chore(release): publish [skip ci]

- @ohif/extension-dicom-segmentation@0.7.18
 - @ohif/viewer@4.12.47

extensions/cornerstone/CHANGELOG.md

@@ -3,6 +3,14 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [2.12.15](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.14...@ohif/extension-cornerstone@2.12.15) (2022-09-20)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
 ## [2.12.14](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.13...@ohif/extension-cornerstone@2.12.14) (2022-09-01)
 
 **Note:** Version bump only for package @ohif/extension-cornerstone

extensions/cornerstone/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone",
-  "version": "2.12.14",
+  "version": "2.12.15",
   "description": "OHIF extension for Cornerstone",
   "author": "OHIF",
   "license": "MIT",
@@ -35,7 +35,7 @@
     "cornerstone-core": "^2.6.1",
     "cornerstone-math": "^0.1.9",
     "cornerstone-tools": "^6.0.6",
-    "cornerstone-wado-image-loader": "^4.1.0",
+    "cornerstone-wado-image-loader": "^4.2.1",
     "dcmjs": "0.24.10",
     "dicom-parser": "^1.8.11",
     "hammerjs": "^2.0.8",

extensions/dicom-segmentation/CHANGELOG.md

@@ -3,6 +3,52 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [0.7.18](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.17...@ohif/extension-dicom-segmentation@0.7.18) (2022-12-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.7.17](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.16...@ohif/extension-dicom-segmentation@0.7.17) (2022-12-12)
+
+
+### Bug Fixes
+
+* [#2964](https://github.com/OHIF/Viewers/issues/2964) Reword message for segmentation error loading due to orientation tolerance ([#3017](https://github.com/OHIF/Viewers/issues/3017)) ([597ac11](https://github.com/OHIF/Viewers/commit/597ac11c4daee1b1e14148804551e20611cfef08))
+
+
+
+
+
+## [0.7.16](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.15...@ohif/extension-dicom-segmentation@0.7.16) (2022-10-28)
+
+
+### Bug Fixes
+
+* [#2964](https://github.com/OHIF/Viewers/issues/2964) Update message for segmentation error loading due to orientation tolerance ([#2982](https://github.com/OHIF/Viewers/issues/2982)) ([545161d](https://github.com/OHIF/Viewers/commit/545161d5e8d92bb6652f17dc24a36dac8aa7b3a4))
+
+
+
+
+
+## [0.7.15](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.14...@ohif/extension-dicom-segmentation@0.7.15) (2022-09-19)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.7.14](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.13...@ohif/extension-dicom-segmentation@0.7.14) (2022-09-12)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
 ## [0.7.13](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.12...@ohif/extension-dicom-segmentation@0.7.13) (2022-09-01)
 
 **Note:** Version bump only for package @ohif/extension-dicom-segmentation

extensions/dicom-segmentation/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-segmentation",
-  "version": "0.7.13",
+  "version": "0.7.18",
   "description": "OHIF extension for viewing segmentations in the 2D MPR view",
   "author": "OHIF",
   "license": "MIT",

extensions/dicom-segmentation/src/components/SegmentItem/SegmentItem.css

@@ -62,8 +62,8 @@
 }
 
 .dcmseg-segment-item .segment-label span {
-  overflow-wrap: normal;
+  overflow-wrap: break-word;
-  white-space: nowrap;
+  white-space: normal;
   overflow: hidden;
   max-width: calc(100% - 40px); /* calc(100% - 50px); 20px = eye icon */
   text-overflow: ellipsis;
@@ -71,6 +71,7 @@
 
 .dcmseg-segment-item .segment-label .eye-icon {
   cursor: pointer;
+  min-width: 20px;
   color: var(--active-color);
 }
 

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

@@ -36,6 +36,7 @@ const { studyMetadataManager } = utils;
  * @param {Function} props.onConfigurationChange - Configuration change handler
  * @param {Function} props.activeContexts - List of active application contexts
  * @param {Function} props.contexts - List of available application contexts
+ * @param {Function} props.servicesManager - Services manager
  * @returns component
  */
 const SegmentationPanel = ({
@@ -50,6 +51,7 @@ const SegmentationPanel = ({
   onSelectedSegmentationChange,
   activeContexts = [],
   contexts = {},
+  servicesManager,
 }) => {
   const isVTK = () => activeContexts.includes(contexts.VTK);
   const isCornerstone = () => activeContexts.includes(contexts.CORNERSTONE);
@@ -59,6 +61,9 @@ const SegmentationPanel = ({
    * store with context to make these kind of things less blurry.
    */
   const { configuration } = cornerstoneTools.getModule('segmentation');
+  if (configuration.segsTolerance === undefined) {
+    configuration.segsTolerance = 1e-2;
+  }
   const DEFAULT_BRUSH_RADIUS = configuration.radius || 10;
 
