feat(dicomJSON): Add Loading Other Display Sets and JSON Metadata Gen…

…eration script (#3777)

.scripts/dicom-json-generator.js

@@ -0,0 +1,265 @@
+/*
+ * This script uses nodejs to generate a JSON file from a DICOM study folder.
+ * You need to have dcmjs installed in your project.
+ * The JSON file can be used to load the study into the OHIF Viewer. You can get more detail
+ * in the DICOM JSON Data source on docs.ohif.org
+ *
+ * Usage: node dicomStudyToJSONLaunch.js <studyFolder> <urlPrefix> <outputJSONPath>
+ *
+ * params:
+ * - studyFolder: path to the study folder
+ * - urlPrefix: prefix to the url that will be used to load the study into the viewer. For instance
+ *   we use https://ohif-assets.s3.us-east-2.amazonaws.com/dicom-json/data as the urlPrefix for the
+ *   example since the data is hosted on S3 and each study is in a folder. So the url in the generated
+ *   json file for the first instance of the first series of the first study will be
+ *   dicomweb:https://ohif-assets.s3.us-east-2.amazonaws.com/dicom-json/data/Series1/Instance1
+ * - outputJSONPath: path to the output JSON file
+ */
+const dcmjs = require('dcmjs');
+const path = require('path');
+const fs = require('fs').promises;
+
+const args = process.argv.slice(2);
+const [studyDirectory, urlPrefix, outputPath] = args;
+
+if (args.length !== 3) {
+  console.error('Usage: node dicomStudyToJSONLaunch.js <studyFolder> <urlPrefix> <outputJSONPath>');
+  process.exit(1);
+}
+
+const model = {
+  studies: [],
+};
+
+async function convertDICOMToJSON(studyDirectory, urlPrefix, outputPath) {
+  try {
+    const files = await recursiveReadDir(studyDirectory);
+    console.debug('Processing...');
+
+    for (const file of files) {
+      if (!file.includes('.DS_Store') && !file.includes('.xml')) {
+        const arrayBuffer = await fs.readFile(file);
+        const dicomDict = dcmjs.data.DicomMessage.readFile(arrayBuffer.buffer);
+        const instance = dcmjs.data.DicomMetaDictionary.naturalizeDataset(dicomDict.dict);
+
+        instance.fileLocation = createImageId(file, urlPrefix, studyDirectory);
+        processInstance(instance);
+      }
+    }
+
+    console.log('Successfully loaded data');
+
+    model.studies.forEach(study => {
+      study.NumInstances = findInstancesNumber(study);
+      study.Modalities = findModalities(study).join('/');
+    });
+
+    await fs.writeFile(outputPath, JSON.stringify(model, null, 2));
+    console.log('JSON saved');
+  } catch (error) {
+    console.error(error);
+  }
+}
+
+async function recursiveReadDir(dir) {
+  let results = [];
+  const list = await fs.readdir(dir);
+  for (const file of list) {
+    const filePath = path.resolve(dir, file);
+    const stat = await fs.stat(filePath);
+    if (stat.isDirectory()) {
+      const res = await recursiveReadDir(filePath);
+      results = results.concat(res);
+    } else {
+      results.push(filePath);
+    }
+  }
+  return results;
+}
+
+function createImageId(fileLocation, urlPrefix, studyDirectory) {
+  const relativePath = path.relative(studyDirectory, fileLocation);
+  const normalizedPath = path.normalize(relativePath).replace(/\\/g, '/');
+  return `dicomweb:${urlPrefix}${normalizedPath}`;
+}
+
+function processInstance(instance) {
+  const { StudyInstanceUID, SeriesInstanceUID } = instance;
+  let study = getStudy(StudyInstanceUID);
+
+  if (!study) {
+    study = createStudyMetadata(StudyInstanceUID, instance);
+    model.studies.push(study);
+  }
+
+  let series = getSeries(StudyInstanceUID, SeriesInstanceUID);
+
+  if (!series) {
+    series = createSeriesMetadata(instance);
+    study.series.push(series);
+  }
+
+  const instanceMetaData =
+    instance.NumberOfFrames > 1
+      ? createInstanceMetaDataMultiFrame(instance)
+      : createInstanceMetaData(instance);
+
+  series.instances.push(...[].concat(instanceMetaData));
+}
+
+function getStudy(StudyInstanceUID) {
+  return model.studies.find(study => study.StudyInstanceUID === StudyInstanceUID);
+}
+
+function getSeries(StudyInstanceUID, SeriesInstanceUID) {
+  const study = getStudy(StudyInstanceUID);
+  return study
+    ? study.series.find(series => series.SeriesInstanceUID === SeriesInstanceUID)
+    : undefined;
+}
+
+const findInstancesNumber = study => {
+  let numInstances = 0;
+  study.series.forEach(aSeries => {
+    numInstances = numInstances + aSeries.instances.length;
+  });
+  return numInstances;
+};
+
+const findModalities = study => {
+  let modalities = new Set();
+  study.series.forEach(aSeries => {
+    modalities.add(aSeries.Modality);
+  });
+  return Array.from(modalities);
+};
+
+function createStudyMetadata(StudyInstanceUID, instance) {
+  return {
+    StudyInstanceUID,
+    StudyDescription: instance.StudyDescription,
+    StudyDate: instance.StudyDate,
+    StudyTime: instance.StudyTime,
+    PatientName: instance.PatientName,
+    PatientID: instance.PatientID || '1234', // this is critical to have
+    AccessionNumber: instance.AccessionNumber,
