feat: visualize overlapping segments in cornerstone (#2185)

* feat: visualize overlapping segments

load multiple labelMaps (splitted by dcmjs because overlapping) in a segmentations [IDC2164]

Dynamically update active labelmap [IDC2164]

Co-authored-by: Davide Punzo <punzodavide@hotmail.it>
Co-authored-by: Igor Octaviano <igoroctaviano@gmail.com>

extensions/cornerstone/package.json

@@ -36,7 +36,7 @@
     "cornerstone-math": "^0.1.8",
     "cornerstone-tools": "^4.20.1",
     "cornerstone-wado-image-loader": "^3.1.0",
-    "dcmjs": "0.16.5",
+    "dcmjs": "0.17.0",
     "dicom-parser": "^1.8.3",
     "hammerjs": "^2.0.8",
     "prop-types": "^15.6.2",

extensions/dicom-html/package.json

@@ -29,7 +29,7 @@
   },
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
-    "dcmjs": "0.16.5",
+    "dcmjs": "0.17.0",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6"

extensions/dicom-rt/package.json

@@ -31,7 +31,7 @@
     "@ohif/core": "^0.50.0",
     "cornerstone-core": "^2.2.8",
     "cornerstone-tools": "^4.20.1",
-    "dcmjs": "0.16.5",
+    "dcmjs": "0.17.0",
     "gl-matrix": "^3.3.0",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",

extensions/dicom-segmentation/package.json

@@ -31,7 +31,7 @@
     "@ohif/core": "^0.50.0",
     "cornerstone-core": "^2.2.8",
     "cornerstone-tools": "^4.20.1",
-    "dcmjs": "0.16.5",
+    "dcmjs": "0.17.0",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6"

extensions/dicom-segmentation/src/components/SegmentationPanel/SegmentationPanel.js

@@ -159,12 +159,12 @@ const SegmentationPanel = ({
         const labelmapList = getLabelmapList(
           brushStackState,
           firstImageId,
-          activeViewport
+          activeViewport,
         );
         const segmentList = getSegmentList(
           labelmap3D,
           firstImageId,
-          brushStackState
+          brushStackState,
         );
         setState(state => ({
           ...state,
@@ -292,10 +292,13 @@ const SegmentationPanel = ({
 
         const sameSegment = state.selectedSegment === segmentNumber;
         const setCurrentSelectedSegment = () => {
+          const activeViewport = viewports[activeIndex];
+
           _setActiveSegment(
             firstImageId,
             segmentNumber,
-            labelmap3D.activeSegmentIndex
+            labelmap3D.activeSegmentIndex,
+            activeViewport
           );
           updateState('selectedSegment', sameSegment ? null : segmentNumber);
 
@@ -640,7 +643,7 @@ const _getReferencedSegDisplaysets = (StudyInstanceUID, SeriesInstanceUID) => {
  * @param {*} activeSegmentIndex
  * @returns
  */
-const _setActiveSegment = (firstImageId, segmentIndex, activeSegmentIndex) => {
+const _setActiveSegment = (firstImageId, segmentIndex, activeSegmentIndex, activeViewport) => {
   if (segmentIndex === activeSegmentIndex) {
     log.info(`${activeSegmentIndex} is already the active segment`);
     return;
@@ -653,8 +656,27 @@ const _setActiveSegment = (firstImageId, segmentIndex, activeSegmentIndex) => {
     brushStackState.labelmaps3D[brushStackState.activeLabelmapIndex];
   labelmap3D.activeSegmentIndex = segmentIndex;
 
-  refreshViewports();
+  /**
+   * Activates the correct label map if clicked segment
+   * does not belong to the active labelmap
+   */
+  const { StudyInstanceUID } = activeViewport;
+  const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
+  const allDisplaySets = studyMetadata.getDisplaySets();
+  let newLabelmapIndex = brushStackState.activeLabelmapIndex;
+  allDisplaySets.forEach(displaySet => {
+    if (displaySet.labelmapSegments) {
+      Object.keys(displaySet.labelmapSegments).forEach(labelmapIndex => {
+        if (displaySet.labelmapSegments[labelmapIndex].includes(segmentIndex)) {
+          newLabelmapIndex = labelmapIndex;
+        }
+      });
+    }
+  });
 