   /*
@@ -87,6 +92,25 @@ const SegmentationPanel = ({
     return studyMetadata.getFirstImageId(displaySetInstanceUID);
   };
 
+  const getAllSegDisplaySets = () => {
+    const { StudyInstanceUID } = getActiveViewport();
+    const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
+    return studyMetadata.getDerivedDatasets({
+      Modality: 'SEG',
+    });
+  };
+
+  const updateSegDisplaySetsTolerance = tolerance => {
+    const segDisplaySets = getAllSegDisplaySets();
+    segDisplaySets.forEach(segDisplaySet => {
+      // update tol value
+      segDisplaySet.tolerance = tolerance;
+      // reset load flags for allowing retry for seg parsing.
+      segDisplaySet.isLoaded = false;
+      segDisplaySet.loadError = false;
+    });
+  };
+
   const getActiveLabelMaps3D = () => {
     const { labelmaps3D, activeLabelmapIndex } = getBrushStackState();
     return labelmaps3D[activeLabelmapIndex];
@@ -598,7 +622,9 @@ const SegmentationPanel = ({
     configuration.outlineWidth = newConfiguration.outlineWidth;
     configuration.fillAlphaInactive = newConfiguration.fillAlphaInactive;
     configuration.outlineAlphaInactive = newConfiguration.outlineAlphaInactive;
+    configuration.segsTolerance = newConfiguration.segsTolerance;
     onConfigurationChange(newConfiguration);
+    updateSegDisplaySetsTolerance(configuration.segsTolerance);
     refreshViewports();
   };
 
@@ -647,6 +673,7 @@ const SegmentationPanel = ({
         configuration={configuration}
         onBack={() => setState(state => ({ ...state, showSettings: false }))}
         onChange={updateConfiguration}
+        servicesManager={servicesManager}
       />
     );
   } else {

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

@@ -4,7 +4,7 @@ import { Range } from '@ohif/ui';
 
 import './SegmentationSettings.css';
 
-const SegmentationSettings = ({ configuration, onBack, onChange, disabledFields = [] }) => {
+const SegmentationSettings = ({ configuration, onBack, onChange, servicesManager, disabledFields = [] }) => {
   const [state, setState] = useState({
     renderFill: configuration.renderFill,
     renderOutline: configuration.renderOutline,
@@ -13,7 +13,8 @@ const SegmentationSettings = ({ configuration, onBack, onChange, disabledFields
     outlineAlpha: configuration.outlineAlpha,
     outlineWidth: configuration.outlineWidth,
     fillAlphaInactive: configuration.fillAlphaInactive,
-    outlineAlphaInactive: configuration.outlineAlphaInactive
+    outlineAlphaInactive: configuration.outlineAlphaInactive,
+    segsTolerance: configuration.segsTolerance,
   });
 
   useEffect(() => {
@@ -133,6 +134,40 @@ const SegmentationSettings = ({ configuration, onBack, onChange, disabledFields
           )}
         </div>
       )}
+      <div className="settings-group" style={{ marginBottom: 15 }}>
+        <label style={{ margin: '0 15px' }}>
+          Tolerance:
+          <input
+            style={{ margin: '0 15px' }}
+            label="Tolerance"
+            onKeyPress={event => {
+              const validate = string => {
+                let rgx = /[^-.e0-9]+/g;
+                return string.match(rgx);
+              };
+
+              if (validate(event.key)) {
+                event.preventDefault();
+              }
+            }}
+            onChange={event => {
+              save('segsTolerance', event.target.value);
+
+              const { UINotificationService, LoggerService } = servicesManager.services;
+              const error = new Error('Segmentation loader tolerance changed. This operation can potentially generate errors in the Segmentation parsing.');
+              LoggerService.error({ error, message: error.message });
+              UINotificationService.show({
+                title: 'Segmentation panel',
+                message: error.message,
+                type: 'warning',
+                autoClose: true,
+              });
+              }
+            }
+            value={state.segsTolerance}
+          />
+        </label>
+      </div>
     </div>
   );
 };
@@ -169,11 +204,12 @@ SegmentationSettings.propTypes = {
     renderFill: PropTypes.bool.isRequired,
     renderOutline: PropTypes.bool.isRequired,
     shouldRenderInactiveLabelmaps: PropTypes.bool.isRequired,
-    fillAlpha: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired, /* TODO: why fillAlpha is string? */
+    fillAlpha: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired,
-    outlineAlpha: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired, /* TODO: why fillAlpha is string? */
+    outlineAlpha: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired,
     outlineWidth: PropTypes.number.isRequired,
-    fillAlphaInactive: PropTypes.number.isRequired,
+    fillAlphaInactive: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired,
-    outlineAlphaInactive: PropTypes.number.isRequired,
+    outlineAlphaInactive: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired,
+    segsTolerance: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired,
   }).isRequired,
   onBack: PropTypes.func.isRequired,
   onChange: PropTypes.func.isRequired,

extensions/dicom-segmentation/src/getOHIFDicomSegSopClassHandler.js

@@ -62,6 +62,7 @@ export default function getSopClassHandlerModule({ servicesManager }) {
         SeriesNumber,
         SeriesDescription,
         metadata,
+        tolerance: 1e-2,
       };
 
       segDisplaySet.getSourceDisplaySet = function(
@@ -93,7 +94,7 @@ export default function getSopClassHandlerModule({ servicesManager }) {
           referencedDisplaySet.SeriesInstanceUID
         );
 