+    PatientAge: instance.PatientAge,
+    PatientSex: instance.PatientSex,
+    PatientWeight: instance.PatientWeight,
+    series: [],
+  };
+}
+function createSeriesMetadata(instance) {
+  return {
+    SeriesInstanceUID: instance.SeriesInstanceUID,
+    SeriesDescription: instance.SeriesDescription,
+    SeriesNumber: instance.SeriesNumber,
+    SeriesTime: instance.SeriesTime,
+    Modality: instance.Modality,
+    SliceThickness: instance.SliceThickness,
+    instances: [],
+  };
+}
+function commonMetaData(instance) {
+  return {
+    Columns: instance.Columns,
+    Rows: instance.Rows,
+    InstanceNumber: instance.InstanceNumber,
+    SOPClassUID: instance.SOPClassUID,
+    AcquisitionNumber: instance.AcquisitionNumber,
+    PhotometricInterpretation: instance.PhotometricInterpretation,
+    BitsAllocated: instance.BitsAllocated,
+    BitsStored: instance.BitsStored,
+    PixelRepresentation: instance.PixelRepresentation,
+    SamplesPerPixel: instance.SamplesPerPixel,
+    PixelSpacing: instance.PixelSpacing,
+    HighBit: instance.HighBit,
+    ImageOrientationPatient: instance.ImageOrientationPatient,
+    ImagePositionPatient: instance.ImagePositionPatient,
+    FrameOfReferenceUID: instance.FrameOfReferenceUID,
+    ImageType: instance.ImageType,
+    Modality: instance.Modality,
+    SOPInstanceUID: instance.SOPInstanceUID,
+    SeriesInstanceUID: instance.SeriesInstanceUID,
+    StudyInstanceUID: instance.StudyInstanceUID,
+    WindowCenter: instance.WindowCenter,
+    WindowWidth: instance.WindowWidth,
+    RescaleIntercept: instance.RescaleIntercept,
+    RescaleSlope: instance.RescaleSlope,
+  };
+}
+
+function conditionalMetaData(instance) {
+  return {
+    ...(instance.ConceptNameCodeSequence && {
+      ConceptNameCodeSequence: instance.ConceptNameCodeSequence,
+    }),
+    ...(instance.SeriesDate && { SeriesDate: instance.SeriesDate }),
+    ...(instance.ReferencedSeriesSequence && {
+      ReferencedSeriesSequence: instance.ReferencedSeriesSequence,
+    }),
+    ...(instance.SharedFunctionalGroupsSequence && {
+      SharedFunctionalGroupsSequence: instance.SharedFunctionalGroupsSequence,
+    }),
+    ...(instance.PerFrameFunctionalGroupsSequence && {
+      PerFrameFunctionalGroupsSequence: instance.PerFrameFunctionalGroupsSequence,
+    }),
+    ...(instance.ContentSequence && { ContentSequence: instance.ContentSequence }),
+    ...(instance.ContentTemplateSequence && {
+      ContentTemplateSequence: instance.ContentTemplateSequence,
+    }),
+    ...(instance.CurrentRequestedProcedureEvidenceSequence && {
+      CurrentRequestedProcedureEvidenceSequence: instance.CurrentRequestedProcedureEvidenceSequence,
+    }),
+    ...(instance.CodingSchemeIdentificationSequence && {
+      CodingSchemeIdentificationSequence: instance.CodingSchemeIdentificationSequence,
+    }),
+    ...(instance.RadiopharmaceuticalInformationSequence && {
+      RadiopharmaceuticalInformationSequence: instance.RadiopharmaceuticalInformationSequence,
+    }),
+    ...(instance.ROIContourSequence && {
+      ROIContourSequence: instance.ROIContourSequence,
+    }),
+    ...(instance.StructureSetROISequence && {
+      StructureSetROISequence: instance.StructureSetROISequence,
+    }),
+    ...(instance.ReferencedFrameOfReferenceSequence && {
+      ReferencedFrameOfReferenceSequence: instance.ReferencedFrameOfReferenceSequence,
+    }),
+    ...(instance.CorrectedImage && { CorrectedImage: instance.CorrectedImage }),
+    ...(instance.Units && { Units: instance.Units }),
+    ...(instance.DecayCorrection && { DecayCorrection: instance.DecayCorrection }),
+    ...(instance.AcquisitionDate && { AcquisitionDate: instance.AcquisitionDate }),
+    ...(instance.AcquisitionTime && { AcquisitionTime: instance.AcquisitionTime }),
+    ...(instance.PatientWeight && { PatientWeight: instance.PatientWeight }),
+    ...(instance.NumberOfFrames && { NumberOfFrames: instance.NumberOfFrames }),
+    ...(instance.FrameTime && { FrameTime: instance.FrameTime }),
+    ...(instance.EncapsulatedDocument && { EncapsulatedDocument: instance.EncapsulatedDocument }),
+    ...(instance.SequenceOfUltrasoundRegions && {
+      SequenceOfUltrasoundRegions: instance.SequenceOfUltrasoundRegions,
+    }),
+  };
+}
+
+function createInstanceMetaData(instance) {
+  const metadata = {
+    ...commonMetaData(instance),
+    ...conditionalMetaData(instance),
+  };
+  return { metadata, url: instance.fileLocation };
+}
+
+function createInstanceMetaDataMultiFrame(instance) {
+  const instances = [];
+  const commonData = commonMetaData(instance);
+  const conditionalData = conditionalMetaData(instance);
+
+  for (let i = 1; i <= instance.NumberOfFrames; i++) {
+    const metadata = { ...commonData, ...conditionalData };
+    const result = { metadata, url: instance.fileLocation + `?frame=${i}` };
+    instances.push(result);
+  }
+  return instances;
+}
+
+convertDICOMToJSON(studyDirectory, urlPrefix, outputPath);

