Merge pull request #1811 from OHIF/feat/OHIF-177

[OHIF-177] - First pass at SR STOW with Arrow Annotate, Ellipse, Length and Bidirectional.

extensions/cornerstone/package.json

@@ -34,7 +34,7 @@
     "cornerstone-core": "^2.3.0",
     "cornerstone-math": "^0.1.8",
     "cornerstone-tools": "4.16.0",
-    "dcmjs": "^0.12.3",
+    "dcmjs": "0.14.0",
     "cornerstone-wado-image-loader": "^3.1.2",
     "dicom-parser": "^1.8.3",
     "hammerjs": "^2.0.8",

extensions/cornerstone/src/utils/measurementServiceMappings/ArrowAnnotate.js

@@ -1,5 +1,4 @@
 import SUPPORTED_TOOLS from './constants/supportedTools';
-import getHandlesFromPoints from './utils/getHandlesFromPoints';
 import getPointsFromHandles from './utils/getPointsFromHandles';
 import getSOPInstanceAttributes from './utils/getSOPInstanceAttributes';
 

extensions/default/package.json

@@ -32,7 +32,7 @@
     "react": "^16.13.1",
     "react-dom": "^16.13.1",
     "webpack": "^4.0.0",
-    "dcmjs": "^0.12.4"
+    "dcmjs": "0.14.0"
   },
   "dependencies": {
     "@babel/runtime": "7.7.6"

extensions/default/src/DicomWebDataSource/index.js

@@ -12,9 +12,14 @@ import getImageId from './utils/getImageId';
 import * as dcmjs from 'dcmjs';
 import { retrieveStudyMetadata } from './retrieveStudyMetadata.js';
 
-const { naturalizeDataset } = dcmjs.data.DicomMetaDictionary;
+const { DicomMetaDictionary, DicomDict } = dcmjs.data;
+
+const { naturalizeDataset, denaturalizeDataset } = DicomMetaDictionary;
 const { urlUtil } = utils;
 
+const VERSION_NAME = 'OHIF-0.1';
+const SR_TRANSFER_SYNTAX_UID = '1.2.840.10008.1.2.1';
+
 /**
  *
  * @param {string} name - Data source name
@@ -128,6 +133,32 @@ function createDicomWebApi(dicomWebConfig) {
         },
       },
     },
+    store: {
+      dicom: async dataset => {
+        const meta = {
+          FileMetaInformationVersion:
+            dataset._meta.FileMetaInformationVersion.Value,
+          MediaStorageSOPClassUID: dataset.SOPClassUID,
+          MediaStorageSOPInstanceUID: dataset.SOPInstanceUID,
+          TransferSyntaxUID: SR_TRANSFER_SYNTAX_UID,
+          ImplementationClassUID: DicomMetaDictionary.uid(),
+          ImplementationVersionName: VERSION_NAME,
+        };
+
+        const denaturalized = denaturalizeDataset(meta);
+        const dicomDict = new DicomDict(denaturalized);
+
+        dicomDict.dict = denaturalizeDataset(dataset);
+
+        const part10Buffer = dicomDict.write();
+
+        const options = {
+          datasets: [part10Buffer],
+        };
+
+        await wadoDicomWebClient.storeInstances(options);
+      },
+    },
     retrieveSeriesMetadata: async ({ StudyInstanceUID } = {}) => {
       if (!StudyInstanceUID) {
         throw new Error(

extensions/default/src/Panels/WrappedPanelStudyBrowser.jsx

@@ -20,7 +20,7 @@ function WrappedPanelStudyBrowser({
 }) {
   // TODO: This should be made available a different way; route should have
   // already determined our datasource
-  const dataSource = extensionManager.getDataSources('dicomweb')[0];
+  const dataSource = extensionManager.getDataSources()[0];
   const _getStudiesForPatientByStudyInstanceUID = getStudiesForPatientByStudyInstanceUID.bind(
     null,
     dataSource

extensions/dicom-html/package.json

@@ -28,7 +28,7 @@
   },
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
-    "dcmjs": "^0.12.3",
+    "dcmjs": "0.14.0",
     "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": "4.16.0",
-    "dcmjs": "^0.12.3",
+    "dcmjs": "0.14.0",
     "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": "4.15.1",
-    "dcmjs": "^0.12.2",
+    "dcmjs": "0.14.0",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6"

