Re IDC #2765: fix loading of segmentations at first startup (#2768)

Re IDC #2761: fix loading of segmentations

update dcmjs to 0.19.9

extensions/cornerstone/package.json

@@ -36,7 +36,7 @@
     "cornerstone-math": "^0.1.9",
     "cornerstone-tools": "^6.0.6",
     "cornerstone-wado-image-loader": "^4.1.0",
-    "dcmjs": "0.19.8",
+    "dcmjs": "0.19.9",
     "dicom-parser": "^1.8.11",
     "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": "0.19.8",
+    "dcmjs": "0.19.9",
     "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": "^2.6.1",
     "cornerstone-tools": "^6.0.6",
-    "dcmjs": "0.19.8",
+    "dcmjs": "0.19.9",
     "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": "^2.6.1",
     "cornerstone-tools": "^6.0.6",
-    "dcmjs": "0.19.8",
+    "dcmjs": "0.19.9",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6"

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

@@ -226,7 +226,6 @@ const SegmentationPanel = ({
     };
   }, [
     activeIndex,
-    updateSegmentationComboBox,
     viewports,
   ]);
 
@@ -234,23 +233,9 @@ const SegmentationPanel = ({
     const index = e.detail.activatedLabelmapIndex;
     if (index !== -1) {
       setState(state => ({ ...state, selectedSegmentation: index }));
-    } else {
-      cleanSegmentationComboBox();
     }
   };
 
-  const cleanSegmentationComboBox = () => {
-    setState(state => ({
-      ...state,
-      segmentsHidden: [],
-      segmentNumbers: [],
-      labelMapList: [],
-      segmentList: [],
-      isDisabled: true,
-      selectedSegmentation: -1,
-    }));
-  };
-
   const refreshSegmentations = () => {
     const activeViewport = getActiveViewport();
     const isDisabled = !activeViewport || !activeViewport.StudyInstanceUID;
@@ -709,7 +694,7 @@ const SegmentationPanel = ({
           count={state.segmentList.length}
           isVisible={
             state.segmentsHidden.filter(isHidden => isHidden === true).length <
-            state.segmentNumbers.length
+            state.segmentNumbers.length && state.segmentNumbers.length > 0
           }
           onVisibilityChange={onVisibilityChangeHandler}
         >

extensions/dicom-segmentation/src/utils/setActiveLabelMap.js

@@ -47,14 +47,23 @@ export default async function setActiveLabelmap(
     return labelmapIndex;
   }
 
-  if (!displaySet.isLoaded) {
+  if (!displaySet.isLoaded && !displaySet.loadError) {
     try {
       await displaySet.load(referencedDisplaySet, studies);
     } catch (error) {
       displaySet.isLoaded = false;
       displaySet.loadError = true;
+      displaySet.segLoadErrorMessagge = error.message;
       onDisplaySetLoadFailure(error);
 
+      /*
+       * TODO: Improve the way we notify parts of the app
+       * that depends on derived display sets to be loaded.
+       * (Implement pubsub for better tracking of derived display sets)
+       */
+      const event = new CustomEvent('segmentationLoadingError');
+      document.dispatchEvent(event);
+
       return -1;
     }
   }

extensions/dicom-tag-browser/package.json

@@ -28,7 +28,7 @@
   },
   "peerDependencies": {
     "@ohif/core": "^2.6.0",
-    "dcmjs": "0.19.8",
+    "dcmjs": "0.19.9",
     "react": "^16.8.6"
   },
   "dependencies": {

extensions/vtk/package.json

@@ -35,7 +35,7 @@
     "cornerstone-core": "^2.6.1",
     "cornerstone-tools": "^6.0.6",
     "cornerstone-wado-image-loader": "^4.1.0",
-    "dcmjs": "0.19.8",
+    "dcmjs": "0.19.9",
     "dicom-parser": "^1.8.11",
     "i18next": "^17.0.3",
     "i18next-browser-languagedetector": "^3.0.1",

platform/core/package.json

@@ -39,7 +39,7 @@
   "dependencies": {
     "@babel/runtime": "^7.5.5",
     "ajv": "^6.10.0",
-    "dcmjs": "0.19.8",
+    "dcmjs": "0.19.9",
     "dicomweb-client": "^0.8.3",
     "immer": "9.0.12",
     "isomorphic-base64": "^1.0.2",

