fix: OHIF 3.9 Recovery 3 (#4697)

Co-authored-by: Ibrahim <93064150+IbrahimCSAE@users.noreply.github.com>
Co-authored-by: Bill Wallace <wayfarer3130@gmail.com>
Co-authored-by: Chao Sui <chao.sui@curvebeamai.com>
Co-authored-by: Jaseel-trenser <108331536+Jaseel-trenser@users.noreply.github.com>

addOns/externals/devDependencies/package.json

@@ -68,7 +68,7 @@
     "prettier-plugin-tailwindcss": "^0.5.4",
     "react-refresh": "^0.14.2",
     "semver": "^7.5.1",
-    "serve": "^14.2.0",
+    "serve": "^14.2.4",
     "shader-loader": "^1.3.1",
     "shx": "^0.3.3",
     "source-map-loader": "^4.0.1",

extensions/cornerstone-dicom-pmap/src/viewports/OHIFCornerstonePMAPViewport.tsx

@@ -97,6 +97,7 @@ function OHIFCornerstonePMAPViewport(props: withAppTypes) {
           viewportType: 'volume',
           orientation: viewportOptions.orientation,
           viewportId: viewportOptions.viewportId,
+          presentationIds: viewportOptions.presentationIds,
         }}
         displaySetOptions={[{}, pmapDisplaySetOptions]}
       ></Component>

extensions/cornerstone-dicom-rt/src/loadRTStruct.js

@@ -126,6 +126,7 @@ export default async function loadRTStruct(extensionManager, rtStructDisplaySet,
     SeriesInstanceUID: instance.SeriesInstanceUID,
     ROIContours: [],
     visible: true,
+    ReferencedSOPInstanceUIDsSet: new Set(),
   };
 
   for (let i = 0; i < ROIContourSequence.length; i++) {
@@ -142,7 +143,8 @@ export default async function loadRTStruct(extensionManager, rtStructDisplaySet,
 
     const contourPoints = [];
     for (let c = 0; c < ContourSequenceArray.length; c++) {
-      const { ContourData, NumberOfContourPoints, ContourGeometricType } = ContourSequenceArray[c];
+      const { ContourData, NumberOfContourPoints, ContourGeometricType, ContourImageSequence } =
+        ContourSequenceArray[c];
 
       let isSupported = false;
 
@@ -172,6 +174,12 @@ export default async function loadRTStruct(extensionManager, rtStructDisplaySet,
         type: ContourGeometricType,
         isSupported,
       });
+
+      if (ContourImageSequence?.ReferencedSOPInstanceUID) {
+        structureSet.ReferencedSOPInstanceUIDsSet.add(
+          ContourImageSequence?.ReferencedSOPInstanceUID
+        );
+      }
     }
 
     _setROIContourMetadata(

extensions/cornerstone-dicom-rt/src/viewports/OHIFCornerstoneRTViewport.tsx

@@ -6,7 +6,7 @@ import promptHydrateRT from '../utils/promptHydrateRT';
 import _getStatusComponent from './_getStatusComponent';
 
 import createRTToolGroupAndAddTools from '../utils/initRTToolGroup';
-import { SegmentationRepresentations } from '@cornerstonejs/tools/enums';
+import { usePositionPresentationStore } from '@ohif/extension-cornerstone';
 
 const RT_TOOLGROUP_BASE_NAME = 'RTToolGroup';
 
@@ -43,8 +43,8 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
   const [viewportGrid, viewportGridService] = useViewportGrid();
 
   // States
-  const [isToolGroupCreated, setToolGroupCreated] = useState(false);
   const [selectedSegment, setSelectedSegment] = useState(1);
+  const { setPositionPresentation } = usePositionPresentationStore();
 
   // Hydration means that the RT is opened and segments are loaded into the
   // segmentation panel, and RT is also rendered on any viewport that is in the
@@ -123,6 +123,7 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
           toolGroupId: toolGroupId,
           orientation: viewportOptions.orientation,
           viewportId: viewportOptions.viewportId,
+          presentationIds: viewportOptions.presentationIds,
         }}
         onElementEnabled={evt => {
           props.onElementEnabled?.(evt);
@@ -185,6 +186,19 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
           setRtIsLoading(false);
         }
 
+        if (rtDisplaySet?.firstSegmentedSliceImageId && viewportOptions?.presentationIds) {
+          const { firstSegmentedSliceImageId } = rtDisplaySet;
+          const { presentationIds } = viewportOptions;
+
+          setPositionPresentation(presentationIds.positionPresentationId, {
+            viewportType: 'stack',
+            viewReference: {
+              referencedImageId: firstSegmentedSliceImageId,
+            },
+            viewPresentation: {},
+          });
+        }
+
         if (evt.overlappingSegments) {
           uiNotificationService.show({
             title: 'Overlapping Segments',
@@ -247,8 +261,6 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
 
     toolGroup = createRTToolGroupAndAddTools(toolGroupService, customizationService, toolGroupId);
 
