refactor: 💡 Move DICOMSR code to @ohif/core project (#1310)

* Move DICOMSR to @ohif/core

* refactor: 💡 Move DICOMSR code to @ohif/core project

We've just merged support for DICOM Structured Reports. Today, support
for this feature lives in the @ohif/viewer project in it's lib folder.
Ideally, it should be moved to @ohif/core and given a clear public API
and unit tests.

Closes: #1282

* Update imports

* CR Update: Update imports

platform/core/src/DICOMSR/dataExchange.js

@@ -0,0 +1,80 @@
+import log from '../log';
+import studies from '../studies';
+import utils from '../utils';
+import {
+  retrieveMeasurementFromSR,
+  stowSRFromMeasurements,
+} from './handleStructuredReport';
+import findMostRecentStructuredReport from './utils/findMostRecentStructuredReport';
+
+/**
+ *
+ * @typedef serverType
+ * @property {string} type - type of the server
+ * @property {string} wadoRoot - server wado root url
+ *
+ */
+
+/**
+ * Function to be registered into MeasurementAPI to retrieve measurements from DICOM Structured Reports
+ *
+ * @param {serverType} server
+ * @returns {Promise} Should resolve with OHIF measurementData object
+ */
+const retrieveMeasurements = server => {
+  log.info('[DICOMSR] retrieveMeasurements');
+
+  if (!server || server.type !== 'dicomWeb') {
+    log.error('[DICOMSR] DicomWeb server is required!');
+    return Promise.reject({});
+  }
+
+  const serverUrl = server.wadoRoot;
+  const studies = utils.studyMetadataManager.all();
+  const latestSeries = findMostRecentStructuredReport(studies);
+
+  if (!latestSeries) return Promise.resolve({});
+
+  return retrieveMeasurementFromSR(latestSeries, studies, serverUrl);
+};
+
+/**
+ *  Function to be registered into MeasurementAPI to store measurements into DICOM Structured Reports
+ *
+ * @param {Object} measurementData - OHIF measurementData object
+ * @param {Object} filter
+ * @param {serverType} server
+ * @returns {Object} With message to be displayed on success
+ */
+const storeMeasurements = async (measurementData, filter, server) => {
+  log.info('[DICOMSR] storeMeasurements');
+
+  if (!server || server.type !== 'dicomWeb') {
+    log.error('[DICOMSR] DicomWeb server is required!');
+    return Promise.reject({});
+  }
+
+  const serverUrl = server.wadoRoot;
+  const firstMeasurementKey = Object.keys(measurementData)[0];
+  const firstMeasurement = measurementData[firstMeasurementKey][0];
+  const studyInstanceUid =
+    firstMeasurement && firstMeasurement.studyInstanceUid;
+
+  try {
+    await stowSRFromMeasurements(measurementData, serverUrl);
+    if (studyInstanceUid) {
+      studies.deleteStudyMetadataPromise(studyInstanceUid);
+    }
+
+    return {
+      message: 'Measurements were saved with success',
+    };
+  } catch (error) {
+    log.error(
+      `[DICOMSR] Error while saving the measurements: ${error.message}`
+    );
+    throw new Error('Error while saving the measurements.');
+  }
+};
+
+export { retrieveMeasurements, storeMeasurements };

