feat(PDF):Add PDF viewer (#2730)

Display DICOM encapsulated PDF documents in a PDF viewer.
Addressed the remaining PR comments, and am merging this.

extensions/default/src/DicomWebDataSource/index.js

@@ -25,7 +25,6 @@ import StaticWadoClient from './utils/StaticWadoClient.js';
 const { DicomMetaDictionary, DicomDict } = dcmjs.data;
 
 const { naturalizeDataset, denaturalizeDataset } = DicomMetaDictionary;
-const { urlUtil } = utils;
 
 const ImplementationClassUID =
   '2.25.270695996825855179949881587723571202391.2.0.0';
@@ -43,6 +42,7 @@ const EXPLICIT_VR_LITTLE_ENDIAN = '1.2.840.10008.1.2.1';
  * @param {string} thumbnailRendering - wadors | ? (unsure of where/how this is used)
  * @param {bool} supportsReject - Whether the server supports reject calls (i.e. DCM4CHEE)
  * @param {bool} lazyLoadStudy - "enableStudyLazyLoad"; Request series meta async instead of blocking
+ * @param {string|bool} singlepart - indicates of the retrieves can fetch singlepart.  Options are bulkdata, video, image or boolean true
  */
 function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
   const {
@@ -53,17 +53,20 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
     supportsWildcard,
     supportsReject,
     staticWado,
+    singlepart,
   } = dicomWebConfig;
 
   const qidoConfig = {
     url: qidoRoot,
     staticWado,
+    singlepart,
     headers: UserAuthenticationService.getAuthorizationHeader(),
     errorInterceptor: errorHandler.getHTTPErrorHandler(),
   };
 
   const wadoConfig = {
     url: wadoRoot,
+    singlepart,
     headers: UserAuthenticationService.getAuthorizationHeader(),
     errorInterceptor: errorHandler.getHTTPErrorHandler(),
   };
@@ -91,7 +94,7 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
     query: {
       studies: {
         mapParams: mapParams.bind(),
-        search: async function(origParams) {
+        search: async function (origParams) {
           const headers = UserAuthenticationService.getAuthorizationHeader();
           if (headers) {
             qidoDicomWebClient.headers = headers;
@@ -116,7 +119,7 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
       },
       series: {
         // mapParams: mapParams.bind(),
-        search: async function(studyInstanceUid) {
+        search: async function (studyInstanceUid) {
           const headers = UserAuthenticationService.getAuthorizationHeader();
           if (headers) {
             qidoDicomWebClient.headers = headers;
@@ -149,13 +152,46 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
       },
     },
     retrieve: {
-      /* Generates a URL that can be used for direct retrieve of the bulkdata */
+      /**
+       * Generates a URL that can be used for direct retrieve of the bulkdata
+       *
+       * @param {object} params
+       * @param {string} params.tag is the tag name of the URL to retrieve
+       * @param {object} params.instance is the instance object that the tag is in
+       * @param {string} params.defaultType is the mime type of the response