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

@@ -200,7 +200,11 @@ function _checkIfCanAddMeasurementsToDisplaySet(srDisplaySet, newDisplaySet, dat
     return;
   }
 
-  const { sopClassUids, images } = newDisplaySet;
+  if (newDisplaySet.unsupported) {
+    return;
+  }
+
+  const { sopClassUids } = newDisplaySet;
 
   // Check if any have the newDisplaySet is the correct SOPClass.
   unloadedMeasurements = unloadedMeasurements.filter(measurement =>

extensions/cornerstone/src/utils/dicomLoaderService.js

@@ -176,6 +176,7 @@ class DicomLoaderService {
       authorizationHeaders,
       wadoRoot,
       wadoUri,
+      instance,
     } = dataset;
     // Retrieve wadors or just try to fetch wadouri
     if (!someInvalidStrings(wadoRoot)) {
@@ -188,6 +189,13 @@ class DicomLoaderService {
       );
     } else if (!someInvalidStrings(wadoUri)) {
       return fetchIt(wadoUri, { headers: authorizationHeaders });
+    } else if (!someInvalidStrings(instance?.url)) {
+      // make sure the url is absolute, remove the scope
+      // from it if it is not absolute. For instance it might be dicomweb:http://....
+      // and we need to remove the dicomweb: part
+      const url = instance.url;
+      const absoluteUrl = url.startsWith('http') ? url : url.substring(url.indexOf(':') + 1);
+      return fetchIt(absoluteUrl, { headers: authorizationHeaders });
     }
   }
 

extensions/default/src/DicomJSONDataSource/index.js

@@ -25,6 +25,23 @@ let _store = {
   // }
 };
 
+function wrapSequences(obj) {
+  return Object.keys(obj).reduce(
+    (acc, key) => {
+      if (typeof obj[key] === 'object' && obj[key] !== null) {
+        // Recursively wrap sequences for nested objects
+        acc[key] = wrapSequences(obj[key]);
+      } else {
+        acc[key] = obj[key];
+      }
+      if (key.endsWith('Sequence')) {
+        acc[key] = OHIF.utils.addAccessors(acc[key]);
+      }
+      return acc;
+    },
+    Array.isArray(obj) ? [] : {}
+  );
+}
 const getMetaDataByURL = url => {
   return _store.urls.find(metaData => metaData.url === url);
 };
@@ -190,8 +207,14 @@ function createDicomJSONApi(dicomJsonConfig) {
           const numberOfSeries = series.length;
           series.forEach((series, index) => {
             const instances = series.instances.map(instance => {
+              // for instance.metadata if the key ends with sequence then
+              // we need to add a proxy to the first item in the sequence
+              // so that we can access the value of the sequence
+              // by using sequenceName.value
+              const modifiedMetadata = wrapSequences(instance.metadata);
+
               const obj = {
-                ...instance.metadata,
+                ...modifiedMetadata,
                 url: instance.url,
                 imageId: instance.url,
                 ...series,