-        const results = await _parseSeg(segArrayBuffer, imageIds);
+        const results = await _parseSeg(segArrayBuffer, imageIds, segDisplaySet.tolerance);
         if (results === undefined) {
           return;
         }
@@ -149,10 +150,13 @@ export default function getSopClassHandlerModule({ servicesManager }) {
   };
 }
 
-function _parseSeg(arrayBuffer, imageIds) {
+function _parseSeg(
-  const skipOverlapping = false;
+  arrayBuffer,
-  const tolerance = 1e-2;
+  imageIds,
-  const cornerstoneToolsVersion = 4;
+  tolerance = 1e-2,
+  skipOverlapping = false,
+  cornerstoneToolsVersion = 4
+) {
   return dcmjs.adapters.Cornerstone.Segmentation.generateToolState(
     imageIds,
     arrayBuffer,

extensions/dicom-segmentation/src/index.js

@@ -32,12 +32,18 @@ export default {
 
     const ExtendedSegmentationPanel = props => {
       const { activeContexts } = api.hooks.useAppContext();
-
       const onDisplaySetLoadFailureHandler = error => {
-        LoggerService.error({ error, message: error.message });
+        const message =
+          error.message.includes('orthogonal') ||
+          error.message.includes('oblique')
+            ? 'The segmentation has been detected as non coplanar,\
+              If you really think it is coplanar,\
+              please adjust the tolerance in the segmentation panel settings (at your own peril!)'
+            : error.message;
+        LoggerService.error({ error, message });
         UINotificationService.show({
           title: 'DICOM Segmentation Loader',
-          message: error.message,
+          message,
           type: 'error',
           autoClose: false,
         });
@@ -78,6 +84,7 @@ export default {
           onConfigurationChange={onConfigurationChangeHandler}
           onSelectedSegmentationChange={onSelectedSegmentationChangeHandler}
           onDisplaySetLoadFailure={onDisplaySetLoadFailureHandler}
+          servicesManager={servicesManager}
         />
       );
     };

extensions/vtk/CHANGELOG.md

@@ -3,6 +3,78 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [1.12.40](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.39...@ohif/extension-vtk@1.12.40) (2022-12-12)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.39](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.38...@ohif/extension-vtk@1.12.39) (2022-11-12)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.38](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.37...@ohif/extension-vtk@1.12.38) (2022-11-02)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.37](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.36...@ohif/extension-vtk@1.12.37) (2022-10-28)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.36](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.35...@ohif/extension-vtk@1.12.36) (2022-10-25)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.35](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.34...@ohif/extension-vtk@1.12.35) (2022-09-26)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.34](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.33...@ohif/extension-vtk@1.12.34) (2022-09-20)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.33](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.32...@ohif/extension-vtk@1.12.33) (2022-09-19)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.32](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.31...@ohif/extension-vtk@1.12.32) (2022-09-12)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
 ## [1.12.31](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.30...@ohif/extension-vtk@1.12.31) (2022-09-02)
 
 **Note:** Version bump only for package @ohif/extension-vtk

extensions/vtk/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-vtk",
-  "version": "1.12.31",
+  "version": "1.12.40",
   "description": "OHIF extension for VTK.js",
   "author": "OHIF",
   "license": "MIT",
@@ -34,7 +34,7 @@
     "@ohif/ui": "^0.50.0",
     "cornerstone-core": "^2.6.1",
     "cornerstone-tools": "^6.0.6",
-    "cornerstone-wado-image-loader": "^4.1.0",
+    "cornerstone-wado-image-loader": "^4.2.1",
     "dcmjs": "0.24.10",
     "dicom-parser": "^1.8.11",
     "i18next": "^17.0.3",
@@ -50,13 +50,13 @@
   "dependencies": {
     "@babel/runtime": "^7.5.5",
     "lodash.throttle": "^4.1.1",
-    "react-vtkjs-viewport": "^0.14.4"
+    "react-vtkjs-viewport": "^0.14.5"
   },
   "devDependencies": {
-    "@ohif/core": "^2.16.26",
+    "@ohif/core": "^2.16.34",
     "@ohif/ui": "^1.10.10",
     "cornerstone-tools": "^6.0.6",
-    "cornerstone-wado-image-loader": "^4.1.0",
+    "cornerstone-wado-image-loader": "^4.2.1",
     "dicom-parser": "^1.8.11",
     "gh-pages": "^2.0.1",
     "i18next": "^17.0.3",

