Gradient rebase Viewer v3.8.0 stable

.github/workflows/deploy_ghpages.yml

@@ -0,0 +1,105 @@
+name: Deploy viewer to github pages
+
+on:
+  push:
+    branches: [ "gradienthealth/segmentation_mode_sheet_integration" ]
+  #pull_request:
+    #branches: [ "main" ]
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        node-version: [16.x]
+
+    steps:
+        - name: Use Node.js ${{ matrix.node-version }}
+          uses: actions/setup-node@v3
+          with:
+            node-version: ${{ matrix.node-version }}
+
+        - name: Checkout cornerstone3D
+          uses: actions/checkout@v3
+          with:
+            repository: gradienthealth/cornerstone3D-beta
+            ref: gradienthealth/segmentation_mode_sheet_integration
+            path: ./cornerstone3D
+
+        - name: Build cornerstone3D
+          run: |
+            cd ./cornerstone3D
+            yarn install
+            yarn build:all
+
+        - name: Checkout GradientExtensionsAndModes
+          uses: actions/checkout@v3
+          with:
+            repository: gradienthealth/GradientExtensionsAndModes
+            ref: gradienthealth/segmentation_mode_sheet_integration
+            path: ./GradientExtensionsAndModes
+
+        #- name: Build GradientExtensionsAndModes
+        #  run: |
+        #   cd ./GradientExtensionsAndModes/extensions/ohif-gradienthealth-extension
+        #   yarn install
+        #   yarn build:package
+        #   cd ./modes/cohort
+        #   yarn install
+        #   yarn build:package
+
+        - name: Checkout Viewers
+          uses: actions/checkout@v3
+          with:
+            repository: gradienthealth/Viewers
+            path: ./Viewers
+
+        - name: Link
+          run: |
+            cd ./cornerstone3D/packages/adapters/dist
+            yarn link
+            cd ../../core/dist
+            yarn link
+            cd ../../dicomImageLoader/dist
+            yarn link
+            #cd ../../nifti-volume-loader/dist
+            #yarn link
+            cd ../../streaming-image-volume-loader/dist
+            yarn link
+            cd ../../tools/dist
+            yarn link
+            cd ../../../../Viewers
+            yarn link @cornerstonejs/adapters
+            yarn link @cornerstonejs/core
+            yarn link @cornerstonejs/dicom-image-loader
+            #yarn link @cornerstonejs/nifti-volume-loader
+            yarn link @cornerstonejs/streaming-image-volume-loader
+            yarn link @cornerstonejs/tools
+            yarn install
+            yarn run cli link-extension ../GradientExtensionsAndModes/extensions/ohif-gradienthealth-extension
+            yarn run cli link-mode ../GradientExtensionsAndModes/modes/cohort
+            yarn run cli link-mode ../GradientExtensionsAndModes/modes/breast-density-mode
+            yarn run build:gradient
+
+        - name: Checkout gh page
+          uses: actions/checkout@v3
+          with:
+            repository: gradienthealth/gradienthealth.github.io
+            path: ./gradienthealth.github.io
+            token: ${{ secrets.GH_DEPLOY_TOKEN }}
+
+        - name: Copy
+          run: |
+            mv ./gradienthealth.github.io/.git /tmp/
+            rm -r ./gradienthealth.github.io
+            cp -r ./Viewers/platform/app/dist/ ./gradienthealth.github.io
+            mv /tmp/.git ./gradienthealth.github.io
+            cd ./gradienthealth.github.io
+            cp index.html 404.html
+            git config --global user.name "maya-mohan"
+            git config --global user.email "[email protected]"
+            git remote set-url origin https://maya-mohan:${{ secrets.GH_DEPLOY_TOKEN }}@github.com/gradienthealth/gradienthealth.github.io
+            git add .
+            git commit -a -m "publishing viewer"
+            git push -u origin

extensions/cornerstone-dicom-seg/src/commandsModule.ts

@@ -19,8 +19,10 @@ import {
   getUpdatedViewportsForSegmentation,
   getTargetViewport,
 } from './utils/hydrationUtils';
-const { segmentation: segmentationUtils } = utilities;
+import generateLabelmaps2DFromImageIdMap from './utils/generateLabelmaps2DFromImageIdMap';
+import getSegmentLabel from './utils/getSegmentLabel';
 
+const { segmentation: segmentationUtils } = utilities;
 const { datasetToBlob } = dcmjs.data;
 
 const {
@@ -80,17 +82,6 @@ const commandsModule = ({
       // Todo: add support for multiple display sets
       const displaySetInstanceUID = viewport.displaySetInstanceUIDs[0];
 
-      const displaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
-
-      if (!displaySet.isReconstructable) {
-        uiNotificationService.show({
-          title: 'Segmentation',
-          message: 'Segmentation is not supported for non-reconstructible displaysets yet',
-          type: 'error',
-        });
-        return;
-      }
-
       updateViewportsForSegmentationRendering({
         viewportId,
         servicesManager,
@@ -113,7 +104,7 @@ const commandsModule = ({
             toolGroupId,
             segmentIndex: 1,
             properties: {
-              label: 'Segment 1',
+              label: getSegmentLabel(segmentationService.getSegmentation(segmentationId)),
             },
           });
 
@@ -245,14 +236,23 @@ const commandsModule = ({
      */
     generateSegmentation: ({ segmentationId, options = {} }) => {
       const segmentation = cornerstoneToolsSegmentation.state.getSegmentation(segmentationId);
+      const segmentationLabelmapData = segmentation.representationData.LABELMAP;
+
+      let referencedImages, labelmapObj;
+      if (segmentationLabelmapData.imageIdReferenceMap) {
+        const { imageIdReferenceMap } = segmentationLabelmapData;
 
