chore(release): publish [skip ci]

- @ohif/extension-dicom-segmentation@0.7.14
 - @ohif/viewer@4.12.38

extensions/dicom-segmentation/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.
 
+## [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": "0.7.14",
   "description": "OHIF extension for viewing segmentations in the 2D MPR view",
   "author": "OHIF",
   "license": "MIT",

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

@@ -78,6 +78,7 @@ export default {
           onConfigurationChange={onConfigurationChangeHandler}
           onSelectedSegmentationChange={onSelectedSegmentationChangeHandler}
           onDisplaySetLoadFailure={onDisplaySetLoadFailureHandler}
+          servicesManager={servicesManager}
         />
       );
     };

extensions/vtk/CHANGELOG.md

@@ -3,6 +3,22 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [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
+
+
+
+
+
 ## [1.12.30](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.29...@ohif/extension-vtk@1.12.30) (2022-09-01)
 
 **Note:** Version bump only for package @ohif/extension-vtk

extensions/vtk/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-vtk",
-  "version": "1.12.30",
+  "version": "1.12.32",
   "description": "OHIF extension for VTK.js",
   "author": "OHIF",
   "license": "MIT",
@@ -53,7 +53,7 @@
     "react-vtkjs-viewport": "^0.14.4"
   },
   "devDependencies": {
-    "@ohif/core": "^2.16.25",
+    "@ohif/core": "^2.16.27",
     "@ohif/ui": "^1.10.10",
     "cornerstone-tools": "^6.0.6",
     "cornerstone-wado-image-loader": "^4.1.0",

platform/core/CHANGELOG.md

@@ -3,6 +3,22 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [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
+
+
+
+
+
 ## [2.16.25](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.24...@ohif/core@2.16.25) (2022-09-01)
 
 **Note:** Version bump only for package @ohif/core

platform/core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/core",
-  "version": "2.16.25",
+  "version": "2.16.27",
   "description": "Generic business logic for web-based medical imaging applications",
   "author": "OHIF Core Team",
   "license": "MIT",

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

@@ -12,8 +12,7 @@ const parseSCOORD3D = ({ servicesManager, displaySets }) => {
     ds =>
       ds.Modality !== 'SR' &&
       ds.Modality !== 'SEG' &&
-      ds.Modality !== 'RTSTRUCT' &&
+      ds.Modality !== 'RTSTRUCT'
-      ds.Modality !== 'RTDOSE'
   );
 
   imageDisplaySets.forEach(imageDisplaySet => {

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/classes/metadata/StudyMetadata.js

@@ -275,6 +275,8 @@ class StudyMetadata extends Metadata {
 
     const otherDisplaySets = allDisplaySets.filter(
       ds =>
+        ds &&
+        derivatedDisplaySet &&
         ds.displaySetInstanceUID !== derivatedDisplaySet.displaySetInstanceUID
     );
 

platform/core/src/studies/retrieveStudyMetadata.test.js

@@ -19,17 +19,4 @@ describe('retrieveStudyMetadata.js', () => {
 
     expect(callWithNoStudyInstanceUID).toThrow(Error);
   });
-
-  it('caches and returns the same promise for identical studyInstanceUIDs', () => {
-    const firstPromise = retrieveStudyMetadata(
-      fakeDicomWebServer,
-      'fake-study-instance-uid'
-    );
-    const secondPromise = retrieveStudyMetadata(
-      fakeDicomWebServer,
-      'fake-study-instance-uid'
-    );
-
-    expect(firstPromise).toBe(secondPromise);
-  });
 });

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

@@ -102,6 +102,35 @@ async function makeSOPInstance(server, study, instance) {
     SOPInstanceUID,
   } = naturalizedInstance;
 
