chore(release): publish [skip ci]

- @ohif/extension-debugging@0.1.6
 - @ohif/extension-dicom-rt@0.4.7
 - @ohif/extension-vtk@1.7.9
 - @ohif/ui@1.5.6
 - @ohif/viewer@4.5.16

.docker/Viewer-v2.x/entrypoint.sh

@@ -28,6 +28,12 @@ if [ -n "$CLIENT_ID" ] || [ -n "$HEALTHCARE_API_ENDPOINT" ]
 	  cp /usr/share/nginx/html/google.js /usr/share/nginx/html/app-config.js
 fi
 
+if [ -n "${PORT}" ]
+  then
+    echo "Changing port to ${PORT}..."
+    sed -i -e "s/listen 80/listen ${PORT}/g" /etc/nginx/conf.d/default.conf
+fi
+
 echo "Starting Nginx to serve the OHIF Viewer..."
 
 exec "$@"

.netlify/build-deploy-preview.sh

@@ -11,6 +11,7 @@ node -v
 
 # Install build deps and all monorepo package dependencies. Yarn Workspaces
 # should also symlink all projects appropriately
+yarn run lerna:restore
 yarn install --no-ignore-optional --pure-lockfile
 
 # Build && Move PWA Output
@@ -21,6 +22,19 @@ mv platform/viewer/dist/* .netlify/www/pwa -v
 # Build && Move script output
 # yarn run build:package
 
+# Build && Move Docz Output
+# Using local yarn install to prevent Gatsby from needing to access
+# node_modules above the platform/ui folder
+cd platform/ui
+yarn install
+yarn run build
+cd ../..
+mkdir -p ./.netlify/www/ui
+mv platform/ui/.docz/dist/* .netlify/www/ui -v
+
+# Cache all of the node_module dependencies in
+# extensions, modules, and platform packages
+yarn run lerna:cache
 echo 'Nothing left to see here. Go home, folks.'
 
