fix: 🐛 Add DicomLoaderService & FileLoaderService to fix SR, PDF, and SEG support in local file and WADO-RS-only use cases (#862)

* fix: 🐛 Local file: failing when retrieving segmentation data

Fix segmentation data retrieval issues for local file. Changed from
fecthing to use cornerstone loadAndCache method

BREAKING CHANGE: DICOM Seg

Closes: part of #838

* Switch SEG retrieval to WADO-RS

* Forgot a debugger

* refactor: 💡 Code refactor. Minor changes into methods

* fix: 🐛 Load local files: PDF

Items:
1. FileLoaderService: used for serveral operations on local files(load it,  get list of studies, group them, accepting dicom and pdf)
2. DicomLoaderService: used for loading dicom based on dataset and studies. Depending on type of dicom loader might change. WIP
3. Refactor PDF and handleSegmentationStorage to use DicomLoaderService

* fix: 🐛 Code review

* fix: 🐛 Code review. Changed:Folder organization and dicom file

Move fileLoaderService and others to a specific folder. When loading
dicom file change to only retrieve the file(not use cornerstone to cache
or anything else).

* fix: 🐛 Code review. Move dicomLoaderService to core

Moved dicomLoaderService to ohif/core and localFileLoaders to a specific
folder.

* fix: 🐛 Code review

Simplified method to get study for dicom file. Added error handling on
file loading. DicomLoaderService to be exposed on ohif/core/utils
instead.

* fix: 🐛 Reduce local load to one method only

Reduced local file load to one method only

* fix: 🐛 HTML to use dicomLoaderService. Prefer wadors than (uri)

* fix: 🐛 Code implementation for multiframe files

* fix: 🐛 Code review. Default local loader to dicom

Closes: 838

* fix: 🐛 Code review. Use relative path to require DICOMWeb

Closes: 838

* fix: 🐛 Code review. Fix unit test. Added DicomLoaderService mod

Closes: 838

* fix: 🐛 Code review. Add 'Seg' on left thumb

When getting/creating dataset get modality for file/image read

Closes: 838

extensions/cornerstone/src/handleSegmentationStorage.js

@@ -4,7 +4,7 @@ import OHIF from '@ohif/core';
 import cornerstone from 'cornerstone-core';
 import cornerstoneTools from 'cornerstone-tools';
 
-const { StackManager } = OHIF.utils;
+const { StackManager, DicomLoaderService } = OHIF.utils;
 
 function getDisplaySet(studies, studyInstanceUid, displaySetInstanceUid) {
   const study = studies.find(
@@ -52,14 +52,6 @@ function addSegMetadataToCornerstoneToolState(
   }
 }
 
-function retrieveDicomData(wadoUri) {
-  // TODO: Authorization header depends on the server. If we ever have multiple servers
-  // we will need to figure out how / when to pass this information in.
-  return fetch(wadoUri, {
-    headers: OHIF.DICOMWeb.getAuthorizationHeader(),
-  }).then(response => response.arrayBuffer());
-}
-
 async function handleSegmentationStorage(
   studies,
   studyInstanceUid,
@@ -73,8 +65,11 @@ async function handleSegmentationStorage(
     studyInstanceUid,
     displaySetInstanceUid
   );
-  const segWadoUri = displaySet.images[0].getData().wadouri;
+
-  const arrayBuffer = await retrieveDicomData(segWadoUri);
+  const arrayBuffer = await DicomLoaderService.findDicomDataPromise(
+    displaySet,
+    studies
+  );
   const dicomData = dcmjs.data.DicomMessage.readFile(arrayBuffer);
   const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
     dicomData.dict

extensions/dicom-html/src/OHIFDicomHtmlViewport.js

@@ -1,46 +1,34 @@
 import React, { Component } from 'react';
 import PropTypes from 'prop-types';
 import DicomHtmlViewport from './DicomHtmlViewport';
+import OHIF from '@ohif/core';
+const { DicomLoaderService } = OHIF.utils;
 
 class OHIFDicomHtmlViewport extends Component {
   static propTypes = {
     studies: PropTypes.object,
     displaySet: PropTypes.object,
-    viewportIndex: PropTypes.number
+    viewportIndex: PropTypes.number,
   };
 
   state = {
     byteArray: null,
-    error: null
+    error: null,
   };
 
   componentDidMount() {
-    const { displaySet } = this.props.viewportData;
+    const { displaySet, studies } = this.props.viewportData;
-    const {
-      studyInstanceUid,
-      seriesInstanceUid,
-      sopInstanceUid,
-      wadoRoot,
-      wadoUri,
-      authorizationHeaders
-    } = displaySet;
 
-    this.retrieveDicomData(
+    DicomLoaderService.findDicomDataPromise(displaySet, studies).then(
-      studyInstanceUid,
+      data => {
-      seriesInstanceUid,
+        const byteArray = new Uint8Array(data);
-      sopInstanceUid,
-      wadoRoot,
-      wadoUri,
-      authorizationHeaders
-    ).then(
-      byteArray => {
         this.setState({
-          byteArray
+          byteArray: byteArray,
         });
       },
       error => {
         this.setState({
-          error
+          error,
         });
 
         throw new Error(error);
@@ -48,27 +36,6 @@ class OHIFDicomHtmlViewport extends Component {
     );
   }
 