-    setToolGroupCreated(true);
-
     return () => {
       // remove the segmentation representations if seg displayset changed
       segmentationService.removeSegmentationRepresentations(viewportId);

extensions/cornerstone-dicom-seg/src/viewports/OHIFCornerstoneSEGViewport.tsx

@@ -4,6 +4,7 @@ import { LoadingIndicatorTotalPercent, useViewportGrid, ViewportActionArrows } f
 import createSEGToolGroupAndAddTools from '../utils/initSEGToolGroup';
 import promptHydrateSEG from '../utils/promptHydrateSEG';
 import _getStatusComponent from './_getStatusComponent';
+import { usePositionPresentationStore } from '@ohif/extension-cornerstone';
 import { SegmentationRepresentations } from '@cornerstonejs/tools/enums';
 
 const SEG_TOOLGROUP_BASE_NAME = 'SEGToolGroup';
@@ -41,6 +42,7 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
 
   // States
   const [selectedSegment, setSelectedSegment] = useState(1);
+  const { setPositionPresentation } = usePositionPresentationStore();
 
   // Hydration means that the SEG is opened and segments are loaded into the
   // segmentation panel, and SEG is also rendered on any viewport that is in the
@@ -198,6 +200,17 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
         if (evt.segDisplaySet.displaySetInstanceUID === segDisplaySet.displaySetInstanceUID) {
           setSegIsLoading(false);
         }
+
+        if (segDisplaySet?.firstSegmentedSliceImageId && viewportOptions?.presentationIds) {
+          const { firstSegmentedSliceImageId } = segDisplaySet;
+          const { presentationIds } = viewportOptions;
+
+          setPositionPresentation(presentationIds.positionPresentationId, {
+            viewReference: {
+              referencedImageId: firstSegmentedSliceImageId,
+            },
+          });
+        }
       }
     );
 

extensions/cornerstone-dicom-sr/src/components/OHIFCornerstoneSRMeasurementViewport.tsx

@@ -9,24 +9,20 @@ import { Icon, Tooltip, useViewportGrid, ViewportActionArrows } from '@ohif/ui';
 import hydrateStructuredReport from '../utils/hydrateStructuredReport';
 import { useAppConfig } from '@state';
 import createReferencedImageDisplaySet from '../utils/createReferencedImageDisplaySet';
+import { usePositionPresentationStore } from '@ohif/extension-cornerstone';
 
 const MEASUREMENT_TRACKING_EXTENSION_ID = '@ohif/extension-measurement-tracking';
 
 const SR_TOOLGROUP_BASE_NAME = 'SRToolGroup';
 
 function OHIFCornerstoneSRMeasurementViewport(props: withAppTypes) {
-  const {
+  const { children, dataSource, displaySets, viewportOptions, servicesManager, extensionManager } =
-    commandsManager,
+    props;
-    children,
-    dataSource,
-    displaySets,
-    viewportOptions,
-    servicesManager,
-    extensionManager,
-  } = props;
 
   const [appConfig] = useAppConfig();
 
+  const { setPositionPresentation } = usePositionPresentationStore();
+
   const {
     displaySetService,
     cornerstoneViewportService,
@@ -157,30 +153,13 @@ function OHIFCornerstoneSRMeasurementViewport(props: withAppTypes) {
         setActiveImageDisplaySetData(referencedDisplaySet);
         setReferencedDisplaySetMetadata(referencedDisplaySetMetadata);
 
-        if (
+        const { presentationIds } = viewportOptions;
-          referencedDisplaySet.displaySetInstanceUID ===
+        const measurement = srDisplaySet.measurements[newMeasurementSelected];
-          activeImageDisplaySetData?.displaySetInstanceUID
+        setPositionPresentation(presentationIds.positionPresentationId, {
-        ) {
+          viewReference: {
-          const { measurements } = srDisplaySet;
+            referencedImageId: measurement.imageId,
-
+          },
-          // it means that we have a new referenced display set, and the
+        });
-          // imageIdIndex will handle it by updating the viewport, but if they
-          // are the same we just need to use measurementService to jump to the
-          // new measurement
-          const csViewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
-
-          if (!csViewport) {
-            return;
-          }
-
-          const imageIds = csViewport.getImageIds();
-
-          const imageIdIndex = imageIds.indexOf(measurements[newMeasurementSelected].imageId);
-
-          if (imageIdIndex !== -1) {
-            csViewport.setImageIdIndex(imageIdIndex);
-          }
-        }
       });
     },
     [dataSource, srDisplaySet, activeImageDisplaySetData, viewportId]
@@ -202,10 +181,6 @@ function OHIFCornerstoneSRMeasurementViewport(props: withAppTypes) {
       return null;
     }
 
-    const initialImageIndex = activeImageDisplaySetData.images.findIndex(
-      image => image.imageId === measurement.imageId
-    );
-
     return (
       <Component
         {...props}
@@ -230,7 +205,6 @@ function OHIFCornerstoneSRMeasurementViewport(props: withAppTypes) {
           props.onElementEnabled?.(evt);
           onElementEnabled(evt);
         }}
-        initialImageIndex={initialImageIndex}
         isJumpToMeasurementDisabled={true}
       ></Component>
     );

extensions/cornerstone-dicom-sr/src/utils/formatContentItem.ts

@@ -25,7 +25,7 @@ const contentItemFormatters = {
     return `${NumericValue} ${CodeValue}`;
   },
   PNAME: contentItem => {
-    const personName = contentItem.PersonName?.[0]?.Alphabetic;
+    const personName = contentItem.PersonName?.[0];
     return personName ? utils.formatPN(personName) : undefined;
   },
   DATE: contentItem => {

extensions/cornerstone-dynamic-volume/src/actions/updateSegmentationsChartDisplaySet.ts