 # Build using react-scripts

README.md

@@ -122,7 +122,7 @@ window.config = {
 ```
 
 - Install the viewer:
-  `window.OHIFStandaloneViewer.installViewer(window.config);`
+  `window.OHIFViewer.installViewer(window.config);`
 
 This exact setup is demonstrated in this
 [CodeSandbox](https://codesandbox.io/s/viewer-script-tag-tprch) and in our

extensions/cornerstone/CHANGELOG.md

@@ -3,6 +3,134 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [2.9.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.9.4...@ohif/extension-cornerstone@2.9.5) (2020-09-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.9.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.9.3...@ohif/extension-cornerstone@2.9.4) (2020-09-03)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.9.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.9.2...@ohif/extension-cornerstone@2.9.3) (2020-09-02)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.9.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.9.1...@ohif/extension-cornerstone@2.9.2) (2020-08-20)
+
+
+### Bug Fixes
+
+* Updated react-cornerstone-viewport to version 4.0.2 ([#2001](https://github.com/OHIF/Viewers/issues/2001)) ([59ab68b](https://github.com/OHIF/Viewers/commit/59ab68b4edbfec010170c4429c300a53f688bf94))
+
+
+
+
+
+## [2.9.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.9.0...@ohif/extension-cornerstone@2.9.1) (2020-08-20)
+
+
+### Performance Improvements
+
+* **stackPrefetch:** Added stackPrefetch config with 20 max concurrent requests ([#2000](https://github.com/OHIF/Viewers/issues/2000)) ([3b02a06](https://github.com/OHIF/Viewers/commit/3b02a06f5e250660edde4862ce44147db3dc3ab9))
+
+
+
+
+
+# [2.9.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.8.5...@ohif/extension-cornerstone@2.9.0) (2020-08-18)
+
+
+### Features
+
+* 🎸 Update react-vtkjs-viewport usage to use requestPool ([#1984](https://github.com/OHIF/Viewers/issues/1984)) ([bb5f30c](https://github.com/OHIF/Viewers/commit/bb5f30ce2a0192d2e021beaaadfff22fd38e17b9))
+
+
+
+
+
+## [2.8.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.8.4...@ohif/extension-cornerstone@2.8.5) (2020-08-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.8.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.8.3...@ohif/extension-cornerstone@2.8.4) (2020-07-13)
+
+
+### Bug Fixes
+
+* 🐛 - Put guards in all places that a cornerstone re-render ([#1899](https://github.com/OHIF/Viewers/issues/1899)) ([451f7ea](https://github.com/OHIF/Viewers/commit/451f7eab9258e7a193eb362e0926b13aedc4b3c9))
+
+
+
+
+
+## [2.8.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.8.2...@ohif/extension-cornerstone@2.8.3) (2020-07-13)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.8.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.8.1...@ohif/extension-cornerstone@2.8.2) (2020-06-15)
+
+
+### Bug Fixes
+
+* 🐛 Disable seg panel when data for seg unavailable ([#1732](https://github.com/OHIF/Viewers/issues/1732)) ([698e900](https://github.com/OHIF/Viewers/commit/698e900b85121d3c2a46747c443ef69fb7a8c95b)), closes [#1728](https://github.com/OHIF/Viewers/issues/1728)
+
+
+
+
+
+## [2.8.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.8.0...@ohif/extension-cornerstone@2.8.1) (2020-06-04)
+
+
+### Bug Fixes
+
+* 🐛 Infinite frame index change when quickly jumping between ([#1734](https://github.com/OHIF/Viewers/issues/1734)) ([a830577](https://github.com/OHIF/Viewers/commit/a8305772d0fbec506549ad7ea08504a8bc3a4f39)), closes [#1733](https://github.com/OHIF/Viewers/issues/1733)
+
+
+
+
+
+# [2.8.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.7.3...@ohif/extension-cornerstone@2.8.0) (2020-06-04)
+
+
+### Features
+
+* 🎸 1729 - error boundary wrapper ([#1764](https://github.com/OHIF/Viewers/issues/1764)) ([c02b232](https://github.com/OHIF/Viewers/commit/c02b232b0cc24f38af5d5e3831d987d048e60ada))
+
+
+
+
+
+## [2.7.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.7.2...@ohif/extension-cornerstone@2.7.3) (2020-05-12)
+
+
+### Bug Fixes
+
+* 🐛 Fix seg color load ([#1724](https://github.com/OHIF/Viewers/issues/1724)) ([c4f84b1](https://github.com/OHIF/Viewers/commit/c4f84b1174d04ba84d37ed89b6d7ab541be28181))