+  const validate = string => {
+    let rgx = /[^.0-9]+/g;
+    return string.match(rgx);
+  };
+
+  if (StudyInstanceUID === undefined || validate(StudyInstanceUID)) {
+    const error =
+      'makeSOPInstance: StudyInstanceUID is not conforming with the UID (DICOM UI VR) character repertoire, skipping SOPInstance.';
+    console.error(error);
+
+    return;
+  }
+
+  if (SeriesInstanceUID === undefined || validate(SeriesInstanceUID)) {
+    const error =
+      'makeSOPInstance: SeriesInstanceUID is not conforming with the UID (DICOM UI VR) character repertoire, skipping SOPInstance.';
+    console.error(error);
+
+    return;
+  }
+
+  if (SOPInstanceUID === undefined || validate(SOPInstanceUID)) {
+    const error =
+      'makeSOPInstance: SOPInstanceUID is not conforming with the UID (DICOM UI VR) character repertoire, skipping SOPInstance.';
+    console.error(error);
+
+    return;
+  }
+
   let series = study.seriesMap[SeriesInstanceUID];
 
   if (!series) {

platform/core/src/utils/loadAndCacheDerivedDisplaySets.js

@@ -124,7 +124,7 @@ async function loadAndCacheDerivedDisplaySets(
                 title: 'DICOM Segmentation Loader',
                 message: error.message,
                 type: 'error',
-                autoClose: true,
+                autoClose: false,
               });
             };
 

platform/viewer/CHANGELOG.md

@@ -3,6 +3,41 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [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
+
+
+
+
+
 ## [4.12.34](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.33...@ohif/viewer@4.12.34) (2022-09-01)
 
 **Note:** Version bump only for package @ohif/viewer

platform/viewer/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/viewer",
-  "version": "4.12.34",
+  "version": "4.12.38",
   "description": "OHIF Viewer",
   "author": "OHIF Contributors",
   "license": "MIT",
@@ -47,16 +47,16 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.5.5",
-    "@ohif/core": "^2.16.25",
+    "@ohif/core": "^2.16.27",
     "@ohif/extension-cornerstone": "^2.12.14",
     "@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": "^0.7.14",
     "@ohif/extension-lesion-tracker": "^0.2.2",
-    "@ohif/extension-vtk": "^1.12.30",
+    "@ohif/extension-vtk": "^1.12.32",
     "@ohif/i18n": "^0.53.0",
     "@ohif/ui": "^1.10.10",
     "@tanem/react-nprogress": "^1.1.25",

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

@@ -25,7 +25,7 @@ const mapDispatchToProps = (dispatch, ownProps) => {
               title: 'DICOM Segmentation Loader',
               message: error.message,
               type: 'error',
-              autoClose: true,
+              autoClose: false,
             });
           };
 

platform/viewer/src/connectedComponents/Viewer.js

@@ -473,7 +473,7 @@ const _checkForDerivedDisplaySets = async function(displaySet, study) {
   let derivedDisplaySetsNumber = 0;
   if (
     displaySet.Modality &&
-    !['SEG', 'SR', 'RTSTRUCT', 'RTDOSE'].includes(displaySet.Modality)
+    !['SEG', 'SR', 'RTSTRUCT'].includes(displaySet.Modality)
   ) {
     const studyMetadata = studyMetadataManager.get(study.StudyInstanceUID);
 
@@ -612,7 +612,6 @@ const _isDisplaySetActive = function(
   if (
     displaySet.Modality !== 'SEG' &&
     displaySet.Modality !== 'RTSTRUCT' &&
-    displaySet.Modality !== 'RTDOSE' &&
     displaySet.Modality !== 'SR'
   ) {
     active = activeDisplaySetInstanceUID === displaySetInstanceUID;

platform/viewer/src/connectedComponents/ViewerMain.js

@@ -150,7 +150,7 @@ class ViewerMain extends Component {
             title: 'DICOM Segmentation Loader',
             message: error.message,
             type: 'error',
-            autoClose: true,
+            autoClose: false,
           });
         };