@@ -262,7 +262,6 @@ function _getInstanceFromSegmentations(segmentations, { servicesManager }) {
 }
 
 function updateSegmentationsChartDisplaySet({ servicesManager }: withAppTypes): void {
-  debugger;
   const { segmentationService } = servicesManager.services;
   const segmentations = segmentationService.getSegmentations();
   const { seriesMetadata, instance } =

extensions/cornerstone/src/Viewport/Overlays/CustomizableViewportOverlay.tsx

@@ -5,12 +5,14 @@ import { metaData, Enums, utilities } from '@cornerstonejs/core';
 import type { ImageSliceData } from '@cornerstonejs/core/types';
 import { ViewportOverlay } from '@ohif/ui';
 import type { InstanceMetadata } from '@ohif/core/src/types';
-import { formatPN, formatDICOMDate, formatDICOMTime, formatNumberPrecision } from './utils';
+import { formatDICOMDate, formatDICOMTime, formatNumberPrecision } from './utils';
+import { utils } from '@ohif/core';
 import { StackViewportData, VolumeViewportData } from '../../types/CornerstoneCacheService';
 
 import './CustomizableViewportOverlay.css';
 
 const EPSILON = 1e-4;
+const { formatPN } = utils;
 
 type ViewportData = StackViewportData | VolumeViewportData;
 

extensions/cornerstone/src/Viewport/Overlays/utils.ts

@@ -52,31 +52,6 @@ export function formatDICOMTime(time, strFormat = 'HH:mm:ss') {
   return moment(time, 'HH:mm:ss').format(strFormat);
 }
 
-/**
- * Formats a patient name for display purposes
- *
- * @param {string} name
- * @returns {string} formatted name.
- */
-export function formatPN(name) {
-  if (!name) {
-    return '';
-  }
-  if (typeof name === 'object') {
-    name = name.Alphabetic;
-    if (!name) {
-      return '';
-    }
-  }
-
-  const cleaned = name
-    .split('^')
-    .filter(s => !!s)
-    .join(', ')
-    .trim();
-  return cleaned === ',' || cleaned === '' ? '' : cleaned;
-}
-
 /**
  * Gets compression type
  *

extensions/cornerstone/src/hps/frameView.ts

@@ -20,7 +20,7 @@ const frameView: Types.HangingProtocol.Protocol = {
         },
         {
           attribute: 'isDisplaySetFromUrl',
-          weight: 10,
+          weight: 20,
           constraint: {
             equals: true,
           },

extensions/cornerstone/src/panels/PanelSegmentation.tsx

@@ -162,6 +162,14 @@ export default function PanelSegmentation({
     const firstImageId = referencedImageIds[0];
 
     const instance = metaData.get('instance', firstImageId);
+
+    if (!instance) {
+      return {
+        segmentationId,
+        isExportable: false,
+      };
+    }
+
     const { SOPInstanceUID, SeriesInstanceUID } = instance;
 
     const displaySet = displaySetService.getDisplaySetForSOPInstanceUID(

extensions/cornerstone/src/services/SegmentationService/SegmentationService.ts

@@ -478,14 +478,24 @@ class SegmentationService extends PubSubService {
     // We should parse the segmentation as separate slices to support overlapping segments.
     // This parsing should occur in the CornerstoneJS library adapters.
     // For now, we use the volume returned from the library and chop it here.
+    let firstSegmentedSliceImageId = null;
     for (let i = 0; i < derivedSegmentationImages.length; i++) {
       const voxelManager = derivedSegmentationImages[i]
         .voxelManager as csTypes.IVoxelManager<number>;
       const scalarData = voxelManager.getScalarData();
-      scalarData.set(volumeScalarData.slice(i * scalarData.length, (i + 1) * scalarData.length));
+      const sliceData = volumeScalarData.slice(i * scalarData.length, (i + 1) * scalarData.length);
+      scalarData.set(sliceData);
       voxelManager.setScalarData(scalarData);
+
+      // Check if this slice has any non-zero voxels and we haven't found one yet
+      if (!firstSegmentedSliceImageId && sliceData.some(value => value !== 0)) {
+        firstSegmentedSliceImageId = derivedSegmentationImages[i].referencedImageId;
+      }
     }
 
+    // assign the first non zero voxel image id to the segDisplaySet
+    segDisplaySet.firstSegmentedSliceImageId = firstSegmentedSliceImageId;
+
     this._broadcastEvent(EVENTS.SEGMENTATION_LOADING_COMPLETE, {
       segmentationId,
       segDisplaySet,
@@ -542,7 +552,19 @@ class SegmentationService extends PubSubService {
     }
 
     const rtDisplaySetUID = rtDisplaySet.displaySetInstanceUID;
+    const referencedDisplaySet = this.servicesManager.services.displaySetService.getDisplaySetByUID(
+      rtDisplaySet.referencedDisplaySetInstanceUID
+    );
 