platform/core/src/utils/loadAndCacheDerivedDisplaySets.js

@@ -49,7 +49,12 @@ import studyMetadataManager from './studyMetadataManager';
  * @param {object} snackbar
  * @returns void
  */
-async function loadAndCacheDerivedDisplaySets(referencedDisplaySet, studies, logger, snackbar) {
+async function loadAndCacheDerivedDisplaySets(
+  referencedDisplaySet,
+  studies,
+  logger,
+  snackbar
+) {
   const { StudyInstanceUID, SeriesInstanceUID } = referencedDisplaySet;
   const promises = [];
   const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
@@ -80,7 +85,8 @@ async function loadAndCacheDerivedDisplaySets(referencedDisplaySet, studies, log
   });
 
   // For each type, see if any are loaded, if not load the most recent.
-  await Promise.all(Object.keys(displaySetsPerModality).map(async (key) => {
+  await Promise.all(
+    Object.keys(displaySetsPerModality).map(async key => {
       const displaySets = displaySetsPerModality[key];
 
       const isLoaded = displaySets.some(displaySet => displaySet.isLoaded);
@@ -107,9 +113,58 @@ async function loadAndCacheDerivedDisplaySets(referencedDisplaySet, studies, log
       });
 
       try {
-      if (recentDisplaySet.hasOwnProperty('getSourceDisplaySet') &&
+        if (
-        typeof recentDisplaySet.getSourceDisplaySet === 'function') {
+          recentDisplaySet.hasOwnProperty('getSourceDisplaySet') &&
+          typeof recentDisplaySet.getSourceDisplaySet === 'function'
+        ) {
+          if (recentDisplaySet.Modality === 'SEG' && logger) {
+            const onDisplaySetLoadFailureHandler = error => {
+              logger.error({ error, message: error.message });
+              snackbar.show({
+                title: 'DICOM Segmentation Loader',
+                message: error.message,
+                type: 'error',
+                autoClose: true,
+              });
+            };
+
+            let activatedLabelmapIndex = -1;
+            while (activatedLabelmapIndex == -1) {
+              const {
+                referencedDisplaySet,
+                activatedLabelmapPromise,
+              } = await recentDisplaySet.getSourceDisplaySet(
+                studies,
+                true,
+                onDisplaySetLoadFailureHandler
+              );
+
+              activatedLabelmapIndex = await activatedLabelmapPromise;
+              const selectionFired = new CustomEvent(
+                'extensiondicomsegmentationsegselected',
+                {
+                  detail: { activatedLabelmapIndex: activatedLabelmapIndex },
+                }
+              );
+              document.dispatchEvent(selectionFired);
+
+              const lastDateTime = Number(
+                `${recentDisplaySet.SeriesDate}${recentDisplaySet.SeriesTime}`
+              );
+              recentDateTime = 0;
+              displaySets.forEach(displaySet => {
+                const dateTime = Number(
+                  `${displaySet.SeriesDate}${displaySet.SeriesTime}`
+                );
+                if (dateTime > recentDateTime && dateTime < lastDateTime) {
+                  recentDateTime = dateTime;
+                  recentDisplaySet = displaySet;
+                }
+              });
+            }
+          } else {
             await recentDisplaySet.getSourceDisplaySet(studies);
+          }
         } else {
           await recentDisplaySet.load(referencedDisplaySet, studies);
         }
@@ -125,7 +180,8 @@ async function loadAndCacheDerivedDisplaySets(referencedDisplaySet, studies, log
           autoClose: false,
         });
       }
-  }));
+    })
+  );
 
   /*
    * TODO: Improve the way we notify parts of the app
@@ -134,6 +190,6 @@ async function loadAndCacheDerivedDisplaySets(referencedDisplaySet, studies, log
    */
   const event = new CustomEvent('deriveddisplaysetsloadedandcached');
   document.dispatchEvent(event);
-};
+}
 
 export default loadAndCacheDerivedDisplaySets;

platform/viewer/package.json

@@ -66,7 +66,7 @@
     "cornerstone-math": "^0.1.9",
     "cornerstone-tools": "^6.0.6",
     "cornerstone-wado-image-loader": "^4.1.0",
-    "dcmjs": "0.19.8",
+    "dcmjs": "0.19.9",
     "dicom-parser": "^1.8.11",
     "dicomweb-client": "^0.8.3",
     "hammerjs": "^2.0.8",

platform/viewer/src/connectedComponents/Viewer.js

@@ -105,6 +105,11 @@ class Viewer extends Component {
     if (this.props.dialog) {
       this.props.dialog.dismissAll();
     }
+
+    document.removeEventListener(
+      'segmentationLoadingError',
+      this._updateThumbnails
+    );
   }
 
   retrieveTimepoints = filter => {
@@ -212,6 +217,12 @@ class Viewer extends Component {
         ),
       });
     }
+
+    document.addEventListener(
+      'segmentationLoadingError',
+      this._updateThumbnails.bind(this),
+      false
+    );
   }
 
   componentDidUpdate(prevProps) {
@@ -255,6 +266,20 @@ class Viewer extends Component {
     }
   }
 
