[OHIF-288] Rehydrating SRs is missing Labels (#1885)

* WIP

* Finish OHIF-288, need to update dcmjs.

* Remove unused copied resources.

* Cleaned up label import code.

* Update for dcmjs Findings -> Finding.

* Update dcmjs

* Remove debuggers

* Respond to reviewer comments.

* update dcmjs version

Co-authored-by: Danny Brown <danny.ri.brown@gmail.com>

extensions/cornerstone/package.json

@@ -35,7 +35,7 @@
     "cornerstone-math": "^0.1.8",
     "cornerstone-tools": "4.18.1",
     "cornerstone-wado-image-loader": "^3.1.2",
-    "dcmjs": "0.14.2",
+    "dcmjs": "0.16.0",
     "dicom-parser": "^1.8.3",
     "hammerjs": "^2.0.8",
     "prop-types": "^15.6.2",

extensions/default/package.json

@@ -34,7 +34,7 @@
     "react": "^16.13.1",
     "react-dom": "^16.13.1",
     "webpack": "^4.0.0",
-    "dcmjs": "0.14.2"
+    "dcmjs": "0.16.0"
   },
   "dependencies": {
     "@babel/runtime": "7.7.6"

extensions/dicom-html/package.json

@@ -28,7 +28,7 @@
   },
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
-    "dcmjs": "0.14.2",
+    "dcmjs": "0.16.0",
     "prop-types": "^15.6.2",
     "react": "^16.11.0",
     "react-dom": "^16.11.0"

extensions/dicom-rt/package.json

@@ -31,7 +31,7 @@
     "@ohif/core": "^0.50.0",
     "cornerstone-core": "^2.2.8",
     "cornerstone-tools": "4.18.1",
-    "dcmjs": "0.14.2",
+    "dcmjs": "0.16.0",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6"

extensions/dicom-segmentation/package.json

@@ -31,7 +31,7 @@
     "@ohif/core": "^0.50.0",
     "cornerstone-core": "^2.2.8",
     "cornerstone-tools": "4.18.1",
-    "dcmjs": "0.14.2",
+    "dcmjs": "0.16.0",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6"

extensions/dicom-sr/package.json

@@ -35,7 +35,7 @@
     "cornerstone-math": "^0.1.8",
     "cornerstone-tools": "4.18.1",
     "cornerstone-wado-image-loader": "^3.1.2",
-    "dcmjs": "0.14.2",
+    "dcmjs": "0.16.0",
     "dicom-parser": "^1.8.3",
     "hammerjs": "^2.0.8",
     "prop-types": "^15.6.2",

extensions/dicom-sr/src/OHIFCornerstoneSRViewport.js

@@ -8,6 +8,7 @@ import { ViewportActionBar, useViewportGrid } from '@ohif/ui';
 import TOOL_NAMES from './constants/toolNames';
 import { adapters } from 'dcmjs';
 import getToolStateToCornerstoneMeasurementSchema from './utils/getToolStateToCornerstoneMeasurementSchema';
+import getLabelFromDCMJSImportedToolData from './utils/getLabelFromDCMJSImportedToolData';
 import id from './id';
 
 const { formatDate } = utils;
@@ -376,6 +377,8 @@ function OHIFCornerstoneSRViewport({
 
         const source = MeasurementService.getSource('CornerstoneTools', '4');
 
+        data.label = getLabelFromDCMJSImportedToolData(data);
+
         MeasurementService.addRawMeasurement(
           source,
           toolType,

extensions/dicom-sr/src/getSopClassHandlerModule.js

@@ -25,13 +25,19 @@ const CodeNameCodeSequenceValues = {
   TrackingUniqueIdentifier: '112040',
   TrackingIdentifier: '112039',
   Finding: '121071',
+  FindingSite: 'G-C0E3', // SRT
+  CornerstoneFreeText: 'CORNERSTONEFREETEXT', // CST4
+};
+
+const CodingSchemeDesignators = {
+  SRT: 'SRT',
+  cornerstoneTools4: 'CST4',
 };
 
 const RELATIONSHIP_TYPE = {
   INFERRED_FROM: 'INFERRED FROM',
 };
 
-const CORNERSTONE_CODING_SCHEME_DESIGNATOR = 'CST4';
 const CORNERSTONE_FREETEXT_CODE_VALUE = 'CORNERSTONEFREETEXT';
 
 /**
@@ -428,12 +434,20 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
       CodeNameCodeSequenceValues.TrackingIdentifier
   );
 
-  const Findings = mergedContentSequence.filter(
+  const Finding = mergedContentSequence.find(
     item =>
       item.ConceptNameCodeSequence.CodeValue ===
       CodeNameCodeSequenceValues.Finding
   );
 
