[OHIF-339] - workflow changes (#1931)

* workflow changes

* Cherry pick OHIF-310 into this PR.

* fix label bug and dead code

* remove comment

* Wire up CreateReportButton

* fix additionalFindingTypes + save interaction

* Remove unused createReportAsync call

* stub for report hydration prompt

* Update PR

* Remove debuggers

* push updated code

* Push updates

* push

* fix sidebar save

* enable tracking of new study or series

* fix for duplicate created report series in sidebard

* fix for unexpected viewport dialog after visiting study list then a new study

* Fix for hydration not marking multiple series as active

* Reviewer changes.

* Respond to final review comment, add series description setting for export.

Co-authored-by: James A. Petts <jamesapetts@gmail.com>

platform/core/src/DICOMSR/dataExchange.js

@@ -6,6 +6,7 @@ import {
   stowSRFromMeasurements,
 } from './handleStructuredReport';
 import findMostRecentStructuredReport from './utils/findMostRecentStructuredReport';
+import cornerstone from 'cornerstone-core';
 import cornerstoneTools from 'cornerstone-tools';
 import dcmjs from 'dcmjs';
 
@@ -47,11 +48,20 @@ const retrieveMeasurements = server => {
  *
  * @param {object[]} measurementData An array of measurements from the measurements service
  * @param {string[]} additionalFindingTypes toolTypes that should be stored with labels as Findings
+ * @param {object} options Naturalized DICOM JSON headers to merge into the displaySet.
  * as opposed to Finding Sites.
  * that you wish to serialize.
  */
-const downloadReport = (measurementData, additionalFindingTypes = []) => {
-  const srDataset = generateReport(measurementData, additionalFindingTypes);
+const downloadReport = (
+  measurementData,
+  additionalFindingTypes,
+  options = {}
+) => {
+  const srDataset = generateReport(
+    measurementData,
+    additionalFindingTypes,
+    options
+  );
   const reportBlob = dcmjs.data.datasetToBlob(srDataset);
 
   //Create a URL for the binary.
@@ -64,19 +74,29 @@ const downloadReport = (measurementData, additionalFindingTypes = []) => {
  * @param {object[]} measurementData An array of measurements from the measurements service
  * that you wish to serialize.
  * @param {string[]} additionalFindingTypes toolTypes that should be stored with labels as Findings
+ * @param {object} options Naturalized DICOM JSON headers to merge into the displaySet.
+ *
  */
-const generateReport = (measurementData, additionalFindingTypes) => {
+const generateReport = (
+  measurementData,
+  additionalFindingTypes,
+  options = {}
+) => {
   const filteredToolState = _getFilteredCornerstoneToolState(
     measurementData,
     additionalFindingTypes
   );
-
   const report = MeasurementReport.generateReport(
     filteredToolState,
     cornerstone.metaData
   );
 
-  return report.dataset;
+  const { dataset } = report;
+
+  // Add in top level series options
+  Object.assign(dataset, options);
+
+  return dataset;
 };
 
 /**
@@ -85,13 +105,14 @@ const generateReport = (measurementData, additionalFindingTypes) => {
  * that you wish to serialize.
  * @param {object} dataSource The dataSource that you wish to use to persist the data.
  * @param {string[]} additionalFindingTypes toolTypes that should be stored with labels as Findings
- * as opposed to Finding Sites.
+ * @param {object} options Naturalized DICOM JSON headers to merge into the displaySet.
  * @return {object} The naturalized report
  */
 const storeMeasurements = async (
   measurementData,
   dataSource,
-  additionalFindingTypes = []
+  additionalFindingTypes,
+  options = {}
 ) => {
   // TODO -> Eventually use the measurements directly and not the dcmjs adapter,
   // But it is good enough for now whilst we only have cornerstone as a datasource.
@@ -105,7 +126,8 @@ const storeMeasurements = async (
   try {
     const naturalizedReport = generateReport(
       measurementData,
-      additionalFindingTypes
+      additionalFindingTypes,
+      options
     );
     const { StudyInstanceUID } = naturalizedReport;
 
@@ -117,6 +139,7 @@ const storeMeasurements = async (
 
     return naturalizedReport;
   } catch (error) {
+    console.warn(error);
     log.error(
       `[DICOMSR] Error while saving the measurements: ${error.message}`
     );
@@ -124,6 +147,8 @@ const storeMeasurements = async (
   }
 };
 
+// _getFilteredCornerstoneToolState
+// DIFFERENT IMPLEMENTATION HERE! What's up?
 function _getFilteredCornerstoneToolState(
   measurementData,
   additionalFindingTypes
@@ -147,7 +172,6 @@ function _getFilteredCornerstoneToolState(
     }
 
     const measurmentDataI = measurementData.find(md => md.id === toolDataI.id);
-
     const toolData = imageIdSpecificToolState[toolType].data;
 
     let finding;

platform/core/src/extensions/ExtensionManager.js

@@ -16,7 +16,7 @@ export default class ExtensionManager {
     this.moduleTypeNames.forEach(moduleType => {
       this.modules[moduleType] = [];
     });
-    this._extensionLifeCycleHooks = { onModeEnter: {} };
+    this._extensionLifeCycleHooks = { onModeEnter: {}, onModeExit: {} };
     this.dataSourceMap = {};
     this.defaultDataSourceName = appConfig.defaultDataSourceName;
     this.activeDataSource = undefined;
@@ -29,12 +29,21 @@ export default class ExtensionManager {
   onModeEnter() {
     const {
       registeredExtensionIds,
-      getModuleEntry,
       _servicesManager,
       _commandsManager,
       _extensionLifeCycleHooks,
     } = this;
 
+    const {
+      MeasurementService,
+      ViewportGridService,
+      HangingProtocolService,
+    } = _servicesManager.services;
+
+    MeasurementService.clearMeasurements();
+    ViewportGridService.reset();
+    HangingProtocolService.reset();
+
     registeredExtensionIds.forEach(extensionId => {
       const onModeEnter = _extensionLifeCycleHooks.onModeEnter[extensionId];
 
@@ -47,6 +56,36 @@ export default class ExtensionManager {
     });
   }
 
+  onModeExit() {
+    const {
+      registeredExtensionIds,
+      _servicesManager,
+      _commandsManager,
+      _extensionLifeCycleHooks,
+    } = this;
+
+    const {
+      MeasurementService,
+      ViewportGridService,
+      HangingProtocolService,
+    } = _servicesManager.services;
+
+    MeasurementService.clearMeasurements();
+    ViewportGridService.reset();
+    HangingProtocolService.reset();
+
+    registeredExtensionIds.forEach(extensionId => {
+      const onModeExit = _extensionLifeCycleHooks.onModeExit[extensionId];
+
+      if (typeof onModeExit === 'function') {
+        onModeExit({
+          servicesManager: _servicesManager,
+          commandsManager: _commandsManager,
+        });
+      }
+    });
+  }
+
   /**
    * An array of extensions, or an array of arrays that contains extension
    * configuration pairs.
@@ -110,6 +149,11 @@ export default class ExtensionManager {
         extension.onModeEnter;
     }
 
+    if (extension.onModeExit) {
+      this._extensionLifeCycleHooks.onModeExit[extensionId] =
+        extension.onModeExit;
+    }
+
     // Register Modules
     this.moduleTypeNames.forEach(moduleType => {
       const extensionModule = this._getExtensionModule(

platform/core/src/measurements/conformance/ConformanceCriteria.js

@@ -77,10 +77,10 @@ class ConformanceCriteria {
     this.nonconformities = nonconformities;
     this.groupedNonConformities = groupedNonConformities;
 
-    console.warn('nonconformities');
-    console.warn(nonconformities);
-    console.warn('groupedNonConformities');
-    console.warn(groupedNonConformities);
+    // console.warn('nonconformities');
+    // console.warn(nonconformities);
+    // console.warn('groupedNonConformities');
+    // console.warn(groupedNonConformities);
 
     return nonconformities;
   }

platform/core/src/services/DicomMetadataStore/DicomMetadataStore.js

@@ -57,9 +57,7 @@ function _getInstance(StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID) {
 const BaseImplementation = {
   EVENTS,
   listeners: {},
-  // TODO: The assumption is that this is called per Study per Series
-  // We should do more to verify/clarify that
-  addInstances(instances) {
+  addInstances(instances, madeInClient = false) {
     const { StudyInstanceUID, SeriesInstanceUID } = instances[0];
 
     let study = _model.studies.find(
@@ -81,6 +79,7 @@ const BaseImplementation = {
     this._broadcastEvent(EVENTS.INSTANCES_ADDED, {
       StudyInstanceUID,
       SeriesInstanceUID,
+      madeInClient,
     });
   },
   addSeriesMetadata(seriesSummaryMetadata) {

platform/core/src/services/DisplaySetService/DisplaySetService.js

@@ -36,6 +36,10 @@ export default class DisplaySetService {
     return displaySetCache;
   }
 
+  getMostRecentDisplaySet() {
+    return this.activeDisplaySets[this.activeDisplaySets.length - 1];
+  }
+
   getActiveDisplaySets() {
     return this.activeDisplaySets;
   }
@@ -69,6 +73,12 @@ export default class DisplaySetService {
       displaySet => displaySet.displaySetInstanceUID === displaySetInstanceUid
     );
 
+  /**
+   *
+   * @param {*} input
+   * @param {*} param1
+   * @returns {string[]} - added displaySetInstanceUIDs
+   */
   makeDisplaySets = (input, { batch = false, madeInClient = false } = {}) => {
     if (!input || !input.length) {
       throw new Error('No instances were provided.');
@@ -84,11 +94,12 @@ export default class DisplaySetService {
     let displaySetsAdded = [];
 
     if (batch) {
-      input.forEach(instances => {
+      for (let i = 0; i < input.length; i++) {
+        const instances = input[i];
         const displaySets = this.makeDisplaySetForInstances(instances);
 
         displaySetsAdded = [...displaySetsAdded, displaySets];
-      });
+      }
     } else {
       const displaySets = this.makeDisplaySetForInstances(input);
 
@@ -109,6 +120,8 @@ export default class DisplaySetService {
         displaySetsAdded,
         options,
       });
+
+      return displaySetsAdded;
     }
   };
 

platform/ui/src/components/ViewportActionBar/ViewportActionBar.jsx

@@ -16,7 +16,6 @@ const ViewportActionBar = ({
   showNavArrows,
   showPatientInfo: patientInfoVisibility,
   onSeriesChange,
-  onHydrationClick,
   onDoubleClick,
 }) => {
   const [showPatientInfo, setShowPatientInfo] = useState(patientInfoVisibility);
@@ -32,7 +31,6 @@ const ViewportActionBar = ({
     label,
     isTracked,
     isLocked,
-    isHydrated,
     modality,
     studyDate,
     currentSeries,
@@ -78,13 +76,7 @@ const ViewportActionBar = ({
               Measurements cannot be duplicated.
             </div>
           )
-        : () => (
-            <div>
-              This SR is unlocked. <br />
-              You can duplicate measurements on your current report <br /> by
-              clicking &apos;Edit&apos;.
-            </div>
-          );
+        : () => <div>This SR is unlocked.</div>;
       return (
         <>
           <Tooltip content={<TooltipMessage />} position="bottom-left">
@@ -101,16 +93,6 @@ const ViewportActionBar = ({
               )}
             </div>
           </Tooltip>
-          {!isLocked && !isHydrated && (
-            <div className="relative flex p-1 ml-1 border rounded cursor-pointer border-primary-light">
-              <span
-                className="text-sm font-bold leading-none text-primary-light"
-                onClick={onHydrationClick}
-              >
-                Edit
-              </span>
-            </div>
-          )}
         </>
       );
     }

platform/viewer/src/routes/Mode/Mode.jsx

@@ -104,14 +104,15 @@ export default function ModeRoute({
     // TODO: For some reason this is running before the Providers
     // are calling setServiceImplementation
     // TOOD -> iterate through services.
-    MeasurementService.clearMeasurements();
-    ViewportGridService.reset();
-    HangingProtocolService.reset();
 
     // Extension
     extensionManager.onModeEnter();
     // Mode
     route.init({ servicesManager, extensionManager });
+
+    return () => {
+      extensionManager.onModeExit();
+    };
   }, [
     mode,
     dataSourceName,
@@ -131,13 +132,16 @@ export default function ModeRoute({
     // DisplaySetService would wire this up?
     const { unsubscribe } = DicomMetadataStore.subscribe(
       DicomMetadataStore.EVENTS.INSTANCES_ADDED,
-      ({ StudyInstanceUID, SeriesInstanceUID }) => {
+      ({ StudyInstanceUID, SeriesInstanceUID, madeInClient = false }) => {
         const seriesMetadata = DicomMetadataStore.getSeries(
           StudyInstanceUID,
           SeriesInstanceUID
         );
 
-        DisplaySetService.makeDisplaySets(seriesMetadata.instances);
+        DisplaySetService.makeDisplaySets(
+          seriesMetadata.instances,
+          madeInClient
+        );
       }
     );
 
@@ -161,9 +165,7 @@ export default function ModeRoute({
     const { unsubscribe } = DicomMetadataStore.subscribe(
       DicomMetadataStore.EVENTS.SERIES_ADDED,
       ({ StudyInstanceUID }) => {
-        const studyMetadata = DicomMetadataStore.getStudy(
-          StudyInstanceUID,
-        );
+        const studyMetadata = DicomMetadataStore.getStudy(StudyInstanceUID);
 
         const sortedSeries = studyMetadata.series.sort((a, b) => {
           const aLowPriority = isLowPriorityModality(a.Modality);
@@ -176,13 +178,12 @@ export default function ModeRoute({
           }
 
           return a.SeriesNumber - b.SeriesNumber;
-        })
+        });
 
-        const { SeriesInstanceUID } = sortedSeries[0]
+        const { SeriesInstanceUID } = sortedSeries[0];
 
-        HangingProtocolService.setHangingProtocol(
-          {
-            /*protocolMatchingRules: [
+        HangingProtocolService.setHangingProtocol({
+          /*protocolMatchingRules: [
               {
                 id: '7tmuq7KzDMCWFeapc',
                 weight: 2,
@@ -195,9 +196,9 @@ export default function ModeRoute({
                 },
               },
             ],*/
-            stages: [
-              {
-                /*id: 'v5PfGt9F6mffZPif5',
+          stages: [
+            {
+              /*id: 'v5PfGt9F6mffZPif5',
                 viewportStructure: {
                   type: 'grid',
                   properties: {
@@ -206,30 +207,29 @@ export default function ModeRoute({
                   },
                   layoutTemplateName: 'gridLayout',
                 },*/
-                viewports: [
-                  {
-                    viewportSettings: {},
-                    imageMatchingRules: [],
-                    seriesMatchingRules: [
-                      {
-                        id: 'mXnsCcNzZL56z7mTZ',
-                        weight: 1,
-                        required: true,
-                        attribute: 'SeriesInstanceUID',
-                        constraint: {
-                          equals: {
-                            value: SeriesInstanceUID,
-                          },
+              viewports: [
+                {
+                  viewportSettings: {},
+                  imageMatchingRules: [],
+                  seriesMatchingRules: [
+                    {
+                      id: 'mXnsCcNzZL56z7mTZ',
+                      weight: 1,
+                      required: true,
+                      attribute: 'SeriesInstanceUID',
+                      constraint: {
+                        equals: {
+                          value: SeriesInstanceUID,
                         },
                       },
-                    ],
-                    studyMatchingRules: [],
-                  },
-                ],
-              }
-            ]
-          }
-        )
+                    },
+                  ],
+                  studyMatchingRules: [],
+                },
+              ],
+            },
+          ],
+        });
       }
     );
     return unsubscribe;