Add DICOM PDF plugin

.gitmodules

@@ -7,3 +7,6 @@
 [submodule "Packages-react/react-cornerstone-viewport"]
 	path = Packages-react/react-cornerstone-viewport
 	url = git@github.com:cornerstonejs/react-cornerstone-viewport.git
+[submodule "Packages-react/plugins/VTKPlugin"]
+	path = Packages-react/plugins/VTKPlugin
+	url = git@github.com:OHIF/VTKPlugin.git

OHIFViewer-react/package.json

@@ -10,6 +10,7 @@
     "cornerstone-tools": "3.0.0-b.1512",
     "cornerstone-wado-image-loader": "2.2.3",
     "dicom-parser": "1.8.3",
+    "dicomweb-client": "^0.4.1",
     "hammerjs": "^2.0.8",
     "lodash.clonedeep": "^4.5.0",
     "lodash.debounce": "^4.0.8",
@@ -27,6 +28,7 @@
     "react-router-dom": "^4.3.1",
     "react-scripts": "^2.1.3",
     "react-viewerbase": "^0.2.1",
+    "react-vtkjs-viewport": "^0.0.1",
     "redux": "^4.0.1",
     "redux-oidc": "^3.1.0"
   },

OHIFViewer-react/src/App.js

@@ -44,6 +44,12 @@ class App extends Component {
 
         const userNotLoggedIn = userManager && (!user || user.expired);
         if (userNotLoggedIn) {
+          const pathname = this.props.location.pathname;
+
+          if (pathname !== '/callback') {
+            sessionStorage.setItem('ohif-redirect-to', pathname);
+          }
+
           return (
             <Switch>
               <Route exact path="/silent-refresh.html" onEnter={reload} />

OHIFViewer-react/src/CallbackPage.js

@@ -14,7 +14,9 @@ class CallbackPage extends Component {
       <CallbackComponent
         userManager={this.props.userManager}
         successCallback={() => {
-          this.props.history.push("/");
+          const pathname = sessionStorage.getItem('ohif-redirect-to');
+
+          this.props.history.push(pathname);
         }}
         errorCallback={error => {
           //this.props.history.push("/");

OHIFViewer-react/src/connectedComponents/FlexboxLayout.js

@@ -35,7 +35,13 @@ class FlexboxLayout extends Component {
 
             const thumbnails = study.displaySets.map((displaySet) => {
                 const { displaySetInstanceUid, seriesDescription, seriesNumber, instanceNumber, numImageFrames } = displaySet;
-                const imageId = displaySet.images[0].getImageId();
+
+
+                let imageId;
+
+                if (displaySet.images && displaySet.images.length) {
+                    imageId = displaySet.images[0].getImageId();
+                }
 
                 return {
                     imageId,

OHIFViewer-react/src/connectedComponents/OHIFComponentPlugin.js

@@ -9,7 +9,7 @@ OHIFComponentPlugin.propTypes = {
   id: PropTypes.string.isRequired,
   init: PropTypes.func.isRequired,
   destroy: PropTypes.func.isRequired,
-  children: PropTypes.node.isRequired
+  children: PropTypes.node
 };
 
 export default OHIFComponentPlugin;

OHIFViewer-react/src/connectedComponents/OHIFCornerstoneViewportPlugin/OHIFCornerstoneViewportPlugin.js

@@ -2,7 +2,7 @@ import React, { Component } from "react";
 import PropTypes from "prop-types";
 import OHIF from 'ohif-core';
 import ConnectedCornerstoneViewport from './ConnectedCornerstoneViewport';
-import OHIFComponentPlugin from './OHIFComponentPlugin.js';
+import OHIFComponentPlugin from '../OHIFComponentPlugin.js';
 
 const { StackManager } = OHIF.utils;
 

OHIFViewer-react/src/connectedComponents/OHIFDicomPDFViewportPlugin/DicomPDFViewport.js

