feat(segmentation): Refactor segmentation and style handling #1449

sedghi · 2024-08-30T17:33:25Z

segmentation representation = segmentation + type + viewport

segmentation style refactored for readability , it is now similar to annotation style

…cedImageId for better overlay matching • Improve VideoViewport rendering by applying device pixel ratio scaling and clearing the canvas before drawing • Update WSIViewport to use getViewReferenceId instead of getReferenceId for consistency • Update MetadataModuleTypes to use numbers for rows, columns, sliceThickness, and sliceLocation • Add preset property to ViewportProperties for future use • Introduce deepClone utility function for deep cloning objects • Update SegmentationStateManager to handle labelmap image references and remove color LUTs when representations are removed

• Add null check for image in Cache class to prevent undefined errors • Update imagePlaneModule to use numeric values for rows and columns • Import and use utilities from @cornerstonejs/core in addColorLUT and ToolGroup • Replace deepClone with utilities.deepClone in ToolGroup • Update BrushTool to dispatch a custom error event instead of throwing an error when no active segmentation is detected

netlify · 2024-08-30T17:33:48Z

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- Introduce `setCameraClippingRange` method in `BaseVolumeViewport` and implement it in `VolumeViewport`, `VolumeViewport3D`, and `Viewport` classes - Move camera clipping range logic from `setCamera` method to `setCameraClippingRange` method to improve code organization and reusability - Update `setCamera` method to call `setCameraClippingRange` method for consistency across classes

…rollTool** - Remove VolumeRotateMouseWheelTool from cornerstoneTools - Update various examples to use StackScrollTool instead of VolumeRotateMouseWheelTool - StackScrollTool now has an additional configuration option to enable rotation - The rotation functionality is implemented in the mouseWheelCallback function of StackScrollTool - The rotation functionality uses the gl-matrix library for 3D transformations

This commit replaces segmentation with labelmap in various parts of the codebase, including core and tools. It updates function names, types, and logic to reflect the change from segmentation to labelmap. Changes include: - Renaming functions from segmentation to labelmap (e.g., `createAndCacheDerivedSegmentationImage` to `createAndCacheDerivedLabelmapImage`) - Updating types and interfaces to reflect the change from segmentation to labelmap - Changing logic and implementation to work with labelmaps instead of segmentations - Updating tests and examples to reflect the change from segmentation to labelmap

• Update Viewport.ts to use BaseVolumeViewport instead of VolumeViewport • Update loaders/index.ts to register cornerstoneStreamingImageVolumeLoader as unknown as VolumeLoaderFn • Update convertLabelmapToSurface.ts to remove isVolume check and handle volumeId directly • Update surfaceComputationStrategies.ts to remove isVolumeSegmentation check • Update addLabelmapToElement.ts to handle missing volume and create a new volume if necessary • Update labelmapDisplay.ts to use BaseVolumeViewport instead of VolumeViewport • Update BrushTool.ts, CircleScissorsTool.ts, PaintFillTool.ts, RectangleScissorsTool.ts, SphereScissorsTool.ts, getStrategyData.ts, and utilities/segmentation/*.ts to use BaseVolumeViewport instead of VolumeViewport • Remove stackVolumeCheck.ts file as it is no longer needed

Update Labelmap tool to handle volume ID correctly and prevent errors when volume ID is missing - Update addLabelmapToElement function to set volumeId property on LabelmapSegmentationDataVolume object - Update getStrategyData function to check for missing volumeId and dispatch an error event if found - Improve error handling and logging for segmentation-related issues

• Refactored SegmentationRenderingEngine to handle viewport cases where the enabled element is not found • Simplified SegmentationStateManager to remove redundant imageIdReferenceMap lookups • Added addSegmentationRepresentationUIDToViewport function to associate a segmentation representation with a given viewport • Updated utilities/index.ts to include pointInSurroundingSphereCallback function • Implemented pointInSurroundingSphereCallback function to run a callback for each point of imageData within a sphere defined by great circle points • Updated labelmapDisplay.ts to include removeRepresentation function and _needsTransferFunctionUpdate function • Updated addLabelmapToElement.ts to trigger segmentation modified event when adding a labelmap to an element

…ports - Remove segmentation representation from state and all viewports - Update segmentation representation removal functions - Remove obsolete functions and imports - Update segmentation state management and display tools - Fix issues with contour, labelmap, and surface display tools