+  brushStackState.activeLabelmapIndex = newLabelmapIndex;
+
+  refreshViewports();
   return segmentIndex;
 };
 

extensions/dicom-segmentation/src/getOHIFDicomSegSopClassHandler.js

@@ -1,6 +1,11 @@
 import { MODULE_TYPES, utils } from '@ohif/core';
 import loadSegmentation from './loadSegmentation';
 import getSourceDisplaySet from './getSourceDisplaySet';
+import OHIF from '@ohif/core';
+import dcmjs from 'dcmjs';
+
+const { DicomLoaderService } = OHIF.utils;
+const { DicomMessage, DicomMetaDictionary } = dcmjs.data;
 
 // TODO: Should probably use dcmjs for this
 const SOP_CLASS_UIDS = {
@@ -46,7 +51,6 @@ export default function getSopClassHandlerModule({ servicesManager }) {
         StudyInstanceUID,
         FrameOfReferenceUID,
         authorizationHeaders,
-        metadata,
         isDerived: true,
         referencedDisplaySetUID: null, // Assigned when loaded.
         labelmapIndex: null, // Assigned when loaded.
@@ -62,11 +66,81 @@ export default function getSopClassHandlerModule({ servicesManager }) {
         return getSourceDisplaySet(studies, segDisplaySet);
       };
 
-      segDisplaySet.load = function(referencedDisplaySet, studies) {
+      segDisplaySet.load = async function (referencedDisplaySet, studies) {
-        return loadSegmentation(segDisplaySet, referencedDisplaySet, studies);
+        segDisplaySet.isLoaded = true;
+        const { StudyInstanceUID } = referencedDisplaySet;
+        const segArrayBuffer = await DicomLoaderService.findDicomDataPromise(
+          segDisplaySet,
+          studies
+        );
+        const dicomData = DicomMessage.readFile(segArrayBuffer);
+        const dataset = DicomMetaDictionary.naturalizeDataset(dicomData.dict);
+        dataset._meta = DicomMetaDictionary.namifyDataset(dicomData.meta);
+        const imageIds = _getImageIdsForDisplaySet(
+          studies,
+          StudyInstanceUID,
+          referencedDisplaySet.SeriesInstanceUID
+        );
+        return new Promise((resolve, reject) => {
+          let results;
+          try {
+            results = _parseSeg(segArrayBuffer, imageIds);
+          } catch (error) {
+            segDisplaySet.isLoaded = false;
+            segDisplaySet.loadError = true;
+            reject(error);
+          }
+          const { labelmapBufferArray, segMetadata, segmentsOnFrame, segmentsOnFrameArray } = results;
+
+          if (labelmapBufferArray.length > 1) {
+            for (let i = 0; i < labelmapBufferArray.length; ++i) {
+              loadSegmentation(imageIds, segDisplaySet, labelmapBufferArray[i], segMetadata, segmentsOnFrame, segmentsOnFrameArray[i]);
+            }
+          } else {
+            loadSegmentation(imageIds, segDisplaySet, labelmapBufferArray[0], segMetadata, segmentsOnFrame, []);
+          }
+          segDisplaySet.labelmapIndex = 0;
+
+          resolve();
+        });
       };
 
       return segDisplaySet;
     },
   };
 }
+
+function _parseSeg(arrayBuffer, imageIds) {
+  return dcmjs.adapters.Cornerstone.Segmentation.generateToolState(
+    imageIds,
+    arrayBuffer,
+    cornerstone.metaData
+  );
+}
+
+function _getImageIdsForDisplaySet(
+  studies,
+  StudyInstanceUID,
+  SeriesInstanceUID
+) {
+  const study = studies.find(
+    study => study.StudyInstanceUID === StudyInstanceUID
+  );
+
+  const displaySets = study.displaySets.filter(displaySet => {
+    return displaySet.SeriesInstanceUID === SeriesInstanceUID;
+  });
+
+  if (displaySets.length > 1) {
+    console.warn(
+      'More than one display set with the same SeriesInstanceUID. This is not supported yet...'
+    );
+    // TODO -> We could make check the instance list and see if any match?
+    // Do we split the segmentation into two cornerstoneTools segmentations if there are images in both series?
+    // ^ Will that even happen?
+  }
+
+  const referencedDisplaySet = displaySets[0];
+
+  return referencedDisplaySet.images.map(image => image.getImageId());
+}

extensions/dicom-segmentation/src/loadSegmentation.js

@@ -1,51 +1,15 @@
-import OHIF from '@ohif/core';
 import dcmjs from 'dcmjs';
 import cornerstone from 'cornerstone-core';
 import cornerstoneTools from 'cornerstone-tools';
 