platform/core/CHANGELOG.md

@@ -3,6 +3,82 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [2.16.34](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.33...@ohif/core@2.16.34) (2022-12-12)
+
+
+### Bug Fixes
+
+* [#2964](https://github.com/OHIF/Viewers/issues/2964) Reword message for segmentation error loading due to orientation tolerance ([#3017](https://github.com/OHIF/Viewers/issues/3017)) ([597ac11](https://github.com/OHIF/Viewers/commit/597ac11c4daee1b1e14148804551e20611cfef08))
+
+
+
+
+
+## [2.16.33](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.32...@ohif/core@2.16.33) (2022-11-12)
+
+
+### Bug Fixes
+
+* handle missing ReferencedInstanceSequence attribute ([#2786](https://github.com/OHIF/Viewers/issues/2786)) ([4473807](https://github.com/OHIF/Viewers/commit/44738078dbd8dc6b27d2d669e25417e37371f48d))
+
+
+
+
+
+## [2.16.32](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.31...@ohif/core@2.16.32) (2022-11-02)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.16.31](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.30...@ohif/core@2.16.31) (2022-10-28)
+
+
+### Bug Fixes
+
+* [#2964](https://github.com/OHIF/Viewers/issues/2964) Update message for segmentation error loading due to orientation tolerance ([#2982](https://github.com/OHIF/Viewers/issues/2982)) ([545161d](https://github.com/OHIF/Viewers/commit/545161d5e8d92bb6652f17dc24a36dac8aa7b3a4))
+
+
+
+
+
+## [2.16.30](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.29...@ohif/core@2.16.30) (2022-10-25)
+
+
+### Bug Fixes
+
+* 2965 Correct Parsing Logic for Qualitative Instance Level SR ([#2972](https://github.com/OHIF/Viewers/issues/2972)) ([f7db74a](https://github.com/OHIF/Viewers/commit/f7db74a84376598065b6fa2c00cd5735415ff651))
+
+
+
+
+
+## [2.16.29](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.28...@ohif/core@2.16.29) (2022-09-20)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.16.28](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.27...@ohif/core@2.16.28) (2022-09-19)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.16.27](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.26...@ohif/core@2.16.27) (2022-09-12)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
 ## [2.16.26](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.25...@ohif/core@2.16.26) (2022-09-02)
 
 **Note:** Version bump only for package @ohif/core

platform/core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/core",
-  "version": "2.16.26",
+  "version": "2.16.34",
   "description": "Generic business logic for web-based medical imaging applications",
   "author": "OHIF Core Team",
   "license": "MIT",
@@ -33,7 +33,7 @@
   "peerDependencies": {
     "cornerstone-core": "^2.6.1",
     "cornerstone-tools": "^6.0.6",
-    "cornerstone-wado-image-loader": "^4.1.0",
+    "cornerstone-wado-image-loader": "^4.2.1",
     "dicom-parser": "^1.8.11"
   },
   "dependencies": {

platform/core/src/DICOMSR/SCOORD3D/parseSCOORD3D.js

@@ -1,6 +1,5 @@
 import { ImageSet } from '../../classes';
 import getMeasurements from './utils/getMeasurements';
-import getReferencedImagesList from './utils/getReferencedImagesList';
 import isRehydratable from './utils/isRehydratable';
 import addMeasurement from './utils/addMeasurement';
 
@@ -27,7 +26,6 @@ const parseSCOORD3D = ({ servicesManager, displaySets }) => {
 
     const { ContentSequence } = firstInstance;
 
-    srDisplaySet.referencedImages = getReferencedImagesList(ContentSequence);
     srDisplaySet.measurements = getMeasurements(ContentSequence);
     const mappings = MeasurementService.getSourceMappings(
       'CornerstoneTools',

platform/core/src/DICOMSR/SCOORD3D/utils/getReferencedImagesList.js

@@ -1,43 +0,0 @@
-import getSequenceAsArray from './getSequenceAsArray';
-import { CodeNameCodeSequenceValues } from '../enums';
-
-const getReferencedImagesList = ImagingMeasurementReportContentSequence => {
-  const referencedImages = [];
-
-  const ImageLibrary = ImagingMeasurementReportContentSequence.find(
-    item =>
-      item.ConceptNameCodeSequence.CodeValue ===
-      CodeNameCodeSequenceValues.ImageLibrary
-  );
-
-  if (!ImageLibrary.ContentSequence) {
-    return referencedImages;
-  }
-
-  const ImageLibraryGroup = getSequenceAsArray(
-    ImageLibrary.ContentSequence
-  ).find(
-    item =>
-      item.ConceptNameCodeSequence.CodeValue ===
-      CodeNameCodeSequenceValues.ImageLibraryGroup
-  );
-
-  getSequenceAsArray(ImageLibraryGroup.ContentSequence).forEach(item => {
-    const { ReferencedSOPSequence } = item;
-    if (ReferencedSOPSequence) {
-      const {
-        ReferencedSOPClassUID,
-        ReferencedSOPInstanceUID,
-      } = ReferencedSOPSequence;
-
-      referencedImages.push({
-        ReferencedSOPClassUID,
-        ReferencedSOPInstanceUID,
-      });
-    }
-  });
-
-  return referencedImages;
-};
-
-export default getReferencedImagesList;