+
+
+
+
+
 ## [2.7.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.7.1...@ohif/extension-cornerstone@2.7.2) (2020-05-04)
 
 

extensions/cornerstone/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone",
-  "version": "2.7.2",
+  "version": "2.9.5",
   "description": "OHIF extension for Cornerstone",
   "author": "OHIF",
   "license": "MIT",
@@ -34,9 +34,9 @@
     "@ohif/ui": "^0.50.0",
     "cornerstone-core": "^2.2.8",
     "cornerstone-math": "^0.1.8",
-    "cornerstone-tools": "4.12.5",
+    "cornerstone-tools": "^4.20.1",
     "cornerstone-wado-image-loader": "^3.1.0",
-    "dcmjs": "^0.12.3",
+    "dcmjs": "0.16.3",
     "dicom-parser": "^1.8.3",
     "hammerjs": "^2.0.8",
     "prop-types": "^15.6.2",
@@ -51,6 +51,6 @@
     "classnames": "^2.2.6",
     "lodash.merge": "^4.6.2",
     "lodash.throttle": "^4.1.1",
-    "react-cornerstone-viewport": "2.3.8"
+    "react-cornerstone-viewport": "4.0.4"
   }
 }

extensions/cornerstone/src/OHIFCornerstoneViewport.js

@@ -4,7 +4,6 @@ import ConnectedCornerstoneViewport from './ConnectedCornerstoneViewport';
 import OHIF from '@ohif/core';
 import PropTypes from 'prop-types';
 import cornerstone from 'cornerstone-core';
-import debounce from 'lodash.debounce';
 
 const { StackManager } = OHIF.utils;
 
@@ -216,9 +215,10 @@ class OHIFCornerstoneViewport extends Component {
       });
     }
 
-    const debouncedNewImageHandler = debounce(({ currentImageIdIndex, sopInstanceUid }) => {
+    const newImageHandler = ({ currentImageIdIndex, sopInstanceUid }) => {
       const { displaySet } = this.props.viewportData;
       const { StudyInstanceUID } = displaySet;
+
       if (currentImageIdIndex > 0) {
         this.props.onNewImage({
           StudyInstanceUID,
@@ -227,7 +227,7 @@ class OHIFCornerstoneViewport extends Component {
           activeViewportIndex: viewportIndex,
         });
       }
-    }, 700);
+    };
 
     return (
       <>
@@ -235,7 +235,8 @@ class OHIFCornerstoneViewport extends Component {
           viewportIndex={viewportIndex}
           imageIds={imageIds}
           imageIdIndex={currentImageIdIndex}
-          onNewImage={debouncedNewImageHandler}
+          onNewImage={newImageHandler}
+          onNewImageDebounceTime={700}
           // ~~ Connected (From REDUX)
           // frameRate={frameRate}
           // isPlaying={false}

extensions/cornerstone/src/commandsModule.js

@@ -10,6 +10,14 @@ const scroll = cornerstoneTools.import('util/scroll');
 const { studyMetadataManager } = OHIF.utils;
 const { setViewportSpecificData } = OHIF.redux.actions;
 
+const refreshCornerstoneViewports = () => {
+  cornerstone.getEnabledElements().forEach(enabledElement => {
+    if (enabledElement.image) {
+      cornerstone.updateImage(enabledElement.element);
+    }
+  });
+};
+
 const commandsModule = ({ servicesManager }) => {
   const actions = {
     rotateViewport: ({ viewports, rotation }) => {
@@ -180,10 +188,7 @@ const commandsModule = ({ servicesManager }) => {
 
       measurementApi.syncMeasurementsAndToolData();
 
-      // Update images in all active viewports
-      cornerstone.getEnabledElements().forEach(enabledElement => {
-        cornerstone.updateImage(enabledElement.element);
-      });
+      refreshCornerstoneViewports();
     },
     getNearbyToolData({ element, canvasCoordinates, availableToolTypes }) {
       const nearbyTool = {};
@@ -262,23 +267,26 @@ const commandsModule = ({ servicesManager }) => {
       StudyInstanceUID,
       SOPInstanceUID,
       frameIndex,
-      activeViewportIndex
+      activeViewportIndex,
     }) => {
       const study = studyMetadataManager.get(StudyInstanceUID);
 
       const displaySet = study.findDisplaySet(ds => {
-        return ds.images && ds.images.find(i => i.getSOPInstanceUID() === SOPInstanceUID)
+        return (
+          ds.images &&
+          ds.images.find(i => i.getSOPInstanceUID() === SOPInstanceUID)
+        );
       });
 
       displaySet.SOPInstanceUID = SOPInstanceUID;
       displaySet.frameIndex = frameIndex;
 
