitar implements the utility the functionenableBrushTool that internally handle brush type and props with a single call.

Syntax

enableBrushTool(viewports: string[], options: BrushProperties)

Parameters

Parameter	Type	Description
viewports	string[]	Viewports Id list on which brush tool will be enabled
options	BrushProperties	Object containing configuration values (eg radius, thresholds, etc...)

NOTE: if options contains thresholds, ThresholdsBrush is activated, otherwise BrushTool is activated.

Returns

"ThresholdsBrush" | "Brush" - the activated tool name

disableBrushTool

To disable brush tools, user can call directly the setToolDisabled api. Otherwise, Larvitar implements the utility the functiondisableBrushTool that internally handle brush type and props with a single call.

Syntax

disableBrushTool(viewports: string[], toolToActivate?: string)

Parameters

Parameter	Type	Description
viewports	string[]	Viewports Id list on which brush tool will be disabled
options	string	The name of the tool to activate after removing the brush @optional

Returns

void - this function disables both brush tools, if found active on viewports

addSegmentationMask

A function to group all settings to load before masks

Syntax

addSegmentationMask(
  props: MaskProperties,
  data: TypedArray,
  elementId: string | HTMLElement
)

Parameters

Parameter	Type	Description
customConfig	SegmentationConfig	Object containing override values for segmentation module config
customConfig	SegmentationConfig	Object containing override values for segmentation module config
customConfig	SegmentationConfig	Object containing override values for segmentation module config

Returns

void - sets segmentation module configuration

setLabelColor

Sets a color for a certain label

Syntax

setLabelColor(labelId: string, color: string)

Parameters

Parameter	Type	Description
labelId	string	The identifier of the label whose color needs to be set.
color	string	The color value to be applied, typically in hexadecimal format (e.g., #FF5733).

Returns

void

getLabelColor

Gets the color for a certain label

Syntax

getLabelColor(labelId: string)

Parameters

Parameter	Type	Description
labelId	string	The identifier of the label whose color needs to be set.

Returns

string - returns the color value for the label, typically in hexadecimal format

loadMaskSlice

Set a new mask slice into the labelmap buffer

Syntax

loadMaskSlice(
  elementId: string | HTMLElement,
  sliceIndex: number,
  pixelData: TypedArray
)

Parameters

Parameter	Type	Description
elementId	HTMLElement or string	The target html element Id or its DOM HTMLElement
sliceIndex	number	The index of the new mask slice
pixelData	TypedArray	The pixelData array

Returns

void

setActiveLabelmap

Activate a specific labelmap through its labelId

Syntax

setActiveLabelmap(
  labelId: number,
  elementId: string | HTMLElement
)

Parameters

Parameter	Type	Description
labelId	number	The labelmap id to activate
elementId	string or HTMLElement	The target html element Id or its DOM HTMLElement

Returns

void

getActiveLabelmapBuffer

Get active labelmap for target element

Syntax

getActiveLabelmapBuffer(elementId: string | HTMLElement)

Parameters

Parameter	Type	Description
elementId	stringg or HTMLElement	The target html element Id or its DOM HTMLElement

Returns

Object - The active labelmap object that contains the buffer

setActiveSegment

Activate a specific segment through its index

Syntax

 setActiveSegment(
  segmentIndex: number,
  elementId: string | HTMLElement
)

Parameters

Parameter	Type	Description
segmentIndex	number	The segment index to activate
elementId	string or HTMLElement	The target html element Id or its DOM HTMLElement

Returns

void

setActiveLabelOpacity

Change opacity for active label

Syntax

setActiveLabelOpacity(opacity: number)

Parameters

Parameter	Type	Description
opacity	number	The desired opacity value

Returns

void

setInactiveLabelOpacity

Change opacity for inactive labels

Syntax

setInactiveLabelOpacity(opacity: number)

Parameters

Parameter	Type	Description
opacity	number	The desired opacity value

Returns

void

toggleVisibility

Toggle mask visibility

Syntax

toggleVisibility(
  elementId: string | HTMLElement,
  labelId: number
)