+    const referencedImageIdsWithGeometry = Array.from(structureSet.ReferencedSOPInstanceUIDsSet);
+
+    const referencedImageIds = referencedDisplaySet.instances.map(image => image.imageId);
+    // find the first image id that contains a referenced SOP instance UID
+    const firstSegmentedSliceImageId = referencedImageIds.find(imageId =>
+      referencedImageIdsWithGeometry.some(referencedId => imageId.includes(referencedId))
+    );
+
+    rtDisplaySet.firstSegmentedSliceImageId = firstSegmentedSliceImageId;
     // Map ROI contours to RT Struct Data
     const allRTStructData = mapROIContoursToRTStructData(structureSet, rtDisplaySetUID);
 

extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts

@@ -605,10 +605,6 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
     let initialImageIndexToUse =
       presentations?.positionPresentation?.initialImageIndex ?? initialImageIndex;
 
-    if (initialImageIndexToUse === undefined || initialImageIndexToUse === null) {
-      initialImageIndexToUse = this._getInitialImageIndexForViewport(viewportInfo, imageIds) || 0;
-    }
-
     const { rotation, flipHorizontal, displayArea } = viewportInfo.getViewportOptions();
 
     const properties = { ...presentations.lutPresentation?.properties };
@@ -637,12 +633,26 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
     });
 
     let imageIdsToSet = imageIds;
-    const res = this._processExtraDisplaySetsForViewport(viewport);
+    const overlayProcessingResult = this._processExtraDisplaySetsForViewport(viewport);
-    imageIdsToSet = res?.imageIds ?? imageIdsToSet;
+    imageIdsToSet = overlayProcessingResult?.imageIds ?? imageIdsToSet;
+
+    const referencedImageId = presentations?.positionPresentation?.viewReference?.referencedImageId;
+    if (referencedImageId) {
+      initialImageIndexToUse = imageIdsToSet.indexOf(referencedImageId);
+    }
+
+    if (initialImageIndexToUse === undefined || initialImageIndexToUse === null) {
+      initialImageIndexToUse = this._getInitialImageIndexForViewport(viewportInfo, imageIds) || 0;
+    }
 
     return viewport.setStack(imageIdsToSet, initialImageIndexToUse).then(() => {
       viewport.setProperties({ ...properties });
       this.setPresentations(viewport.id, presentations, viewportInfo);
+
+      if (overlayProcessingResult?.addOverlayFn) {
+        overlayProcessingResult.addOverlayFn();
+      }
+
       if (displayArea) {
         viewport.setDisplayArea(displayArea);
       }
@@ -827,10 +837,14 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
     });
 
     // For SEG and RT viewports
-    this._processExtraDisplaySetsForViewport(viewport);
+    const { addOverlayFn } = this._processExtraDisplaySetsForViewport(viewport) || {};
 
     await viewport.setVolumes(volumeInputArray);
 
+    if (addOverlayFn) {
+      addOverlayFn();
+    }
+
     volumesProperties.forEach(({ properties, volumeId }) => {
       viewport.setProperties(properties, volumeId);
     });
@@ -880,8 +894,12 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
       segOrRTSOverlayDisplaySet.referencedDisplaySetInstanceUID
     );
     const imageIds = referenceDisplaySet.images.map(image => image.imageId);
-    this.addOverlayRepresentationForDisplaySet(segOrRTSOverlayDisplaySet, viewport);
+
-    return { imageIds };
+    return {
+      imageIds,
+      addOverlayFn: () =>
+        this.addOverlayRepresentationForDisplaySet(segOrRTSOverlayDisplaySet, viewport),
+    };
   }
 
   private addOverlayRepresentationForDisplaySet(

extensions/cornerstone/src/stores/usePositionPresentationStore.ts

@@ -4,7 +4,7 @@ import { PositionPresentation } from '../types/Presentation';
 import { addUniqueIndex, JOIN_STR } from './presentationUtils';
 
 const PRESENTATION_TYPE_ID = 'positionPresentationId';
-const DEBUG_STORE = true;
+const DEBUG_STORE = false;
 
 /**
  * Represents the state and actions for managing position presentations.

extensions/default/src/DicomLocalDataSource/index.js

@@ -142,7 +142,9 @@ function createDicomLocalApi(dicomLocalConfig) {
           study.series.forEach(aSeries => {
             const { SeriesInstanceUID } = aSeries;
 
-            aSeries.instances.forEach(instance => {
+            const isMultiframe = aSeries.instances[0].NumberOfFrames > 1;
+
+            aSeries.instances.forEach((instance, index) => {
               const {
                 url: imageId,
                 StudyInstanceUID,
@@ -151,22 +153,14 @@ function createDicomLocalApi(dicomLocalConfig) {
               } = instance;
 
               instance.imageId = imageId;
-              const numberOfFrames = instance.NumberOfFrames || 1;
+
-              // Process all frames consistently, whether single or multiframe
+              // Add imageId specific mapping to this data as the URL isn't necessarily WADO-URI.
-              for (let i = 0; i < numberOfFrames; i++) {
+              metadataProvider.addImageIdToUIDs(imageId, {
-                const frameNumber = i + 1;
+                StudyInstanceUID,
-                const frameImageId = implementation.getImageIdsForInstance({
+                SeriesInstanceUID,
-                  instance,
+                SOPInstanceUID,
-                  frame: frameNumber,
+                frameIndex: isMultiframe ? index : 1,
-                });
+              });
-                // Add imageId specific mapping to this data as the URL isn't necessarily WADO-URI.
-                metadataProvider.addImageIdToUIDs(frameImageId, {
-                  StudyInstanceUID,
-                  SeriesInstanceUID,
-                  SOPInstanceUID,
-                  frameNumber: numberOfFrames > 1 ? frameNumber : undefined,
-                });
-              }
             });
 