platform/core/src/DICOMSR/parseDicomStructuredReport.js

@@ -21,16 +21,32 @@ const parseDicomStructuredReport = (
   displaySets,
   external
 ) => {
-  if (external && external.servicesManager) {
-    parseSCOORD3D({ servicesManager: external.servicesManager, displaySets });
-  }
-
   // Get the dicom data as an Object
   const dicomData = dcmjs.data.DicomMessage.readFile(part10SRArrayBuffer);
   const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
     dicomData.dict
   );
 
+  const {
+    LoggerService,
+    UINotificationService,
+  } = external.servicesManager.services;
+  if (external && external.servicesManager) {
+    try {
+      parseSCOORD3D({ servicesManager: external.servicesManager, displaySets });
+    } catch (error) {
+      const seriesDescription = dataset.SeriesDescription || '';
+      LoggerService.error({ error, message: error.message });
+      UINotificationService.show({
+        title: `Failed to parse ${seriesDescription} SR display set`,
+        message: error.message,
+        type: 'error',
+        autoClose: false,
+      });
+      return;
+    }
+  }
+
   const { MeasurementReport } = dcmjs.adapters.Cornerstone;
 
   let storedMeasurementByToolType;
@@ -38,11 +54,12 @@ const parseDicomStructuredReport = (
     storedMeasurementByToolType = MeasurementReport.generateToolState(dataset);
   } catch (error) {
     const seriesDescription = dataset.SeriesDescription || '';
-    LogManager.publish(LogManager.EVENTS.OnLog, {
+    LoggerService.error({ error, message: error.message });
+    UINotificationService.show({
       title: `Failed to parse ${seriesDescription} measurement report`,
-      type: 'warning',
+      message: error.message,
-      message: error.message || '',
+      type: 'error',
-      notify: true,
+      autoClose: false,
     });
     return;
   }

platform/core/src/classes/HotkeysManager.js

@@ -67,12 +67,13 @@ export class HotkeysManager {
         UINotificationService,
         LoggerService,
       } = this._servicesManager.services;
-      const message = 'Erro while setting hotkeys';
+      const message = 'Error while setting hotkeys';
       LoggerService.error({ error, message });
       UINotificationService.show({
         title: 'Hotkeys Manager',
         message,
         type: 'error',
+        autoClose: false,
       });
     }
   }

platform/core/src/studies/services/wado/getReferencedSeriesSequence.js

@@ -21,16 +21,18 @@ const getReferencedSeriesSequence = instance => {
       const referencedInstanceSequenceRaw = referencedSeries['0008114A'];
       const referencedInstanceSequence = [];
 
-      referencedInstanceSequenceRaw.Value.forEach(referencedInstance => {
+      if (referencedInstanceSequenceRaw) {
-        referencedInstanceSequence.push({
+        referencedInstanceSequenceRaw.Value.forEach(referencedInstance => {
-          referencedSOPClassUID: DICOMWeb.getString(
+          referencedInstanceSequence.push({
-            referencedInstance['00081150']
+            referencedSOPClassUID: DICOMWeb.getString(
-          ),
+              referencedInstance['00081150']
-          referencedSOPInstanceUID: DICOMWeb.getString(
+            ),
-            referencedInstance['00081155']
+            referencedSOPInstanceUID: DICOMWeb.getString(
-          ),
+              referencedInstance['00081155']
+            ),
+          });
         });
-      });
+      }
 
       referencedSeriesSequence.push({
         referencedSeriesInstanceUID,

platform/core/src/utils/loadAndCacheDerivedDisplaySets.js

@@ -119,12 +119,20 @@ async function loadAndCacheDerivedDisplaySets(
         ) {
           if (recentDisplaySet.Modality === 'SEG' && logger) {
             const onDisplaySetLoadFailureHandler = error => {
-              logger.error({ error, message: error.message });
+              const message =
+                error.message.includes('orthogonal') ||
+                error.message.includes('oblique')
+                  ? 'The segmentation has been detected as non coplanar,\
+                    If you really think it is coplanar,\
+                    please adjust the tolerance in the segmentation panel settings (at your own peril!)'
+                  : error.message;
+
+              logger.error({ error, message });
               snackbar.show({
                 title: 'DICOM Segmentation Loader',
-                message: error.message,
+                message,
                 type: 'error',
-                autoClose: true,
+                autoClose: false,
               });
             };
 