-  retrieveDicomData(
-    studyInstanceUid,
-    seriesInstanceUid,
-    sopInstanceUid,
-    wadoRoot,
-    wadoUri,
-    authorizationHeaders
-  ) {
-    // TODO: Passing in a lot of data we aren't using
-
-    // TODO: Authorization header depends on the server. If we ever have multiple servers
-    // we will need to figure out how / when to pass this information in.
-    return fetch(wadoUri, {
-      headers: authorizationHeaders
-    })
-      .then(response => response.arrayBuffer())
-      .then(arraybuffer => {
-        return new Uint8Array(arraybuffer);
-      });
-  }
-
   render() {
     return (
       <>

extensions/dicom-pdf/src/DicomPDFViewport.js

@@ -4,41 +4,46 @@ import TypedArrayProp from './TypedArrayProp';
 
 // TODO: Should probably use dcmjs for this
 const SOP_CLASS_UIDS = {
-  ENCAPSULATED_PDF: '1.2.840.10008.5.1.4.1.1.104.1'
+  ENCAPSULATED_PDF: '1.2.840.10008.5.1.4.1.1.104.1',
 };
 
 class DicomPDFViewport extends Component {
   state = {
     fileURL: null,
-    error: null
+    error: null,
   };
 
   static propTypes = {
-    byteArray: TypedArrayProp.uint8
+    byteArray: TypedArrayProp.uint8,
   };
 
-  renderPDF = dataSet => {
+  renderPDF = (dataSet, byteArray) => {
-    const sopClassUid = dataSet.string('x00080016');
+    let pdfByteArray = byteArray;
 
-    if (sopClassUid !== SOP_CLASS_UIDS.ENCAPSULATED_PDF) {
+    if (dataSet) {
-      throw new Error('This is not a DICOM-encapsulated PDF');
+      const sopClassUid = dataSet.string('x00080016');
+
+      if (sopClassUid !== SOP_CLASS_UIDS.ENCAPSULATED_PDF) {
+        throw new Error('This is not a DICOM-encapsulated PDF');
+      }
+
+      const fileTag = dataSet.elements.x00420011;
+      const offset = fileTag.dataOffset;
+      const remainder = offset + fileTag.length;
+      pdfByteArray = dataSet.byteArray.slice(offset, remainder);
     }
 
-    const fileTag = dataSet.elements.x00420011;
-    const offset = fileTag.dataOffset;
-    const remainder = offset + fileTag.length;
-    const pdfByteArray = dataSet.byteArray.slice(offset, remainder);
     const PDF = new Blob([pdfByteArray], { type: 'application/pdf' });
     const fileURL = URL.createObjectURL(PDF);
 
     this.setState({
-      fileURL
+      fileURL,
     });
   };
 
   parseByteArray = byteArray => {
     const options = {
-      untilTag: ''
+      untilTag: '',
     };
 
     let dataSet;
@@ -47,7 +52,7 @@ class DicomPDFViewport extends Component {
       dataSet = dicomParser.parseDicom(byteArray, options);
     } catch (error) {
       this.setState({
-        error
+        error,
       });
     }
 
@@ -57,7 +62,7 @@ class DicomPDFViewport extends Component {
   componentDidMount() {
     const dataSet = this.parseByteArray(this.props.byteArray);
 
-    this.renderPDF(dataSet);
+    this.renderPDF(dataSet, this.props.byteArray);
   }
 
   render() {

extensions/dicom-pdf/src/OHIFDicomPDFViewport.js

@@ -1,60 +1,54 @@
-import React, { Component } from "react";
+import React, { Component } from 'react';
-import PropTypes from "prop-types";
+import PropTypes from 'prop-types';
-import OHIF from "@ohif/core";
+import OHIF from '@ohif/core';
-import OHIFComponentPlugin from "./OHIFComponentPlugin.js";
+import OHIFComponentPlugin from './OHIFComponentPlugin.js';
-import DicomPDFViewport from "./DicomPDFViewport";
+import DicomPDFViewport from './DicomPDFViewport';
 
-const { DICOMWeb } = OHIF;
+const { DicomLoaderService } = OHIF.utils;
 
 class OHIFDicomPDFViewport extends Component {
   static propTypes = {
     studies: PropTypes.object,
     displaySet: PropTypes.object,
-    viewportIndex: PropTypes.number
+    viewportIndex: PropTypes.number,
   };
 
   state = {
     byteArray: null,
-    error: null
+    error: null,
   };
 
-  static id = "DicomPDFViewportPDF";
+  static id = 'DicomPDFViewportPDF';
 
   static init() {
-    console.log("DicomPDFViewport init()");
+    console.log('DicomPDFViewport init()');
   }
 
   static destroy() {
-    console.log("DicomPDFViewport destroy()");
+    console.log('DicomPDFViewport destroy()');
   }
 
   componentDidMount() {
-    const { displaySet } = this.props.viewportData;
+    const { displaySet, studies } = this.props.viewportData;
     const {
       studyInstanceUid,
       seriesInstanceUid,
       sopInstanceUid,
       wadoRoot,
       wadoUri,
-      authorizationHeaders
+      authorizationHeaders,
     } = displaySet;
 