@@ -0,0 +1,80 @@
+import React, { Component } from "react";
+import dicomParser from 'dicom-parser';
+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'
+};
+
+class DicomPDFViewport extends Component {
+  state = {
+    fileURL: null,
+    error: null
+  };
+
+  static propTypes = {
+    byteArray: TypedArrayProp.uint8,
+  };
+
+  renderPDF = (dataSet) => {
+    debugger;
+    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;
+    const pdfByteArray = dataSet.byteArray.slice(offset, remainder);
+    const PDF = new Blob([pdfByteArray], {type: 'application/pdf'});
+    const fileURL = URL.createObjectURL(PDF);
+
+    this.setState({
+      fileURL
+    });
+  }
+
+  parseByteArray = (byteArray) => {
+    const options = {
+      untilTag: ''
+    };
+
+    let dataSet;
+
+    try {
+      dataSet = dicomParser.parseDicom(byteArray, options);
+    } catch(error) {
+      this.setState({
+        error
+      });
+    }
+
+    return dataSet
+  }
+
+  componentDidMount() {
+    const dataSet = this.parseByteArray(this.props.byteArray);
+
+    this.renderPDF(dataSet);
+  }
+
+  render() {
+    return (
+      <div className={'DicomPDFViewport'} style={{width: '100%', height: '100%'}}>
+        {this.state.fileURL &&
+          <object data={this.state.fileURL} type="application/pdf" width="100%" height="100%">
+          </object>
+        }
+        {this.state.error &&
+        <h2>{JSON.stringify(this.state.error)}</h2>
+        }
+      </div>
+    );
+  }
+}
+
+
+export default DicomPDFViewport;

OHIFViewer-react/src/connectedComponents/OHIFDicomPDFViewportPlugin/OHIFDicomPDFSopClassHandlerPlugin.js

@@ -0,0 +1,32 @@
+import OHIF from "ohif-core";
+
+const { plugins, utils } = OHIF;
+const { PLUGIN_TYPES } = plugins;
+
+// TODO: Should probably use dcmjs for this
+const SOP_CLASS_UIDS = {
+  ENCAPSULATED_PDF: '1.2.840.10008.5.1.4.1.1.104.1'
+};
+
+const OHIFDicomPDFSopClassHandlerPlugin = {
+  id: 'OHIFDicomPDFSopClassHandlerPlugin',
+  type: PLUGIN_TYPES.SOP_CLASS_HANDLER,
+  sopClassUids: [
+    SOP_CLASS_UIDS.ENCAPSULATED_PDF
+  ],
+  getDisplaySetFromSeries(series, study) {
+    const instance = series.getFirstInstance();
+
+    return {
+      plugin: 'pdf',
+      displaySetInstanceUid: utils.guid(),
+      wadoRoot: study.getData().wadoRoot,
+      wadoUri: instance.getData().wadouri,
+      sopInstanceUid: instance.getSOPInstanceUID(),
+      seriesInstanceUid: series.getSeriesInstanceUID(),
+      studyInstanceUid: study.getStudyInstanceUID()
+    };
+  }
+}
+
+export default OHIFDicomPDFSopClassHandlerPlugin;

OHIFViewer-react/src/connectedComponents/OHIFDicomPDFViewportPlugin/OHIFDicomPDFViewportPlugin.js