platform/viewer/CHANGELOG.md

@@ -3,6 +3,111 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [4.12.47](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.46...@ohif/viewer@4.12.47) (2022-12-21)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
+## [4.12.46](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.45...@ohif/viewer@4.12.46) (2022-12-12)
+
+
+### Bug Fixes
+
+* [#2964](https://github.com/OHIF/Viewers/issues/2964) Reword message for segmentation error loading due to orientation tolerance ([#3017](https://github.com/OHIF/Viewers/issues/3017)) ([597ac11](https://github.com/OHIF/Viewers/commit/597ac11c4daee1b1e14148804551e20611cfef08))
+
+
+
+
+
+## [4.12.45](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.44...@ohif/viewer@4.12.45) (2022-11-12)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
+## [4.12.44](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.43...@ohif/viewer@4.12.44) (2022-11-02)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
+## [4.12.43](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.42...@ohif/viewer@4.12.43) (2022-10-28)
+
+
+### Bug Fixes
+
+* [#2964](https://github.com/OHIF/Viewers/issues/2964) Update message for segmentation error loading due to orientation tolerance ([#2982](https://github.com/OHIF/Viewers/issues/2982)) ([545161d](https://github.com/OHIF/Viewers/commit/545161d5e8d92bb6652f17dc24a36dac8aa7b3a4))
+
+
+
+
+
+## [4.12.42](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.41...@ohif/viewer@4.12.42) (2022-10-25)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
+## [4.12.41](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.40...@ohif/viewer@4.12.41) (2022-09-26)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
+## [4.12.40](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.39...@ohif/viewer@4.12.40) (2022-09-20)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
+## [4.12.39](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.38...@ohif/viewer@4.12.39) (2022-09-19)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
+## [4.12.38](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.37...@ohif/viewer@4.12.38) (2022-09-12)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
+## [4.12.37](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.36...@ohif/viewer@4.12.37) (2022-09-12)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
+## [4.12.36](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.35...@ohif/viewer@4.12.36) (2022-09-08)
+
+
+### Bug Fixes
+
+* hotkey page up/down did not work ([#2910](https://github.com/OHIF/Viewers/issues/2910)) ([d74ad37](https://github.com/OHIF/Viewers/commit/d74ad370e091c8af2d93ec35f688c4ef902bab2b))
+
+
+
+
+
 ## [4.12.35](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.34...@ohif/viewer@4.12.35) (2022-09-02)
 
 **Note:** Version bump only for package @ohif/viewer

platform/viewer/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/viewer",
-  "version": "4.12.35",
+  "version": "4.12.47",
   "description": "OHIF Viewer",
   "author": "OHIF Contributors",
   "license": "MIT",
@@ -47,16 +47,16 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.5.5",
-    "@ohif/core": "^2.16.26",
+    "@ohif/core": "^2.16.34",
-    "@ohif/extension-cornerstone": "^2.12.14",
+    "@ohif/extension-cornerstone": "^2.12.15",
     "@ohif/extension-debugging": "^0.3.3",
     "@ohif/extension-dicom-html": "^1.3.23",
     "@ohif/extension-dicom-microscopy": "^0.52.0",
     "@ohif/extension-dicom-pdf": "^1.1.2",
     "@ohif/extension-dicom-rt": "^0.7.13",
-    "@ohif/extension-dicom-segmentation": "^0.7.13",
+    "@ohif/extension-dicom-segmentation": "^0.7.18",
     "@ohif/extension-lesion-tracker": "^0.2.2",
-    "@ohif/extension-vtk": "^1.12.31",
+    "@ohif/extension-vtk": "^1.12.40",
     "@ohif/i18n": "^0.53.0",
     "@ohif/ui": "^1.10.10",
     "@tanem/react-nprogress": "^1.1.25",
@@ -65,7 +65,7 @@
     "cornerstone-core": "^2.6.1",
     "cornerstone-math": "^0.1.9",
     "cornerstone-tools": "^6.0.6",
-    "cornerstone-wado-image-loader": "^4.1.0",
+    "cornerstone-wado-image-loader": "^4.2.1",
     "dcmjs": "0.24.10",
     "dicom-parser": "^1.8.11",
     "dicomweb-client": "^0.8.3",

platform/viewer/src/appExtensions/GenericViewerCommands/commandsModule.js

@@ -1,4 +1,4 @@
-import { redux } from '@ohif/core';
+import { redux, utils } from '@ohif/core';
 import store from './../../store';
 
