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

Author: ladeirarodolfo

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

@@ -1,74 +1,41 @@
 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 {
-      studyInstanceUid,
-      seriesInstanceUid,
-      sopInstanceUid,
-      wadoRoot,
-      wadoUri,
-      authorizationHeaders
-    } = displaySet;
+    const { displaySet, studies } = this.props.viewportData;
 
-    this.retrieveDicomData(
-      studyInstanceUid,
-      seriesInstanceUid,
-      sopInstanceUid,
-      wadoRoot,
-      wadoUri,
-      authorizationHeaders
-    ).then(
-      byteArray => {
+    DicomLoaderService.findDicomDataPromise(displaySet, studies).then(
+      data => {
+        const byteArray = new Uint8Array(data);
         this.setState({
-          byteArray
+          byteArray: byteArray,
         });
       },
       error => {
         this.setState({
-          error
+          error,
         });
 
         throw new Error(error);
       }
     );
   }
 
-  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 => {
-    const sopClassUid = dataSet.string('x00080016');
+  renderPDF = (dataSet, byteArray) => {
+    let pdfByteArray = byteArray;
 
-    if (sopClassUid !== SOP_CLASS_UIDS.ENCAPSULATED_PDF) {
-      throw new Error('This is not a DICOM-encapsulated PDF');
+    if (dataSet) {
+      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

@@ -1,88 +1,61 @@
-import React, { Component } from "react";
-import PropTypes from "prop-types";
-import OHIF from "@ohif/core";
-import OHIFComponentPlugin from "./OHIFComponentPlugin.js";
-import DicomPDFViewport from "./DicomPDFViewport";
+import React, { Component } from 'react';
+import PropTypes from 'prop-types';
+import OHIF from '@ohif/core';
+import OHIFComponentPlugin from './OHIFComponentPlugin.js';
+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(
-      studyInstanceUid,
-      seriesInstanceUid,
-      sopInstanceUid,
-      wadoRoot,
-      wadoUri,
-      authorizationHeaders
-    ).then(
-      byteArray => {
+    DicomLoaderService.findDicomDataPromise(displaySet, studies).then(
+      data => {
+        const byteArray = new Uint8Array(data);
         this.setState({
-          byteArray
+          byteArray: byteArray,
         });
       },
       error => {
         this.setState({
-          error
+          error,
         });
 
         throw new Error(error);
       }
     );
   }
 
-  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,
       };