-const { DicomLoaderService } = OHIF.utils;
-
 export default async function loadSegmentation(
+  imageIds,
   segDisplaySet,
-  referencedDisplaySet,
+  labelmapBuffer,
-  studies
+  segMetadata,
+  segmentsOnFrame,
+  labelmapSegments
 ) {
-  const { StudyInstanceUID } = referencedDisplaySet;
-
-  // Set here is loading is asynchronous.
-  // If this function throws its set back to false.
-  segDisplaySet.isLoaded = true;
-
-  const segArrayBuffer = await DicomLoaderService.findDicomDataPromise(
-    segDisplaySet,
-    studies
-  );
-
-  const dicomData = dcmjs.data.DicomMessage.readFile(segArrayBuffer);
-  const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
-    dicomData.dict
-  );
-
-  dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(dicomData.meta);
-
-  const imageIds = _getImageIdsForDisplaySet(
-    studies,
-    StudyInstanceUID,
-    referencedDisplaySet.SeriesInstanceUID
-  );
-
-  return new Promise((resolve, reject) => {
-    let results;
-
-    try {
-      results = _parseSeg(segArrayBuffer, imageIds);
-    } catch (error) {
-      segDisplaySet.isLoaded = false;
-      segDisplaySet.loadError = true;
-      reject(error);
-    }
-
-    const { labelmapBuffer, segMetadata, segmentsOnFrame } = results;
   const { setters } = cornerstoneTools.getModule('segmentation');
 
   // TODO: Could define a color LUT based on colors in the SEG.
@@ -62,6 +26,15 @@ export default async function loadSegmentation(
     colorLUTIndex
   );
 
+  if (!segDisplaySet.labelmapSegments) {
+    segDisplaySet.labelmapSegments = {};
+  }
+
+  /**
+   * Cache each labelmap segments.
+   * This data is used to determine the active label map when a given segment is activated/clicked.
+   */
+  segDisplaySet.labelmapSegments[labelmapIndex] = labelmapSegments.length ? Array.from(new Set(labelmapSegments.filter(a => !!a).reduce((a, b) => a.concat(b)))) : [];
   segDisplaySet.labelmapIndex = labelmapIndex;
 
   /*
@@ -84,9 +57,6 @@ export default async function loadSegmentation(
   console.log('Segmentation loaded.');
   const event = new CustomEvent('extensiondicomsegmentationsegloaded');
   document.dispatchEvent(event);
-
-    resolve(labelmapIndex);
-  });
 }
 
 function _getNextLabelmapIndex(firstImageId) {
@@ -172,38 +142,3 @@ function _getNextColorLUTIndex() {
 
   return colorLUTIndex;
 }
-
-function _parseSeg(arrayBuffer, imageIds) {
-  return dcmjs.adapters.Cornerstone.Segmentation.generateToolState(
-    imageIds,
-    arrayBuffer,
-    cornerstone.metaData
-  );
-}
-
-function _getImageIdsForDisplaySet(
-  studies,
-  StudyInstanceUID,
-  SeriesInstanceUID
-) {
-  const study = studies.find(
-    study => study.StudyInstanceUID === StudyInstanceUID
-  );
-
-  const displaySets = study.displaySets.filter(displaySet => {
-    return displaySet.SeriesInstanceUID === SeriesInstanceUID;
-  });
-
-  if (displaySets.length > 1) {
-    console.warn(
-      'More than one display set with the same SeriesInstanceUID. This is not supported yet...'
-    );
-    // TODO -> We could make check the instance list and see if any match?
-    // Do we split the segmentation into two cornerstoneTools segmentations if there are images in both series?
-    // ^ Will that even happen?
-  }
-
-  const referencedDisplaySet = displaySets[0];
-
-  return referencedDisplaySet.images.map(image => image.getImageId());
-}

extensions/dicom-tag-browser/package.json

@@ -28,7 +28,7 @@
   },
   "peerDependencies": {
     "@ohif/core": "^2.6.0",
-    "dcmjs": "0.16.5",
+    "dcmjs": "0.17.0",
     "react": "^16.8.6"
   },
   "dependencies": {