 const commandsModule = ({ commandsManager }) => {

platform/viewer/src/connectedComponents/ConnectedStudyBrowser.js

@@ -20,12 +20,20 @@ const mapDispatchToProps = (dispatch, ownProps) => {
         const { Modality } = displaySet;
         if (Modality === 'SEG' && servicesManager) {
           const onDisplaySetLoadFailureHandler = error => {
-            LoggerService.error({ error, message: error.message });
+            const message =
+              error.message.includes('orthogonal') ||
+              error.message.includes('oblique')
+                ? 'The segmentation has been detected as non coplanar,\
+                If you really think it is coplanar,\
+                please adjust the tolerance in the segmentation panel settings (at your own peril!)'
+                : error.message;
+
+            LoggerService.error({ error, message });
             UINotificationService.show({
               title: 'DICOM Segmentation Loader',
-              message: error.message,
+              message,
               type: 'error',
-              autoClose: true,
+              autoClose: false,
             });
           };
 

platform/viewer/src/connectedComponents/ViewerMain.js

@@ -145,12 +145,19 @@ class ViewerMain extends Component {
       const { Modality } = displaySet;
       if (Modality === 'SEG' && servicesManager) {
         const onDisplaySetLoadFailureHandler = error => {
-          LoggerService.error({ error, message: error.message });
+          const message =
+            error.message.includes('orthogonal') ||
+            error.message.includes('oblique')
+              ? 'The segmentation has been detected as non coplanar,\
+              If you really think it is coplanar,\
+              please adjust the tolerance in the segmentation panel settings (at your own peril!)'
+              : error.message;
+          LoggerService.error({ error, message });
           UINotificationService.show({
             title: 'DICOM Segmentation Loader',
-            message: error.message,
+            message,
             type: 'error',
-            autoClose: true,
+            autoClose: false,
           });
         };
 

runtime.txt

@@ -1 +1 @@
-3.7
+3.8

yarn.lock

@@ -4242,13 +4242,13 @@ capture-exit@^2.0.0:
     rsvp "^4.8.4"
 
 cardboard-vr-display@^1.0.15:
-  version "1.0.16"
+  version "1.0.19"
-  resolved "https://registry.yarnpkg.com/cardboard-vr-display/-/cardboard-vr-display-1.0.16.tgz#f91e2798e8fb70a348599638c6742c72dfeadabc"
+  resolved "https://registry.yarnpkg.com/cardboard-vr-display/-/cardboard-vr-display-1.0.19.tgz#81dcde1804b329b8228b757ac00e1fd2afa9d748"
-  integrity sha512-GFBWPMH/ixy4Ji014BAO1ryddGHphtJlA8gUR6UdKsOpPjUQukCKpgsx2XIJ5oBlqXnDQOcLVRqBWyuvTI32jQ==
+  integrity sha512-+MjcnWKAkb95p68elqZLDPzoiF/dGncQilLGvPBM5ZorABp/ao3lCs7nnRcYBckmuNkg1V/5rdGDKoUaCVsHzQ==
   dependencies:
     gl-preserve-state "^1.0.0"
     nosleep.js "^0.7.0"
-    webvr-polyfill-dpdb "^1.0.11"
+    webvr-polyfill-dpdb "^1.0.17"
 
 cardinal@^2.1.1:
   version "2.1.1"
@@ -5117,10 +5117,10 @@ cornerstone-tools@^6.0.6:
     "@babel/runtime" "7.1.2"
     cornerstone-math "0.1.9"
 
-cornerstone-wado-image-loader@^4.1.0:
+cornerstone-wado-image-loader@^4.2.1:
-  version "4.1.0"
+  version "4.2.1"
-  resolved "https://registry.yarnpkg.com/cornerstone-wado-image-loader/-/cornerstone-wado-image-loader-4.1.0.tgz#a85c206eb23e188181ed3f1dcf3ec715e65efcb4"
+  resolved "https://registry.yarnpkg.com/cornerstone-wado-image-loader/-/cornerstone-wado-image-loader-4.2.1.tgz#ee37797fe8970dcb7e438a6d87b710e817066100"
-  integrity sha512-QRoMqBE5xEc1Jttg3eH6RB4jFY2aIEjd9rcbvJszefl0isow+JwcLv2kh1xkSvqGfHGozcz+F4mrORyTNNLuFQ==
+  integrity sha512-nRu+6GfHFERpZLytH/SCfymODCz1SC1NKRv/xn02pr3PEkzU6fvKI76sSxSFOozxDsYljupTRNi/qGMprfdBHA==
   dependencies:
     "@cornerstonejs/codec-charls" "^0.1.1"
     "@cornerstonejs/codec-libjpeg-turbo-8bit" "^0.0.7"
@@ -11208,7 +11208,7 @@ normalize-url@^3.0.0, normalize-url@^3.3.0:
 nosleep.js@^0.7.0:
   version "0.7.0"
   resolved "https://registry.yarnpkg.com/nosleep.js/-/nosleep.js-0.7.0.tgz#cfd919c25523ca0d0f4a69fb3305c083adaee289"
-  integrity sha1-z9kZwlUjyg0PSmn7MwXAg62u4ok=
+  integrity sha512-Z4B1HgvzR+en62ghwZf6BwAR6x4/pjezsiMcbF9KMLh7xoscpoYhaSXfY3lLkqC68AtW+/qLJ1lzvBIj0FGaTA==
 
 npm-bundled@^1.0.1:
   version "1.0.6"
@@ -13519,10 +13519,10 @@ react-transition-group@^4.1.1:
     loose-envify "^1.4.0"
     prop-types "^15.6.2"
 
