feat(dicomJSON): Add Loading Other Display Sets and JSON Metadata Generation 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,

platform/core/src/utils/addAccessors.js

@@ -0,0 +1,66 @@
+const handler = {
+  /**
+   * Get a proxied value from the array or property value
+   * Note that the property value get works even if you update the underlying object.
+   * Also, return true of proxy.__isProxy in order to distinguish proxies and not double proxy them.
+   */
+  get: (target, prop) => {
+    if (prop == '__isProxy') {
+      return true;
+    }
+    if (prop in target) {
+      return target[prop];
+    }
+    return target[0][prop];
+  },
+
+  set: (obj, prop, value) => {
+    if (typeof prop === 'number' || prop in obj) {
+      obj[prop] = value;
+    } else {
+      obj[0][prop] = value;
+    }
+    return true;
+  },
+};
+
+/**
+ * Add a proxy object for sqZero or the src[0] element if sqZero is unspecified, AND
+ * src is an array of length 1.
+ *
+ * If sqZero isn't passed in, then assume this is a create call on the destination object
+ * itself, by:
+ * 1. If not an object, return dest
+ * 2. If an array of length != 1, return dest
+ * 3. If an array, use dest[0] as sqZero
+ * 4. Use dest as sqZero
+ *
+ * @example
+ * src = [{a:5,b:'string', c:null}]
+ * addAccessors(src)
+ * src.c = 'outerChange'
+ * src[0].b='innerChange'
+ *
+ * assert src.a===5
+ * assert src[0].c === 'outerChange'
+ * assert src.b === 'innerChange'
+ */
+const addAccessors = (dest, sqZero) => {
+  if (dest.__isProxy) {
+    return dest;
+  }
+  let itemZero = sqZero;
+  if (itemZero === undefined) {
+    if (typeof dest !== 'object') {
+      return dest;
+    }
+    if (Array.isArray(dest) && dest.length !== 1) {
+      return dest;
+    }
+    itemZero = Array.isArray(dest) ? dest[0] : dest;
+  }
+  const ret = [itemZero];
+  return new Proxy(ret, handler);
+};
+
+export default addAccessors;

platform/core/src/utils/index.js

@@ -27,6 +27,7 @@ import debounce from './debounce';
 import roundNumber from './roundNumber';
 import downloadCSVReport from './downloadCSVReport';
 import isEqualWithin from './isEqualWithin';
+import addAccessors from './addAccessors';
 import {
   sortStudy,
   sortStudySeries,
@@ -65,6 +66,7 @@ const utils = {
   Queue,
   isDicomUid,
   isEqualWithin,
+  addAccessors,
   resolveObjectPath,
   hierarchicalListUtils,
   progressTrackingUtils,

platform/core/src/utils/index.test.js

@@ -40,6 +40,7 @@ describe('Top level exports', () => {
       'progressTrackingUtils',
       'subscribeToNextViewportGridChange',
       'uuidv4',
+      'addAccessors',
     ].sort();
 
     const exports = Object.keys(utils.default).sort();

platform/docs/docs/configuration/dataSources/dicom-json.md

@@ -28,6 +28,20 @@ dataset. Let's have a look at the JSON file:
 JSON file stores the metadata for the study level, series level and instance
 level. A JSON launch file should follow the same structure as the one below.
 
+:::tip
+You can use our script to generate the JSON file from a hosted endpoint. See
+`.scripts/dicom-json-generator.js`
+
+You could run it like this:
+
+```bash
+node .scripts/dicom-json-generator.js '/path/to/study/folder' 'url/to/dicom/server/folder' 'json/output/file.json'
+```
+
+Some modalities require additional metadata to be added to the JSON file. You can read more about the minimum amount of metadata required for the viewer to work [here](../../faq.md#what-are-the-list-of-required-metadata-for-the-ohif-viewer-to-work). We will handle this in the script. For example, the script will add the CodeSequences for SR in order to display the measurements in the viewer.
+:::
+
+
 Note that at the instance level metadata we are storing both the `metadata` and
 also the `url` for the dicom file on the dicom server. In this case we are
 referring to
@@ -35,6 +49,8 @@ referring to
 which is stored in another directory in our s3. (You can actually try
 downloading the dicom file by opening the url in your browser).
 
+The URL to the script in the given example is `https://ohif-dicom-json-example.s3.amazonaws.com/LIDC-IDRI-0001/01-01-2000-30178`. This URL serves as the parent directory that contains all the series within their respective folders.
+
 ```json
 {
   "studies": [

platform/docs/docs/configuration/url.md

@@ -62,7 +62,9 @@ WorkList by adding the `dataSources` query parameter.
 /?dataSources=orthanc
 ```
 
-Note: you should pass the `sourceName` of the data source in the configuration file (not the friendly name nor the name)
+Note1: You should pass the `sourceName` of the data source in the configuration file (not the friendly name nor the name)
+Note2: Make sure that the configuration file you are using actually includes that data source. You cannot use a data source from another configuration file.
+
 
 :::tip