+  _updateThumbnails() {
+    const { studies, activeViewportIndex, viewports } = this.props;
+
+    const activeViewport = viewports[activeViewportIndex];
+    const activeDisplaySetInstanceUID = activeViewport
+      ? activeViewport.displaySetInstanceUID
+      : undefined;
+
+    this.setState({
+      thumbnails: _mapStudiesToThumbnails(studies, activeDisplaySetInstanceUID),
+      activeDisplaySetInstanceUID,
+    });
+  }
+
   _getActiveViewport() {
     return this.props.viewports[this.props.activeViewportIndex];
   }
@@ -461,9 +486,7 @@ const _checkForDerivedDisplaySets = async function(displaySet, study) {
 /**
  * Async function to check if there are any inconsistences in the series.
  *
- * For segmentation checks that the geometry is consistent with the source images:
+ * For segmentation returns any error during loading.
- * 1) no frames out of plane;
- * 2) have the same width and height.
  *
  * For reconstructable 3D volume:
  * 1) Is series multiframe?
@@ -477,10 +500,7 @@ const _checkForDerivedDisplaySets = async function(displaySet, study) {
  * @param {*object} displaySet
  * @returns {[string]} an array of strings containing the warnings
  */
-const _checkForSeriesInconsistencesWarnings = async function(
+const _checkForSeriesInconsistencesWarnings = async function(displaySet) {
-  displaySet,
-  studies
-) {
   if (displaySet.inconsistencyWarnings) {
     // warnings already checked and cached in displaySet
     return displaySet.inconsistencyWarnings;
@@ -546,98 +566,14 @@ const _checkForSeriesInconsistencesWarnings = async function(
     if (displaySet.isModalitySupported === false) {
       inconsistencyWarnings.push('The datasets modality is not supported.');
     }
-  } else {
-    const segMetadata = displaySet.metadata;
-    if (!segMetadata) {
-      return inconsistencyWarnings;
-    }
-
-    const { referencedDisplaySet } = displaySet.getSourceDisplaySet(
-      studies,
-      false
-    );
-    if (!referencedDisplaySet) {
-      return inconsistencyWarnings;
-    }
-
-    const imageIds = referencedDisplaySet.images.map(image =>
-      image.getImageId()
-    );
-    if (!imageIds || imageIds.length === 0) {
-      return inconsistencyWarnings;
-    }
-
-    for (
-      let i = 0,
-        groupsLen = segMetadata.PerFrameFunctionalGroupsSequence.length;
-      i < groupsLen;
-      ++i
-    ) {
-      const PerFrameFunctionalGroups =
-        segMetadata.PerFrameFunctionalGroupsSequence[i];
-      if (!PerFrameFunctionalGroups) {
-        continue;
-      }
-
-      let SourceImageSequence = undefined;
-      if (segMetadata.SourceImageSequence) {
-        SourceImageSequence = segMetadata.SourceImageSequence[i];
-      } else if (PerFrameFunctionalGroups.DerivationImageSequence) {
-        SourceImageSequence =
-          PerFrameFunctionalGroups.DerivationImageSequence.SourceImageSequence;
-      }
-      if (!SourceImageSequence) {
-        if (inconsistencyWarnings.length === 0) {
-          const warningMessage =
-            'The segmentation ' +
-            'has frames out of plane respect to the source images.';
-          inconsistencyWarnings.push(warningMessage);
-        }
-        continue;
-      }
-
-      const { ReferencedSOPInstanceUID } = SourceImageSequence;
-
-      const imageId = imageIds.find(imageId => {
-        const sopCommonModule = cornerstone.metaData.get(
-          'sopCommonModule',
-          imageId
-        );
-        if (!sopCommonModule) {
-          return;
-        }
-
-        return sopCommonModule.sopInstanceUID === ReferencedSOPInstanceUID;
-      });
-
-      if (!imageId) {
-        continue;
-      }
-
-      const sourceImageMetadata = cornerstone.metaData.get('instance', imageId);
-      if (
-        segMetadata.Rows !== sourceImageMetadata.Rows ||
-        segMetadata.Columns !== sourceImageMetadata.Columns
-      ) {
-        const warningMessage =
-          'The segmentation ' +
-          'has frames with different geometry ' +
-          'dimensions (Rows and Columns) respect to the source images.';
-        inconsistencyWarnings.push(warningMessage);
-        break;
-      }
-    }
-
-    if (inconsistencyWarnings.length !== 0) {
-      const warningMessage =
-        'The segmentation format is not supported yet. ' +
-        'The segmentation data (segments) could not be loaded.';
-      inconsistencyWarnings.push(warningMessage);
-    }
-  }
-
-  // cache the warnings
     displaySet.inconsistencyWarnings = inconsistencyWarnings;
+  } else {
+    if (displaySet.loadError) {
+      inconsistencyWarnings.push(displaySet.segLoadErrorMessagge);
+      displaySet.inconsistencyWarnings = inconsistencyWarnings;
+    }
+  }
+
   return inconsistencyWarnings;
 };
 