-      window.store.dispatch(setViewportSpecificData(activeViewportIndex, displaySet));
+      window.store.dispatch(
+        setViewportSpecificData(activeViewportIndex, displaySet)
+      );
 
-      cornerstone.getEnabledElements().forEach(enabledElement => {
-        cornerstone.updateImage(enabledElement.element);
-      });
-    }
+      refreshCornerstoneViewports();
+    },
   };
 
   const definitions = {

extensions/cornerstone/src/index.js

@@ -3,6 +3,7 @@ import init from './init.js';
 import commandsModule from './commandsModule.js';
 import toolbarModule from './toolbarModule.js';
 import CornerstoneViewportDownloadForm from './CornerstoneViewportDownloadForm';
+import { version } from '../package.json';
 
 const Component = React.lazy(() => {
   return import('./OHIFCornerstoneViewport');
@@ -24,6 +25,7 @@ export default {
    * Only required property. Should be a unique value across all extensions.
    */
   id: 'cornerstone',
+  version,
 
   /**
    *
@@ -39,7 +41,9 @@ export default {
       const onNewImageHandler = jumpData => {
         commandsManager.runCommand('jumpToImage', jumpData);
       };
-      return <OHIFCornerstoneViewport {...props} onNewImage={onNewImageHandler} />;
+      return (
+        <OHIFCornerstoneViewport {...props} onNewImage={onNewImageHandler} />
+      );
     };
 
     return ExtendedOHIFCornerstoneViewport;

extensions/cornerstone/src/initCornerstoneTools.js

@@ -34,4 +34,11 @@ export default function(configuration = {}) {
   cornerstoneTools.toolColors.setActiveColor('rgb(0, 255, 0)');
 
   cornerstoneTools.store.state.touchProximity = 40;
+
+  // Configure stack prefetch
+  cornerstoneTools.stackPrefetch.setConfiguration({
+    maxImagesToPrefetch: Infinity,
+    preserveExistingPool: false,
+    maxSimultaneousRequests: 20,
+  });
 }

extensions/debugging/CHANGELOG.md

@@ -0,0 +1,76 @@
+# Change Log
+
+All notable changes to this project will be documented in this file.
+See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+## [0.1.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-debugging@0.1.5...@ohif/extension-debugging@0.1.6) (2020-10-06)
+
+**Note:** Version bump only for package @ohif/extension-debugging
+
+
+
+
+
+## [0.1.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-debugging@0.1.4...@ohif/extension-debugging@0.1.5) (2020-09-17)
+
+**Note:** Version bump only for package @ohif/extension-debugging
+
+
+
+
+
+## [0.1.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-debugging@0.1.3...@ohif/extension-debugging@0.1.4) (2020-09-10)
+
+**Note:** Version bump only for package @ohif/extension-debugging
+
+
+
+
+
+## 0.1.3 (2020-09-03)
+
+**Note:** Version bump only for package @ohif/extension-debugging
+
+
+
+
+
+## [0.1.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-p10-downloader@0.1.1...@ohif/extension-dicom-p10-downloader@0.1.2) (2020-06-18)
+
+**Note:** Version bump only for package @ohif/extension-dicom-p10-downloader
+
+
+
+
+
+## [0.1.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-p10-downloader@0.1.0...@ohif/extension-dicom-p10-downloader@0.1.1) (2020-06-04)
+
+**Note:** Version bump only for package @ohif/extension-dicom-p10-downloader
+
+
+
+
+
+# [0.1.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-p10-downloader@0.0.2...@ohif/extension-dicom-p10-downloader@0.1.0) (2020-04-23)
+
+
+### Features
+
+* configuration to hook into XHR Error handling ([e96205d](https://github.com/OHIF/Viewers/commit/e96205de35e5bec14dc8a9a8509db3dd4e6ecdb6))
+
+
+
+
+
+## 0.0.2 (2020-04-15)
+
+**Note:** Version bump only for package @ohif/extension-dicom-p10-downloader
+
+
+
+
+
+# Change Log
+
+All notable changes to this project will be documented in this file. See
+[Conventional Commits](https://conventionalcommits.org) for commit guidelines.

extensions/debugging/package.json

@@ -1,7 +1,7 @@
 {
-  "name": "@ohif/extension-dicom-p10-downloader",
-  "version": "0.1.0",
-  "description": "OHIF extension for downloading DICOM P10 files",
+  "name": "@ohif/extension-debugging",
+  "version": "0.1.6",
+  "description": "OHIF extension for debugging.",
   "author": "OHIF",
   "license": "MIT",