…onality and performance - Extracted and refactored common logic in VideoViewport and VolumeViewport3D - Improved voxelManager.forEach method for efficient point iteration - Added resetCameraForResize method to VolumeViewport3D - Enhanced generateVolumePropsFromImageIds utility function - Introduced pointInShapeCallback for efficient shape-based point iteration - Removed deprecated methods and improved code organization

…e code organization and modularity - Extracted internal functions internalComputeVolumeSegmentationFromStack and internalConvertStackToVolumeSegmentation from SegmentationStateManager - Moved external functions computeVolumeSegmentationFromStack and convertStackToVolumeSegmentation to separate files - Updated imports and exports to reflect new file structure - Removed unused function updateSegmentationState and modified internalConvertStackToVolumeSegmentation to directly update segmentation state

…lback - Migrate voxelManager to new system in WSIViewport - Refactor pointInShapeCallback to support new system - Update type imports and usage in pointInShapeCallback - Update type imports in labelmapComputationStrategies and convertLabelmapToSurface

- Initialize globalDefaultProperties with an empty object - Update globalDefaultProperties with new values instead of overwriting them - Remove unused cameraFocalPointOnRender property - Simplify _setPropertiesFromCache method by removing unused variables - Update camera event triggering to use the current camera state - Remove _restoreCameraProps method as it is no longer needed - Refactor _getVOIFromCache method to return the voiRange - Update setVOI method to use the returned voiRange - Remove console.log statements and unused code - Improve code readability and consistency

- Change boundsIJK to private and add getDefaultBounds method in VoxelManager - Add clearSegmentValue function to clear specified segment value from a segmentation - Update segmentation helpers and index - Update Labelmap display to use perSegment labelmap config - Update BrushStrategy to include isInObject and isInObjectBoundsIJK in InitializedOperationData - Update various segmentation strategies to use operationData.isInObject and operationData.isInObjectBoundsIJK

- Extract imageIdToURI function to handle image ID to URI conversion - Update imageLoader to store referencedImageId in localImage - Simplify imageChangeEventListener and remove unnecessary logic for segmentation actor updates

fix all examples based on new segmentation

wayfarer3130 · 2024-09-12T12:19:05Z

packages/tools/src/stateManagement/segmentation/config/segmentationColor.ts

 segmentIndex: number,
 color: Types.Color
 ): void {
 // Get the reference to the color in the colorLUT.
 const colorReference = getSegmentIndexColor(
- segmentationRepresentationUID,
+ viewportId,
+ segmentationId,
 segmentIndex
 );



Since the color values are directly modified, when we add color luts, do we ensure we take a full copy so we don't later on modify it?

Yes during add we do

packages/tools/src/stateManagement/segmentation/getSegmentationRepresentation.ts

packages/tools/src/stateManagement/segmentation/getViewportIdsWithSegmentation.ts

packages/tools/src/stateManagement/segmentation/getViewportSegmentations.ts

packages/tools/src/stateManagement/segmentation/helpers/computeStackLabelmapFromVolume.ts

packages/tools/src/stateManagement/segmentation/setActiveSegmentation.ts

wayfarer3130 · 2024-09-12T13:09:46Z

packages/tools/src/stateManagement/segmentation/setActiveSegmentation.ts

+ */
+export function setActiveSegmentation(
+ viewportId: string,
+ segmentationId: string


Should this include the segmentation type? Also, should it be possible to have 1 active of each type of segmentation? That is, to have both the active labelmap and the active contour.

No, in the concept of activeness, only one segmentation (not representation) is active at a time. We can't have the contour of one segmentation active while the labelmap of another segmentation is active.

packages/tools/src/store/ToolGroupManager/ToolGroup.ts

wayfarer3130 · 2024-09-12T13:12:30Z

packages/tools/src/store/ToolGroupManager/ToolGroup.ts

@@ -765,7 +773,7 @@ export default class ToolGroup {
 get(this._toolInstances[toolName].configuration, configurationPath) ||
 this._toolInstances[toolName].configuration;

- return structuredClone(_configuration);
+ return utilities.deepClone(_configuration);


Why is this one deepClone and not structuredClone?