+  const FindingSites = mergedContentSequence.filter(
+    item =>
+      item.ConceptNameCodeSequence.CodingSchemeDesignator ===
+        CodingSchemeDesignators.SRT &&
+      item.ConceptNameCodeSequence.CodeValue ===
+        CodeNameCodeSequenceValues.FindingSite
+  );
+
   const measurement = {
     loaded: false,
     labels: [],
@@ -442,19 +456,33 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
     TrackingIdentifier: TrackingIdentifierContentItem.TextValue,
   };
 
-  if (Findings.length) {
+  if (
-    // TODO -> Pull in labels when we have them, just free text for now.
+    Finding &&
-    const cornerstoneFreeTextFinding = Findings.find(
+    Finding.ConceptCodeSequence.CodingSchemeDesignator ===
-      Finding =>
+      CodingSchemeDesignators.cornerstoneTools4 &&
-        Finding.ConceptCodeSequence.CodingSchemeDesignator ===
+    Finding.ConceptCodeSequence.CodeValue ===
-          CORNERSTONE_CODING_SCHEME_DESIGNATOR &&
+      CodeNameCodeSequenceValues.CornerstoneFreeText
-        Finding.ConceptCodeSequence.CodeValue ===
+  ) {
-          CORNERSTONE_FREETEXT_CODE_VALUE
+    measurement.labels.push({
+      label: CORNERSTONE_FREETEXT_CODE_VALUE,
+      value: Finding.ConceptCodeSequence.CodeMeaning,
+    });
+  }
+
+  // TODO -> Eventually hopefully support SNOMED or some proper code library, just free text for now.
+  if (FindingSites.length) {
+    const cornerstoneFreeTextFindingSite = FindingSites.find(
+      FindingSite =>
+        FindingSite.ConceptCodeSequence.CodingSchemeDesignator ===
+          CodingSchemeDesignators.cornerstoneTools4 &&
+        FindingSite.ConceptCodeSequence.CodeValue ===
+          CodeNameCodeSequenceValues.CornerstoneFreeText
     );
-    if (cornerstoneFreeTextFinding) {
+
+    if (cornerstoneFreeTextFindingSite) {
       measurement.labels.push({
         label: CORNERSTONE_FREETEXT_CODE_VALUE,
-        value: cornerstoneFreeTextFinding.ConceptCodeSequence.CodeMeaning,
+        value: cornerstoneFreeTextFindingSite.ConceptCodeSequence.CodeMeaning,
       });
     }
   }

extensions/dicom-sr/src/tools/DICOMSRDisplayTool.js

@@ -280,10 +280,9 @@ export default class DICOMSRDisplayTool extends BaseTool {
 }
 
 function _getTextBoxLinesFromLabels(labels) {
-  // TODO -> max 2 for now, need a generic solution for this!
+  // TODO -> max 3 for now (label + shortAxis + longAxis), need a generic solution for this!
-
-  const labelLength = Math.min(labels.length, 2);
 
+  const labelLength = Math.min(labels.length, 3);
   const lines = [];
 
   for (let i = 0; i < labelLength; i++) {

extensions/dicom-sr/src/utils/getLabelFromDCMJSImportedToolData.js

@@ -0,0 +1,23 @@
+/**
+ * Extracts the label from the toolData imported from dcmjs. We need to do this
+ * as dcmjs does not depeend on OHIF/the MeasurementService, it just produces data for cornestoneTools.
+ * This optional data is available for the consumer to process if they wish to.
+ * @param {object} toolData The tooldata relating to the
+ *
+ * @returns {string} The extracted label.
+ */
+export default function getLabelFromDCMJSImportedToolData(toolData) {
+  const { findingSites = [], finding } = toolData;
+
+  let freeTextLabel = findingSites.find(
+    fs => fs.CodeValue === 'CORNERSTONEFREETEXT'
+  );
+
+  if (freeTextLabel) {
+    return freeTextLabel.CodeMeaning;
+  }
+
+  if (finding && finding.CodeValue === 'CORNERSTONEFREETEXT') {
+    return finding.CodeMeaning;
+  }
+}

extensions/dicom-sr/src/utils/getToolStateToCornerstoneMeasurementSchema.js

@@ -51,7 +51,7 @@ function Length(measurementData, imageId, _getValueTypeFromToolType) {
     StudyInstanceUID,
   } = instance;
 
-  const { handles } = measurementData;
+  const { handles, label } = measurementData;
 
   const points = [];
   Object.keys(handles).map(handle => {
@@ -75,6 +75,7 @@ function Length(measurementData, imageId, _getValueTypeFromToolType) {
     length: measurementData.length,
     type: _getValueTypeFromToolType(tool),
     points,
+    label,
   };
 }
 
@@ -88,7 +89,7 @@ function Bidirectional(measurementData, imageId, _getValueTypeFromToolType) {
     StudyInstanceUID,
   } = instance;
 
