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

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',
-          });
-        }
       }
     );