-    this.retrieveDicomData(
+    DicomLoaderService.findDicomDataPromise(displaySet, studies).then(
-      studyInstanceUid,
+      data => {
-      seriesInstanceUid,
+        const byteArray = new Uint8Array(data);
-      sopInstanceUid,
-      wadoRoot,
-      wadoUri,
-      authorizationHeaders
-    ).then(
-      byteArray => {
         this.setState({
-          byteArray
+          byteArray: byteArray,
         });
       },
       error => {
         this.setState({
-          error
+          error,
         });
 
         throw new Error(error);
@@ -62,27 +56,6 @@ class OHIFDicomPDFViewport extends Component {
     );
   }
 
-  retrieveDicomData(
-    studyInstanceUid,
-    seriesInstanceUid,
-    sopInstanceUid,
-    wadoRoot,
-    wadoUri,
-    authorizationHeaders
-  ) {
-    // TODO: Passing in a lot of data we aren't using
-
-    // TODO: Authorization header depends on the server. If we ever have multiple servers
-    // we will need to figure out how / when to pass this information in.
-    return fetch(wadoUri, {
-      headers: authorizationHeaders
-    })
-      .then(response => response.arrayBuffer())
-      .then(arraybuffer => {
-        return new Uint8Array(arraybuffer);
-      });
-  }
-
   render() {
     const { id, init, destroy } = OHIFDicomPDFViewport;
     const pluginProps = { id, init, destroy };

platform/core/src/classes/metadata/StudyMetadata.js

@@ -129,6 +129,7 @@ export class StudyMetadata extends Metadata {
         );
 
         if (displaySet) {
+          displaySet.sopClassModule = true;
           displaySets.push(displaySet);
 
           return;
@@ -214,7 +215,7 @@ export class StudyMetadata extends Metadata {
    * @returns {boolean} True on success, false on failure.
    */
   addDisplaySet(displaySet) {
-    if (displaySet instanceof ImageSet) {
+    if (displaySet instanceof ImageSet || displaySet.sopClassModule) {
       this._displaySets.push(displaySet);
       return true;
     }

platform/core/src/studies/services/wado/retrieveMetadata.js

@@ -402,6 +402,7 @@ async function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
         baseWadoRsUri: baseWadoRsUri,
         wadouri: WADOProxy.convertURL(wadouri, server),
         wadorsuri: WADOProxy.convertURL(wadorsuri, server),
+        wadoRoot: server.wadoRoot,
         imageRendering: server.imageRendering,
         thumbnailRendering: server.thumbnailRendering,
       };

