Fix palette colour display in OHIF v3 (#2731)

* fix(OHIFv3):Fix palette colour data display

* PR comments - added params description

extensions/default/src/getSopClassHandlerModule.js

@@ -162,6 +162,7 @@ const sopClassDictionary = {
   MRSpectroscopyStorage: '1.2.840.10008.5.1.4.1.1.4.2',
   EnhancedMRColorImageStorage: '1.2.840.10008.5.1.4.1.1.4.3',
   LegacyConvertedEnhancedMRImageStorage: '1.2.840.10008.5.1.4.1.1.4.4',
+  UltrasoundImageStorageRET: '1.2.840.10008.5.1.4.1.1.6',
   UltrasoundImageStorage: '1.2.840.10008.5.1.4.1.1.6.1',
   EnhancedUSVolumeStorage: '1.2.840.10008.5.1.4.1.1.6.2',
   SecondaryCaptureImageStorage: '1.2.840.10008.5.1.4.1.1.7',
@@ -288,6 +289,7 @@ const sopClassUids = [
   sopClassDictionary.EnhancedMRColorImageStorage,
   sopClassDictionary.LegacyConvertedEnhancedMRImageStorage,
   sopClassDictionary.UltrasoundImageStorage,
+  sopClassDictionary.UltrasoundImageStorageRET,
   sopClassDictionary.SecondaryCaptureImageStorage,
   sopClassDictionary.MultiframeSingleBitSecondaryCaptureImageStorage,
   sopClassDictionary.MultiframeGrayscaleByteSecondaryCaptureImageStorage,

platform/core/src/classes/MetadataProvider.js

@@ -2,6 +2,7 @@ import queryString from 'query-string';
 import dicomParser from 'dicom-parser';
 import getPixelSpacingInformation from '../utils/metadataProvider/getPixelSpacingInformation';
 import DicomMetadataStore from '../services/DicomMetadataStore';
+import fetchPaletteColorLookupTableData from '../utils/metadataProvider/fetchPaletteColorLookupTableData';
 
 class MetadataProvider {
   constructor() {
@@ -20,46 +21,6 @@ class MetadataProvider {
     });
   }
 
-  /*async addInstance(dicomJSONDatasetOrP10ArrayBuffer, options = {}) {
-    let dicomJSONDataset;
-
-    // If Arraybuffer, parse to DICOMJSON before naturalizing.
-    if (dicomJSONDatasetOrP10ArrayBuffer instanceof ArrayBuffer) {
-      const dicomData = DicomMessage.readFile(dicomJSONDatasetOrP10ArrayBuffer);
-
-      dicomJSONDataset = dicomData.dict;
-    } else {
-      dicomJSONDataset = dicomJSONDatasetOrP10ArrayBuffer;
-    }
-
-    // Check if dataset is already naturalized.
-
-    let naturalizedDataset;
-
-    if (dicomJSONDataset['SeriesInstanceUID'] === undefined) {
-      naturalizedDataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
-        dicomJSONDataset
-      );
-    } else {
-      naturalizedDataset = dicomJSONDataset;
-    }
-
-    const {
-      StudyInstanceUID,
-      SeriesInstanceUID,
-      SOPInstanceUID,
-    } = naturalizedDataset;
-
-    const study = this._getAndCacheStudy(StudyInstanceUID);
-    const series = this._getAndCacheSeriesFromStudy(study, SeriesInstanceUID);
-    const instance = this._getAndCacheInstanceFromStudy(series, SOPInstanceUID);
-
-    Object.assign(instance, naturalizedDataset);
-
-    await this._checkBulkDataAndInlineBinaries(instance, options.server);
-
-    return instance;
-  }*/
 
   addImageIdToUIDs(imageId, uids) {
     // This method is a fallback for when you don't have WADO-URI or WADO-RS.
@@ -69,40 +30,6 @@ class MetadataProvider {
     this.imageIdToUIDs.set(imageId, uids);
   }
 
