fix(segmentation): upgrade cs3d to fix various segmentation bugs (#3885)

extensions/cornerstone-dicom-rt/src/viewports/OHIFCornerstoneRTViewport.tsx

@@ -168,6 +168,8 @@ function OHIFCornerstoneRTViewport(props) {
   }, [servicesManager, viewportId, rtDisplaySet, rtIsLoading]);
 
   useEffect(() => {
+    // I'm not sure what is this, since in RT we support Overlapping segmnets
+    // via contours
     const { unsubscribe } = segmentationService.subscribe(
       segmentationService.EVENTS.SEGMENTATION_LOADING_COMPLETE,
       evt => {

extensions/cornerstone-dicom-seg/package.json

@@ -44,9 +44,9 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/adapters": "^1.40.3",
-    "@cornerstonejs/tools": "^1.40.3",
-    "@kitware/vtk.js": "27.3.1",
+    "@cornerstonejs/adapters": "^1.43.7",
+    "@cornerstonejs/tools": "^1.43.7",
+    "@kitware/vtk.js": "29.3.0",
     "react-color": "^2.19.3"
   }
 }

extensions/cornerstone-dicom-seg/src/getSopClassHandlerModule.js

@@ -189,6 +189,15 @@ async function _loadSegments({ extensionManager, servicesManager, segDisplaySet,
     }
   });
 
+  if (results.overlappingSegments) {
+    uiNotificationService.show({
+      title: 'Overlapping Segments',
+      message:
+        'Unsupported overlapping segments detected, segmentation rendering results may be incorrect.',
+      type: 'warning',
+    });
+  }
+
   if (!usedRecommendedDisplayCIELabValue) {
     // Display a notification about the non-utilization of RecommendedDisplayCIELabValue
     uiNotificationService.show({

extensions/cornerstone-dicom-seg/src/panels/PanelSegmentation.tsx

@@ -1,7 +1,7 @@
 import { createReportAsync } from '@ohif/extension-default';
 import React, { useEffect, useState, useCallback } from 'react';
 import PropTypes from 'prop-types';
-import { SegmentationGroupTable, LegacyButtonGroup, LegacyButton } from '@ohif/ui';
+import { SegmentationGroupTable } from '@ohif/ui';
 
 import callInputDialog from './callInputDialog';
 import callColorPickerDialog from './colorPickerDialog';

extensions/cornerstone-dicom-seg/src/panels/SegmentationToolbox.tsx

@@ -37,7 +37,7 @@ const initialState = {
   },
   ThresholdBrush: {
     brushSize: 15,
-    thresholdRange: [-500, 500],
+    thresholdRange: null,
   },
   activeTool: null,
 };
@@ -88,6 +88,8 @@ function SegmentationToolbox({ servicesManager, extensionManager }) {
 
   const setToolActive = useCallback(
     toolName => {
+      initializeThresholdValue(toolName);
+
       toolbarService.recordInteraction({
         interactionType: 'tool',
         commands: [
@@ -178,6 +180,24 @@ function SegmentationToolbox({ servicesManager, extensionManager }) {
     [toolGroupService]
   );
 
+  function initializeThresholdValue(toolName: any) {
+    if (state.ThresholdBrush.thresholdRange === null) {
+      // set the default threshold range from the tool configuration
+      const toolGroupIds = toolGroupService.getToolGroupIds();
+      const toolGroupId = toolGroupIds[0];
+      const toolGroup = toolGroupService.getToolGroup(toolGroupId);
+      const toolConfig = toolGroup.getToolConfiguration(toolName);
+      const defaultThresholdRange = toolConfig?.strategySpecificConfiguration?.THRESHOLD?.threshold;
+      dispatch({
+        type: ACTIONS.SET_TOOL_CONFIG,
+        payload: {
+          tool: 'ThresholdBrush',
+          config: { thresholdRange: defaultThresholdRange },
+        },
+      });
+    }
+  }
+
   const onBrushSizeChange = useCallback(
     (valueAsStringOrNumber, toolCategory) => {
       const value = Number(valueAsStringOrNumber);
@@ -200,8 +220,8 @@ function SegmentationToolbox({ servicesManager, extensionManager }) {
   const handleRangeChange = useCallback(
     newRange => {
       if (
-        newRange[0] === state.ThresholdBrush.thresholdRange[0] &&
-        newRange[1] === state.ThresholdBrush.thresholdRange[1]
+        newRange[0] === state.ThresholdBrush.thresholdRange?.[0] &&
+        newRange[1] === state.ThresholdBrush.thresholdRange?.[1]
       ) {
         return;
       }
@@ -213,7 +233,7 @@ function SegmentationToolbox({ servicesManager, extensionManager }) {
           const toolGroup = toolGroupService.getToolGroup(toolGroupId);
           toolGroup.setToolConfiguration(toolName, {
             strategySpecificConfiguration: {
-              THRESHOLD_INSIDE_CIRCLE: {
+              THRESHOLD: {
                 threshold: newRange,
               },
             },
@@ -365,7 +385,7 @@ function SegmentationToolbox({ servicesManager, extensionManager }) {
                     <InputDoubleRange
                       values={state.ThresholdBrush.thresholdRange}
                       onChange={handleRangeChange}
-                      minValue={-1000}
+                      minValue={-1000} // Todo: these should be configurable
                       maxValue={1000}
                       step={1}
                       showLabel={true}