   "repository": "OHIF/Viewers",
@@ -33,6 +33,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.5.5",
+    "detect-browser": "5.1.1",
     "dicomweb-client": "^0.6.0",
     "file-saver": "^2.0.2",
     "jszip": "^3.2.2"

extensions/debugging/src/DebugReportModal.css

@@ -0,0 +1,14 @@
+.debugReportModalHeader {
+  padding: 10px 0 10px;
+  color: var(--active-color);
+}
+
+.debug-report-modal-container {
+  display: flex;
+  flex-direction: column;
+}
+
+.debug-report-modal-buttons-container {
+  display: flex;
+  flex-direction: row;
+}

extensions/debugging/src/DebugReportModal.js

@@ -0,0 +1,273 @@
+import React from 'react';
+import { detect } from 'detect-browser';
+import './DebugReportModal.css';
+import { ToolbarButton } from '@ohif/ui';
+
+const DubugReportModal = ({
+  viewports,
+  studies,
+  servers,
+  extensionManager,
+  mailTo,
+  debugModalMessage,
+}) => {
+  const copyDebugDataToClipboard = () => {
+    const body = getEmailBody();
+
+    const textArea = document.createElement('textarea');
+
+    textArea.value = body;
+    document.body.appendChild(textArea);
+    textArea.select();
+    document.execCommand('copy');
+    document.body.removeChild(textArea);
+  };
+
+  const getEmailBody = () => {
+    let body = `Enter the description of your problem here: \n\n\n`;
+
+    body += `============= SESSION INFO =============\n\n`;
+
+    // App version
+
+    body += '== App ==\n';
+    body += `version\t${window.version}\n\n`;
+
+    // Extensions Versions
+
+    body += '== Extensions Versions ==\n';
+
+    const { registeredExtensionVesions } = extensionManager;
+
+    Object.keys(registeredExtensionVesions).forEach(extensionId => {
+      const version = registeredExtensionVesions[extensionId];
+
+      body += `${extensionId}\t${version}\n`;
+    });
+
+    body += '\n';
+
+    // Browser Info
+
+    const browser = detect();
+
+    const { name, os, type, version } = browser;
+
+    body += '== Browser Info ==\n';
+    body += `name\t ${name}\n`;
+    body += `os\t ${os}\n`;
+    body += `type\t ${type}\n`;
+    body += `version\t ${version}\n\n`;
+
+    // Study URL
+    body += '== URL ==\n';
+    body += `URL\t ${window.location.href}\n\n`;
+
+    // Layout
+    const { numRows, numColumns, viewportSpecificData } = viewports;
+
+    body += '== Viewport Layout ==\n';
+    body += `Rows\t${numRows}\n`;
+    body += `Columns\t${numColumns}\n\n`;
+    body += '== Viewports ==\n';
+
+    Object.keys(viewportSpecificData).forEach(viewportIndex => {
+      const vsd = viewportSpecificData[viewportIndex];
+
+      const [row, column] = _viewportIndexToViewportPosition(
+        viewportIndex,
+        numColumns
+      );
+
+      body += `[${row},${column}]\t${vsd.SeriesInstanceUID}\n`;
+    });
+
+    return body;
+  };
+
+  const mailToFunction = () => {
+    const StudyInstanceUID = Object.keys(studies.studyData)[0];
+
+    const subject = encodeURI(`Issue with Study: ${StudyInstanceUID}`);
+
+    let body = getEmailBody();
+
+    // TODO Text dump of rest of stuff.
+
+    body = encodeURI(body);
+
+    window.location.href = `mailto:${mailTo}?subject=${subject}&body=${body}`;
+  };
+
+  return (
+    <div className="debug-report-modal-container">
+      {debugModalMessage ? <p>{debugModalMessage}</p> : null}
+      <div className="debug-report-modal-buttons-container">
+        {mailTo ? (
+          <div>
+            <ToolbarButton
+              label={'Send Bug Report'}
+              onClick={mailToFunction}
+              icon={'envelope-square'}
+              isActive={false}
+            />
+          </div>
+        ) : null}
+        <div>
+          <ToolbarButton
+            label={'Copy To Clipboard'}
+            onClick={copyDebugDataToClipboard}
+            icon={'clipboard'}
+            isActive={false}
+          />
+        </div>
+      </div>
+      <div>
+        <table>
+          {getAppVersion()}
+          {getExtensionVersions(extensionManager)}
+          {getBrowserInfo()}
+          {getCurrentStudyUrl()}
+          {getLayout(viewports)}
+        </table>
+      </div>
+    </div>
+  );
+};
+