Parameters

Parameter	Type	Description
elementId	string or HTMLElement	The target html element Id or its DOM HTMLElement
labelId	number	The id of the mask label

Returns

void

toggleContourMode

Toggle between 'contours mode' and 'filled mode'

Syntax

toggleContourMode(toggle: boolean)

Parameters

Parameter	Type	Description
toggle	boolean	Contour mode enabled if true

Returns

void - forces a new render with chosen modality

setMaskProps

Set mask appearance props:

• labelId
• visualization [0=filled, 1=contour, 2=hidden]
• opacity (if mode=0), between 0 and 1

Syntax

setMaskProps(props: MaskProperties)

Parameters

Parameter	Type	Description
props	MaskProperties	The mask appearance props

Returns

void - forces a new render with chosen appearance props

clearSegmentationState

Clear state for segmentation module

Syntax

clearSegmentationState();

Returns

void

setBrushProps

Change the brush props:

• radius: number[px]
• thresholds: array[min,max]

Syntax

setBrushProps(props: BrushProperties)

Parameters

Parameter	Type	Description
props	BrushProperties	The new brush props

Returns

void - forces a new render with chosen brush props

undoLastStroke

Undo last brush operation (stroke)

Syntax

undoLastStroke(elementId: string | HTMLElement)

Parameters

Parameter	Type	Description
elementId	string or HTMLElement	The target html element Id or its DOM HTMLElement

Returns

void - forces a new render with undone brush operations

redoLastStroke

Redo last brush operation (stroke)

Syntax

redoLastStroke(elementId: string | HTMLElement)

Parameters

Parameter	Type	Description
elementId	string or HTMLElement	The target html element Id or its DOM HTMLElement

Returns

void - forces a new render with redone brush operations

deleteMask

Delete mask from state

Syntax

deleteMask(labelId: number )

Parameters

Parameter	Type	Description
labelId	number	The labelmap id to delete

Returns

void - forces a new render with deleted label

setLabelmap3DByFirstImageId

Takes an 16-bit encoded ArrayBuffer and stores it as a Labelmap3D for the BrushStackState associated with the firstImageId.

Syntax

setLabelmap3DByFirstImageId(
  firstImageId: string,
  buffer: ArrayBuffer,
  labelmapIndex: number,
  metadata: Object[] = [],
  numberOfFrames: number,
  segmentsOnLabelmapArray: number[][],
  colorLUTIndex: number = 0
)

Parameters

Parameter	Type	Description
firstImageId	string	The firstImageId of the series to store the segmentation on.
buffer	ArrayBuffer	The array buffer to store as labelMap
labelmapIndex	number	The index to store the labelmap under.
metadata	Object[]	Any metadata about the segments.
numberOfFrames	number	The number of frames to set up the relevant labelmap2D views.
segmentsOnLabelmapArray	number[][]	An array of array of segments on each imageIdIndex.
colorLUTIndex	number	The index of the colorLUT to use to render the segmentation.

Returns

Promise<...> - the function is async

setLabelmap3DForElement

Takes a 16-bit encoded ArrayBuffer and stores it as a Labelmap3D for the BrushStackState associated with the element.

Syntax

setLabelmap3DForElement(
  elementOrEnabledElementUID: EnabledElement | string,
  buffer: ArrayBuffer,
  labelmapIndex: number,
  metadata: Object[] = [],
  segmentsOnLabelmapArray: number[][],
  colorLUTIndex = 0
)

Parameters

Parameter	Type	Description
elementOrEnabledElementUID	EnabledElement	The firstImageId of the series to store the segmentation on.
buffer	ArrayBuffer	The array buffer to store as labelMap
labelmapIndex	number	The index to store the labelmap under.
metadata	Object[]	Any metadata about the segments.
segmentsOnLabelmapArray	number[][]	An array of array of segments on each imageIdIndex.
colorLUTIndex	number	The index of the colorLUT to use to render the segmentation.

Returns

Promise<...> - the function is async

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