platform/core/src/utils/dicomLoaderService.js

@@ -0,0 +1,199 @@
+import cornerstone from 'cornerstone-core';
+import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader';
+import { api } from 'dicomweb-client';
+import DICOMWeb from '../DICOMWeb';
+
+const getImageId = imageObj => {
+  if (!imageObj) {
+    return;
+  }
+
+  return typeof imageObj.getImageId === 'function'
+    ? imageObj.getImageId()
+    : imageObj.url;
+};
+
+const findImageIdOnStudies = (studies, displaySetInstanceUid) => {
+  const study = studies.find(study => {
+    const displaySet = study.displaySets.some(
+      displaySet => displaySet.displaySetInstanceUid === displaySetInstanceUid
+    );
+    return displaySet;
+  });
+  const { seriesList = [] } = study;
+  const { instances = [] } = seriesList[0] || {};
+  const instance = instances[0];
+
+  return getImageId(instance);
+};
+
+const someInvalidStrings = strings => {
+  const stringsArray = Array.isArray(strings) ? strings : [strings];
+  const emptyString = string => !string;
+  let invalid = stringsArray.some(emptyString);
+  return invalid;
+};
+
+const getImageInstance = dataset => {
+  return dataset && dataset.images && dataset.images[0];
+};
+
+const getImageInstanceId = imageInstance => {
+  return getImageId(imageInstance);
+};
+
+const fetchIt = (url, headers = DICOMWeb.getAuthorizationHeader()) => {
+  return fetch(url, headers).then(response => response.arrayBuffer());
+};
+
+const cornerstoneRetriever = imageId => {
+  return cornerstone.loadAndCacheImage(imageId).then(image => {
+    return image && image.data && image.data.byteArray.buffer;
+  });
+};
+
+const wadorsRetriever = (
+  url,
+  studyInstanceUID,
+  seriesInstanceUID,
+  sopInstanceUID,
+  headers = DICOMWeb.getAuthorizationHeader()
+) => {
+  const config = {
+    url,
+    headers,
+  };
+  const dicomWeb = new api.DICOMwebClient(config);
+
+  return dicomWeb.retrieveInstance({
+    studyInstanceUID,
+    seriesInstanceUID,
+    sopInstanceUID,
+  });
+};
+
+const getImageLoaderType = imageId => {
+  const loaderRegExp = /^\w+\:/;
+  const loaderType = loaderRegExp.exec(imageId);
+
+  return (
+    (loaderRegExp.lastIndex === 0 &&
+      loaderType &&
+      loaderType[0] &&
+      loaderType[0].replace(':', '')) ||
+    ''
+  );
+};
+
+const DicomLoaderService = new (class {
+  getLocalData(dataset, studies) {
+    if (dataset && dataset.localFile) {
+      // Use referenced imageInstance
+      const imageInstance = getImageInstance(dataset);
+      let imageId = getImageInstanceId(imageInstance);
+
+      // or Try to get it from studies
+      if (someInvalidStrings(imageId)) {
+        imageId = findImageIdOnStudies(studies, dataset.displaySetInstanceUid);
+      }
+
+      if (!someInvalidStrings(imageId)) {
+        return cornerstoneWADOImageLoader.wadouri.loadFileRequest(imageId);
+      }
+    }
+  }
+
+  getDataByImageType(dataset) {
+    const imageInstance = getImageInstance(dataset);
+
+    if (imageInstance) {
+      const imageId = getImageInstanceId(imageInstance);
+      let getDicomDataMethod = fetchIt;
+      const loaderType = getImageLoaderType(imageId);
+
+      switch (loaderType) {
+        case 'dicomfile':
+          getDicomDataMethod = cornerstoneRetriever.bind(this, imageId);
+          break;
+        case 'wadors':
+          const url = imageInstance.getData().wadoRoot;
+          const studyInstanceUID = imageInstance.getStudyInstanceUID();
+          const seriesInstanceUID = imageInstance.getSeriesInstanceUID();
+          const sopInstanceUID = imageInstance.getSOPInstanceUID();
+          const invalidParams = someInvalidStrings([
+            url,
+            studyInstanceUID,
+            seriesInstanceUID,
+            sopInstanceUID,
+          ]);
+          if (invalidParams) {
+            return;
+          }
+
+          getDicomDataMethod = wadorsRetriever.bind(
+            this,
+            url,
+            studyInstanceUID,
+            seriesInstanceUID,
+            sopInstanceUID
+          );
+          break;
+        case 'wadouri':
+          // Strip out the image loader specifier
+          imageId = imageId.substring(imageId.indexOf(':') + 1);
+
+          if (someInvalidStrings(imageId)) {
+            return;
+          }
+          getDicomDataMethod = fetchIt.bind(this, imageId);
+          break;
+      }
+
+      return getDicomDataMethod();
+    }
+  }
+
+  getDataByDatasetType(dataset) {
+    const {
+      studyInstanceUid,
+      seriesInstanceUid,
+      sopInstanceUid,
+      authorizationHeaders,
+      wadoRoot,
+      wadoUri,
+    } = dataset;
+    // Retrieve wadors or just try to fetch wadouri
+    if (!someInvalidStrings(wadoRoot)) {
+      return wadorsRetriever(
+        wadoRoot,
+        studyInstanceUid,
+        seriesInstanceUid,
+        sopInstanceUid,
+        authorizationHeaders
+      );
+    } else if (!someInvalidStrings(wadoUri)) {
+      return fetchIt(wadoUri, { headers: authorizationHeaders });
+    }
+  }
+
+  *getLoaderIterator(dataset, studies) {
+    yield this.getLocalData(dataset, studies);
+    yield this.getDataByImageType(dataset);
+    yield this.getDataByDatasetType(dataset);
+  }
+
+  findDicomDataPromise(dataset, studies) {
+    const loaderIterator = this.getLoaderIterator(dataset, studies);
+    // it returns first valid retriever method.
+    for (const loader of loaderIterator) {
+      if (loader) {
+        return loader;
+      }
+    }
+
+    // in case of no valid loader
+    throw new Error('Invalid dicom data loader');
+  }
+})();
+
+export default DicomLoaderService;

platform/core/src/utils/getWADORSImageId.js

@@ -5,11 +5,16 @@ function getWADORSImageUrl(instance, frame) {
     return;
   }
 
-  // We need to sum 1 because WADO-RS frame number is 1-based
+  // Use null to obtain an imageId which represents the instance
-  frame = frame ? parseInt(frame) + 1 : 1;
+  if (frame === null) {
+    wadorsuri = wadorsuri.replace(/frames\/(\d+)/, '');
+  } else {
+    // We need to sum 1 because WADO-RS frame number is 1-based
+    frame = frame ? parseInt(frame) + 1 : 1;
 
-  // Replaces /frame/1 by /frame/{frame}
+    // Replaces /frame/1 by /frame/{frame}
-  wadorsuri = wadorsuri.replace(/frames\/(\d+)/, `frames/${frame}`);
+    wadorsuri = wadorsuri.replace(/frames\/(\d+)/, `frames/${frame}`);
+  }
 
   return wadorsuri;
 }

platform/core/src/utils/index.js

@@ -8,6 +8,7 @@ import sortBy from './sortBy.js';
 import studyMetadataManager from './studyMetadataManager';
 import updateMetaDataManager from './updateMetaDataManager.js';
 import writeScript from './writeScript.js';
+import DicomLoaderService from './dicomLoaderService.js';
 
 const utils = {
   guid,
@@ -21,6 +22,7 @@ const utils = {
   // Updates WADO-RS metaDataManager
   updateMetaDataManager,
   DICOMTagDescriptions,
+  DicomLoaderService,
 };
 
 export {
@@ -35,6 +37,7 @@ export {
   // Updates WADO-RS metaDataManager
   updateMetaDataManager,
   DICOMTagDescriptions,
+  DicomLoaderService,
 };
 
 export default utils;

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

@@ -14,6 +14,7 @@ describe('Top level exports', () => {
       // Updates WADO-RS metaDataManager
       'updateMetaDataManager',
       'DICOMTagDescriptions',
+      'DicomLoaderService',
     ].sort();
 
     const exports = Object.keys(utils.default).sort();

platform/viewer/src/connectedComponents/ViewerLocalFileData.js

@@ -79,6 +79,9 @@ class ViewerLocalFileData extends Component {
         studyMetadata.createDisplaySets(sopClassHandlerModules);
       studyMetadata.setDisplaySets(study.displaySets);
 