-  // _getAndCacheStudy(StudyInstanceUID) {
-  //   const studies = this.studies;
-
-  //   let study = studies.get(StudyInstanceUID);
-
-  //   if (!study) {
-  //     study = { series: new Map() };
-  //     studies.set(StudyInstanceUID, study);
-  //   }
-
-  //   return study;
-  // }
-  // _getAndCacheSeriesFromStudy(study, SeriesInstanceUID) {
-  //   let series = study.series.get(SeriesInstanceUID);
-
-  //   if (!series) {
-  //     series = { instances: new Map() };
-  //     study.series.set(SeriesInstanceUID, series);
-  //   }
-
-  //   return series;
-  // }
-
-  // _getAndCacheInstanceFromStudy(series, SOPInstanceUID) {
-  //   let instance = series.instances.get(SOPInstanceUID);
-
-  //   if (!instance) {
-  //     instance = {};
-  //     series.instances.set(SOPInstanceUID, instance);
-  //   }
-
-  //   return instance;
-  // }
-
   _getInstance(imageId) {
     const uids = this._getUIDsFromImageID(imageId);
 
@@ -254,14 +181,14 @@ class MetadataProvider {
           bluePaletteColorLookupTableDescriptor: validNumber(
             instance.BluePaletteColorLookupTableDescriptor
           ),
-          redPaletteColorLookupTableData: validNumber(
+          redPaletteColorLookupTableData: fetchPaletteColorLookupTableData(
-            instance.RedPaletteColorLookupTableData
+            instance, "RedPaletteColorLookupTableData", "RedPaletteColorLookupTableDescriptor"
           ),
-          greenPaletteColorLookupTableData: validNumber(
+          greenPaletteColorLookupTableData: fetchPaletteColorLookupTableData(
-            instance.GreenPaletteColorLookupTableData
+            instance, "GreenPaletteColorLookupTableData", "GreenPaletteColorLookupTableDescriptor"
           ),
-          bluePaletteColorLookupTableData: validNumber(
+          bluePaletteColorLookupTableData: fetchPaletteColorLookupTableData(
-            instance.BluePaletteColorLookupTableData
+            instance, "BluePaletteColorLookupTableData", "BluePaletteColorLookupTableDescriptor"
           ),
         };
 

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

@@ -1,165 +1,72 @@
-import { api } from 'dicomweb-client';
+/**
-import DICOMWeb from '../../DICOMWeb';
+ * Gets the palette color data for the specified tag - red/green/blue,
-import str2ab from '../str2ab';
+ * either from the given UID or from the tag itself.
-
+ * Returns an array if the data is immediately available, or a promise
-import errorHandler from '../../errorHandler';
+ * which resolves to the data if the data needs to be loaded.
-
+ * Returns undefined if the palette isn't specified.
-export default async function fetchPaletteColorLookupTableData(
+ *
-  instance,
+ * @param {*} item containing the palette colour data and description
-  server
+ * @param {*} tag is the tag for the palette data
+ * @param {*} descriptorTag is the tag for the descriptor
+ * @returns Array view containing the palette data, or a promise to return one.
+ * Returns undefined if the palette data is absent.
+ */
+export default function fetchPaletteColorLookupTableData(
+  item, tag, descriptorTag
 ) {
-  const {
+  const { PaletteColorLookupTableUID } = item;
-    PaletteColorLookupTableUID,
+  const paletteData = item[tag];
-    RedPaletteColorLookupTableDescriptor,
+  if (paletteData === undefined && PaletteColorLookupTableUID === undefined) return;
-    GreenPaletteColorLookupTableDescriptor,
+  // performance optimization - read UID and cache by UID
-    BluePaletteColorLookupTableDescriptor,
+  return _getPaletteColor(
-    RedPaletteColorLookupTableData,
+    item[tag],
-    GreenPaletteColorLookupTableData,
+    item[descriptorTag]
-    BluePaletteColorLookupTableData,
+  )
-  } = instance;
-
-  return new Promise((resolve, reject) => {
-    let entry;
-    if (_paletteColorCache.isValidUID(PaletteColorLookupTableUID)) {
-      entry = _paletteColorCache.get(PaletteColorLookupTableUID);
-
-      if (entry) {
-        return resolve(entry);
-      }
-    }
-
-    // no entry in cache... Fetch remote data.
-    const promises = [
-      _getPaletteColor(
-        server,
-        RedPaletteColorLookupTableData,
-        RedPaletteColorLookupTableDescriptor
-      ),
-      _getPaletteColor(
-        server,
-        GreenPaletteColorLookupTableData,
-        GreenPaletteColorLookupTableDescriptor
-      ),
-      _getPaletteColor(
-        server,
-        BluePaletteColorLookupTableData,
-        BluePaletteColorLookupTableDescriptor
-      ),
-    ];
-
-    Promise.all(promises).then(
-      ([
-        RedPaletteColorLookupTableData,
-        GreenPaletteColorLookupTableData,
-        BluePaletteColorLookupTableData,
-      ]) => {
-        // when PaletteColorLookupTableUID is present, the entry can be cached...
-        _paletteColorCache.add({
-          RedPaletteColorLookupTableData,
-          GreenPaletteColorLookupTableData,
-          BluePaletteColorLookupTableData,
-          PaletteColorLookupTableUID,
-        });
-
-        instance.RedPaletteColorLookupTableData = RedPaletteColorLookupTableData;
-        instance.GreenPaletteColorLookupTableData = GreenPaletteColorLookupTableData;
-        instance.BluePaletteColorLookupTableData = BluePaletteColorLookupTableData;
-
-        resolve();
-      }
-    );
-  });
 }
 