             DicomMetadataStore._broadcastEvent(EVENTS.INSTANCES_ADDED, {

extensions/default/src/Panels/WrappedPanelStudyBrowser.tsx

@@ -30,6 +30,7 @@ function WrappedPanelStudyBrowser({ commandsManager, extensionManager, servicesM
   return (
     <PanelStudyBrowser
       servicesManager={servicesManager}
+      commandsManager={commandsManager}
       dataSource={dataSource}
       getImageSrc={_getImageSrcFromImageId}
       getStudiesForPatientByMRN={_getStudiesForPatientByMRN}

extensions/default/src/getHangingProtocolModule.js

@@ -63,7 +63,7 @@ const defaultProtocol = {
         // It has no affect if nothing is specified in the URL.
         {
           attribute: 'isDisplaySetFromUrl',
-          weight: 10,
+          weight: 20,
           constraint: {
             equals: true,
           },

extensions/default/src/hangingprotocols/hpCompare.ts

@@ -24,7 +24,7 @@ const defaultDisplaySetSelector = {
     // It has no affect if nothing is specified in the URL.
     {
       attribute: 'isDisplaySetFromUrl',
-      weight: 10,
+      weight: 20,
       constraint: {
         equals: true,
       },
@@ -56,7 +56,7 @@ const priorDisplaySetSelector = {
     // It has no affect if nothing is specified in the URL.
     {
       attribute: 'isDisplaySetFromUrl',
-      weight: 10,
+      weight: 20,
       constraint: {
         equals: true,
       },

extensions/default/src/hangingprotocols/hpMNGrid.ts

@@ -50,7 +50,7 @@ const hpMN: Types.HangingProtocol.Protocol = {
         // It has no affect if nothing is specified in the URL.
         {
           attribute: 'isDisplaySetFromUrl',
-          weight: 10,
+          weight: 20,
           constraint: {
             equals: true,
           },

extensions/default/src/hangingprotocols/hpScale.ts

@@ -43,7 +43,7 @@ const hpScale: Types.HangingProtocol.Protocol = {
         // It has no affect if nothing is specified in the URL.
         {
           attribute: 'isDisplaySetFromUrl',
-          weight: 10,
+          weight: 20,
           constraint: {
             equals: true,
           },

extensions/default/src/hooks/usePatientInfo.tsx

@@ -38,7 +38,7 @@ function usePatientInfo(servicesManager: AppTypes.ServicesManager) {
     }
     setPatientInfo({
       PatientID: instance.PatientID || null,
-      PatientName: instance.PatientName ? formatPN(instance.PatientName.Alphabetic) : null,
+      PatientName: instance.PatientName ? formatPN(instance.PatientName) : null,
       PatientSex: instance.PatientSex || null,
       PatientDOB: formatDate(instance.PatientBirthDate) || null,
     });

extensions/default/src/stores/useViewportsByPositionStore.ts

@@ -2,7 +2,7 @@ import { create } from 'zustand';
 import { devtools } from 'zustand/middleware';
 
 const PRESENTATION_TYPE_ID = 'viewportsByPositionId';
-const DEBUG_STORE = true;
+const DEBUG_STORE = false;
 
 /**
  * Represents the state and actions for managing viewports by position.

extensions/dicom-microscopy/src/components/ViewportOverlay/index.tsx

@@ -3,7 +3,10 @@ import classnames from 'classnames';
 
 import listComponentGenerator from './listComponentGenerator';
 import './ViewportOverlay.css';
-import { formatDICOMDate, formatDICOMTime, formatNumberPrecision, formatPN } from './utils';
+import { formatDICOMDate, formatDICOMTime, formatNumberPrecision } from './utils';
+import { utils } from '@ohif/core';
+
+const { formatPN } = utils;
 
 interface OverlayItem {
   id: string;

extensions/dicom-microscopy/src/components/ViewportOverlay/utils.ts

@@ -52,28 +52,6 @@ export function formatDICOMTime(time, strFormat = 'HH:mm:ss') {
   return moment(time, 'HH:mm:ss').format(strFormat);
 }
 
-/**
- * Formats a patient name for display purposes
- *
- * @param {string} name
- * @returns {string} formatted name.
- */
-export function formatPN(name) {
-  if (!name) {
-    return;
-  }
-
-  // Convert the first ^ to a ', '. String.replace() only affects
-  // the first appearance of the character.
-  const commaBetweenFirstAndLast = name.replace('^', ', ');
-
-  // Replace any remaining '^' characters with spaces
-  const cleaned = commaBetweenFirstAndLast.replace(/\^/g, ' ');
-
-  // Trim any extraneous whitespace
-  return cleaned.trim();
-}
-
 /**
  * Gets compression type
  *

extensions/test-extension/src/hpTestSwitch.ts

@@ -188,7 +188,7 @@ const hpTestSwitch: Types.HangingProtocol.Protocol = {
         // It has no affect if nothing is specified in the URL.
         {
           attribute: 'isDisplaySetFromUrl',
-          weight: 10,
+          weight: 20,
           constraint: {
             equals: true,
           },

extensions/tmtv/src/commandsModule.ts

@@ -9,8 +9,10 @@ import dicomRTAnnotationExport from './utils/dicomRTAnnotationExport/RTStructure
 