extensions/dicom-sr/package.json

@@ -34,7 +34,7 @@
     "cornerstone-core": "^2.3.0",
     "cornerstone-math": "^0.1.8",
     "cornerstone-tools": "4.16.0",
-    "dcmjs": "^0.12.3",
+    "dcmjs": "0.14.0",
     "cornerstone-wado-image-loader": "^3.1.2",
     "dicom-parser": "^1.8.3",
     "hammerjs": "^2.0.8",

extensions/measurement-tracking/package.json

@@ -28,11 +28,12 @@
   },
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
-    "dcmjs": "^0.12.4",
+    "dcmjs": "0.14.0",
     "prop-types": "^15.6.2",
     "react": "^16.13.1",
     "react-dom": "^16.13.1",
-    "webpack": "^4.0.0"
+    "webpack": "^4.0.0",
+    "cornerstone-tools": "4.15.1"
   },
   "dependencies": {
     "@babel/runtime": "7.7.6",

extensions/measurement-tracking/src/panels/PanelMeasurementTableTracking/ActionButtons.jsx

@@ -2,10 +2,10 @@ import React from 'react';
 import PropTypes from 'prop-types';
 import { Button, ButtonGroup, Icon, IconButton } from '@ohif/ui';
 
-function ActionButtons() {
+function ActionButtons({ onExportClick, onCreateReportClick }) {
   return (
     <React.Fragment>
-      <ButtonGroup onClick={() => alert('Export')}>
+      <ButtonGroup onClick={onExportClick}>
         <Button
           className="px-2 py-2 text-base text-white bg-black border-primary-main"
           size="initial"
@@ -26,7 +26,7 @@ function ActionButtons() {
         variant="outlined"
         size="initial"
         color="inherit"
-        onClick={() => alert('Create Report')}
+        onClick={onCreateReportClick}
       >
         Create Report
       </Button>
@@ -34,4 +34,14 @@ function ActionButtons() {
   );
 }
 
+ActionButtons.propTypes = {
+  onExportClick: PropTypes.func,
+  onCreateReportClick: PropTypes.func,
+};
+
+ActionButtons.defaultProps = {
+  onExportClick: () => alert('Export'),
+  onCreateReportClick: () => alert('Create Report'),
+};
+
 export default ActionButtons;

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

@@ -1,10 +1,13 @@
 import React, { useEffect, useState } from 'react';
 import PropTypes from 'prop-types';
 import { StudySummary, MeasurementTable } from '@ohif/ui';
-import { DicomMetadataStore } from '@ohif/core';
+import { DicomMetadataStore, DICOMSR } from '@ohif/core';
 import { useDebounce } from '@hooks';
 import ActionButtons from './ActionButtons';
 import { useTrackedMeasurements } from '../../getContextModule';
+import cornerstoneTools from 'cornerstone-tools';
+import cornerstone from 'cornerstone-core';
+import dcmjs from 'dcmjs';
 
 const DISPLAY_STUDY_SUMMARY_INITIAL_VALUE = {
   key: undefined, //
@@ -13,7 +16,7 @@ const DISPLAY_STUDY_SUMMARY_INITIAL_VALUE = {
   description: undefined, // 'CHEST/ABD/PELVIS W CONTRAST',
 };
 
-function PanelMeasurementTableTracking({ servicesManager, commandsManager }) {
+function PanelMeasurementTableTracking({ servicesManager, extensionManager }) {
   const [measurementChangeTimestamp, setMeasurementsUpdated] = useState(
     Date.now().toString()
   );
@@ -102,6 +105,35 @@ function PanelMeasurementTableTracking({ servicesManager, commandsManager }) {
 
   const activeMeasurementItem = 0;
 
+  const onExportClick = () => {
+    const measurements = MeasurementService.getMeasurements();
+    const trackedMeasurements = measurements.filter(
+      m =>
+        trackedStudy === m.referenceStudyUID &&
+        trackedSeries.includes(m.referenceSeriesUID)
+    );
+
+    // TODO -> local download.
+    DICOMSR.downloadReport(trackedMeasurements, dataSource);
+  };
+
+  const onCreateReportClick = () => {
+    const measurements = MeasurementService.getMeasurements();
+    const trackedMeasurements = measurements.filter(
+      m =>
+        trackedStudy === m.referenceStudyUID &&
+        trackedSeries.includes(m.referenceSeriesUID)
+    );
+
+
+    const dataSources = extensionManager.getDataSources();
+    // TODO -> Eventually deal with multiple dataSources.
+    // Would need some way of saying which one is the "push" dataSource
+    const dataSource = dataSources[0];
+
+    DICOMSR.storeMeasurements(trackedMeasurements, dataSource);
+  };
+
   return (
     <>
       <div className="overflow-x-hidden overflow-y-auto invisible-scrollbar">
@@ -121,7 +153,10 @@ function PanelMeasurementTableTracking({ servicesManager, commandsManager }) {
         />
       </div>
       <div className="flex justify-center p-4">
-        <ActionButtons />
+        <ActionButtons
+          onExportClick={onExportClick}
+          onCreateReportClick={onCreateReportClick}
+        />
       </div>
     </>
   );