+       * @param {string} params.singlepart is the type of the part to retrieve
+       * @returns an absolute URL to the resource, if the absolute URL can be retrieved as singlepart,
+       *    or is already retrieved, or a promise to a URL for such use if a BulkDataURI
+       */
       directURL: (params) => {
-        const { instance, tag = "PixelData", defaultPath = "/pixeldata", defaultType = "video/mp4" } = params;
-        const { StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID } = instance;
-        // If the BulkDataURI isn't present, then assume it uses the pixeldata endpoint
-        // The standard isn't quite clear on that, but appears to be what is expected
+        const {
+          instance,
+          tag = "PixelData",
+          defaultPath = "/pixeldata",
+          defaultType = "video/mp4",
+          singlepart: fetchPart = "video",
+        } = params;
         const value = instance[tag];
+        if (!value) return undefined;
+
+        if (value.DirectRetrieveURL) return value.DirectRetrieveURL;
+        if (value.InlineBinary) {
+          const blob = utils.b64toBlob(value.InlineBinary, defaultType);
+          value.DirectRetrieveURL = URL.createObjectURL(blob);
+          return value.DirectRetrieveURL;
+        }
+        if (!singlepart || singlepart !== true && singlepart.indexOf(fetchPart) === -1) {
+          if (value.retrieveBulkData) {
+            return value.retrieveBulkData().then(arr => {
+              value.DirectRetrieveURL = URL.createObjectURL(new Blob([arr], { type: defaultType }));
+              return value.DirectRetrieveURL;
+            });
+          }
+          console.warn('Unable to retrieve', tag, 'from', instance);
+          return undefined;
+        }
+
+        const { StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID } = instance;
         const BulkDataURI =
           (value && value.BulkDataURI) ||
           `series/${SeriesInstanceUID}/instances/${SOPInstanceUID}${defaultPath}`;
@@ -164,8 +200,8 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
         const acceptUri =
           BulkDataURI +
           (hasAccept ? '' : (hasQuery ? '&' : '?') + `accept=${defaultType}`);
-        if (BulkDataURI.indexOf('http') == 0) return acceptUri;
-        if (BulkDataURI.indexOf('/') == 0) {
+        if (BulkDataURI.indexOf('http') === 0) return acceptUri;
+        if (BulkDataURI.indexOf('/') === 0) {
           return wadoRoot + acceptUri;
         }
         if (BulkDataURI.indexOf('series/') == 0) {
@@ -174,6 +210,9 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
         if (BulkDataURI.indexOf('instances/') === 0) {
           return `${wadoRoot}/studies/${StudyInstanceUID}/series/${SeriesInstanceUID}/${acceptUri}`;
         }
+        if (BulkDataURI.indexOf('bulkdata/') === 0) {
+          return `${wadoRoot}/studies/${StudyInstanceUID}/${acceptUri}`;
+        }
         throw new Error('BulkDataURI in unknown format:' + BulkDataURI);
       },
       series: {