-react-vtkjs-viewport@^0.14.4:
+react-vtkjs-viewport@^0.14.5:
-  version "0.14.4"
+  version "0.14.5"
-  resolved "https://registry.yarnpkg.com/react-vtkjs-viewport/-/react-vtkjs-viewport-0.14.4.tgz#8cc5a49738fff3fee75ead61c98307bc24710151"
+  resolved "https://registry.yarnpkg.com/react-vtkjs-viewport/-/react-vtkjs-viewport-0.14.5.tgz#95cda594370e557d43aa966392ed92926e6c53c1"
-  integrity sha512-WKU87iqH6AQ1R8zp1hUXU4hsGwfbkkoUhzSCjbBGZ9Di0ELYNx/xY9DtdmgsKOU5Y5Arp5+VQW/ziFsq2KTcTA==
+  integrity sha512-DE+Ytub6veya3DTvItJdZhkTR8MppoLkrq57qhN9vd2meykeS1fZp9cDyWmq92dJ7IHSuS5FPof8ucsae9ci5w==
   dependencies:
     date-fns "^2.2.1"
     gl-matrix "^3.1.0"
@@ -14499,7 +14499,7 @@ scriptjs@^2.5.9:
 seedrandom@2.4.3:
   version "2.4.3"
   resolved "https://registry.yarnpkg.com/seedrandom/-/seedrandom-2.4.3.tgz#2438504dad33917314bff18ac4d794f16d6aaecc"
-  integrity sha1-JDhQTa0zkXMUv/GKxNeU8W1qrsw=
+  integrity sha512-2CkZ9Wn2dS4mMUWQaXLsOAfGD+irMlLEeSP3cMxpGbgyOOzJGFa+MWCOMTOCMyZinHRPxyOj/S/C57li/1to6Q==
 
 seedrandom@^3.0.5:
   version "3.0.5"
@@ -14715,7 +14715,7 @@ shebang-regex@^3.0.0:
 shelljs@0.7.8:
   version "0.7.8"
   resolved "https://registry.yarnpkg.com/shelljs/-/shelljs-0.7.8.tgz#decbcf874b0d1e5fb72e14b164a9683048e9acb3"
-  integrity sha1-3svPh0sNHl+3LhSxZKloMEjprLM=
+  integrity sha512-/YF5Uk8hcwi7ima04ppkbA4RaRMdPMBfwAvAf8sufYOxsJRtbdoBsT8vGvlb+799BrlGdYrd+oczIA2eN2JdWA==
   dependencies:
     glob "^7.0.0"
     interpret "^1.0.0"
@@ -16662,10 +16662,10 @@ websocket-extensions@>=0.1.1:
   resolved "https://registry.yarnpkg.com/websocket-extensions/-/websocket-extensions-0.1.3.tgz#5d2ff22977003ec687a4b87073dfbbac146ccf29"
   integrity sha512-nqHUnMXmBzT0w570r2JpJxfiSD1IzoI+HGVdd3aZ0yNi3ngvQ4jv1dtHt5VGxfI2yj5yqImPhOK4vmIh2xMbGg==
 
-webvr-polyfill-dpdb@^1.0.11:
+webvr-polyfill-dpdb@^1.0.17:
-  version "1.0.16"
+  version "1.0.18"
-  resolved "https://registry.yarnpkg.com/webvr-polyfill-dpdb/-/webvr-polyfill-dpdb-1.0.16.tgz#7f2cf88460c002a5f10ff69b2bf3a5663e0ad9dd"
+  resolved "https://registry.yarnpkg.com/webvr-polyfill-dpdb/-/webvr-polyfill-dpdb-1.0.18.tgz#258484ce06b057bf18898acc911bd173847bce11"
-  integrity sha512-FCciTtPhwkYYHGL0K67G8k7ZnNVqnEx3u4NVHLJ0+Ya6f2VTZUl/GJpaEo1Id2pBP/2l0RYZ3IGZE4Pe8fRalg==
+  integrity sha512-O0S1ZGEWyPvyZEkS2VbyV7mtir/NM9MNK3EuhbHPoJ8EHTky2pTXehjIl+IiDPr+Lldgx129QGt3NGly7rwRPw==
 
 webvr-polyfill@0.10.8:
   version "0.10.8"