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": "0.12.2",
+    "dcmjs": "0.14.0",
     "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": "^0.12.4",
+    "dcmjs": "0.14.0",
     "dicomweb-client": "^0.6.0",
     "immer": "6.0.2",
     "isomorphic-base64": "^1.0.2",

platform/core/src/DICOMSR/dataExchange.js

@@ -6,6 +6,10 @@ import {
   stowSRFromMeasurements,
 } from './handleStructuredReport';
 import findMostRecentStructuredReport from './utils/findMostRecentStructuredReport';
+import cornerstoneTools from 'cornerstone-tools';
+import dcmjs from 'dcmjs';
+
+const { MeasurementReport } = dcmjs.adapters.Cornerstone;
 
 /**
  *
@@ -47,7 +51,7 @@ const retrieveMeasurements = server => {
  * @param {serverType} server
  * @returns {Object} With message to be displayed on success
  */
-const storeMeasurements = async (measurementData, filter, server) => {
+const storeMeasurementsOld = async (measurementData, filter, server) => {
   log.info('[DICOMSR] storeMeasurements');
 
   if (!server || server.type !== 'dicomWeb') {
@@ -78,4 +82,112 @@ const storeMeasurements = async (measurementData, filter, server) => {
   }
 };
 
-export { retrieveMeasurements, storeMeasurements };
+const downloadReport = measurementData => {
+  const srDataset = generateReport(measurementData);
+  const reportBlob = dcmjs.data.datasetToBlob(srDataset);
+
+  //Create a URL for the binary.
+  var objectUrl = URL.createObjectURL(reportBlob);
+  window.location.assign(objectUrl);
+};
+
+const generateReport = measurementData => {
+  const ids = measurementData.map(md => md.id);
+  const filteredToolState = _getFilteredCornerstoneToolState(ids);
+
+  const report = MeasurementReport.generateReport(
+    filteredToolState,
+    cornerstone.metaData
+  );
+
+  return report.dataset;
+};
+
+const storeMeasurements = async (measurementData, dataSource) => {
+  // 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');
+
+  if (!dataSource || !dataSource.store || !dataSource.store.dicom) {
+    log.error('[DICOMSR] datasource has no dataSource.store.dicom endpoint!');
+    return Promise.reject({});
+  }
+
+  const naturalizedReport = generateReport(measurementData);
+  const { StudyInstanceUID } = naturalizedReport;
+
+  try {
+    await dataSource.store.dicom(naturalizedReport);
+
+    if (StudyInstanceUID) {
+      studies.deleteStudyMetadataPromise(StudyInstanceUID);
+    }
+
+    return {
+      message: 'Measurements saved successfully',
+    };
+  } catch (error) {
+    log.error(
+      `[DICOMSR] Error while saving the measurements: ${error.message}`
+    );
+    throw new Error('Error while saving the measurements.');
+  }
+};
+
+function _getFilteredCornerstoneToolState(uidFilter) {
+  const globalToolState = cornerstoneTools.globalImageIdSpecificToolStateManager.saveToolState();
+  const filteredToolState = {};
+
+  function addToFilteredToolState(imageId, toolType, toolDataI) {
+    if (!filteredToolState[imageId]) {
+      filteredToolState[imageId] = {};
+    }
+
+    const imageIdSpecificToolState = filteredToolState[imageId];
+
+    if (!imageIdSpecificToolState[toolType]) {
+      imageIdSpecificToolState[toolType] = {
+        data: [],
+      };
+    }
+
+    const toolData = imageIdSpecificToolState[toolType].data;
+
+    toolData.push(toolDataI);
+  }
+
+  const uids = uidFilter.slice();
+  const imageIds = Object.keys(globalToolState);
+
+  for (let i = 0; i < imageIds.length; i++) {
+    const imageId = imageIds[i];
+    const imageIdSpecificToolState = globalToolState[imageId];
+
+    const toolTypes = Object.keys(imageIdSpecificToolState);
+
+    for (let j = 0; j < toolTypes.length; j++) {
+      const toolType = toolTypes[j];
+      const toolData = imageIdSpecificToolState[toolType].data;
+
+      if (toolData) {
+        for (let k = 0; k < toolData.length; k++) {
+          const toolDataK = toolData[k];
+          const uidIndex = uids.findIndex(uid => uid === toolDataK.id);
+
+          if (uidIndex !== -1) {
+            addToFilteredToolState(imageId, toolType, toolDataK);
+            uids.splice(uidIndex, 1);
+
+            if (!uids.length) {
+              return filteredToolState;
+            }
+          }
+        }
+      }
+    }
+  }
+
+  return filteredToolState;
+}
+
+export { retrieveMeasurements, storeMeasurements, downloadReport };