@@ -736,10 +672,7 @@ const _mapStudiesToThumbnails = function(studies, activeDisplaySetInstanceUID) {
         altImageText = displaySet.Modality ? displaySet.Modality : 'UN';
       }
 
-      const hasWarnings = _checkForSeriesInconsistencesWarnings(
+      const hasWarnings = _checkForSeriesInconsistencesWarnings(displaySet);
-        displaySet,
-        studies
-      );
 
       const hasDerivedDisplaySets = _checkForDerivedDisplaySets(
         displaySet,

platform/viewer/src/connectedComponents/ViewerMain.js

@@ -154,12 +154,25 @@ class ViewerMain extends Component {
           });
         };
 
-        const { referencedDisplaySet } = displaySet.getSourceDisplaySet(
+        const {
+          referencedDisplaySet,
+          activatedLabelmapPromise,
+        } = displaySet.getSourceDisplaySet(
           this.props.studies,
           true,
           onDisplaySetLoadFailureHandler
         );
         displaySet = referencedDisplaySet;
+
+        activatedLabelmapPromise.then(activatedLabelmapIndex => {
+          const selectionFired = new CustomEvent(
+            'extensiondicomsegmentationsegselected',
+            {
+              detail: { activatedLabelmapIndex: activatedLabelmapIndex },
+            }
+          );
+          document.dispatchEvent(selectionFired);
+        });
       } else {
         displaySet = displaySet.getSourceDisplaySet(this.props.studies);
       }

platform/viewer/src/googleCloud/DicomStorePickerModal.js

@@ -36,7 +36,7 @@ function DicomStorePickerModal({
           user,
           url,
         },
-        onClose
+        onClose,
       });
     }
   };

yarn.lock

@@ -5449,10 +5449,10 @@ dateformat@^3.0.0:
   resolved "https://registry.yarnpkg.com/dateformat/-/dateformat-3.0.3.tgz#a6e37499a4d9a9cf85ef5872044d62901c9889ae"
   integrity sha512-jyCETtSl3VMZMWeRo7iY1FL19ges1t55hMo5yaam4Jrsm5EPL89UQkoQRyiI+Yf4k8r2ZpdngkV8hr1lIdjb3Q==
 
-dcmjs@0.19.8:
+dcmjs@0.19.9:
-  version "0.19.8"
+  version "0.19.9"
-  resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.19.8.tgz#9be7471f8f2e20d4e09489b5f0c51dfa56621ec1"
+  resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.19.9.tgz#be500101b1f75a28ea9eb7ef845a8ed197355e76"
-  integrity sha512-po/GWh7pXF+diO/umpqOfpF0Kk7MzAmhFlscOR+KchCIZbN0pmt2npFT3p8jMii/FBre++k+8PIvFa/LKh0P2A==
+  integrity sha512-V+0tND+SPX5e7WFeLzeoooaTsZbiKmEP2i3AyERsojaXXfaDV5E+pta5IqId4Ok1yfRT5qfTFwLGstGT6nLplA==
   dependencies:
     "@babel/polyfill" "^7.8.3"
     "@babel/runtime" "^7.8.4"