-  const { handles } = measurementData;
+  const { handles, label } = measurementData;
 
   const longAxis = [handles.start, handles.end];
   const shortAxis = [handles.perpendicularStart, handles.perpendicularEnd];
@@ -106,6 +107,7 @@ function Bidirectional(measurementData, imageId, _getValueTypeFromToolType) {
     longestDiameter: measurementData.longestDiameter,
     type: _getValueTypeFromToolType(tool),
     points: { longAxis, shortAxis },
+    label,
   };
 }
 
@@ -119,7 +121,8 @@ function EllipticalRoi(measurementData, imageId, _getValueTypeFromToolType) {
     StudyInstanceUID,
   } = instance;
 
-  const { start, end } = measurementData.handles;
+  const { handles, label } = measurementData;
+  const { start, end } = handles;
 
   const halfXLength = Math.abs(start.x - end.x) / 2;
   const halfYLength = Math.abs(start.y - end.y) / 2;
@@ -161,6 +164,7 @@ function EllipticalRoi(measurementData, imageId, _getValueTypeFromToolType) {
         .area /* TODO: Add concept names instead (descriptor) */,
     type: _getValueTypeFromToolType(tool),
     points,
+    label,
   };
 }
 
@@ -198,5 +202,6 @@ function ArrowAnnotate(measurementData, imageId, _getValueTypeFromToolType) {
     text: measurementData.text,
     type: _getValueTypeFromToolType(tool),
     points,
+    label,
   };
 }

extensions/measurement-tracking/package.json

@@ -29,7 +29,7 @@
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
     "cornerstone-tools": "4.18.1",
-    "dcmjs": "0.14.2",
+    "dcmjs": "0.16.0",
     "prop-types": "^15.6.2",
     "react": "^16.13.1",
     "react-dom": "^16.13.1",

extensions/measurement-tracking/src/_shared/createReportAsync.js

@@ -18,7 +18,8 @@ async function createReportAsync(servicesManager, dataSource, measurements) {
   try {
     const naturalizedReport = await DICOMSR.storeMeasurements(
       measurements,
-      dataSource
+      dataSource,
+      ['ArrowAnnotate']
     );
 
     DisplaySetService.makeDisplaySets([naturalizedReport], {

extensions/measurement-tracking/src/panels/PanelMeasurementTableTracking/index.js

@@ -147,8 +147,6 @@ function PanelMeasurementTableTracking({ servicesManager, extensionManager }) {
   }
 
   function exportReport() {
-    const dataSources = extensionManager.getDataSources();
-    const dataSource = dataSources[0];
     const measurements = MeasurementService.getMeasurements();
     const trackedMeasurements = measurements.filter(
       m =>
@@ -156,8 +154,9 @@ function PanelMeasurementTableTracking({ servicesManager, extensionManager }) {
         trackedSeries.includes(m.referenceSeriesUID)
     );
 
-    // TODO -> local download.
+    const additionalFindings = ['ArrowAnnotate'];
-    DICOMSR.downloadReport(trackedMeasurements, dataSource);
+
+    DICOMSR.downloadReport(trackedMeasurements, additionalFindings);
   }
 
   const jumpToImage = ({ id, isActive }) => {

extensions/vtk/package.json

@@ -33,7 +33,7 @@
     "@ohif/ui": "^2.0.0",
     "cornerstone-core": "^2.3.0",
     "cornerstone-wado-image-loader": "^3.1.2",
-    "dcmjs": "0.14.2",
+    "dcmjs": "0.16.0",
     "dicom-parser": "^1.8.3",
     "i18next": "^17.0.3",
     "i18next-browser-languagedetector": "^3.0.1",

platform/core/package.json

@@ -38,7 +38,7 @@
   "dependencies": {
     "@babel/runtime": "7.7.6",
     "ajv": "^6.10.0",
-    "dcmjs": "0.14.2",
+    "dcmjs": "0.16.0",
     "dicomweb-client": "^0.6.0",
     "immer": "6.0.2",
     "isomorphic-base64": "^1.0.2",

platform/core/src/DICOMSR/dataExchange.js

@@ -46,10 +46,12 @@ 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
+ * as opposed to Finding Sites.
  * that you wish to serialize.
  */
-const downloadReport = measurementData => {
+const downloadReport = (measurementData, additionalFindingTypes = []) => {
-  const srDataset = generateReport(measurementData);
+  const srDataset = generateReport(measurementData, additionalFindingTypes);
   const reportBlob = dcmjs.data.datasetToBlob(srDataset);
 