platform/core/src/DICOMSR/index.js

@@ -1,9 +1,14 @@
-import { retrieveMeasurements, storeMeasurements } from './dataExchange';
+import {
+  retrieveMeasurements,
+  storeMeasurements,
+  downloadReport,
+} from './dataExchange';
 import isToolSupported from './utils/isToolSupported';
 
 const DICOMSR = {
   retrieveMeasurements,
   storeMeasurements,
+  downloadReport,
   isToolSupported,
 };
 

platform/core/src/DataSources/IWebApiDataSource.js

@@ -15,6 +15,7 @@ import { DicomMetadataStore } from '@ohif/core';
 function create({
   query,
   retrieve,
+  store,
   retrieveSeriesMetadata,
   getImageIdsForDisplaySet,
 }) {
@@ -44,13 +45,20 @@ function create({
     series: {},
   };
 
+  const defaultStore = {
+    dicom: async naturalizedDataset => {
+      throw new Error(
+        'store.dicom(naturalizedDicom, StudyInstanceUID) not implemented for dataSource.'
+      );
+    },
+  };
+
   return {
     query: query || defaultQuery,
     retrieve: retrieve || defaultRetrieve,
+    store: store || defaultStore,
     getImageIdsForDisplaySet,
     retrieveSeriesMetadata,
-    // then go get all series level metadata.
-    // Store this in the DICOM MetadataStore.
   };
 }
 

platform/viewer/package.json

@@ -69,7 +69,7 @@
     "cornerstone-math": "^0.1.8",
     "cornerstone-tools": "4.16.0",
     "cornerstone-wado-image-loader": "^3.1.2",
-    "dcmjs": "^0.12.2",
+    "dcmjs": "0.14.0",
     "dicom-parser": "^1.8.3",
     "dicomweb-client": "^0.4.4",
     "dotenv-webpack": "^1.7.0",

yarn.lock

@@ -7353,10 +7353,10 @@ dateformat@^3.0.0:
   resolved "https://registry.yarnpkg.com/dateformat/-/dateformat-3.0.3.tgz#a6e37499a4d9a9cf85ef5872044d62901c9889ae"
   integrity sha512-jyCETtSl3VMZMWeRo7iY1FL19ges1t55hMo5yaam4Jrsm5EPL89UQkoQRyiI+Yf4k8r2ZpdngkV8hr1lIdjb3Q==
 
-dcmjs@^0.12.2, dcmjs@^0.12.4:
+dcmjs@0.14.0:
-  version "0.12.4"
+  version "0.14.0"
-  resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.12.4.tgz#82c24abdc357ea5281b78eb2cae8b781f7392aa3"
+  resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.14.0.tgz#0dc6cb2d15ddcff759bc9002f2a9704537735d1c"
-  integrity sha512-N1ZsXqZIysirqdytb7h572TyIjmxpvCjrzdjtQsuPN8gC2EpxsUHQ598CPzaJBpBy9i1kfKuq4h2Jwt99cr/QQ==
+  integrity sha512-VL/Ibxe5RDsc5j5SEv3aEqdlKuBXz81/bBuW59Or0cos9vgK3XnVl3rr0ct6DWXJGK8vGIUMBOguyd/NRvlN0w==
   dependencies:
     "@babel/polyfill" "^7.8.3"
     "@babel/runtime" "^7.8.4"