extensions/cornerstone-dicom-seg/src/viewports/OHIFCornerstoneSEGViewport.tsx

@@ -172,14 +172,6 @@ function OHIFCornerstoneSEGViewport(props) {
         if (evt.segDisplaySet.displaySetInstanceUID === segDisplaySet.displaySetInstanceUID) {
           setSegIsLoading(false);
         }
-
-        if (evt.overlappingSegments) {
-          uiNotificationService.show({
-            title: 'Overlapping Segments',
-            message: 'Overlapping segments detected which is not currently supported',
-            type: 'warning',
-          });
-        }
       }
     );
 

extensions/cornerstone-dicom-sr/package.json

@@ -44,9 +44,9 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/adapters": "^1.40.3",
-    "@cornerstonejs/core": "^1.40.3",
-    "@cornerstonejs/tools": "^1.40.3",
+    "@cornerstonejs/adapters": "^1.43.7",
+    "@cornerstonejs/core": "^1.43.7",
+    "@cornerstonejs/tools": "^1.43.7",
     "classnames": "^2.3.2"
   }
 }

extensions/cornerstone/package.json

@@ -36,7 +36,7 @@
     "@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2",
     "@cornerstonejs/codec-openjpeg": "^1.2.2",
     "@cornerstonejs/codec-openjph": "^2.4.2",
-    "@cornerstonejs/dicom-image-loader": "^1.40.3",
+    "@cornerstonejs/dicom-image-loader": "^1.43.7",
     "@ohif/core": "3.8.0-beta.42",
     "@ohif/ui": "3.8.0-beta.42",
     "dcmjs": "^0.29.12",
@@ -52,11 +52,11 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/adapters": "^1.40.3",
-    "@cornerstonejs/core": "^1.40.3",
-    "@cornerstonejs/streaming-image-volume-loader": "^1.40.3",
-    "@cornerstonejs/tools": "^1.40.3",
-    "@kitware/vtk.js": "27.3.1",
+    "@cornerstonejs/adapters": "^1.43.7",
+    "@cornerstonejs/core": "^1.43.7",
+    "@cornerstonejs/streaming-image-volume-loader": "^1.43.7",
+    "@cornerstonejs/tools": "^1.43.7",
+    "@kitware/vtk.js": "29.3.01",
     "html2canvas": "^1.4.1",
     "lodash.debounce": "4.0.8",
     "lodash.merge": "^4.6.2",

extensions/cornerstone/src/init.tsx

@@ -253,10 +253,10 @@ export default async function init({
 
   /**
    * Runs error handler for failed requests.
-   * @param event 
+   * @param event
    */
   const imageLoadFailedHandler = ({ detail }) => {
-    const handler = errorHandler.getHTTPErrorHandler()
+    const handler = errorHandler.getHTTPErrorHandler();
     handler(detail.error);
   };
 
@@ -290,7 +290,7 @@ export default async function init({
   });
   eventTarget.addEventListener(EVENTS.IMAGE_LOAD_FAILED, imageLoadFailedHandler);
   eventTarget.addEventListener(EVENTS.IMAGE_LOAD_ERROR, imageLoadFailedHandler);
-  
+
   function elementEnabledHandler(evt) {
     const { element } = evt.detail;
 

extensions/cornerstone/src/services/SegmentationService/SegmentationService.ts

@@ -1,5 +1,3 @@
-import cloneDeep from 'lodash.clonedeep';
-
 import { Types as OhifTypes, ServicesManager, PubSubService } from '@ohif/core';
 import {
   cache,
@@ -11,7 +9,6 @@ import {
   volumeLoader,
 } from '@cornerstonejs/core';
 import {
-  CONSTANTS as cstConstants,
   Enums as csToolsEnums,
   segmentation as cstSegmentation,
   Types as cstTypes,
@@ -23,7 +20,6 @@ import { easeInOutBell, reverseEaseInOutBell } from '../../utils/transitions';
 import { Segment, Segmentation, SegmentationConfig } from './SegmentationServiceTypes';
 import { mapROIContoursToRTStructData } from './RTSTRUCT/mapROIContoursToRTStructData';
 
-const { COLOR_LUT } = cstConstants;
 const LABELMAP = csToolsEnums.SegmentationRepresentations.Labelmap;
 const CONTOUR = csToolsEnums.SegmentationRepresentations.Contour;
 
@@ -465,15 +461,6 @@ class SegmentationService extends PubSubService {
       },
     ]);
 