-      const { referencedVolumeId } = segmentation.representationData.LABELMAP;
+        ({ referencedImages, labelmapObj } =
+          generateLabelmaps2DFromImageIdMap(imageIdReferenceMap));
+      } else {
+        const { referencedVolumeId } = segmentationLabelmapData;
 
-      const segmentationVolume = cache.getVolume(segmentationId);
-      const referencedVolume = cache.getVolume(referencedVolumeId);
-      const referencedImages = referencedVolume.getCornerstoneImages();
+        const segmentationVolume = cache.getVolume(segmentationId);
+        const referencedVolume = cache.getVolume(referencedVolumeId);
+        referencedImages = referencedVolume.getCornerstoneImages();
 
-      const labelmapObj = generateLabelMaps2DFrom3D(segmentationVolume);
+        labelmapObj = generateLabelMaps2DFrom3D(segmentationVolume);
+      }
 
       // Generate fake metadata as an example
       labelmapObj.metadata = [];
@@ -326,28 +326,45 @@ const commandsModule = ({
      * @returns {Object|void} Returns the naturalized report if successfully stored,
      * otherwise throws an error.
      */
-    storeSegmentation: async ({ segmentationId, dataSource }) => {
-      const promptResult = await createReportDialogPrompt(uiDialogService, {
-        extensionManager,
-      });
-
-      if (promptResult.action !== 1 && promptResult.value) {
-        return;
-      }
-
+    storeSegmentation: async ({ segmentationId, dataSource, skipLabelDialog = false }) => {
       const segmentation = segmentationService.getSegmentation(segmentationId);
 
       if (!segmentation) {
         throw new Error('No segmentation found');
       }
+      const { label, displaySetInstanceUID } = segmentation;
+
+      const displaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
+      const shouldOverWrite = displaySet && displaySet.Modality === 'SEG';
+
+      let promptResult: { action?: number; value?: string } = {};
+
+      if (!(skipLabelDialog || shouldOverWrite)) {
+        promptResult = await createReportDialogPrompt(uiDialogService, {
+          extensionManager,
+        });
+
+        if (promptResult.action !== 1 && !promptResult.value) {
+          return;
+        }
+      }
 
-      const { label } = segmentation;
       const SeriesDescription = promptResult.value || label || 'Research Derived Series';
+      segmentation.label = SeriesDescription;
 
       const generatedData = actions.generateSegmentation({
         segmentationId,
         options: {
           SeriesDescription,
+          // Use SeriesInstanceUID, SOPInstanceUID, SeriesNumber, Manufacturer and SeriesDate
+          // if displaySet of the segmentation already exists.
+          // Study level and patient metadata will be used automatically.
+          ...(shouldOverWrite && {
+            SeriesInstanceUID: displaySet.SeriesInstanceUID,
+            SOPInstanceUID: displaySet.instances[0].SOPInstanceUID,
+            SeriesNumber: displaySet.SeriesNumber,
+            Manufacturer: displaySet.instances[0].Manufacturer,
+          }),
         },
       });
 
@@ -366,8 +383,6 @@ const commandsModule = ({
       // add the information for where we stored it to the instance as well
       naturalizedReport.wadoRoot = dataSource.getConfig().wadoRoot;
 
-      DicomMetadataStore.addInstances([naturalizedReport], true);
-
       return naturalizedReport;
     },
     /**

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

@@ -142,20 +142,27 @@ async function _loadSegments({ extensionManager, servicesManager, segDisplaySet,
     '@ohif/extension-cornerstone.utilityModule.common'
   );
 
-  const { segmentationService, uiNotificationService } = servicesManager.services;
+  const { segmentationService, uiNotificationService, displaySetService } =
+    servicesManager.services;
 
   const { dicomLoaderService } = utilityModule.exports;
   const arrayBuffer = await dicomLoaderService.findDicomDataPromise(segDisplaySet, null, headers);
 
-  const cachedReferencedVolume = cache.getVolume(segDisplaySet.referencedVolumeId);
+  const referencedDisplaySet = displaySetService.getDisplaySetByUID(
+    segDisplaySet.referencedDisplaySetInstanceUID
+  );
+  let imageIds;
 
-  if (!cachedReferencedVolume) {
-    throw new Error(
-      'Referenced Volume is missing for the SEG, and stack viewport SEG is not supported yet'
-    );
-  }
+  if (referencedDisplaySet.isReconstructable) {
+    const cachedReferencedVolume = cache.getVolume(segDisplaySet.referencedVolumeId);
+    if (!cachedReferencedVolume) {
+      throw new Error('Referenced Volume is missing for the SEG');
+    }
 
-  const { imageIds } = cachedReferencedVolume;
+    imageIds = cachedReferencedVolume.imageIds || cachedReferencedVolume._imageIds;
+  } else {
+    imageIds = referencedDisplaySet.instances.map(instance => instance.imageId);
+  }
 
   // Todo: what should be defaults here
   const tolerance = 0.001;
@@ -198,6 +205,7 @@ async function _loadSegments({ extensionManager, servicesManager, segDisplaySet,
     });
   }
 
+  /* Skip the warning message as it is annoying on auto segmentations loading.
   if (!usedRecommendedDisplayCIELabValue) {
     // Display a notification about the non-utilization of RecommendedDisplayCIELabValue
     uiNotificationService.show({
@@ -207,7 +215,7 @@ async function _loadSegments({ extensionManager, servicesManager, segDisplaySet,
       type: 'warning',
       duration: 5000,
     });
-  }
+  }*/
 
   Object.assign(segDisplaySet, results);
 }