@@ -0,0 +1,77 @@
+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;
+
+class OHIFDicomPDFViewportPlugin extends Component {
+  static propTypes = {
+    studies: PropTypes.object,
+    displaySet: PropTypes.object,
+    viewportIndex: PropTypes.number,
+  };
+
+  state = {
+    byteArray: null,
+    error: null
+  }
+
+  static id = 'DicomPDFViewportPlugin';
+
+  static init() {
+    console.log('DicomPDFViewportPlugin init()');
+  }
+
+  static destroy() {
+    console.log('DicomPDFViewportPlugin destroy()');
+  }
+
+  componentDidMount() {
+    const { displaySet } = this.props.viewportData;
+    const { studyInstanceUid, seriesInstanceUid, sopInstanceUid, wadoRoot, wadoUri } = displaySet;
+
+    this.retrieveDicomData(studyInstanceUid, seriesInstanceUid, sopInstanceUid, wadoRoot, wadoUri).then(byteArray => {
+      this.setState({
+        byteArray
+      });
+    }, error => {
+      this.setState({
+        error
+      });
+
+      throw new Error(error);
+    });
+  }
+
+  retrieveDicomData(studyInstanceUid, seriesInstanceUid, sopInstanceUid, wadoRoot, wadoUri) {
+    // 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: DICOMWeb.getAuthorizationHeader()
+    }).then(response => response.arrayBuffer()).then(arraybuffer => {
+      debugger;
+      return new Uint8Array(arraybuffer);
+    });
+  }
+
+  render() {
+    const { id, init, destroy } = OHIFDicomPDFViewportPlugin;
+    const pluginProps = { id, init, destroy };
+
+    return (
+      <OHIFComponentPlugin {...pluginProps}>
+        {this.state.byteArray && <DicomPDFViewport byteArray={this.state.byteArray}/>}
+        {this.state.error &&
+        <h2>{JSON.stringify(this.state.error)}</h2>
+        }
+      </OHIFComponentPlugin>
+    );
+  }
+}
+
+
+export default OHIFDicomPDFViewportPlugin;

OHIFViewer-react/src/connectedComponents/OHIFDicomPDFViewportPlugin/TypedArrayProp.js

@@ -0,0 +1,137 @@
+// https://github.com/facebook/prop-types/issues/69
+
+export const TypedArrayProp = {
+  any: (props, propName, componentName) => {
+    let obj = props[propName];
+    if (!(obj instanceof Float64Array ||
+      obj instanceof Float32Array ||
+      obj instanceof Int32Array ||
+      obj instanceof Int16Array ||
+      obj instanceof Int8Array ||
+      obj instanceof Uint32Array ||
+      obj instanceof Uint16Array ||
+      obj instanceof Uint8Array ||
+      obj instanceof Uint8ClampedArray)) {
+      return new Error(
+        'Invalid prop `' + propName + '` supplied to' +
+        ' `' + componentName + '`. Expected a typed array.'
+      );
+    }
+  },
+
+  float64: (props, propName, componentName) => {
+    if (!(props[propName] instanceof Float64Array)) {
+      return new Error(
+        'Invalid prop `' + propName + '` supplied to' +
+        ' `' + componentName + '`. Expected a Float64Array.'
+      );
+    }
+  },
+
+  float32: (props, propName, componentName) => {
+    if (!(props[propName] instanceof Float32Array)) {
+      return new Error(
+        'Invalid prop `' + propName + '` supplied to' +
+        ' `' + componentName + '`. Expected a Float32Array.'
+      );
+    }
+  },
+
+  float: (props, propName, componentName) => {
+    if (!(props[propName] instanceof Float64Array ||
+      props[propName] instanceof Float32Array)) {
+      return new Error(
+        'Invalid prop `' + propName + '` supplied to' +
+        ' `' + componentName + '`. Expected a Float32Array or Float64Array.'
+      );
+    }
+  },
+
+  int32: (props, propName, componentName) => {
+    if (!(props[propName] instanceof Int32Array)) {
+      return new Error(
+        'Invalid prop `' + propName + '` supplied to' +
+        ' `' + componentName + '`. Expected an Int32Array.'
+      );
+    }
+  },
+
+  int16: (props, propName, componentName) => {
+    if (!(props[propName] instanceof Int16Array)) {
+      return new Error(
+        'Invalid prop `' + propName + '` supplied to' +
+        ' `' + componentName + '`. Expected an In16Array.'
+      );
+    }
+  },
+
+  int8: (props, propName, componentName) => {
+    if (!(props[propName] instanceof Int8Array)) {
+      return new Error(
+        'Invalid prop `' + propName + '` supplied to' +
+        ' `' + componentName + '`. Expected an Int8Array.'
+      );
+    }
+  },
+
+  int: (props, propName, componentName) => {
+    if (!(props[propName] instanceof Int32Array ||
+      props[propName] instanceof Int16Array ||
+      props[propName] instanceof Int8Array)) {
+      return new Error(
+        'Invalid prop `' + propName + '` supplied to' +
+        ' `' + componentName + '`. Expected an Int32Array, In16Array, or Int8Array.'
+      );
+    }
+  },
+
+  uint32: (props, propName, componentName) => {
+    if (!(props[propName] instanceof Uint32Array)) {
+      return new Error(
+        'Invalid prop `' + propName + '` supplied to' +
+        ' `' + componentName + '`. Expected a Uint32Array.'
+      );
+    }
+  },
+
+  uint16: (props, propName, componentName) => {
+    if (!(props[propName] instanceof Uint16Array)) {
+      return new Error(
+        'Invalid prop `' + propName + '` supplied to' +
+        ' `' + componentName + '`. Expected a Uint16Array.'
+      );
+    }
+  },
+
+  uint8: (props, propName, componentName) => {
+    if (!(props[propName] instanceof Uint8Array)) {
+      return new Error(
+        'Invalid prop `' + propName + '` supplied to' +
+        ' `' + componentName + '`. Expected a Uint8Array.'
+      );
+    }
+  },
+
+  uint8clamped: (props, propName, componentName) => {
+    if (!(props[propName] instanceof Uint8ClampedArray)) {
+      return new Error(
+        'Invalid prop `' + propName + '` supplied to' +
+        ' `' + componentName + '`. Expected a Uint8ClampedArray.'
+      );
+    }
+  },
+
+  uint: (props, propName, componentName) => {
+    if (!(props[propName] instanceof Uint32Array ||
+      props[propName] instanceof Uint16Array ||
+      props[propName] instanceof Uint8Array ||
+      props[propName] instanceof Uint8ClampedArray)) {
+      return new Error(
+        'Invalid prop `' + propName + '` supplied to' +
+        ' `' + componentName + '`. Expected a Uint32Array, Uint16Array, Uint8Array, or Uint8ClampedArray.'
+      );
+    }
+  },
+};
+
+export { TypedArrayProp as default };