Since structuredClone cannot copy functions or classes, our custom deepClone function uses structuredClone for objects while also handling functions and classes.

packages/tools/src/tools/base/ContourSegmentationBaseTool.ts

packages/tools/src/tools/displayTools/Labelmap/addLabelmapToElement.ts

packages/tools/src/tools/displayTools/Surface/removeSurfaceFromElement.ts

wayfarer3130 · 2024-09-12T13:51:24Z

packages/tools/src/tools/segmentation/strategies/fillCircle.ts

@@ -67,12 +66,13 @@ const initializeCircle = {
 segmentationImageData.getDimensions()
 );

- segmentationVoxelManager.boundsIJK = boundsIJK;
- imageVoxelManager.isInObject = createPointInEllipse({
+ operationData.isInObject = createPointInEllipse({


Here is a spot where getting the object iterator as a complete options object which includes currently the is in object and the bounds ijk would allow us in the future to define it using more efficient maps, and as long as it is just an instance of the right type, then the type can be extended in the future to allow for improved definitions. I believe this should be part of CS3D 2 as it fixes the types now, and then allows for better future extension.

We have the options for the forEach, i added it to the pointInShape too

packages/tools/src/tools/StackScrollTool.ts

packages/tools/test/segmentationState_test.js

wayfarer3130

A few bug fixes as noted, plus some naming changes a few small improvements are needed, but overall this is a much cleaner design than the CS3D 1 version.

- Introduce `hasVolumeURI` method to `BaseVolumeViewport` to check if a volume with a given URI exists - Update `getViewportsWithImageURI` and `getViewportsWithVolumeId` to use `getRenderingEngines` instead of `getRenderingEngine` - Introduce `getViewportsWithVolumeURI` utility - Update various tools to use `getTargetImageData` instead of `getTargetIdImage` and remove `renderingEngine` dependency - Remove `getTargetVolumeId` method from `BaseTool` and update tools to use `getVolumeId` directly from `viewport` instance - Update segmentation tools to use `getTargetImageData` instead of `getTargetIdImage` and remove `renderingEngine` dependency

…ViewportsWithImageURI - Remove renderingEngineId from getViewportsWithVolumeId in WindowLevelTool - Remove renderingEngineId from getViewportsWithImageURI in ProbeTool - Remove renderingEngineId from getViewportsWithVolumeId in ViewportColorbar

…x/source-maps

wayfarer3130 · 2024-09-12T20:45:42Z

packages/core/src/utilities/pointInShapeCallback.ts

- * every point in the shape.
- * @param boundsIJK - The bounds of the volume in IJK coordinates.
+ * @param options - Configuration options for the shape callback.
+ * @returns An array of points in the shape if returnPoints is true, otherwise undefined.
 */
 export function pointInShapeCallback(


Thank you - this feels like a better interface.

wayfarer3130

Thank you for all these changes - I think they are really looking pretty good now

sedghi added 10 commits August 26, 2024 15:56

try to not publish source maps

f2bd87c

wip for ohif changes

1981388

annotation fix

c439fbf

fix camera sync

269f210

actor uid should not be volume id

23cc6d0

fix the invert and colormap issue

9c39713

fix stuff

2b567db

wip

b55e060

sedghi added 19 commits August 30, 2024 14:46

Core: Refactor image ID handling and segmentation rendering

56ce4df

- Extract imageIdToURI function to handle image ID to URI conversion - Update imageLoader to store referencedImageId in localImage - Simplify imageChangeEventListener and remove unnecessary logic for segmentation actor updates

fix overlay

2ee988b

fix remove render

111de8c

fix

ae98c4f

towards viewport based segmentation representation

3031f25

fix more build issues

6bd9085

fix various build issues

5968bf8

fix all examples based on new segmentation

wayfarer3130 reviewed Sep 12, 2024

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sedghi added 7 commits September 12, 2024 14:33

apply review comments

e25bcba

api

c187f0c

fix tests

fd54eb1

Merge branch 'beta' of github.com:cornerstonejs/cornerstone3D into fi…

125a7a0

…x/source-maps

fix deploy

193bfac

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sedghi changed the title ~~more fixes~~ feat(segmentation): Refactor segmentation and style handling Sep 12, 2024

sedghi merged commit 51f7cde into beta Sep 12, 2024
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feat(segmentation): Refactor segmentation and style handling #1449

feat(segmentation): Refactor segmentation and style handling #1449

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feat(segmentation): Refactor segmentation and style handling #1449

feat(segmentation): Refactor segmentation and style handling #1449

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sedghi commented Aug 30, 2024 •

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