+      studyMetadata.forEachDisplaySet(displayset => {
+        displayset.localFile = true;
+      });
       // Updates WADO-RS metaDataManager
       updateMetaDataManager(study);
 

platform/viewer/src/lib/filesToStudies.js

@@ -1,160 +1,26 @@
-import cornerstone from 'cornerstone-core';
+import FileLoaderService from './localFileLoaders/fileLoaderService';
-import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader';
-import * as dcmjs from 'dcmjs';
 
-function datasetsToStudies(datasets) {
+const processFile = async file => {
-  const StudyInstanceUIDs = new Set();
+  try {
-  datasets.forEach(ds => {
+    const fileLoaderService = new FileLoaderService(file);
-    StudyInstanceUIDs.add(ds.StudyInstanceUID);
+    const imageId = fileLoaderService.addFile(file);
-  });
+    const image = await fileLoaderService.loadFile(file, imageId);
+    const dataset = await fileLoaderService.getDataset(image, imageId);
+    const studies = await fileLoaderService.getStudies(dataset, imageId);
 
-  const studies = [];
+    return studies;
-  Array.from(StudyInstanceUIDs).forEach(studyInstanceUid => {
+  } catch (error) {
-    const studyDatasets = datasets.filter(
+    console.log(
-      ds => ds.StudyInstanceUID === studyInstanceUid
+      error.name,
+      ':Error when trying to load and process local files:',
+      error.message
     );
-    const firstDataset = studyDatasets[0];
+  }
-    const study = {
+};
-      studyInstanceUid: firstDataset.StudyInstanceUID,
-      studyDate: firstDataset.StudyDate,
-      studyTime: firstDataset.StudyTime,
-      accessionNumber: firstDataset.AccessionNumber,
-      referringPhysicianName: firstDataset.ReferringPhysicianName,
-      patientName: firstDataset.PatientName,
-      patientId: firstDataset.PatientID,
-      patientBirthdate: firstDataset.PatientBirthDate,
-      patientSex: firstDataset.PatientSex,
-      studyId: firstDataset.StudyID,
-      studyDescription: firstDataset.StudyDescription,
-      //numberOfStudyRelatedSeries: DICOMWeb.getString(study['00201206']),
-      //numberOfStudyRelatedInstances: DICOMWeb.getString(study['00201208']),
-      // modality: DICOMWeb.getString(study['00080060']),
-      // modalitiesInStudy: DICOMWeb.getString(study['00080061']),
-      //modalities:
-      seriesList: [],
-    };
-
-    const SeriesInstanceUIDs = new Set();
-    studyDatasets.forEach(ds => {
-      SeriesInstanceUIDs.add(ds.SeriesInstanceUID);
-    });
-
-    Array.from(SeriesInstanceUIDs).forEach(seriesInstanceUid => {
-      const seriesDatasets = studyDatasets.filter(
-        ds => ds.SeriesInstanceUID === seriesInstanceUid
-      );
-
-      const SOPInstanceUIDs = new Set();
-      seriesDatasets.forEach(ds => {
-        SOPInstanceUIDs.add(ds.SOPInstanceUID);
-
-        study.seriesList.push({
-          seriesInstanceUid: ds.SeriesInstanceUID,
-          seriesDescription: ds.SeriesDescription,
-          seriesNumber: ds.SeriesNumber,
-          instances: [],
-        });
-      });
-
-      Array.from(SOPInstanceUIDs).forEach(sopInstanceUid => {
-        const instance = seriesDatasets.find(
-          a => a.SOPInstanceUID === sopInstanceUid
-        );
-        const series = study.seriesList.find(
-          a => a.seriesInstanceUid === seriesInstanceUid
-        );
-
-        series.instances.push({
-          sopInstanceUid: instance.SOPInstanceUID,
-          sopClassUid: instance.SOPClassUID,
-          rows: instance.Rows,
-          columns: instance.Columns,
-          numberOfFrames: instance.NumberOfFrames,
-          instanceNumber: instance.InstanceNumber,
-          getImageId: () => instance.imageId, // TODO: Change getImageId to check for instance.imageId property first.
-          /*imageType: DICOMWeb.getString(instance['00080008']),
-          modality: DICOMWeb.getString(instance['00080060']),
-          instanceNumber: DICOMWeb.getNumber(instance['00200013']),
-          imagePositionPatient: DICOMWeb.getString(instance['00200032']),
-          imageOrientationPatient: DICOMWeb.getString(instance['00200037']),
-          frameOfReferenceUID: DICOMWeb.getString(instance['00200052']),
-          sliceLocation: DICOMWeb.getNumber(instance['00201041']),
-          samplesPerPixel: DICOMWeb.getNumber(instance['00280002']),
-          photometricInterpretation: DICOMWeb.getString(instance['00280004']),
-          planarConfiguration: DICOMWeb.getNumber(instance['00280006']),
-          pixelSpacing: DICOMWeb.getString(instance['00280030']),
-          pixelAspectRatio: DICOMWeb.getString(instance['00280034']),
-          bitsAllocated: DICOMWeb.getNumber(instance['00280100']),
-          bitsStored: DICOMWeb.getNumber(instance['00280101']),
-          highBit: DICOMWeb.getNumber(instance['00280102']),
-          pixelRepresentation: DICOMWeb.getNumber(instance['00280103']),
-          smallestPixelValue: DICOMWeb.getNumber(instance['00280106']),
-          largestPixelValue: DICOMWeb.getNumber(instance['00280107']),
-          windowCenter: DICOMWeb.getString(instance['00281050']),
-          windowWidth: DICOMWeb.getString(instance['00281051']),
-          rescaleIntercept: DICOMWeb.getNumber(instance['00281052']),
-          rescaleSlope: DICOMWeb.getNumber(instance['00281053']),
-          rescaleType: DICOMWeb.getNumber(instance['00281054']),
-          sourceImageInstanceUid: getSourceImageInstanceUid(instance),
-          laterality: DICOMWeb.getString(instance['00200062']),
-          viewPosition: DICOMWeb.getString(instance['00185101']),
-          acquisitionDateTime: DICOMWeb.getString(instance['0008002A']),
-          frameIncrementPointer: getFrameIncrementPointer(instance['00280009']),
-          frameTime: DICOMWeb.getNumber(instance['00181063']),
-          frameTimeVector: parseFloatArray(
-            DICOMWeb.getString(instance['00181065'])
-          ),
-          sliceThickness: DICOMWeb.getNumber(instance['00180050']),
-          spacingBetweenSlices: DICOMWeb.getString(instance['00180088']),
-          lossyImageCompression: DICOMWeb.getString(instance['00282110']),
-          derivationDescription: DICOMWeb.getString(instance['00282111']),
-          lossyImageCompressionRatio: DICOMWeb.getString(instance['00282112']),
-          lossyImageCompressionMethod: DICOMWeb.getString(instance['00282114']),
-          echoNumber: DICOMWeb.getString(instance['00180086']),
-          contrastBolusAgent: DICOMWeb.getString(instance['00180010']),
-          radiopharmaceuticalInfo: getRadiopharmaceuticalInfo(instance),
-          wadouri: WADOProxy.convertURL(wadouri, server),
-          wadorsuri: WADOProxy.convertURL(wadorsuri, server),*/
-        });
-      });
-    });
-
-    studies.push(study);
-  });
-
-  console.warn(studies);
-
-  return studies;
-}
 