   //Create a URL for the binary.
@@ -61,10 +63,13 @@ const downloadReport = measurementData => {
  *
  * @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
  */
-const generateReport = measurementData => {
+const generateReport = (measurementData, additionalFindingTypes) => {
-  const ids = measurementData.map(md => md.id);
+  const filteredToolState = _getFilteredCornerstoneToolState(
-  const filteredToolState = _getFilteredCornerstoneToolState(ids);
+    measurementData,
+    additionalFindingTypes
+  );
 
   const report = MeasurementReport.generateReport(
     filteredToolState,
@@ -79,9 +84,15 @@ const generateReport = measurementData => {
  * @param {object[]} measurementData An array of measurements from the measurements service
  * 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.
  * @return {object} The naturalized report
  */
-const storeMeasurements = async (measurementData, dataSource) => {
+const storeMeasurements = async (
+  measurementData,
+  dataSource,
+  additionalFindingTypes = []
+) => {
   // 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.
   log.info('[DICOMSR] storeMeasurements');
@@ -92,7 +103,10 @@ const storeMeasurements = async (measurementData, dataSource) => {
   }
 
   try {
-    const naturalizedReport = generateReport(measurementData);
+    const naturalizedReport = generateReport(
+      measurementData,
+      additionalFindingTypes
+    );
     const { StudyInstanceUID } = naturalizedReport;
 
     await dataSource.store.dicom(naturalizedReport);
@@ -110,7 +124,12 @@ const storeMeasurements = async (measurementData, dataSource) => {
   }
 };
 
-function _getFilteredCornerstoneToolState(uidFilter) {
+function _getFilteredCornerstoneToolState(
+  measurementData,
+  additionalFindingTypes
+) {
+  const uidFilter = measurementData.map(md => md.id);
+
   const globalToolState = cornerstoneTools.globalImageIdSpecificToolStateManager.saveToolState();
   const filteredToolState = {};
 
@@ -127,9 +146,38 @@ function _getFilteredCornerstoneToolState(uidFilter) {
       };
     }
 
+    const measurmentDataI = measurementData.find(md => md.id === toolDataI.id);
+
     const toolData = imageIdSpecificToolState[toolType].data;
 
-    toolData.push(toolDataI);
+    let finding;
+    const findingSites = [];
+
+    // NOTE -> Any kind of freetext value abuses the DICOM standard,
+    // As CodeValues should map 1:1 with CodeMeanings.
+    // Ideally we would actually use SNOMED codes for this.
+    if (measurmentDataI.label) {
+      if (additionalFindingTypes.includes(toolType)) {
+        finding = {
+          CodeValue: 'CORNERSTONEFREETEXT',
+          CodingSchemeDesignator: 'CST4',
+          CodeMeaning: measurmentDataI.label,
+        };
+      } else {
+        findingSites.push({
+          CodeValue: 'CORNERSTONEFREETEXT',
+          CodingSchemeDesignator: 'CST4',
+          CodeMeaning: measurmentDataI.label,
+        });
+      }
+    }
+
+    const measurement = Object.assign({}, toolDataI, {
+      finding,
+      findingSites,
+    });
+
+    toolData.push(measurement);
   }
 
   const uids = uidFilter.slice();

platform/viewer/package.json

@@ -69,7 +69,7 @@
     "cornerstone-math": "^0.1.8",
     "cornerstone-tools": "4.18.1",
     "cornerstone-wado-image-loader": "^3.1.2",
-    "dcmjs": "0.14.2",
+    "dcmjs": "0.16.0",
     "dicom-parser": "^1.8.3",
     "dicomweb-client": "^0.4.4",
     "dotenv-webpack": "^1.7.0",

yarn.lock

@@ -7364,10 +7364,10 @@ dateformat@^3.0.0:
   resolved "https://registry.yarnpkg.com/dateformat/-/dateformat-3.0.3.tgz#a6e37499a4d9a9cf85ef5872044d62901c9889ae"
   integrity sha512-jyCETtSl3VMZMWeRo7iY1FL19ges1t55hMo5yaam4Jrsm5EPL89UQkoQRyiI+Yf4k8r2ZpdngkV8hr1lIdjb3Q==
 
-dcmjs@0.14.2:
+dcmjs@0.16.0:
-  version "0.14.2"
+  version "0.16.0"
-  resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.14.2.tgz#bc4926c3312632ec61a5d68753c0857aebb65793"
+  resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.16.0.tgz#714755d006c3a49cf65ef13e627ff7a23151d35a"
-  integrity sha512-W4/f34Ph6Nrc95QhL/7f1kPlfR2YJMbyEsbPELt3xml17SFnkEgXAeO41qHZ7KywozO/lBW5sXGOpMenuYVV2g==
+  integrity sha512-41nY3Isg5i5FoSd1s67aUgUHi146r+fb8JuiRvDsxvm7MEkkdjIzMYMtxjsrVwKRW1xRH+x34nxbV9+8cc7WQw==
   dependencies:
     "@babel/polyfill" "^7.8.3"
     "@babel/runtime" "^7.8.4"