extensions/default/src/DicomWebDataSource/utils/StaticWadoClient.js

@@ -70,7 +70,7 @@ export default class StaticWadoClient extends api.DICOMwebClient {
       if (actual.length === 0) return true;
       if (desired.length === 0 || desired === '*') return true;
       if (desired[0] === '*' && desired[desired.length - 1] === '*') {
-        console.log(`Comparing ${actual} to ${desired.substring(1, desired.length - 1)}`)
+        // console.log(`Comparing ${actual} to ${desired.substring(1, desired.length - 1)}`)
         return actual.indexOf(desired.substring(1, desired.length - 1)) != -1;
       } else if (desired[desired.length - 1] === '*') {
         return actual.indexOf(desired.substring(0, desired.length - 1)) != -1;

extensions/dicom-pdf/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 Open Health Imaging Foundation
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

extensions/dicom-pdf/README.md

@@ -0,0 +1,5 @@
+# DICOM Encapsulated PDF
+This extension adds support for displaying DICOM encapsulated PDF documents.
+
+The extension is a "standard" extension in that it is installed and available
+by default.

extensions/dicom-pdf/package.json

@@ -0,0 +1,49 @@
+{
+  "name": "@ohif/extension-dicom-pdf",
+  "version": "3.0.1",
+  "description": "OHIF extension for PDF display",
+  "author": "OHIF",
+  "license": "MIT",
+  "repository": "OHIF/Viewers",
+  "main": "dist/index.umd.js",
+  "module": "src/index.js",
+  "engines": {
+    "node": ">=10",
+    "npm": ">=6",
+    "yarn": ">=1.16.0"
+  },
+  "files": [
+    "dist",
+    "README.md"
+  ],
+  "publishConfig": {
+    "access": "public"
+  },
+  "scripts": {
+    "dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --debug --output-pathinfo",
+    "dev:cornerstone": "yarn run dev",
+    "build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
+    "build:package": "yarn run build",
+    "start": "yarn run dev",
+    "test:unit": "jest --watchAll",
+    "test:unit:ci": "jest --ci --runInBand --collectCoverage --passWithNoTests"
+  },
+  "peerDependencies": {
+    "@ohif/core": "^0.50.0",
+    "@ohif/ui": "^0.50.0",
+    "cornerstone-core": "^2.6.0",
+    "cornerstone-math": "^0.1.9",
+    "cornerstone-tools": "6.0.2",
+    "cornerstone-wado-image-loader": "4.0.4",
+    "dcmjs": "0.16.1",
+    "dicom-parser": "^1.8.9",
+    "hammerjs": "^2.0.8",
+    "prop-types": "^15.6.2",
+    "react": "^17.0.2",
+    "react-cornerstone-viewport": "4.1.2"
+  },
+  "dependencies": {
+    "@babel/runtime": "7.7.6",
+    "classnames": "^2.2.6"
+  }
+}

extensions/dicom-pdf/src/getSopClassHandlerModule.js

@@ -0,0 +1,70 @@
+import { Name, SOPClassHandlerId } from './id';
+import { utils, classes } from '@ohif/core';
+
+const { ImageSet } = classes;
+
+const SOP_CLASS_UIDS = {
+  ENCAPSULATED_PDF: '1.2.840.10008.5.1.4.1.1.104.1',
+};
+
+const sopClassUids = Object.values(SOP_CLASS_UIDS);
+
+
+const _getDisplaySetsFromSeries = (instances, servicesManager, extensionManager) => {
+  const dataSource = extensionManager.getActiveDataSource()[0];
+  return instances
+    .map(instance => {
+      const { Modality, SOPInstanceUID, EncapsulatedDocument } = instance;
+      const { SeriesDescription = "PDF", MIMETypeOfEncapsulatedDocument, } = instance;
+      const { SeriesNumber, SeriesDate, SeriesInstanceUID, StudyInstanceUID, } = instance;
+      const pdfUrl = dataSource.retrieve.directURL({
+        instance,
+        tag: 'EncapsulatedDocument',
+        defaultType: MIMETypeOfEncapsulatedDocument || "application/pdf",
+        singlepart: "pdf",
+      });
+
+      const displaySet = {
+        //plugin: id,
+        Modality,
+        displaySetInstanceUID: utils.guid(),
+        SeriesDescription,
+        SeriesNumber,
+        SeriesDate,
+        SOPInstanceUID,
+        SeriesInstanceUID,
+        StudyInstanceUID,
+        SOPClassHandlerId,
+        referencedImages: null,
+        measurements: null,
+        pdfUrl,
+        others: [instance],
+        thumbnailSrc: dataSource.retrieve.directURL({ instance, defaultPath: "/thumbnail", defaultType: "image/jpeg", tag: "Absent" }),
+        isDerivedDisplaySet: true,
+        isLoaded: false,
+        sopClassUids,
+        numImageFrames: 0,
+        numInstances: 1,
+        instance,
+      };
+      return displaySet;
+    });
+};
+
+export default function getSopClassHandlerModule({ servicesManager, extensionManager }) {
+  const getDisplaySetsFromSeries = instances => {
+    return _getDisplaySetsFromSeries(
+      instances,
+      servicesManager,
+      extensionManager
+    );
+  };
+
+  return [
+    {
+      name: Name,
+      sopClassUids,
+      getDisplaySetsFromSeries,
+    },
+  ];
+}

extensions/dicom-pdf/src/id.js

@@ -0,0 +1,8 @@
+const Name = 'dicom-pdf';
+const id = `org.ohif.${Name}`;
+
+export default id;
+
+const SOPClassHandlerId = `${id}.sopClassHandlerModule.${Name}`;
+
+export { Name, SOPClassHandlerId, };