 import { getWebWorkerManager } from '@cornerstonejs/core';
 import { Enums } from '@cornerstonejs/tools';
+import { utils } from '@ohif/core';
 
 const { SegmentationRepresentations } = Enums;
+const { formatPN } = utils;
 
 const metadataProvider = classes.MetadataProvider;
 const ROI_THRESHOLD_MANUAL_TOOL_IDS = [
@@ -595,7 +597,7 @@ const commandsModule = ({ servicesManager, commandsManager, extensionManager }:
         report[id] = {
           ...segReport,
           PatientID: instance.PatientID ?? '000000',
-          PatientName: instance.PatientName.Alphabetic,
+          PatientName: formatPN(instance.PatientName),
           StudyInstanceUID: instance.StudyInstanceUID,
           SeriesInstanceUID: instance.SeriesInstanceUID,
           StudyDate: instance.StudyDate,

platform/app/public/config/local_orthanc.js

@@ -23,6 +23,7 @@ window.config = {
         wadoRoot: 'http://localhost/dicom-web',
         qidoSupportsIncludeField: true,
         supportsReject: true,
+        dicomUploadEnabled: true,
         imageRendering: 'wadors',
         thumbnailRendering: 'wadors',
         enableStudyLazyLoad: true,

platform/core/src/classes/MetadataProvider.ts

@@ -6,10 +6,10 @@ import DicomMetadataStore from '../services/DicomMetadataStore';
 import fetchPaletteColorLookupTableData from '../utils/metadataProvider/fetchPaletteColorLookupTableData';
 import toNumber from '../utils/toNumber';
 import combineFrameInstance from '../utils/combineFrameInstance';
+import formatPN from '../utils/formatPN';
 
 class MetadataProvider {
   private readonly imageURIToUIDs: Map<string, any> = new Map();
-  private readonly imageUIDsByImageId: Map<string, any> = new Map();
   // Can be used to store custom metadata for a specific type.
   // For instance, the scaling metadata for PET can be stored here
   // as type "scalingModule"
@@ -25,7 +25,6 @@ class MetadataProvider {
     // An example would be dicom hosted at some random site.
     const imageURI = imageIdToURI(imageId);
     this.imageURIToUIDs.set(imageURI, uids);
-    this.imageUIDsByImageId.set(imageId, uids);
   }
 
   addCustomMetadata(imageId, type, metadata) {
@@ -347,7 +346,7 @@ class MetadataProvider {
 
         let patientName;
         if (PatientName) {
-          patientName = PatientName.Alphabetic;
+          patientName = formatPN(PatientName);
         }
 
         metadata = {
@@ -462,11 +461,6 @@ class MetadataProvider {
   }
 
   getUIDsFromImageID(imageId) {
-    const cachedUIDs = this.imageUIDsByImageId.get(imageId);
-    if (cachedUIDs) {
-      return cachedUIDs;
-    }
-
     if (imageId.startsWith('wadors:')) {
       const strippedImageId = imageId.split('/studies/')[1];
       const splitImageId = strippedImageId.split('/');

platform/core/src/utils/combineFrameInstance.ts

@@ -1,4 +1,5 @@
 import { vec3 } from 'gl-matrix';
+import { dicomSplit } from './dicomSplit';
 
 /**
  * Combine the Per instance frame data, the shared frame data
@@ -15,24 +16,13 @@ const combineFrameInstance = (frame, instance) => {
     PerFrameFunctionalGroupsSequence,
     SharedFunctionalGroupsSequence,
     NumberOfFrames,
-    SpacingBetweenSlices,
+    ImageType,
   } = instance;
 
+  instance.ImageType = dicomSplit(ImageType);
+
   if (PerFrameFunctionalGroupsSequence || NumberOfFrames > 1) {
     const frameNumber = Number.parseInt(frame || 1);
-    const shared = SharedFunctionalGroupsSequence
-      ? Object.values(SharedFunctionalGroupsSequence[0])
-          .filter(Boolean)
-          .map(it => it[0])
-          .filter(it => typeof it === 'object')
-      : [];
-
-    const perFrame = PerFrameFunctionalGroupsSequence
-      ? Object.values(PerFrameFunctionalGroupsSequence[frameNumber - 1])
-          .filter(Boolean)
-          .map(it => it[0])
-          .filter(it => typeof it === 'object')
-      : [];
 
     // this is to fix NM multiframe datasets with position and orientation
     // information inside DetectorInformationSequence
@@ -44,8 +34,12 @@ const combineFrameInstance = (frame, instance) => {
     let ImagePositionPatientToUse = instance.ImagePositionPatient;
 
     if (!instance.ImagePositionPatient && instance.DetectorInformationSequence) {
-      const imagePositionPatient = instance.DetectorInformationSequence[0].ImagePositionPatient;
+      let imagePositionPatient = instance.DetectorInformationSequence[0].ImagePositionPatient;
-      const imageOrientationPatient = instance.ImageOrientationPatient;
+      let imageOrientationPatient = instance.ImageOrientationPatient;
+
+      imagePositionPatient = imagePositionPatient.map(it => Number(it));
+      imageOrientationPatient = imageOrientationPatient.map(it => Number(it));
+      const SpacingBetweenSlices = Number(instance.SpacingBetweenSlices);
 