 export default async function filesToStudies(files) {
-  const imagePromises = files.map(file => {
+  const processFilesPromises = files.map(processFile);
-    const imageId = cornerstoneWADOImageLoader.wadouri.fileManager.add(file);
+  const studies = await Promise.all(processFilesPromises);
-    return cornerstone
-      .loadAndCacheImage(imageId)
-      .catch(error => console.warn(error));
-  });
 
-  const images = await Promise.all(imagePromises);
+  return FileLoaderService.groupSeries(studies.flat());
-  const datasets = [];
-
-  images.forEach(image => {
-    if (!image || !image.data) {
-      return;
-    }
-
-    const arrayBuffer = image.data.byteArray.buffer;
-    const dicomData = dcmjs.data.DicomMessage.readFile(arrayBuffer);
-    const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
-      dicomData.dict
-    );
-    dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(
-      dicomData.meta
-    );
-    dataset.imageId = image.imageId;
-
-    datasets.push(dataset);
-  });
-
-  return datasetsToStudies(datasets);
 }

platform/viewer/src/lib/localFileLoaders/dicomFileLoader.js

@@ -0,0 +1,192 @@
+import * as dcmjs from 'dcmjs';
+import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader';
+import FileLoader from './fileLoader';
+
+const DICOMFileLoader = new (class extends FileLoader {
+  fileType = 'application/dicom';
+  loadFile(file, imageId) {
+    return cornerstoneWADOImageLoader.wadouri.loadFileRequest(imageId);
+  }
+
+  getDataset(image, imageId) {
+    let dataset = {};
+    try {
+      const dicomData = dcmjs.data.DicomMessage.readFile(image);
+      dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
+        dicomData.dict
+      );
+      dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(
+        dicomData.meta
+      );
+    } catch (e) {
+      console.log('Error on getting dicom file dataset. It defaults to empty');
+    }
+    // Set imageId on dataset to be consumed later on
+    dataset.imageId = imageId;
+
+    return dataset;
+  }
+
+  getStudies(dataset, imageId) {
+    return this.getStudyFromDataset(dataset);
+  }
+
+  getStudyFromDataset(dataset = {}) {
+    const {
+      StudyInstanceUID,
+      StudyDate,
+      StudyTime,
+      AccessionNumber,
+      ReferringPhysicianName,
+      PatientName,
+      PatientID,
+      PatientBirthDate,
+      PatientSex,
+      StudyID,
+      StudyDescription,
+      /*
+      NumberOfStudyRelatedSeries,
+      NumberOfStudyRelatedInstances,
+      Modality,
+      ModalitiesInStudy,
+      */
+      SeriesInstanceUID,
+      SeriesDescription,
+      SeriesNumber,
+      SOPInstanceUID,
+      SOPClassUID,
+      Rows,
+      Columns,
+      NumberOfFrames,
+      InstanceNumber,
+      imageId,
+      Modality,
+      /*ImageType,
+        InstanceNumber,
+        ImagePositionPatient,
+        ImageOrientationPatient,
+        FrameOfReferenceUID,
+        SliceLocation,
+        SamplesPerPixel,
+        PhotometricInterpretation,
+        PlanarConfiguration,
+        PixelSpacing,
+        PixelAspectRatio,
+        BitsAllocated,
+        BitsStored,
+        HighBit,
+        PixelRepresentation,
+        SmallestPixelValue,
+        LargestPixelValue,
+        WindowCenter,
+        WindowWidth,
+        RescaleIntercept,
+        RescaleSlope,
+        RescaleType,
+        Laterality,
+        ViewPosition,
+        AcquisitionDateTime,
+        FrameIncrementPointer,
+        FrameTime,
+        FrameTimeVector,
+        SliceThickness,
+        SpacingBetweenSlices,
+        LossyImageCompression,
+        DerivationDescription,
+        LossyImageCompressionRatio,
+        LossyImageCompressionMethod,
+        EchoNumber,
+        ContrastBolusAgent,
+        */
+    } = dataset;
+
+    const instance = {
+      sopInstanceUid: SOPInstanceUID,
+      sopClassUid: SOPClassUID,
+      rows: Rows,
+      columns: Columns,
+      numberOfFrames: NumberOfFrames,
+      instanceNumber: InstanceNumber,
+      url: imageId,
+      modality: Modality,
+      /*
+        TODO: in case necessary to uncoment this block, double check every property
+        imageType: ImageType || DICOMWeb.getString(dataset['00080008']),
+        instanceNumber: InstanceNumber || DICOMWeb.getNumber(dataset['00200013']),
+        imagePositionPatient: ImagePositionPatient || DICOMWeb.getString(dataset['00200032']),
