[WIP] feat: Save DICOM SR to the same series

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

@@ -41,6 +41,8 @@ const _generateReport = (
   if (typeof dataset.SpecificCharacterSet === 'undefined') {
     dataset.SpecificCharacterSet = 'ISO_IR 192';
   }
+  dataset.InstanceNumber = 1 + (options.InstanceNumber || 0);
+
   return dataset;
 };
 

extensions/cornerstone-dicom-sr/src/getSopClassHandlerModule.ts

@@ -124,7 +124,7 @@ function _getDisplaySetsFromSeries(
   if (
     !ConceptNameCodeSequence ||
     ConceptNameCodeSequence.CodeValue !==
-      CodeNameCodeSequenceValues.ImagingMeasurementReport
+    CodeNameCodeSequenceValues.ImagingMeasurementReport
   ) {
     servicesManager.services.uiNotificationService.show({
       title: 'DICOM SR',
@@ -364,7 +364,7 @@ function _getMeasurements(ImagingMeasurementReportContentSequence) {
     trackingUniqueIdentifier => {
       const mergedContentSequence =
         mergedContentSequencesByTrackingUniqueIdentifiers[
-          trackingUniqueIdentifier
+        trackingUniqueIdentifier
         ];
 
       const measurement = _processMeasurement(mergedContentSequence);
@@ -404,7 +404,7 @@ function _getMergedContentSequencesByTrackingUniqueIdentifiers(
 
     if (
       mergedContentSequencesByTrackingUniqueIdentifiers[
-        trackingUniqueIdentifier
+      trackingUniqueIdentifier
       ] === undefined
     ) {
       // Add the full ContentSequence
@@ -519,9 +519,9 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
   const findingSites = mergedContentSequence.filter(
     item =>
       item.ConceptNameCodeSequence.CodingSchemeDesignator ===
-        CodingSchemeDesignators.SRT &&
+      CodingSchemeDesignators.SRT &&
       item.ConceptNameCodeSequence.CodeValue ===
-        CodeNameCodeSequenceValues.FindingSite
+      CodeNameCodeSequenceValues.FindingSite
   );
 
   const measurement = {
@@ -538,7 +538,7 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
       finding.ConceptCodeSequence.CodingSchemeDesignator
     ) &&
     finding.ConceptCodeSequence.CodeValue ===
-      CodeNameCodeSequenceValues.CornerstoneFreeText
+    CodeNameCodeSequenceValues.CornerstoneFreeText
   ) {
     measurement.labels.push({
       label: CORNERSTONE_FREETEXT_CODE_VALUE,
@@ -554,7 +554,7 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
           FindingSite.ConceptCodeSequence.CodingSchemeDesignator
         ) &&
         FindingSite.ConceptCodeSequence.CodeValue ===
-          CodeNameCodeSequenceValues.CornerstoneFreeText
+        CodeNameCodeSequenceValues.CornerstoneFreeText
     );
 
     if (cornerstoneFreeTextFindingSite) {

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

@@ -10,6 +10,7 @@ import { id } from './id.js';
 import toolNames from './tools/toolNames';
 import hydrateStructuredReport from './utils/hydrateStructuredReport';
 import createReferencedImageDisplaySet from './utils/createReferencedImageDisplaySet';
+import convertCode from './utils/convertCode';
 
 const Component = React.lazy(() => {
   return import(
@@ -74,4 +75,4 @@ const dicomSRExtension = {
 export default dicomSRExtension;
 
 // Put static exports here so they can be type checked
-export { hydrateStructuredReport, createReferencedImageDisplaySet, srProtocol };
+export { hydrateStructuredReport, createReferencedImageDisplaySet, srProtocol, convertCode };