OHIFViewer-react/src/connectedComponents/ViewerMain.js

@@ -21,13 +21,11 @@ class ViewerMain extends Component {
     studies: PropTypes.array.isRequired
   };
 
-  getDisplaySetsWithImages(studies) {
+  getDisplaySets(studies) {
     const displaySets = [];
     studies.forEach((study) => {
       study.displaySets.forEach(dSet => {
-        if (dSet.images.length) {
+        displaySets.push(dSet);
-          displaySets.push(dSet);
-        }
       });
     });
 
@@ -53,7 +51,7 @@ class ViewerMain extends Component {
     //window.addEventListener('beforeunload', unloadHandlers.beforeUnload);
 
     // Get all the display sets for the viewer studies
-    const displaySets = this.getDisplaySetsWithImages(this.props.studies);
+    const displaySets = this.getDisplaySets(this.props.studies);
 
     this.setState({
       viewportData: displaySets
@@ -66,14 +64,10 @@ class ViewerMain extends Component {
 
     // Note: Use Slice because React does a shallow equality check. Mutating the array
     // would not trigger a re-render. We have to create a copy.
-    debugger;
-    console.warn(item);
     const updatedViewportData = this.state.viewportData.slice(0);
 
     const displaySet = this.findDisplaySet(this.props.studies, item.studyInstanceUid, item.displaySetInstanceUid);
 
-    console.warn(displaySet);
-
     updatedViewportData[viewportIndex] = Object.assign({}, displaySet);
 
     this.setState({
@@ -101,9 +95,6 @@ class ViewerMain extends Component {
     OHIF.viewer.updateImageSynchronizer.destroy();
 
     // TODO: Instruct all plugins to clean up themselves
-    //
-    // Clear references to all stacks in the StackManager
-    //StackManager.clearStacks();
 