+        imageOrientationPatient: ImageOrientationPatient || DICOMWeb.getString(dataset['00200037']),
+        frameOfReferenceUID: FrameOfReferenceUID || DICOMWeb.getString(dataset['00200052']),
+        sliceLocation: SliceLocation || DICOMWeb.getNumber(dataset['00201041']),
+        samplesPerPixel: SamplesPerPixel || DICOMWeb.getNumber(dataset['00280002']),
+        photometricInterpretation: PhotometricInterpretation || DICOMWeb.getString(dataset['00280004']),
+        planarConfiguration: PlanarConfiguration || DICOMWeb.getNumber(dataset['00280006']),
+        pixelSpacing: PixelSpacing || DICOMWeb.getString(dataset['00280030']),
+        pixelAspectRatio: PixelAspectRatio || DICOMWeb.getString(dataset['00280034']),
+        bitsAllocated: BitsAllocated || DICOMWeb.getNumber(dataset['00280100']),
+        bitsStored: BitsStored || DICOMWeb.getNumber(dataset['00280101']),
+        highBit: HighBit || DICOMWeb.getNumber(dataset['00280102']),
+        pixelRepresentation: PixelRepresentation || DICOMWeb.getNumber(dataset['00280103']),
+        smallestPixelValue: SmallestPixelValue || DICOMWeb.getNumber(dataset['00280106']),
+        largestPixelValue: LargestPixelValue || DICOMWeb.getNumber(dataset['00280107']),
+        windowCenter: WindowCenter || DICOMWeb.getString(dataset['00281050']),
+        windowWidth: WindowWidth || DICOMWeb.getString(dataset['00281051']),
+        rescaleIntercept: RescaleIntercept || DICOMWeb.getNumber(dataset['00281052']),
+        rescaleSlope: RescaleSlope || DICOMWeb.getNumber(dataset['00281053']),
+        rescaleType: RescaleType || DICOMWeb.getNumber(dataset['00281054']),
+        sourceImageInstanceUid: getSourceImageInstanceUid(dataset),
+        laterality: Laterality || DICOMWeb.getString(dataset['00200062']),
+        viewPosition: ViewPosition || DICOMWeb.getString(dataset['00185101']),
+        acquisitionDateTime: AcquisitionDateTime || DICOMWeb.getString(dataset['0008002A']),
+        frameIncrementPointer: FrameIncrementPointer || getFrameIncrementPointer(dataset['00280009']),
+        frameTime: FrameTime || DICOMWeb.getNumber(dataset['00181063']),
+        frameTimeVector: FrameTimeVector || parseFloatArray(
+          DICOMWeb.getString(dataset['00181065'])
+        ),
+        sliceThickness: SliceThickness || DICOMWeb.getNumber(dataset['00180050']),
+        spacingBetweenSlices: SpacingBetweenSlices || DICOMWeb.getString(dataset['00180088']),
+        lossyImageCompression: LossyImageCompression || DICOMWeb.getString(dataset['00282110']),
+        derivationDescription: DerivationDescription || DICOMWeb.getString(dataset['00282111']),
+        lossyImageCompressionRatio: LossyImageCompressionRatio || DICOMWeb.getString(dataset['00282112']),
+        lossyImageCompressionMethod: LossyImageCompressionMethod || DICOMWeb.getString(dataset['00282114']),
+        echoNumber: EchoNumber || DICOMWeb.getString(dataset['00180086']),
+        contrastBolusAgent: ContrastBolusAgent || DICOMWeb.getString(dataset['00180010']),
+        radiopharmaceuticalInfo: getRadiopharmaceuticalInfo(dataset),
+        wadouri: WADOProxy.convertURL(wadouri, server),
+        wadorsuri: WADOProxy.convertURL(wadorsuri, server),*/
+    };
+
+    const series = {
+      seriesInstanceUid: SeriesInstanceUID,
+      seriesDescription: SeriesDescription,
+      seriesNumber: SeriesNumber,
+      instances: [instance],
+    };
+
+    const study = {
+      studyInstanceUid: StudyInstanceUID,
+      studyDate: StudyDate,
+      studyTime: StudyTime,
+      accessionNumber: AccessionNumber,
+      referringPhysicianName: ReferringPhysicianName,
+      patientName: PatientName,
+      patientId: PatientID,
+      patientBirthdate: PatientBirthDate,
+      patientSex: PatientSex,
+      studyId: StudyID,
+      studyDescription: StudyDescription,
+      /*
+      TODO: in case necessary to uncomment this block, double check every property
+      numberOfStudyRelatedSeries: NumberOfStudyRelatedSeries || DICOMWeb.getString(dataset['00201206']),
+      numberOfStudyRelatedInstances: NumberOfStudyRelatedInstances || DICOMWeb.getString(dataset['00201208']),
+      modality: Modality || DICOMWeb.getString(dataset['00080060']),
+      modalitiesInStudy: ModalitiesInStudy || DICOMWeb.getString(dataset['00080061']),
+      modalities:
+      */
+      seriesList: [series],
+    };
+
+    return study;
+  }
+})();
+
+export default DICOMFileLoader;