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

@@ -0,0 +1,24 @@
+/**
+ * Converts a DICOM code value into an object with more information such
+ * as whether the code is a key value, any colouring etc.
+ *
+ * @param codingValues - map from string codes to code information
+ * @param code - the code we want more inofrmation about
+ * @returns An enhanced code value that includes the DICOM coding information
+ *   as well as other information.
+ */
+const convertCode = (codingValues, code) => {
+  if (!code || code.CodingSchemeDesignator === 'CORNERSTONEJS') return;
+  const ref = `${code.CodingSchemeDesignator}:${code.CodeValue}`;
+  const codeLookup = codingValues[ref];
+  const ret = {
+    ref,
+    ...code,
+    ...codeLookup,
+    CodeMeaning: codeLookup?.text || code.codeMeaning,
+    text: codeLookup?.text || code.CodeMeaning,
+  };
+  return ret;
+};
+
+export default convertCode;

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

@@ -2,6 +2,7 @@ import { utilities, metaData } from '@cornerstonejs/core';
 import OHIF, { DicomMetadataStore } from '@ohif/core';
 import getLabelFromDCMJSImportedToolData from './getLabelFromDCMJSImportedToolData';
 import { adaptersSR } from '@cornerstonejs/adapters';
+import convertCode from './convertCode';
 
 const { guid } = OHIF.utils;
 const { MeasurementReport, CORNERSTONE_3D_TAG } = adaptersSR.Cornerstone3D;
@@ -11,13 +12,10 @@ const CORNERSTONE_3D_TOOLS_SOURCE_VERSION = '0.1';
 
 const supportedLegacyCornerstoneTags = ['cornerstoneTools@^4.0.0'];
 
-const convertCode = (codingValues, code) => {
-  if (!code || code.CodingSchemeDesignator === 'CORNERSTONEJS') return;
-  const ref = `${code.CodingSchemeDesignator}:${code.CodeValue}`;
-  const ret = { ...codingValues[ref], ref, ...code, text: code.CodeMeaning };
-  return ret;
-};
-
+/**
+ * Takes a list of codes and runs them through convert, only adding the ones
+ * which are not CORNERSTONEJS issued to the result.
+ */
 const convertSites = (codingValues, sites) => {
   if (!sites || !sites.length) return;
   const ret = [];
@@ -32,7 +30,6 @@ const convertSites = (codingValues, sites) => {
 
 /**
  * Hydrates a structured report, for default viewports.
- *
  */
 export default function hydrateStructuredReport(
   { servicesManager, extensionManager },
@@ -287,7 +284,7 @@ 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

@@ -1,14 +1,20 @@
 import PropTypes from 'prop-types';
 import React, { useCallback, useContext, useEffect, useState } from 'react';
 import { useTranslation } from 'react-i18next';
-import OHIF, { utils, ServicesManager, ExtensionManager } from '@ohif/core';
+import OHIF, {
+  utils,
+  ServicesManager,
+  ExtensionManager,
+  classes,
+} from '@ohif/core';
 
 import { setTrackingUniqueIdentifiersForElement } from '../tools/modules/dicomSRModule';
 
 import { Icon, Tooltip, useViewportGrid, ViewportActionBar } from '@ohif/ui';
 import hydrateStructuredReport from '../utils/hydrateStructuredReport';
 
 const { formatDate } = utils;
+const { ImageSet } = classes;
 