platform/core/src/DICOMSR/handleStructuredReport.js

@@ -0,0 +1,84 @@
+import * as dcmjs from 'dcmjs';
+import { api } from 'dicomweb-client';
+
+import DICOMWeb from '../DICOMWeb';
+import parseDicomStructuredReport from './parseDicomStructuredReport';
+import parseMeasurementsData from './parseMeasurementsData';
+import getAllDisplaySets from './utils/getAllDisplaySets';
+
+const VERSION_NAME = 'dcmjs-0.0';
+const TRANSFER_SYNTAX_UID = '1.2.840.10008.1.2.1';
+
+/**
+ * Function to retrieve measurements from DICOM Structured Reports coming from determined server
+ *
+ * @param {Array} series - List of all series metaData loaded
+ * @param {Array} studies - List of all studies metaData loaded
+ * @param {string} serverUrl - Server URL to be used on request
+ * @returns {Object} MeasurementData
+ */
+const retrieveMeasurementFromSR = async (series, studies, serverUrl) => {
+  const config = {
+    url: serverUrl,
+    headers: DICOMWeb.getAuthorizationHeader(),
+  };
+
+  const dicomWeb = new api.DICOMwebClient(config);
+
+  const instance = series.getFirstInstance();
+  const options = {
+    studyInstanceUID: instance.getStudyInstanceUID(),
+    seriesInstanceUID: instance.getSeriesInstanceUID(),
+    sopInstanceUID: instance.getSOPInstanceUID(),
+  };
+
+  const part10SRArrayBuffer = await dicomWeb.retrieveInstance(options);
+  const displaySets = getAllDisplaySets(studies);
+  const measurementsData = parseDicomStructuredReport(
+    part10SRArrayBuffer,
+    displaySets
+  );
+
+  return measurementsData;
+};
+
+/**
+ * Function to store measurements to DICOM Structured Reports in determined server
+ *
+ * @param {Object} measurements - OHIF measurementData object
+ * @param {string} serverUrl - Server URL to be used on request
+ * @returns {Promise}
+ */
+const stowSRFromMeasurements = async (measurements, serverUrl) => {
+  const { dataset } = parseMeasurementsData(measurements);
+  const { DicomMetaDictionary, DicomDict } = dcmjs.data;
+  const meta = {
+    FileMetaInformationVersion: dataset._meta.FileMetaInformationVersion.Value,
+    MediaStorageSOPClassUID: dataset.SOPClassUID,
+    MediaStorageSOPInstanceUID: dataset.SOPInstanceUID,
+    TransferSyntaxUID: TRANSFER_SYNTAX_UID,
+    ImplementationClassUID: DicomMetaDictionary.uid(),
+    ImplementationVersionName: VERSION_NAME,
+  };
+
+  const denaturalized = DicomMetaDictionary.denaturalizeDataset(meta);
+  const dicomDict = new DicomDict(denaturalized);
+
+  dicomDict.dict = DicomMetaDictionary.denaturalizeDataset(dataset);
+
+  const part10Buffer = dicomDict.write();
+
+  const config = {
+    url: serverUrl,
+    headers: DICOMWeb.getAuthorizationHeader(),
+  };
+
+  const dicomWeb = new api.DICOMwebClient(config);
+  const options = {
+    datasets: [part10Buffer],
+  };
+
+  await dicomWeb.storeInstances(options);
+};
+
+export { retrieveMeasurementFromSR, stowSRFromMeasurements };

platform/core/src/DICOMSR/index.js

@@ -0,0 +1,10 @@
+import { retrieveMeasurements, storeMeasurements } from './dataExchange';
+import isToolSupported from './utils/isToolSupported';
+
+const DICOMSR = {
+  retrieveMeasurements,
+  storeMeasurements,
+  isToolSupported,
+};
+
+export default DICOMSR;