platform/viewer/src/lib/localFileLoaders/fileLoader.js

@@ -0,0 +1,6 @@
+export default class FileLoader {
+  fileType;
+  loadFile(file, imageId) { }
+  getDataset(image, imageId) { }
+  getStudies(dataset, imageId) { }
+}

platform/viewer/src/lib/localFileLoaders/fileLoaderService.js

@@ -0,0 +1,82 @@
+import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader';
+import FileLoader from './fileLoader';
+import PDFFileLoader from './pdfFileLoader';
+import DICOMFileLoader from './dicomFileLoader';
+
+class FileLoaderService extends FileLoader {
+  fileType;
+  loader;
+  constructor(file) {
+    super();
+    const fileType = file && file.type;
+    this.loader = this.getLoader(fileType);
+    this.fileType = this.loader.fileType;
+  }
+
+  static groupSeries(studies) {
+    const groupBy = (list, groupByKey, listKey) => {
+      let nonKeyCounter = 1;
+
+      return list.reduce((acc, obj) => {
+        let key = obj[groupByKey];
+        const list = obj[listKey];
+
+        // in case key not found, group it using counter
+        key = !!key ? key : '' + nonKeyCounter++;
+
+        if (!acc[key]) {
+          acc[key] = { ...obj };
+          acc[key][listKey] = [];
+        }
+
+        acc[key][listKey].push(...list);
+
+        return acc;
+      }, {});
+    };
+
+    const studiesGrouped = Object.values(
+      groupBy(studies, 'studyInstanceUid', 'seriesList')
+    );
+
+    const result = studiesGrouped.map(studyGroup => {
+      const seriesGrouped = groupBy(
+        studyGroup.seriesList,
+        'seriesInstanceUid',
+        'instances'
+      );
+      studyGroup.seriesList = Object.values(seriesGrouped);
+
+      return studyGroup;
+    });
+
+    return result;
+  }
+
+  addFile(file) {
+    return cornerstoneWADOImageLoader.wadouri.fileManager.add(file);
+  }
+
+  loadFile(file, imageId) {
+    return this.loader.loadFile(file, imageId);
+  }
+
+  getDataset(image, imageId) {
+    return this.loader.getDataset(image, imageId);
+  }
+
+  getStudies(dataset, imageId) {
+    return this.loader.getStudies(dataset, imageId);
+  }
+
+  getLoader(fileType) {
+    if (fileType === 'application/pdf') {
+      return PDFFileLoader;
+    } else {
+      // Default to dicom loader
+      return DICOMFileLoader;
+    }
+  }
+}
+
+export default FileLoaderService;

platform/viewer/src/lib/localFileLoaders/pdfFileLoader.js

@@ -0,0 +1,58 @@
+import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader';
+import FileLoader from './fileLoader';
+
+const PDFFileLoader = new (class extends FileLoader {
+  fileType = 'application/pdf';
+  loadFile(file, imageId) {
+    return cornerstoneWADOImageLoader.wadouri.loadFileRequest(imageId);
+  }
+
+  getDataset(image, imageId) {
+    const dataset = {};
+    dataset.imageId = image.imageId || imageId;
+    return dataset;
+  }
+
+  getStudies(dataset, imageId) {
+    return this.getDefaultStudy(imageId);
+  }
+
+  getDefaultStudy(imageId) {
+    const study = {
+      studyInstanceUid: '',
+      studyDate: '',
+      studyTime: '',
+      accessionNumber: '',
+      referringPhysicianName: '',
+      patientName: '',
+      patientId: '',
+      patientBirthdate: '',
+      patientSex: '',
+      studyId: '',
+      studyDescription: '',
+      seriesList: [
+        {
+          seriesInstanceUid: '',
+          seriesDescription: '',
+          seriesNumber: '',
+          instances: [
+            {
+              sopInstanceUid: '',
+              sopClassUid: '1.2.840.10008.5.1.4.1.1.104.1',
+              rows: '',
+              columns: '',
+              numberOfFrames: 0,
+              instanceNumber: 1,
+              getImageId: () => imageId,
+              isLocalFile: true,
+            },
+          ],
+        },
+      ],
+    };
+
+    return study;
+  }
+})();
+
+export default PDFFileLoader;