 const MEASUREMENT_TRACKING_EXTENSION_ID =
   '@ohif/extension-measurement-tracking';
@@ -74,22 +80,26 @@ function OHIFCornerstoneSRViewport(props) {
     // if no panels from measurement-tracking extension is used, this code will run
     trackedMeasurements = null;
     sendTrackedMeasurementsEvent = (eventName, { displaySetInstanceUID }) => {
-      measurementService.clearMeasurements();
+      const { StudyInstanceUID } = srDisplaySet;
+      measurementService.clearStudyMeasurements(StudyInstanceUID);
       const { SeriesInstanceUIDs } = hydrateStructuredReport(
         { servicesManager, extensionManager },
         displaySetInstanceUID
       );
-      const displaySets = displaySetService.getDisplaySetsForSeries(
-        SeriesInstanceUIDs[0]
-      );
+      const displaySets =
+        (srDisplaySet.keyImageDisplaySet && [
+          srDisplaySet.keyImageDisplaySet,
+        ]) ||
+        displaySetService.getDisplaySetsForSeries(SeriesInstanceUIDs[0]);
       if (displaySets.length) {
         viewportGridService.setDisplaySetsForViewports([
           {
-            viewportIndex: activeViewportIndex,
-            displaySetInstanceUIDs: [displaySets[0].displaySetInstanceUID],
+          viewportIndex: activeViewportIndex,
+          displaySetInstanceUIDs: [displaySets[0].displaySetInstanceUID],
           },
         ]);
       }
+      measurementService.setSeriesInformation(StudyInstanceUID, srDisplaySet);
     };
   }
 
@@ -424,19 +434,76 @@ OHIFCornerstoneSRViewport.defaultProps = {
   customProps: {},
 };
 
+const findInstance = (measurement, displaySetService: DisplaySetService) => {
+  const {
+    displaySetInstanceUID,
+    ReferencedSOPInstanceUID: sopUid,
+  } = measurement;
+  const referencedDisplaySet = displaySetService.getDisplaySetByUID(
+    displaySetInstanceUID
+  );
+  if (!referencedDisplaySet.images) return;
+  return referencedDisplaySet.images.find(it => it.SOPInstanceUID === sopUid);
+};
+
 async function _getViewportReferencedDisplaySetData(
   displaySet,
   measurementSelected,
   displaySetService
 ) {
   const { measurements } = displaySet;
-  const measurement = measurements[measurementSelected];
 
-  const { displaySetInstanceUID } = measurement;
+  if (!displaySet.keyImageDisplaySet) {
+    const findReferences = ds => {
+      const instances = [];
+      const instanceByUrl = {};
+      for (const measurement of ds.measurements) {
+        const instance = findInstance(measurement, displaySetService);
+        if (!instance) {
+          console.log('Measurement', measurement, 'had no instances found');
+          continue;
+        }
 
-  const referencedDisplaySet = displaySetService.getDisplaySetByUID(
-    displaySetInstanceUID
-  );
+        // TODO - find actual URL
+        const { imageId } = measurement;
+        if (!imageId) continue;
+        if (instanceByUrl[imageId]) continue;
+        instanceByUrl[imageId] = instance;
+        instances.push(instance);
+      }
+      return instances;
+    };
+    const instances = findReferences(displaySet);
+    const updateInstances = function() {
+      this.images.splice(0, this.images.length, ...findReferences(displaySet));
+      this.numImageFrames = this.images.length;
+    };
+    const imageSet = new ImageSet(instances);
+    const instance = instances[0];
+    imageSet.setAttributes({
+      displaySetInstanceUID: imageSet.uid, // create a local alias for the imageSet UID
+      SeriesDate: instance.SeriesDate,
+      SeriesTime: instance.SeriesTime,
+      SeriesInstanceUID: imageSet.uid,
+      StudyInstanceUID: instance.StudyInstanceUID,
+      SeriesNumber: instance.SeriesNumber || 0,
+      SOPClassUID: instance.SOPClassUID,
+      SeriesDescription: `${displaySet.SeriesDescription} KO ${displaySet.instance.SeriesNumber}`,
+      Modality: 'KO',
+      isMultiFrame: false,
+      numImageFrames: instances.length,
+      SOPClassHandlerId: `@ohif/extension-default.sopClassHandlerModule.stack`,
+      isReconstructable: false,
+      madeInClient: true,
+      updateInstances,
+    });
+
+    displaySetService.addDisplaySets(imageSet);
+
+    displaySet.keyImageDisplaySet = imageSet;
+  }
+
+  const referencedDisplaySet = displaySet.keyImageDisplaySet;
 
   const image0 = referencedDisplaySet.images[0];
   const referencedDisplaySetMetadata = {