fix: Overlays were broken. (#2614)

* fix(OHIFv3):Overlays were broken.

Adds a retrieveBulkData to elements containing BulkDataURI so that
anyone display the data can retrieve the required information.

* fix(OHIFv3):Added a call in the wrong spot, removed it.

* docs(OHIFv3):Added some documentation as requested

extensions/default/src/DicomWebDataSource/index.js

@@ -162,9 +162,9 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
             );
           }
 
+
           const storeInstances = instances => {
             const naturalizedInstances = instances.map(naturalizeDataset);
-
             DicomMetadataStore.addInstances(naturalizedInstances);
             callback(naturalizedInstances);
           };
@@ -252,9 +252,47 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
         sortFunction
       );
 
+      /**
+       * naturalizes the dataset, and adds a retrieve bulkdata method
+       * to any values containing BulkDataURI.
+       * @param {*} instance
+       * @returns naturalized dataset, with retrieveBulkData methods
+       */
+      const addRetrieveBulkData = instance => {
+        const naturalized = naturalizeDataset(instance);
+        Object.keys(naturalized).forEach(key => {
+          const value = naturalized[key];
+          // The value.Value will be set with the bulkdata read value
+          // in which case it isn't necessary to re-read this.
+          if (value && value.BulkDataURI && !value.Value) {
+            // Provide a method to fetch bulkdata
+            value.retrieveBulkData = () => {
+              const options = {
+                // The bulkdata fetches work with either multipart or
+                // singlepart, so set multipart to false to let the server
+                // decide which type to respond with.
+                multipart: false,
+                BulkDataURI: value.BulkDataURI,
+                // The study instance UID is required if the bulkdata uri
+                // is relative - that isn't disallowed by DICOMweb, but
+                // isn't well specified in the standard, but is needed in
+                // any implementation that stores static copies of the metadata
+                StudyInstanceUID: naturalized.StudyInstanceUID,
+              };
+              return qidoDicomWebClient.retrieveBulkData(options).then(val => {
+                const ret = val && val[0] || undefined;
+                value.Value = ret;
+                return ret;
+              });
+            };
+          }
+        });
+        return naturalized
+      };
+
       // Async load series, store as retrieved
       function storeInstances(instances) {
-        const naturalizedInstances = instances.map(naturalizeDataset);
+        const naturalizedInstances = instances.map(addRetrieveBulkData);
 
         DicomMetadataStore.addInstances(naturalizedInstances, madeInClient);
       }

platform/core/src/classes/MetadataProvider.js

@@ -1,8 +1,6 @@
 import queryString from 'query-string';
 import dicomParser from 'dicom-parser';
 import getPixelSpacingInformation from '../utils/metadataProvider/getPixelSpacingInformation';
-import fetchPaletteColorLookupTableData from '../utils/metadataProvider/fetchPaletteColorLookupTableData';
-import fetchOverlayData from '../utils/metadataProvider/fetchOverlayData';
 import DicomMetadataStore from '../services/DicomMetadataStore';
 
 class MetadataProvider {
@@ -105,14 +103,6 @@ class MetadataProvider {
   //   return instance;
   // }
 
-  // async _checkBulkDataAndInlineBinaries(instance, server) {
-  //   await fetchOverlayData(instance, server);
-
-  //   if (instance.PhotometricInterpretation === 'PALETTE COLOR') {
-  //     await fetchPaletteColorLookupTableData(instance, server);
-  //   }
-  // }
-
   _getInstance(imageId) {
     const uids = this._getUIDsFromImageID(imageId);
 
@@ -508,4 +498,3 @@ const WADO_IMAGE_LOADER_TAGS = {
 };
 
 const INSTANCE = 'instance';
-const DICOMWEB = 'dicomweb';

platform/core/src/utils/metadataProvider/fetchOverlayData.js

@@ -1,82 +0,0 @@
-import { api } from 'dicomweb-client';
-import DICOMWeb from '../../DICOMWeb';
-import str2ab from '../str2ab';
-import unpackOverlay from './unpackOverlay';
-
-import errorHandler from '../../errorHandler';
-
-export default async function fetchOverlayData(instance, server) {
-  const OverlayDataPromises = [];
-  const OverlayDataTags = [];
-
-  return new Promise((resolve, reject) => {
-    for (let overlayGroup = 0x00; overlayGroup <= 0x1e; overlayGroup += 0x02) {
-      let groupStr = `60${overlayGroup.toString(16)}`;
-
-      if (groupStr.length === 3) {
-        groupStr = `600${overlayGroup.toString(16)}`;
-      }
-
-      const OverlayDataTag = `${groupStr}3000`;
-
-      if (instance[OverlayDataTag] && instance[OverlayDataTag].InlineBinary) {
-        const inlineBinaryData = atob(instance[OverlayDataTag].InlineBinary);
-        const arraybuffer = str2ab(inlineBinaryData);
-
-        instance[OverlayDataTag] = unpackOverlay(arraybuffer);
-      } else if (
-        instance[OverlayDataTag] &&
-        instance[OverlayDataTag].BulkDataURI
-      ) {
-        OverlayDataPromises.push(
-          _getOverlayData(instance[OverlayDataTag], server)
-        );
-        OverlayDataTags.push(OverlayDataTag);
-      } else if (
-        instance[OverlayDataTag] &&
-        instance[OverlayDataTag] instanceof ArrayBuffer
-      ) {
-        instance[OverlayDataTag] = unpackOverlay(instance[OverlayDataTag]);
-      }
-    }
-
-    if (OverlayDataPromises.length) {
-      Promise.all(OverlayDataPromises).then(results => {
-        for (let i = 0; i < results.length; i++) {
-          instance[OverlayDataTags[i]] = results[i];
-        }
-
-        resolve();
-      });
-    } else {
-      resolve();
-    }
-  });
-}
-
-async function _getOverlayData(tag, server) {
-  const { BulkDataURI } = tag;
-
-  let uri = BulkDataURI;
-
-  // TODO: Workaround for dcm4chee behind SSL-terminating proxy returning
-  // incorrect bulk data URIs
-  if (server.wadoRoot.indexOf('https') === 0 && !uri.includes('https')) {
-    uri = uri.replace('http', 'https');
-  }
-
-  const config = {
-    url: server.wadoRoot, //BulkDataURI is absolute, so this isn't used
-    headers: DICOMWeb.getAuthorizationHeader(server),
-    errorInterceptor: errorHandler.getHTTPErrorHandler(),
-  };
-  const dicomWeb = new api.DICOMwebClient(config);
-  const options = {
-    BulkDataURI: uri,
-  };
-
-  return dicomWeb
-    .retrieveBulkData(options)
-    .then(result => result[0])
-    .then(unpackOverlay);
-}

platform/core/src/utils/str2ab.js

@@ -4,13 +4,4 @@
  * @param {String} str Input String
  * @return {ArrayBuffer} Output converted ArrayBuffer
  */
-export default function str2ab(str) {
+export default str => Uint8Array.from(atob(str), c => c.charCodeAt(0));
-  const strLen = str.length;
-  const bytes = new Uint8Array(strLen);
-
-  for (let i = 0; i < strLen; i++) {
-    bytes[i] = str.charCodeAt(i);
-  }
-
-  return bytes.buffer;
-}