     // @TypeSafeStudies
     // Clears OHIF.viewer.Studies collection

OHIFViewer-react/src/index.js

@@ -11,6 +11,9 @@ import App from './App.js';
 
 import OHIFCornerstoneViewportPlugin from "./connectedComponents/OHIFCornerstoneViewportPlugin/OHIFCornerstoneViewportPlugin.js";
 //import ConnectedExampleViewportPlugin from './components/ConnectedExampleViewportPlugin.js';
+//import OHIFVTKViewportPlugin from './connectedComponents/OHIFVTKViewportPlugin/OHIFVTKViewportPlugin.js';
+import OHIFDicomPDFViewportPlugin from './connectedComponents/OHIFDicomPDFViewportPlugin/OHIFDicomPDFViewportPlugin.js';
+import OHIFDicomPDFSopClassHandlerPlugin from './connectedComponents/OHIFDicomPDFViewportPlugin/OHIFDicomPDFSopClassHandlerPlugin.js';
 
 const reducers = OHIF.redux.reducers;
 reducers.ui = ui;
@@ -127,21 +130,44 @@ const buttonsAction = OHIF.redux.actions.setAvailableButtons(defaultButtons);
 
 store.dispatch(buttonsAction);
 
+const { plugins } = OHIF;
+const { PLUGIN_TYPES } = plugins;
+
 // Uncomment this and comment the Cornerstone version to see how the
 // example plugin works
 /*const pluginAction = OHIF.redux.actions.addPlugin({
   id: 'example',
-  type: 'viewport',
+  type: PLUGIN_TYPES.VIEWPORT,
   component: ConnectedExampleViewportPlugin
 });*/
 
-const pluginAction = OHIF.redux.actions.addPlugin({
+const cornerstonePluginAction = OHIF.redux.actions.addPlugin({
   id: 'cornerstone',
-  type: 'viewport',
+  type: PLUGIN_TYPES.VIEWPORT,
   component: OHIFCornerstoneViewportPlugin
 });
 
-store.dispatch(pluginAction);
+/*const pluginAction = OHIF.redux.actions.addPlugin({
+  id: 'vtk',
+  type: PLUGIN_TYPES.VIEWPORT,
+  component: OHIFVTKViewportPlugin
+});*/
+
+const pdfPluginAction = OHIF.redux.actions.addPlugin({
+  id: 'pdf',
+  type: PLUGIN_TYPES.VIEWPORT,
+  component: OHIFDicomPDFViewportPlugin
+});
+
+const pdfPluginActionSopClass = OHIF.redux.actions.addPlugin({
+  id: 'pdf_sopClassHandler',
+  type: PLUGIN_TYPES.SOP_CLASS_HANDLER,
+  component: OHIFDicomPDFSopClassHandlerPlugin
+});
+
+store.dispatch(cornerstonePluginAction);
+store.dispatch(pdfPluginAction);
+store.dispatch(pdfPluginActionSopClass);
 
 // TODO[react] Use a provider when the whole tree is React
 window.store = store;

Packages-react/ohif-core

@@ -1 +1 @@
-Subproject commit 305643a1c9d355888643163e8080f06701cb59ed
+Subproject commit 7ab55fe8f5778def698282d9e6381835897c392d

Packages-react/ohif-viewer/src/CallbackPage.js

@@ -15,7 +15,6 @@ class CallbackPage extends Component {
         userManager={this.props.userManager}
         successCallback={() => {
           const pathname = sessionStorage.getItem('ohif-redirect-to');
-          debugger;
 
           this.props.history.push(pathname);
         }}

Packages-react/ohif-viewer/src/OHIFStandaloneViewer.js

@@ -38,7 +38,6 @@ class OHIFStandaloneViewer extends Component {
 
     const userNotLoggedIn = userManager && (!user || user.expired);
     if (userNotLoggedIn) {
-      debugger;
       const pathname = this.props.location.pathname;
 
       if (pathname !== '/callback') {

Packages-react/plugins/VTKPlugin

@@ -0,0 +1 @@
+Subproject commit dd8b3a7edddc5bc97af49bd4ceeb89c5f7d56dfb

Packages-react/react-viewerbase

@@ -1 +1 @@
-Subproject commit 34b0df571866dcd374d6189944c16a863b79e0bd
+Subproject commit 6baa2cc97f224cc2baef62436014385b9cc6ac4d