extensions/vtk/package.json

@@ -35,7 +35,7 @@
     "cornerstone-core": "^2.2.8",
     "cornerstone-tools": "^4.20.1",
     "cornerstone-wado-image-loader": "^3.1.0",
-    "dcmjs": "0.16.5",
+    "dcmjs": "0.17.0",
     "dicom-parser": "^1.8.3",
     "i18next": "^17.0.3",
     "i18next-browser-languagedetector": "^3.0.1",

extensions/vtk/src/OHIFVTKViewport.js

@@ -159,6 +159,15 @@ class OHIFVTKViewport extends Component {
       const { activeLabelmapIndex } = brushStackState;
       const labelmap3D = brushStackState.labelmaps3D[activeLabelmapIndex];
 
+      if (brushStackState.labelmaps3D.length > 1 && this.props.viewportIndex === 0) {
+        const { UINotificationService } = this.props.servicesManager.services;
+        UINotificationService.show({
+          title: 'Overlapping Segmentation Found',
+          message: 'Overlapping segmentations cannot be displayed when in MPR mode',
+          type: 'info',
+        });
+      }
+
       this.segmentsDefaultProperties = labelmap3D.segmentsHidden.map(
         isHidden => {
           return { visible: !isHidden };

platform/core/package.json

@@ -39,7 +39,7 @@
   "dependencies": {
     "@babel/runtime": "^7.5.5",
     "ajv": "^6.10.0",
-    "dcmjs": "0.16.5",
+    "dcmjs": "0.17.0",
     "dicomweb-client": "^0.6.0",
     "immer": "6.0.2",
     "isomorphic-base64": "^1.0.2",

platform/ui/src/contextProviders/SnackbarProvider.js

@@ -37,6 +37,10 @@ const SnackbarProvider = ({ children, service }) => {
         return null;
       }
 
+      if (options.type === 'error') {
+        console.error(options.error);
+      }
+
       const newItem = {
         ...DEFAULT_OPTIONS,
         ...options,

platform/viewer/package.json

@@ -68,7 +68,7 @@
     "cornerstone-math": "^0.1.8",
     "cornerstone-tools": "^4.20.1",
     "cornerstone-wado-image-loader": "^3.1.0",
-    "dcmjs": "0.16.5",
+    "dcmjs": "0.17.0",
     "dicom-parser": "^1.8.3",
     "dicomweb-client": "^0.4.4",
     "hammerjs": "^2.0.8",

platform/viewer/src/components/ViewportGrid/ViewportGrid.js

@@ -48,6 +48,7 @@ const ViewportGrid = function(props) {
               title: 'Error loading derived display set:',
               message: error.message,
               type: 'error',
+              error,
               autoClose: false,
             });
           });

yarn.lock

@@ -6619,14 +6619,15 @@ dateformat@^3.0.0:
   resolved "https://registry.yarnpkg.com/dateformat/-/dateformat-3.0.3.tgz#a6e37499a4d9a9cf85ef5872044d62901c9889ae"
   integrity sha512-jyCETtSl3VMZMWeRo7iY1FL19ges1t55hMo5yaam4Jrsm5EPL89UQkoQRyiI+Yf4k8r2ZpdngkV8hr1lIdjb3Q==
 
-dcmjs@0.16.5:
+dcmjs@0.17.0:
-  version "0.16.5"
+  version "0.17.0"
-  resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.16.5.tgz#05aa0c8d539a4d5777f996b9b796932d1f848993"
+  resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.17.0.tgz#dbfd6db3efd2936f9bead9c902b7db396f64e9f5"
-  integrity sha512-Y92KAx4JSfev79xjYhaukQZjWgyJlaHnXSTdbtkGkJAHERjIakgHcCIPmACuVmtW/nHViTu04zIGAB0pmZ4GaA==
+  integrity sha512-7JnNqNWXqjGyspLRwKM4nn+TU/+w3iMl9boU4eHrr831M4crMWWIiSQDejpOnfDT9+opqyeaYcNkiekr7p6TFg==
   dependencies:
     "@babel/polyfill" "^7.8.3"
     "@babel/runtime" "^7.8.4"
     gl-matrix "^3.1.0"
+    lodash.clonedeep "^4.5.0"
     loglevelnext "^3.0.1"
     ndarray "^1.0.19"