platform/core/src/DICOMSR/parseDicomStructuredReport.js

@@ -0,0 +1,95 @@
+import * as dcmjs from 'dcmjs';
+
+import findInstanceMetadataBySopInstanceUid from './utils/findInstanceMetadataBySopInstanceUid';
+
+/**
+ * Function to parse the part10 array buffer that comes from a DICOM Structured report into measurementData
+ * measurementData format is a viewer specific format to be stored into the redux and consumed by other components
+ * (e.g. measurement table)
+ *
+ * @param {ArrayBuffer} part10SRArrayBuffer
+ * @param {Array} displaySets
+ * @returns
+ */
+const parseDicomStructuredReport = (part10SRArrayBuffer, displaySets) => {
+  // Get the dicom data as an Object
+  const dicomData = dcmjs.data.DicomMessage.readFile(part10SRArrayBuffer);
+  const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
+    dicomData.dict
+  );
+
+  const { MeasurementReport } = dcmjs.adapters.Cornerstone;
+  const storedMeasurementByToolType = MeasurementReport.generateToolState(
+    dataset
+  );
+  const measurementData = {};
+  let measurementNumber = 0;
+
+  Object.keys(storedMeasurementByToolType).forEach(toolName => {
+    const measurements = storedMeasurementByToolType[toolName];
+    measurementData[toolName] = [];
+
+    measurements.forEach(measurement => {
+      const instanceMetadata = findInstanceMetadataBySopInstanceUid(
+        displaySets,
+        measurement.sopInstanceUid
+      );
+      const { _study: study, _series: series } = instanceMetadata;
+      const { studyInstanceUid, patientId } = study;
+      const { seriesInstanceUid } = series;
+      const { sopInstanceUid, frameIndex } = measurement;
+      const imagePath = getImagePath(
+        studyInstanceUid,
+        seriesInstanceUid,
+        sopInstanceUid,
+        frameIndex
+      );
+
+      const imageId = instanceMetadata.getImageId();
+      if (!imageId) {
+        return;
+      }
+
+      // TODO: We need the currentTimepointID set into the viewer
+      const currentTimepointId = 'TimepointId';
+
+      const toolData = Object.assign({}, measurement, {
+        imageId,
+        imagePath,
+        seriesInstanceUid,
+        studyInstanceUid,
+        patientId,
+        measurementNumber: ++measurementNumber,
+        timepointId: currentTimepointId,
+        toolType: toolName,
+        _id: imageId + measurementNumber,
+      });
+
+      measurementData[toolName].push(toolData);
+    });
+  });
+
+  return measurementData;
+};
+
+/**
+ * Function to create imagePath with all imageData related
+ *
+ * @param {string} studyInstanceUid
+ * @param {string} seriesInstanceUid
+ * @param {string} sopInstanceUid
+ * @param {string} frameIndex
+ * @returns
+ */
+const getImagePath = (
+  studyInstanceUid,
+  seriesInstanceUid,
+  sopInstanceUid,
+  frameIndex
+) => {
+  return [studyInstanceUid, seriesInstanceUid, sopInstanceUid, frameIndex].join(
+    '_'
+  );
+};
+
+export default parseDicomStructuredReport;

platform/core/src/DICOMSR/parseMeasurementsData.js

@@ -0,0 +1,57 @@
+import * as dcmjs from 'dcmjs';
+import cornerstone from 'cornerstone-core';
+
+import log from '../log';
+import measurements from '../measurements';
+import isToolSupported from './utils/isToolSupported';
+
+/**
+ * Function to parse OHIF viewer measurementData into a dcmjs MeasurementReport
+ *
+ * @param {Object} measurementsData - OHIF measurementData object
+ * @returns {Object} Dataset: measurement report from dcmjs
+ */
+const parseMeasurementsData = measurementsData => {
+  const { MeasurementReport } = dcmjs.adapters.Cornerstone;
+  const { getImageIdForImagePath } = measurements;
+
+  const toolState = {};
+  const unsupportedTools = [];
+
+  Object.keys(measurementsData).forEach(measurementType => {
+    const annotations = measurementsData[measurementType];
+
+    annotations.forEach(annotation => {
+      const { toolType, imagePath } = annotation;
+
+      if (isToolSupported(toolType)) {
+        const imageId = getImageIdForImagePath(imagePath);
+        toolState[imageId] = toolState[imageId] || {};
+        toolState[imageId][toolType] = toolState[imageId][toolType] || {
+          data: [],
+        };
+
+        toolState[imageId][toolType].data.push(annotation);
+      } else {
+        unsupportedTools.push(toolType);
+      }
+    });
+  });
+
+  if (unsupportedTools.length > 0) {
+    log.warn(
+      `[DICOMSR] Tooltypes not supported: ${unsupportedTools.join(', ')}`
+    );
+  }
+
+  const report = MeasurementReport.generateReport(
+    toolState,
+    cornerstone.metaData
+  );
+
+  return {
+    dataset: report.dataset,
+  };
+};
+
+export default parseMeasurementsData;

platform/core/src/DICOMSR/utils/findInstanceMetadataBySopInstanceUid.js

@@ -0,0 +1,24 @@
+/**
+ *  Should Find the requested instance metadata into the displaySets and return
+ *
+ * @param {Array} displaySets - List of displaySets
+ * @param {string} sopInstanceUid - sopInstanceUID to look for
+ * @returns {Object} - instance metadata found
+ */
+const findInstanceMetadataBySopInstanceUid = (displaySets, sopInstanceUid) => {
+  let instanceFound;
+
+  displaySets.find(displaySet => {
+    if (!displaySet.images) return false;
+
+    instanceFound = displaySet.images.find(
+      instanceMetadata => instanceMetadata._sopInstanceUID === sopInstanceUid
+    );
+
+    return !!instanceFound;
+  });
+
+  return instanceFound;
+};
+
+export default findInstanceMetadataBySopInstanceUid;