-    // if first segmentation, we can use the default colorLUT, otherwise
-    // we need to generate a new one and use a new colorLUT
-    const colorLUTIndex = 0;
-    if (Object.keys(this.segmentations).length !== 0) {
-      const newColorLUT = this.generateNewColorLUT();
-      const colorLUTIndex = this.getNextColorLUTIndex();
-      cstSegmentation.config.color.addColorLUT(newColorLUT, colorLUTIndex);
-    }
-
     this.segmentations[segmentationId] = {
       ...segmentation,
       label: segmentation.label || '',
@@ -482,7 +469,6 @@ class SegmentationService extends PubSubService {
       segmentCount: segmentation.segmentCount ?? 0,
       isActive: false,
       isVisible: true,
-      colorLUTIndex,
     };
 
     cachedSegmentation = this.segmentations[segmentationId];
@@ -1037,8 +1023,6 @@ class SegmentationService extends PubSubService {
       segmentation.hydrated = true;
     }
 
-    const { colorLUTIndex } = segmentation;
-
     // Based on the segmentationId, set the colorLUTIndex.
     const segmentationRepresentationUIDs = await cstSegmentation.addSegmentationRepresentations(
       toolGroupId,
@@ -1057,12 +1041,6 @@ class SegmentationService extends PubSubService {
       segmentationRepresentationUIDs[0]
     );
 
-    cstSegmentation.config.color.setColorLUT(
-      toolGroupId,
-      segmentationRepresentationUIDs[0],
-      colorLUTIndex
-    );
-
     // add the segmentation segments properly
     for (const segment of segmentation.segments) {
       if (segment === null || segment === undefined) {
@@ -1530,7 +1508,6 @@ class SegmentationService extends PubSubService {
       segments: [],
       isVisible: true,
       isActive: false,
-      colorLUTIndex: 0,
     };
   }
 
@@ -2124,23 +2101,6 @@ class SegmentationService extends PubSubService {
     return viewportInfo.getToolGroupId();
   };
 
-  private getNextColorLUTIndex = (): number => {
-    let i = 0;
-    while (true) {
-      if (cstSegmentation.state.getColorLUT(i) === undefined) {
-        return i;
-      }
-
-      i++;
-    }
-  };
-
-  private generateNewColorLUT() {
-    const newColorLUT = cloneDeep(COLOR_LUT);
-
-    return newColorLUT;
-  }
-
   /**
    * Converts object of objects to array.
    *

extensions/cornerstone/src/services/ViewportService/Viewport.ts

@@ -1,5 +1,5 @@
 import { Types, Enums } from '@cornerstonejs/core';
-import { Types as UITypes } from '@ohif/ui';
+import { Types as CoreTypes } from '@ohif/core';
 import { StackViewportData, VolumeViewportData } from '../../types/CornerstoneCacheService';
 import getCornerstoneBlendMode from '../../utils/getCornerstoneBlendMode';
 import getCornerstoneOrientation from '../../utils/getCornerstoneOrientation';
@@ -18,7 +18,7 @@ export type ViewportOptions = {
   toolGroupId: string;
   viewportId: string;
   // Presentation ID to store/load presentation state from
-  presentationIds?: UITypes.PresentationIds;
+  presentationIds?: CoreTypes.PresentationIds;
   orientation?: Enums.OrientationAxis;
   background?: Types.Point3;
   displayArea?: Types.DisplayArea;
@@ -36,7 +36,7 @@ export type PublicViewportOptions = {
   id?: string;
   viewportType?: string;
   toolGroupId?: string;
-  presentationIds?: UITypes.PresentationIds;
+  presentationIds?: CoreTypes.PresentationIds;
   viewportId?: string;
   orientation?: Enums.OrientationAxis;
   background?: Types.Point3;
@@ -71,7 +71,7 @@ export type DisplaySetOptions = {
   voiInverted: boolean;
   blendMode?: Enums.BlendModes;
   slabThickness?: number;
-  colormap?: { name: string, opacity?: number };
+  colormap?: { name: string; opacity?: number };
   displayPreset?: string;
 };
 

extensions/cornerstone/src/types/Presentation.ts

@@ -1,12 +1,12 @@
 /** Store presentation data for either stack viewports or volume viewports */
 import { Types } from '@cornerstonejs/core';
-import { Types as UITypes } from '@ohif/ui';
+import { Types as CoreTypes } from '@ohif/core';
 
 /**
  * Has information on the presentation of the viewport.
  */
 export interface Presentation extends Types.StackViewportProperties {
-  presentationIds: UITypes.PresentationIds;
+  presentationIds: CoreTypes.PresentationIds;
   viewportType: string;
   initialImageIndex: number;
   camera: Types.ICamera;

extensions/measurement-tracking/package.json

@@ -30,8 +30,8 @@
     "start": "yarn run dev"
   },
   "peerDependencies": {
-    "@cornerstonejs/core": "^1.40.3",
-    "@cornerstonejs/tools": "^1.40.3",
+    "@cornerstonejs/core": "^1.43.7",
+    "@cornerstonejs/tools": "^1.43.7",
     "@ohif/core": "3.8.0-beta.42",
     "@ohif/extension-cornerstone-dicom-sr": "3.8.0-beta.42",
     "@ohif/ui": "3.8.0-beta.42",