       // Calculate the position for the current frame
       if (imageOrientationPatient && SpacingBetweenSlices) {
@@ -73,27 +67,77 @@ const combineFrameInstance = (frame, instance) => {
         ImagePositionPatientToUse = [position[0], position[1], position[2]];
       }
     }
-    console.debug('🚀 ~ ImagePositionPatientToUse:', ImagePositionPatientToUse);
 
-    const newInstance = Object.assign(instance, { frameNumber: frameNumber });
+    // Cache the _parentInstance at the top level as a full copy to prevent
-
+    // setting values hard.
-    // merge the shared first then the per frame to override
+    if (!instance._parentInstance) {
-    [...shared, ...perFrame].forEach(item => {
+      Object.defineProperty(instance, '_parentInstance', {
-      Object.entries(item).forEach(([key, value]) => {
+        value: { ...instance },
-        newInstance[key] = value;
       });
-    });
+    }
+    const sharedInstance = createCombinedValue(
+      instance._parentInstance,
+      SharedFunctionalGroupsSequence?.[0],
+      '_shared'
+    );
+    const newInstance = createCombinedValue(
+      sharedInstance,
+      PerFrameFunctionalGroupsSequence?.[frameNumber - 1],
+      frameNumber
+    );
 
-    // Todo: we should cache this combined instance somewhere, maybe add it
+    newInstance.ImagePositionPatient = ImagePositionPatientToUse ??
-    // back to the dicomMetaStore so we don't have to do this again.
+      newInstance.ImagePositionPatient ?? [0, 0, frameNumber];
-    return {
+
-      ...newInstance,
+    Object.defineProperty(newInstance, 'frameNumber', {
-      ImagePositionPatient: ImagePositionPatientToUse ??
+      value: frameNumber,
-        newInstance.ImagePositionPatient ?? [0, 0, frameNumber],
+      writable: true,
-    };
+      enumerable: true,
+      configurable: true,
+    });
+    return newInstance;
   } else {
     return instance;
   }
 };
 
+/**
+ * Creates a combined instance stored in the parent object which
+ * inherits from the parent instance the attributes in the functional groups.
+ * The storage key in the parent is in key
+ */
+function createCombinedValue(parent, functionalGroups, key) {
+  if (parent[key]) {
+    return parent[key];
+  }
+  // Exclude any proxying values
+  const newInstance = Object.create(parent);
+  Object.defineProperty(parent, key, {
+    value: newInstance,
+    writable: false,
+    enumerable: false,
+  });
+  if (!functionalGroups) {
+    return newInstance;
+  }
+  const shared = functionalGroups
+    ? Object.values(functionalGroups)
+        .filter(Boolean)
+        .map(it => it[0])
+        .filter(it => typeof it === 'object')
+    : [];
+
+  // merge the shared first then the per frame to override
+  [...shared].forEach(item => {
+    if (item.SOPInstanceUID) {
+      // This sub-item is a previous value information item, so don't merge it
+      return;
+    }
+    Object.entries(item).forEach(([key, value]) => {
+      newInstance[key] = value;
+    });
+  });
+  return newInstance;
+}
+
 export default combineFrameInstance;

platform/core/src/utils/dicomSplit.ts

@@ -0,0 +1,5 @@
+export function dicomSplit(value) {
+  return (
+    (Array.isArray(value) && value) || (typeof value === 'string' && value.split('\\')) || value
+  );
+}

platform/core/src/utils/downloadCSVReport.js

@@ -1,4 +1,5 @@
 import { DicomMetadataStore } from '../services/DicomMetadataStore/DicomMetadataStore';
+import formatPN from './formatPN';
 
 export default function downloadCSVReport(measurementData) {
   if (measurementData.length === 0) {
@@ -86,7 +87,7 @@ function _getCommonRowItems(measurement, seriesMetadata) {
 
   return {
     'Patient ID': firstInstance.PatientID, // Patient ID
-    'Patient Name': firstInstance.PatientName?.Alphabetic || '', // Patient Name
+    'Patient Name': formatPN(firstInstance.PatientName) || '', // Patient Name
     StudyInstanceUID: measurement.referenceStudyUID, // StudyInstanceUID
     SeriesInstanceUID: measurement.referenceSeriesUID, // SeriesInstanceUID
     SOPInstanceUID: measurement.SOPInstanceUID, // SOPInstanceUID

platform/ui/src/components/HeaderPatientInfo/HeaderPatientInfo.tsx

@@ -48,7 +48,7 @@ function usePatientInfo(servicesManager: AppTypes.ServicesManager) {
     }
     setPatientInfo({
       PatientID: instance.PatientID || null,
-      PatientName: instance.PatientName ? formatPN(instance.PatientName.Alphabetic) : null,
+      PatientName: instance.PatientName ? formatPN(instance.PatientName) : null,
       PatientSex: instance.PatientSex || null,
       PatientDOB: formatDate(instance.PatientBirthDate) || null,
     });

version.txt

@@ -1 +1 @@
-3.9.2
+3.9.3

yarn.lock

@@ -12594,13 +12594,6 @@ fast-uri@^3.0.1:
   resolved "https://registry.yarnpkg.com/fast-uri/-/fast-uri-3.0.2.tgz#d78b298cf70fd3b752fd951175a3da6a7b48f024"
   integrity sha512-GR6f0hD7XXyNJa25Tb9BuIdN0tdr+0BMi6/CJPH3wJO1JjNG3n/VsSw38AwRdKZABm8lGbPfakLRkYzx2V9row==
 