extensions/dicom-pdf/src/index.js

@@ -0,0 +1,76 @@
+import React from 'react';
+import getSopClassHandlerModule from './getSopClassHandlerModule';
+import id from './id.js';
+
+const Component = React.lazy(() => {
+  return import(
+    /* webpackPrefetch: true */ './viewports/OHIFCornerstonePdfViewport'
+  );
+});
+
+const OHIFCornerstonePdfViewport = props => {
+  return (
+    <React.Suspense fallback={<div>Loading...</div>}>
+      <Component {...props} />
+    </React.Suspense>
+  );
+};
+
+/**
+ *
+ */
+export default {
+  /**
+   * Only required property. Should be a unique value across all extensions.
+   */
+  id,
+  dependencies: [
+    // TODO -> This isn't used anywhere yet, but we do have a hard dependency, and need to check for these in the future.
+    // OHIF-229
+    {
+      id: 'org.ohif.cornerstone',
+      version: '3.0.0',
+    },
+    {
+      id: 'org.ohif.measurement-tracking',
+      version: '^0.0.1',
+    },
+  ],
+
+  preRegistration({ servicesManager, configuration = {} }) {
+    // No-op for now
+  },
+
+  /**
+   *
+   *
+   * @param {object} [configuration={}]
+   * @param {object|array} [configuration.csToolsConfig] - Passed directly to `initCornerstoneTools`
+   */
+  getViewportModule({ servicesManager, extensionManager }) {
+    const ExtendedOHIFCornerstonePdfViewport = props => {
+      return (
+        <OHIFCornerstonePdfViewport
+          servicesManager={servicesManager}
+          extensionManager={extensionManager}
+          {...props}
+        />
+      );
+    };
+
+    return [{ name: 'dicom-pdf', component: ExtendedOHIFCornerstonePdfViewport }];
+  },
+  getCommandsModule({ servicesManager }) {
+    return {
+      definitions: {
+        setToolActive: {
+          commandFn: () => null,
+          storeContexts: [],
+          options: {},
+        },
+      },
+      defaultContext: 'ACTIVE_VIEWPORT::PDF',
+    };
+  },
+  getSopClassHandlerModule,
+};

extensions/dicom-pdf/src/viewports/OHIFCornerstonePdfViewport.js

@@ -0,0 +1,26 @@
+import React, { useEffect, useState } from 'react';
+import PropTypes from 'prop-types';
+
+function OHIFCornerstonePdfViewport({
+  displaySet,
+}) {
+  const [url, setUrl] = useState(null);
+  const { pdfUrl } = displaySet;
+  useEffect(async () => {
+    setUrl(await pdfUrl);
+  });
+
+  return (
+    <div className="bg-primary-black w-full h-full">
+      <object data={url} type="application/pdf" className="w-full h-full">
+        <div>No online PDF viewer installed</div>
+      </object>
+    </div>
+  )
+}
+
+OHIFCornerstonePdfViewport.propTypes = {
+  displaySet: PropTypes.object.isRequired,
+};
+
+export default OHIFCornerstonePdfViewport;

extensions/dicom-video/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-video",
-  "version": "0.0.1",
+  "version": "3.0.1",
   "description": "OHIF extension for video display",
   "author": "OHIF",
   "license": "MIT",

extensions/dicom-video/src/getSopClassHandlerModule.js

@@ -1,7 +1,5 @@
-import { SOPClassHandlerName, SOPClassHandlerId } from './id';
-import { utils, classes } from '@ohif/core';
-
-const { ImageSet } = classes;
+import { Name, SOPClassHandlerId } from './id';
+import { utils, } from '@ohif/core';
 