-/**
+function _getPaletteColor(paletteColorLookupTableData, lutDescriptor) {
- * Simple cache schema for retrieved color palettes.
- */
-const _paletteColorCache = {
-  count: 0,
-  maxAge: 24 * 60 * 60 * 1000, // 24h cache?
-  entries: {},
-  isValidUID: function(PaletteColorLookupTableUID) {
-    return (
-      typeof PaletteColorLookupTableUID === 'string' &&
-      PaletteColorLookupTableUID.length > 0
-    );
-  },
-  get: function(PaletteColorLookupTableUID) {
-    let entry = null;
-    if (this.entries.hasOwnProperty(PaletteColorLookupTableUID)) {
-      entry = this.entries[PaletteColorLookupTableUID];
-      // check how the entry is...
-      if (Date.now() - entry.time > this.maxAge) {
-        // entry is too old... remove entry.
-        delete this.entries[PaletteColorLookupTableUID];
-        this.count--;
-        entry = null;
-      }
-    }
-    return entry;
-  },
-  add: function(entry) {
-    if (this.isValidUID(entry.uid)) {
-      let PaletteColorLookupTableUID = entry.uid;
-      if (this.entries.hasOwnProperty(PaletteColorLookupTableUID) !== true) {
-        this.count++; // increment cache entry count...
-      }
-      entry.time = Date.now();
-      this.entries[PaletteColorLookupTableUID] = entry;
-      // @TODO: Add logic to get rid of old entries and reduce memory usage...
-    }
-  },
-};
-
-function _getPaletteColor(server, paletteColorLookupTableData, lutDescriptor) {
   const numLutEntries = lutDescriptor[0];
   const bits = lutDescriptor[2];
 
+  if (!paletteColorLookupTableData) return undefined;
+
   const arrayBufferToPaletteColorLUT = arraybuffer => {
-    const byteArray =
-      bits === 16 ? new Uint16Array(arraybuffer) : new Uint8Array(arraybuffer);
     const lut = [];
 
-    for (let i = 0; i < numLutEntries; i++) {
+    if (bits === 16) {
-      lut[i] = byteArray[i];
+      let j = 0;
-    }
+      for (let i = 0; i < numLutEntries; i++) {
+        lut[i] = arraybuffer[j++] + arraybuffer[j++] << 8;
+      }
+    } else {
+      for (let i = 0; i < numLutEntries; i++) {
+        lut[i] = byteArray[i];
+      }
 
+    }
     return lut;
   };
 
-  if (paletteColorLookupTableData.BulkDataURI) {
+  if (paletteColorLookupTableData.palette) {
-    let uri = paletteColorLookupTableData.BulkDataURI;
+    return paletteColorLookupTableData.palette;
-
-    // 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(arrayBufferToPaletteColorLUT);
-  } else if (paletteColorLookupTableData.InlineBinary) {
-    const inlineBinaryData = atob(paletteColorLookupTableData.InlineBinary);
-    const arraybuffer = str2ab(inlineBinaryData);
-
-    return new Promise(resolve => {
-      resolve(arrayBufferToPaletteColorLUT(arraybuffer));
-    });
-  } else {
-    return Promise.resolve(
-      arrayBufferToPaletteColorLUT(paletteColorLookupTableData)
-    );
   }
+
+  if (paletteColorLookupTableData.InlineBinary) {
+    try {
+      const arraybuffer = Uint8Array.from(atob(paletteColorLookupTableData.InlineBinary), c =>
+        c.charCodeAt(0)
+      );
+      return (paletteColorLookupTableData.palette = arrayBufferToPaletteColorLUT(arraybuffer));
+    } catch (e) {
+      console.log("Couldn't decode", paletteColorLookupTableData.InlineBinary, e);
+      return undefined;
+    }
+  }
+
+  if (paletteColorLookupTableData.retrieveBulkData) {
+    return paletteColorLookupTableData.retrieveBulkData().then(val =>
+      (paletteColorLookupTableData.palette = arrayBufferToPaletteColorLUT(val)));
+  }
+
+  throw new Error(`No data found for ${paletteColorLookupTableData} palette`)
 }

yarn.lock

@@ -1236,7 +1236,7 @@
     core-js-pure "^3.20.2"
     regenerator-runtime "^0.13.4"
 
-"@babel/runtime@7.1.2", "@babel/runtime@7.16.3", "@babel/runtime@^7.0.0", "@babel/runtime@^7.1.2", "@babel/runtime@^7.10.2", "@babel/runtime@^7.10.3", "@babel/runtime@^7.11.2", "@babel/runtime@^7.12.1", "@babel/runtime@^7.12.13", "@babel/runtime@^7.12.5", "@babel/runtime@^7.14.6", "@babel/runtime@^7.14.8", "@babel/runtime@^7.16.3", "@babel/runtime@^7.16.7", "@babel/runtime@^7.2.0", "@babel/runtime@^7.3.1", "@babel/runtime@^7.4.4", "@babel/runtime@^7.4.5", "@babel/runtime@^7.5.0", "@babel/runtime@^7.5.5", "@babel/runtime@^7.7.2", "@babel/runtime@^7.7.4", "@babel/runtime@^7.7.6", "@babel/runtime@^7.8.4", "@babel/runtime@^7.9.2":
+"@babel/runtime@7.1.2", "@babel/runtime@7.16.3", "@babel/runtime@7.7.6", "@babel/runtime@^7.0.0", "@babel/runtime@^7.1.2", "@babel/runtime@^7.10.2", "@babel/runtime@^7.10.3", "@babel/runtime@^7.11.2", "@babel/runtime@^7.12.1", "@babel/runtime@^7.12.13", "@babel/runtime@^7.12.5", "@babel/runtime@^7.14.6", "@babel/runtime@^7.14.8", "@babel/runtime@^7.16.3", "@babel/runtime@^7.16.7", "@babel/runtime@^7.2.0", "@babel/runtime@^7.3.1", "@babel/runtime@^7.4.4", "@babel/runtime@^7.4.5", "@babel/runtime@^7.5.0", "@babel/runtime@^7.5.5", "@babel/runtime@^7.7.2", "@babel/runtime@^7.7.4", "@babel/runtime@^7.7.6", "@babel/runtime@^7.8.4", "@babel/runtime@^7.9.2":
   version "7.16.3"
   resolved "https://registry.yarnpkg.com/@babel/runtime/-/runtime-7.16.3.tgz#b86f0db02a04187a3c17caa77de69840165d42d5"
   integrity sha512-WBwekcqacdY2e9AF/Q7WLFUWmdJGJTkbjqTjoMDgXkVZ3ZRUvOPsLb5KdwISoQVsbP+DQzVZW4Zhci0DvpbNTQ==