-fast-url-parser@1.1.3:
-  version "1.1.3"
-  resolved "https://registry.yarnpkg.com/fast-url-parser/-/fast-url-parser-1.1.3.tgz#f4af3ea9f34d8a271cf58ad2b3759f431f0b318d"
-  integrity sha512-5jOCVXADYNuRkKFzNJ0dCCewsZiYo0dz8QNYljkOpFC6r2U4OBmKtvm/Tsuh4w1YYdDqDb31a8TVhBJ2OJKdqQ==
-  dependencies:
-    punycode "^1.3.2"
-
 fastest-levenshtein@^1.0.12:
   version "1.0.16"
   resolved "https://registry.yarnpkg.com/fastest-levenshtein/-/fastest-levenshtein-1.0.16.tgz#210e61b6ff181de91ea9b3d1b84fdedd47e034e5"
@@ -19130,7 +19123,7 @@ path-to-regexp@1.9.0, path-to-regexp@^1.7.0:
   dependencies:
     isarray "0.0.1"
 
-path-to-regexp@2.2.1, path-to-regexp@3.3.0:
+path-to-regexp@3.3.0:
   version "3.3.0"
   resolved "https://registry.yarnpkg.com/path-to-regexp/-/path-to-regexp-3.3.0.tgz#f7f31d32e8518c2660862b644414b6d5c63a611b"
   integrity sha512-qyCH421YQPS2WFDxDjftfc1ZR5WKQzVzqsp4n9M2kQhVOo/ByahFoUNJfl58kOcEGfQ//7weFTDhm+ss8Ecxgw==
@@ -20438,7 +20431,7 @@ pumpify@^1.3.3:
     inherits "^2.0.3"
     pump "^2.0.0"
 
-punycode@^1.3.2, punycode@^1.4.1:
+punycode@^1.4.1:
   version "1.4.1"
   resolved "https://registry.yarnpkg.com/punycode/-/punycode-1.4.1.tgz#c0d5a63b2718800ad8e1eb0fa5269c84dd41845e"
   integrity sha512-jmYNElW7yvO7TV33CjSmvSiE2yco3bV2czu/OzDKdMNVZQWfxCblURLhf+47syQRBntjfLdd/H0egrzIG+oaFQ==
@@ -22034,21 +22027,7 @@ serialize-javascript@^6.0.0, serialize-javascript@^6.0.1:
   dependencies:
     randombytes "^2.1.0"
 
-serve-handler@6.1.5:
+serve-handler@6.1.6, serve-handler@^6.1.6:
-  version "6.1.5"
-  resolved "https://registry.yarnpkg.com/serve-handler/-/serve-handler-6.1.5.tgz#a4a0964f5c55c7e37a02a633232b6f0d6f068375"
-  integrity sha512-ijPFle6Hwe8zfmBxJdE+5fta53fdIY0lHISJvuikXB3VYFafRjMRpOffSPvCYsbKyBA7pvy9oYr/BT1O3EArlg==
-  dependencies:
-    bytes "3.0.0"
-    content-disposition "0.5.2"
-    fast-url-parser "1.1.3"
-    mime-types "2.1.18"
-    minimatch "3.1.2"
-    path-is-inside "1.0.2"
-    path-to-regexp "2.2.1"
-    range-parser "1.2.0"
-
-serve-handler@^6.1.6:
   version "6.1.6"
   resolved "https://registry.yarnpkg.com/serve-handler/-/serve-handler-6.1.6.tgz#50803c1d3e947cd4a341d617f8209b22bd76cfa1"
   integrity sha512-x5RL9Y2p5+Sh3D38Fh9i/iQ5ZK+e4xuXRd/pGbM4D13tgo/MGwbttUk8emytcr1YYzBYs+apnUngBDFYfpjPuQ==
@@ -22084,10 +22063,10 @@ serve-static@1.16.2:
     parseurl "~1.3.3"
     send "0.19.0"
 
-serve@^14.2.0:
+serve@^14.2.4:
-  version "14.2.3"
+  version "14.2.4"
-  resolved "https://registry.yarnpkg.com/serve/-/serve-14.2.3.tgz#047ba2b349354255bc09e0332cd41a92787836c9"
+  resolved "https://registry.yarnpkg.com/serve/-/serve-14.2.4.tgz#ba4c425c3c965f496703762e808f34b913f42fb0"
-  integrity sha512-VqUFMC7K3LDGeGnJM9h56D3XGKb6KGgOw0cVNtA26yYXHCcpxf3xwCTUaQoWlVS7i8Jdh3GjQkOB23qsXyjoyQ==
+  integrity sha512-qy1S34PJ/fcY8gjVGszDB3EXiPSk5FKhUa7tQe0UPRddxRidc2V6cNHPNewbE1D7MAkgLuWEt3Vw56vYy73tzQ==
   dependencies:
     "@zeit/schemas" "2.36.0"
     ajv "8.12.0"
@@ -22098,7 +22077,7 @@ serve@^14.2.0:
     clipboardy "3.0.0"
     compression "1.7.4"
     is-port-reachable "4.0.0"
-    serve-handler "6.1.5"
+    serve-handler "6.1.6"
     update-check "1.5.4"
 
 set-blocking@^2.0.0: