Fix/sr hydration non tracking (#3080)

* fix:DICOM SR hydration - remove redundancies

feat:Allow save and restore on non-tracking view

* PR comments

extensions/cornerstone-dicom-sr/src/commandsModule.js

@@ -37,6 +37,12 @@ const _generateReport = (
   // Add in top level series options
   Object.assign(dataset, options);
 
+  // Set the default character set as UTF-8
+  // https://dicom.innolitics.com/ciods/nm-image/sop-common/00080005
+  if (typeof dataset.SpecificCharacterSet === 'undefined') {
+    dataset.SpecificCharacterSet = 'ISO_IR 192';
+  }
+
   return dataset;
 };
 

extensions/cornerstone-dicom-sr/src/index.tsx

@@ -5,6 +5,7 @@ import commandsModule from './commandsModule';
 import init from './init';
 import { id } from './id.js';
 import toolNames from './tools/toolNames';
+import hydrateStructuredReport from './utils/hydrateStructuredReport';
 
 const Component = React.lazy(() => {
   return import(
@@ -74,3 +75,4 @@ const dicomSRExtension = {
 };
 
 export default dicomSRExtension;
+export { hydrateStructuredReport };

extensions/cornerstone-dicom-sr/src/utils/hydrateStructuredReport.js

@@ -1,6 +1,6 @@
 import { utilities, metaData } from '@cornerstonejs/core';
 import OHIF, { DicomMetadataStore } from '@ohif/core';
-import getLabelFromDCMJSImportedToolData from './utils/getLabelFromDCMJSImportedToolData';
+import getLabelFromDCMJSImportedToolData from './getLabelFromDCMJSImportedToolData';
 import { adapters } from 'dcmjs';
 
 const { guid } = OHIF.utils;
@@ -12,9 +12,10 @@ const CORNERSTONE_3D_TOOLS_SOURCE_VERSION = '0.1';
 const supportedLegacyCornerstoneTags = ['cornerstoneTools@^4.0.0'];
 
 /**
+ * Hydrates a structured report, for default viewports.
  *
  */
-export default function _hydrateStructuredReport(
+export default function hydrateStructuredReport(
   { servicesManager, extensionManager },
   displaySetInstanceUID
 ) {
@@ -250,7 +251,7 @@ function _mapLegacyDataSet(dataset) {
   return dataset;
 }
 
-const toArray = function(x) {
+const toArray = function (x) {
   return Array.isArray(x) ? x : [x];
 };
 

extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx

@@ -13,6 +13,7 @@ import {
   Icon,
 } from '@ohif/ui';
 import classNames from 'classnames';
+import hydrateStructuredReport from '../utils/hydrateStructuredReport';
 
 const { formatDate } = utils;
 
@@ -37,6 +38,7 @@ function OHIFCornerstoneSRViewport(props) {
   const {
     DisplaySetService,
     CornerstoneViewportService,
+    MeasurementService,
   } = servicesManager.services;
 
   // SR viewport will always have a single display set
@@ -69,18 +71,25 @@ function OHIFCornerstoneSRViewport(props) {
     MEASUREMENT_TRACKING_EXTENSION_ID
   );
 
-  // TODO: this is a hook that fails if we register/de-register
   if (hasMeasurementTrackingExtension) {
     const contextModule = extensionManager.getModuleEntry(
       '@ohif/extension-measurement-tracking.contextModule.TrackedMeasurementsContext'
     );
 
-    const useTrackedMeasurements = () => useContext(contextModule.context);
-
-    [
-      trackedMeasurements,
-      sendTrackedMeasurementsEvent,
-    ] = useTrackedMeasurements();
+    const tracked = useContext(contextModule.context);
+    trackedMeasurements = tracked?.[0];
+    sendTrackedMeasurementsEvent = tracked?.[1];
+  }
+  if (!sendTrackedMeasurementsEvent) {
+    // if no panels from measurement-tracking extension is used, this code will trun
+    trackedMeasurements = null;
+    sendTrackedMeasurementsEvent = (eventName, { displaySetInstanceUID }) => {
+      MeasurementService.clearMeasurements();
+      hydrateStructuredReport(
+        { servicesManager, extensionManager },
+        displaySetInstanceUID
+      );
+    };
   }
 
   /**
@@ -362,7 +371,7 @@ function OHIFCornerstoneSRViewport(props) {
           useAltStyling: true,
           studyDate: formatDate(StudyDate),
           currentSeries: SeriesNumber,
-          seriesDescription: SeriesDescription,
+          seriesDescription: SeriesDescription || '',
           patientInformation: {
             patientName: PatientName
               ? OHIF.utils.formatPN(PatientName.Alphabetic)

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

@@ -23,6 +23,11 @@ export type ViewportOptions = {
   syncGroups?: SyncGroup[];
   initialImageOptions?: InitialImageOptions;
   customViewportProps?: Record<string, unknown>;
+  /*
+   * Allows drag and drop of display sets not matching viewport options, but
+   * doesn't show them initially.  Displays initially blank if no required match
+   */
+  allowUnmatchedView?: boolean;
 };
 
 export type PublicViewportOptions = {
@@ -34,6 +39,7 @@ export type PublicViewportOptions = {
   syncGroups?: SyncGroup[];
   initialImageOptions?: InitialImageOptions;
   customViewportProps?: Record<string, unknown>;
+  allowUnmatchedView?: boolean;
 };
 
 export type PublicDisplaySetOptions = {

extensions/default/src/Actions/createReportAsync.tsx

@@ -0,0 +1,73 @@
+import React from 'react';
+import { DicomMetadataStore } from '@ohif/core';
+
+/**
+ *
+ * @param {*} servicesManager
+ * @param {*} dataSource
+ * @param {*} measurements
+ * @param {*} options
+ * @returns {string[]} displaySetInstanceUIDs
+ */
+async function createReportAsync(
+  servicesManager,
+  commandsManager,
+  dataSource,
+  measurements,
+  options
+) {
+  const {
+    DisplaySetService,
+    UINotificationService,
+    UIDialogService,
+  } = servicesManager.services;
+  const loadingDialogId = UIDialogService.create({
+    showOverlay: true,
+    isDraggable: false,
+    centralize: true,
+    // TODO: Create a loading indicator component + zeplin design?
+    content: Loading,
+  });
+
+  try {
+    const naturalizedReport = await commandsManager.runCommand(
+      'storeMeasurements',
+      {
+        measurementData: measurements,
+        dataSource,
+        additionalFindingTypes: ['ArrowAnnotate'],
+        options,
+      },
+      'CORNERSTONE_STRUCTURED_REPORT'
+    );
+
+    // The "Mode" route listens for DicomMetadataStore changes
+    // When a new instance is added, it listens and
+    // automatically calls makeDisplaySets
+    DicomMetadataStore.addInstances([naturalizedReport], true);
+
+    const displaySetInstanceUID = DisplaySetService.getMostRecentDisplaySet();
+
+    UINotificationService.show({
+      title: 'Create Report',
+      message: 'Measurements saved successfully',
+      type: 'success',
+    });
+
+    return [displaySetInstanceUID];
+  } catch (error) {
+    UINotificationService.show({
+      title: 'Create Report',
+      message: error.message || 'Failed to store measurements',
+      type: 'error',
+    });
+  } finally {
+    UIDialogService.dismiss({ id: loadingDialogId });
+  }
+}
+
+function Loading() {
+  return <div className="text-primary-active">Loading...</div>;
+}
+
+export default createReportAsync;

extensions/default/src/Panels/ActionButtons.tsx

@@ -13,16 +13,10 @@ function ActionButtons({ onExportClick, onCreateReportClick }) {
         <Button className="px-2 py-2 text-base" onClick={onExportClick}>
           {t('Export CSV')}
         </Button>
+        <Button className="px-2 py-2 text-base" onClick={onCreateReportClick}>
+          {t('Create Report')}
+        </Button>
       </ButtonGroup>
-      {/* <Button
-        className="ml-2 text-base"
-        variant="outlined"
-        size="small"
-        color="black"
-        onClick={onCreateReportClick}
-      >
-        {t('Create Report')}
-      </Button> */}
     </React.Fragment>
   );
 }

extensions/default/src/Panels/PanelMeasurementTable.tsx

@@ -5,15 +5,27 @@ import ActionButtons from './ActionButtons';
 import debounce from 'lodash.debounce';
 
 import { utils } from '@ohif/core';
+import createReportDialogPrompt, {
+  CREATE_REPORT_DIALOG_RESPONSE,
+} from './createReportDialogPrompt';
+import createReportAsync from '../Actions/createReportAsync';
+import getNextSRSeriesNumber from '../utils/getNextSRSeriesNumber';
 
 const { downloadCSVReport } = utils;
 
 export default function PanelMeasurementTable({
   servicesManager,
   commandsManager,
+  extensionManager,
 }) {
   const [viewportGrid, viewportGridService] = useViewportGrid();
-  const { MeasurementService, UIDialogService } = servicesManager.services;
+  const { activeViewportIndex, viewports } = viewportGrid;
+  const {
+    MeasurementService,
+    UIDialogService,
+    UINotificationService,
+    DisplaySetService,
+  } = servicesManager.services;
   const [displayMeasurements, setDisplayMeasurements] = useState([]);
 
   useEffect(() => {
@@ -56,6 +68,62 @@ export default function PanelMeasurementTable({
     downloadCSVReport(measurements, MeasurementService);
   }
 
+  async function clearMeasurements() {
+    MeasurementService.clearMeasurements();
+  }
+
+  async function createReport() {
+    // filter measurements that are added to the active study
+    const activeViewport = viewports[activeViewportIndex];
+    const measurements = MeasurementService.getMeasurements();
+    const displaySet = DisplaySetService.getDisplaySetByUID(
+      activeViewport.displaySetInstanceUIDs[0]
+    );
+    const trackedMeasurements = measurements.filter(
+      m => displaySet.StudyInstanceUID === m.referenceStudyUID
+    );
+
+    if (trackedMeasurements.length <= 0) {
+      UINotificationService.show({
+        title: 'No Measurements',
+        message: 'No Measurements are added to the current Study.',
+        type: 'info',
+        duration: 3000,
+      });
+      return;
+    }
+
+    const promptResult = await createReportDialogPrompt(UIDialogService, {
+      extensionManager,
+    });
+
+    if (promptResult.action === CREATE_REPORT_DIALOG_RESPONSE.CREATE_REPORT) {
+      const dataSources = extensionManager.getDataSources(
+        promptResult.dataSourceName
+      );
+      const dataSource = dataSources[0];
+
+      const SeriesDescription =
+        // isUndefinedOrEmpty
+        promptResult.value === undefined || promptResult.value === ''
+          ? 'Research Derived Series' // default
+          : promptResult.value; // provided value
+
+      const SeriesNumber = getNextSRSeriesNumber(DisplaySetService);
+
+      const displaySetInstanceUIDs = await createReportAsync(
+        servicesManager,
+        commandsManager,
+        dataSource,
+        trackedMeasurements,
+        {
+          SeriesDescription,
+          SeriesNumber,
+        }
+      );
+    }
+  }
+
   const jumpToImage = ({ uid, isActive }) => {
     MeasurementService.jumpToMeasurement(viewportGrid.activeViewportIndex, uid);
 
@@ -142,7 +210,7 @@ export default function PanelMeasurementTable({
   return (
     <>
       <div
-        className="overflow-x-hidden overflow-y-auto invisible-scrollbar"
+        className="overflow-x-hidden overflow-y-auto ohif-scrollbar"
         data-cy={'measurements-panel'}
       >
         <MeasurementTable
@@ -155,7 +223,8 @@ export default function PanelMeasurementTable({
       <div className="flex justify-center p-4">
         <ActionButtons
           onExportClick={exportReport}
-          onCreateReportClick={() => {}}
+          onClearMeasurementsClick={clearMeasurements}
+          onCreateReportClick={createReport}
         />
       </div>
     </>

extensions/default/src/Panels/createReportDialogPrompt.tsx

@@ -0,0 +1,143 @@
+/* eslint-disable react/display-name */
+import React from 'react';
+import { Dialog, Input, Select } from '@ohif/ui';
+
+export const CREATE_REPORT_DIALOG_RESPONSE = {
+  CANCEL: 0,
+  CREATE_REPORT: 1,
+};
+
+export default function createReportDialogPrompt(
+  UIDialogService,
+  { extensionManager }
+) {
+  return new Promise(function (resolve, reject) {
+    let dialogId = undefined;
+
+    const _handleClose = () => {
+      // Dismiss dialog
+      UIDialogService.dismiss({ id: dialogId });
+      // Notify of cancel action
+      resolve({
+        action: CREATE_REPORT_DIALOG_RESPONSE.CANCEL,
+        value: undefined,
+        dataSourceName: undefined,
+      });
+    };
+
+    /**
+     *
+     * @param {string} param0.action - value of action performed
+     * @param {string} param0.value - value from input field
+     */
+    const _handleFormSubmit = ({ action, value }) => {
+      UIDialogService.dismiss({ id: dialogId });
+      switch (action.id) {
+        case 'save':
+          resolve({
+            action: CREATE_REPORT_DIALOG_RESPONSE.CREATE_REPORT,
+            value: value.label,
+            dataSourceName: value.dataSourceName,
+          });
+          break;
+        case 'cancel':
+          resolve({
+            action: CREATE_REPORT_DIALOG_RESPONSE.CANCEL,
+            value: undefined,
+            dataSourceName: undefined,
+          });
+          break;
+      }
+    };
+
+    const dataSourcesOpts = Object.keys(extensionManager.dataSourceMap)
+      .filter(ds => {
+        const configuration =
+          extensionManager.dataSourceDefs[ds]?.configuration;
+        const supportsStow =
+          configuration?.supportsStow ?? configuration?.wadoRoot;
+        return supportsStow;
+      })
+      .map(ds => {
+        return {
+          value: ds,
+          label: ds,
+          placeHolder: ds,
+        };
+      });
+
+    dialogId = UIDialogService.create({
+      centralize: true,
+      isDraggable: false,
+      content: Dialog,
+      useLastPosition: false,
+      showOverlay: true,
+      contentProps: {
+        title: 'Provide a name for your report',
+        value: {
+          label: '',
+          dataSourceName: extensionManager.activeDataSource,
+        },
+        noCloseButton: true,
+        onClose: _handleClose,
+        actions: [
+          { id: 'cancel', text: 'Cancel', type: 'primary' },
+          { id: 'save', text: 'Save', type: 'secondary' },
+        ],
+        // TODO: Should be on button press...
+        onSubmit: _handleFormSubmit,
+        body: ({ value, setValue }) => {
+          const onChangeHandler = event => {
+            event.persist();
+            setValue(value => ({ ...value, label: event.target.value }));
+          };
+          const onKeyPressHandler = event => {
+            if (event.key === 'Enter') {
+              UIDialogService.dismiss({ id: dialogId });
+              resolve({
+                action: CREATE_REPORT_DIALOG_RESPONSE.CREATE_REPORT,
+                value: value.label,
+              });
+            }
+          };
+          return (
+            <>
+              <div className="p-4 bg-primary-dark">
+                {dataSourcesOpts.length > 1 && (
+                  <Select
+                    closeMenuOnSelect={true}
+                    className="mr-2 bg-black border-primary-main"
+                    options={dataSourcesOpts}
+                    placeholder={
+                      dataSourcesOpts.find(
+                        option => option.value === value.dataSourceName
+                      ).placeHolder
+                    }
+                    value={value.dataSourceName}
+                    onChange={evt => {
+                      setValue(v => ({ ...v, dataSourceName: evt.value }));
+                    }}
+                    isClearable={false}
+                  />
+                )}
+              </div>
+              <div className="p-4 bg-primary-dark">
+                <Input
+                  autoFocus
+                  className="mt-2 bg-black border-primary-main"
+                  type="text"
+                  placeholder="Enter Report Name"
+                  containerClassName="mr-2"
+                  value={value.label}
+                  onChange={onChangeHandler}
+                  onKeyPress={onKeyPressHandler}
+                  required
+                />
+              </div>
+            </>
+          );
+        },
+      },
+    });
+  });
+}

extensions/default/src/getHangingProtocolModule.js

@@ -14,7 +14,16 @@ const defaultProtocol = {
       // Unused currently
       imageMatchingRules: [],
       // Matches displaysets, NOT series
-      seriesMatchingRules: [],
+      seriesMatchingRules: [
+        // Try to match series with images by default, to prevent weird display
+        // on SEG/SR containing studies
+        {
+          attribute: 'numImageFrames',
+          constraint: {
+            greaterThan: { value: 0 },
+          },
+        },
+      ],
       studyMatchingRules: [],
     },
   },
@@ -40,7 +49,6 @@ const defaultProtocol = {
           },
           displaySets: [
             {
-              options: [],
               id: 'defaultDisplaySetId',
             },
           ],

extensions/default/src/getPanelModule.tsx

@@ -16,6 +16,7 @@ function getPanelModule({
       <PanelMeasurementTable
         commandsManager={commandsManager}
         servicesManager={servicesManager}
+        extensionManager={extensionManager}
       />
     );
   };

extensions/default/src/utils/getNextSRSeriesNumber.js

@@ -0,0 +1,10 @@
+const MIN_SR_SERIES_NUMBER = 4700;
+
+export default function getNextSRSeriesNumber(DisplaySetService) {
+  const activeDisplaySets = DisplaySetService.getActiveDisplaySets();
+  const srDisplaySets = activeDisplaySets.filter(ds => ds.Modality === 'SR');
+  const srSeriesNumbers = srDisplaySets.map(ds => ds.SeriesNumber);
+  const maxSeriesNumber = Math.max(...srSeriesNumbers, MIN_SR_SERIES_NUMBER);
+
+  return maxSeriesNumber + 1;
+}

extensions/measurement-tracking/src/contexts/TrackedMeasurementsContext/promptHydrateStructuredReport.js

@@ -1,4 +1,4 @@
-import hydrateStructuredReport from './_hydrateStructuredReport.js';
+import hydrateStructuredReport from '@ohif/extension-cornerstone-dicom-sr';
 
 const RESPONSE = {
   NO_NEVER: -1,