 const SOP_CLASS_UIDS = {
   VIDEO_MICROSCOPIC_IMAGE_STORAGE: '1.2.840.10008.5.1.4.1.1.77.1.2.1',
@@ -36,8 +34,7 @@ const _getDisplaySetsFromSeries = (instances, servicesManager, extensionManager)
       return supportedTransferSyntaxUIDs.includes(tsuid);
     })
     .map(instance => {
-      const { Modality, FrameOfReferenceUID, SOPInstanceUID } = instance;
-      const { SeriesDescription, ContentDate, ContentTime } = instance;
+      const { Modality, SOPInstanceUID, SeriesDescription = "VIDEO" } = instance;
       const { SeriesNumber, SeriesDate, SeriesInstanceUID, StudyInstanceUID, NumberOfFrames } = instance;
       const displaySet = {
         //plugin: id,
@@ -52,7 +49,7 @@ const _getDisplaySetsFromSeries = (instances, servicesManager, extensionManager)
         SOPClassHandlerId,
         referencedImages: null,
         measurements: null,
-        videoUrl: dataSource.retrieve.directURL({ instance }),
+        videoUrl: dataSource.retrieve.directURL({ instance, singlepart: "video", tag: "PixelData", }),
         others: [instance],
         thumbnailSrc: dataSource.retrieve.directURL({ instance, defaultPath: "/thumbnail", defaultType: "image/jpeg", tag: "Absent" }),
         isDerivedDisplaySet: true,
@@ -76,7 +73,7 @@ export default function getSopClassHandlerModule({ servicesManager, extensionMan
 
   return [
     {
-      name: SOPClassHandlerName,
+      name: Name,
       sopClassUids,
       getDisplaySetsFromSeries,
     },

extensions/dicom-video/src/id.js

@@ -1,7 +1,8 @@
-const id = 'org.ohif.dicom-video';
+const Name = 'dicom-video';
+const id = `org.ohif.${Name}`;
 
 export default id;
 
-const SOPClassHandlerName = 'dicom-video';
-const SOPClassHandlerId = `${id}.sopClassHandlerModule.${SOPClassHandlerName}`;
-export { SOPClassHandlerName, SOPClassHandlerId };
+const SOPClassHandlerId = `${id}.sopClassHandlerModule.${Name}`;
+
+export { Name, SOPClassHandlerId, };

extensions/dicom-video/src/viewports/OHIFCornerstoneVideoViewport.js

@@ -1,51 +1,36 @@
-import React, { useCallback, useContext, useEffect, useState } from 'react';
+import React, { useEffect, useState } from 'react';
 import PropTypes from 'prop-types';
-import cornerstoneTools from 'cornerstone-tools';
-import cornerstone from 'cornerstone-core';
-import CornerstoneViewport from 'react-cornerstone-viewport';
-import OHIF, { DicomMetadataStore, utils } from '@ohif/core';
-import {
-  Notification,
-  ViewportActionBar,
-  useViewportGrid,
-  useViewportDialog,
-} from '@ohif/ui';
-import { adapters } from 'dcmjs';
-import id from '../id';
-
 
 function OHIFCornerstoneVideoViewport({
-  children,
-  dataSource,
   displaySet,
-  viewportIndex,
-  servicesManager,
-  extensionManager,
 }) {
-  const {
-    DisplaySetService,
-    MeasurementService,
-    ToolBarService,
-  } = servicesManager.services;
   const { videoUrl } = displaySet;
   const mimeType = "video/mp4";
+  const [url, setUrl] = useState(null);
+  useEffect(async () => {
+    setUrl(await videoUrl);
+  });
 
   // Need to copies of the source to fix a firefox bug
   return (
     <div className="bg-primary-black w-full h-full">
       <video
-        src={videoUrl}
+        src={url}
         controls
         controlsList="nodownload"
         preload="auto"
         className="w-full h-full"
       >
-        <source src={videoUrl} type={mimeType} />
-        <source src={videoUrl} type={mimeType} />
-        Video src/type not supported: <a href={videoUrl}>{videoUrl} of type {mimeType}</a>
+        <source src={url} type={mimeType} />
+        <source src={url} type={mimeType} />
+        Video src/type not supported: <a href={url}>{url} of type {mimeType}</a>
       </video>
     </div>
   )
 }
 
+OHIFCornerstoneVideoViewport.propTypes = {
+  displaySet: PropTypes.object.isRequired,
+};
+
 export default OHIFCornerstoneVideoViewport;