platform/core/src/DICOMSR/utils/findMostRecentStructuredReport.js

@@ -0,0 +1,60 @@
+/**
+ * Should find the most recent Structured Report metadata
+ *
+ * @param {Array} studies
+ * @returns {Object} Series
+ */
+const findMostRecentStructuredReport = studies => {
+  let mostRecentStructuredReport;
+
+  studies.forEach(study => {
+    const allSeries = study.getSeries ? study.getSeries() : [];
+    allSeries.forEach(series => {
+      if (isStructuredReportSeries(series)) {
+        if (
+          !mostRecentStructuredReport ||
+          compareSeriesDate(series, mostRecentStructuredReport)
+        ) {
+          mostRecentStructuredReport = series;
+        }
+      }
+    });
+  });
+
+  return mostRecentStructuredReport;
+};
+
+/**
+ *  Checks if series sopClassUID matches with the supported Structured Reports sopClassUID
+ *
+ * @param {Object} series - Series metadata
+ * @returns {boolean}
+ */
+const isStructuredReportSeries = series => {
+  const supportedSopClassUIDs = [
+    '1.2.840.10008.5.1.4.1.1.88.22',
+    '1.2.840.10008.5.1.4.1.1.11.1',
+  ];
+
+  const firstInstance = series.getFirstInstance();
+  const sopClassUid = firstInstance._instance.sopClassUid;
+
+  return supportedSopClassUIDs.includes(sopClassUid);
+};
+
+/**
+ *  Checkes if series1 is newer than series2
+ *
+ * @param {Object} series1 - Series Metadata 1
+ * @param {Object} series2 - Series Metadata 2
+ * @returns {boolean} true/false if series1 is newer than series2
+ */
+const compareSeriesDate = (series1, series2) => {
+  return (
+    series1._data.seriesDate > series2._data.seriesDate ||
+    (series1._data.seriesDate === series2._data.seriesDate &&
+      series1._data.seriesTime > series2._data.seriesTime)
+  );
+};
+
+export default findMostRecentStructuredReport;

platform/core/src/DICOMSR/utils/getAllDisplaySets.js

@@ -0,0 +1,19 @@
+/**
+ * Retrieve a list of all displaySets of all studies
+ *
+ * @param {Object} studies - List of studies loaded into the viewer
+ * @returns {Object} List of DisplaySets
+ */
+const getAllDisplaySets = studies => {
+  let allDisplaySets = [];
+
+  studies.forEach(study => {
+    if (study.getDisplaySets) {
+      allDisplaySets = allDisplaySets.concat(study.getDisplaySets());
+    }
+  });
+
+  return allDisplaySets;
+};
+
+export default getAllDisplaySets;

platform/core/src/DICOMSR/utils/isToolSupported.js

@@ -0,0 +1,14 @@
+import * as dcmjs from 'dcmjs';
+
+/**
+ *  Checks if dcmjs has support to determined tool
+ *
+ * @param {string} toolName
+ * @returns {boolean}
+ */
+const isToolSupported = toolName => {
+  const adapter = dcmjs.adapters.Cornerstone;
+  return !!adapter[toolName];
+};
+
+export default isToolSupported;

platform/core/src/index.js

@@ -5,6 +5,7 @@ import { ServicesManager } from './services';
 import classes, { CommandsManager, HotkeysManager } from './classes/';
 
 import DICOMWeb from './DICOMWeb';
+import DICOMSR from './DICOMSR';
 import cornerstone from './cornerstone.js';
 import hangingProtocols from './hanging-protocols';
 import header from './header.js';
@@ -46,6 +47,7 @@ const OHIF = {
   object,
   log,
   DICOMWeb,
+  DICOMSR,
   viewer: {},
   measurements,
   hangingProtocols,
@@ -76,6 +78,7 @@ export {
   object,
   log,
   DICOMWeb,
+  DICOMSR,
   measurements,
   hangingProtocols,
   //

platform/core/src/index.test.js

@@ -28,6 +28,7 @@ describe('Top level exports', () => {
       'object',
       'log',
       'DICOMWeb',
+      'DICOMSR',
       'OHIF', //
       'measurements',
       'hangingProtocols',