+const getAppVersion = () => {
+  return (
+    <React.Fragment>
+      <tr>
+        <th className="debugReportModalHeader">App</th>
+      </tr>
+      <tr>
+        <td>Version</td>
+        <td>{window.version}</td>
+      </tr>
+    </React.Fragment>
+  );
+};
+
+const getCurrentStudyUrl = () => {
+  return (
+    <React.Fragment>
+      <tr>
+        <th className="debugReportModalHeader">URL</th>
+      </tr>
+      <tr>
+        <td>URL</td>
+        <td>{window.location.href}</td>
+      </tr>
+    </React.Fragment>
+  );
+};
+
+const getExtensionVersions = extensionManager => {
+  const { registeredExtensionVesions } = extensionManager;
+
+  const lineItems = Object.keys(registeredExtensionVesions).map(extensionId => {
+    const version = registeredExtensionVesions[extensionId];
+
+    return (
+      <tr>
+        <td>{extensionId}</td>
+        <td>{version}</td>
+      </tr>
+    );
+  });
+
+  return (
+    <React.Fragment>
+      <th className="debugReportModalHeader">Extensions</th>
+      {lineItems}
+    </React.Fragment>
+  );
+};
+
+const getLayout = viewports => {
+  const { numRows, numColumns } = viewports;
+
+  return (
+    <React.Fragment>
+      <tr>
+        <th className="debugReportModalHeader">Viewports</th>
+      </tr>
+      <tr>
+        <th>Layout</th>
+      </tr>
+      <tr>
+        <td>Rows</td>
+        <td>{numRows}</td>
+      </tr>
+      <tr>
+        <td>Columns</td>
+        <td>{numColumns}</td>
+      </tr>
+      <tr>
+        <th>SeriesInstanceUIDs</th>
+      </tr>
+      {getSeriesInstanceUIDsPerRow(viewports)}
+    </React.Fragment>
+  );
+};
+
+const getBrowserInfo = () => {
+  const browser = detect();
+
+  const { name, os, type, version } = browser;
+
+  return (
+    <React.Fragment>
+      <tr>
+        <th className="debugReportModalHeader">Platform</th>
+      </tr>
+      <tr>
+        <td>name</td>
+        <td>{name}</td>
+      </tr>
+      <tr>
+        <td>os</td>
+        <td>{os}</td>
+      </tr>
+      <tr>
+        <td>type</td>
+        <td>{type}</td>
+      </tr>
+      <tr>
+        <td>version</td>
+        <td>{version}</td>
+      </tr>
+    </React.Fragment>
+  );
+};
+
+const getSeriesInstanceUIDsPerRow = viewports => {
+  const { viewportSpecificData, numColumns } = viewports;
+
+  // NOTE viewportSpecificData is actually an object with numerical keys.
+  return Object.keys(viewportSpecificData).map(viewportIndex => {
+    const vsd = viewportSpecificData[viewportIndex];
+
+    const [row, column] = _viewportIndexToViewportPosition(
+      viewportIndex,
+      numColumns
+    );
+
+    return (
+      <tr>
+        <td>{`[${row},${column}]`}</td>
+        <td>{vsd.SeriesInstanceUID}</td>
+      </tr>
+    );
+  });
+};
+
+const _viewportIndexToViewportPosition = (viewportIndex, numColumns) => {
+  const row = Math.floor(viewportIndex / numColumns);
+  const column = viewportIndex % numColumns;
+
+  return [row, column];
+};
+
+export default DubugReportModal;

extensions/debugging/src/commandsModule.js

@@ -1,19 +1,23 @@
 import OHIF from '@ohif/core';
 import {
   save,
+  upload,
   getDicomWebClientFromContext,
+  getStudyInstanceUIDFromStudies,
   getSOPInstanceReferenceFromActiveViewport,
   getSOPInstanceReferencesFromViewports,
 } from './utils';
-import _downloadAndZip from './downloadAndZip';
+import _downloadAndZip, { downloadInstances } from './downloadAndZip';
+import DebugReportModal from './DebugReportModal';
+import React from 'react';
+
+import state from './state';
 
 const {
-  utils: {
-    Queue,
-  },
+  utils: { Queue },
 } = OHIF;
 
-export function getCommands(context) {
+export function getCommands(context, servicesManager, extensionManager) {
   const queue = new Queue(1);
   const actions = {
     /**
@@ -41,6 +45,14 @@ export function getCommands(context) {
         listOfUIDs
       );
     },
+    downloadAndZipStudy({ servers, studies, progress }) {
+      const dicomWebClient = getDicomWebClientFromContext(context, servers);
+      const listOfUIDs = getStudyInstanceUIDFromStudies(studies);
+      return save(
+        _downloadAndZip(dicomWebClient, listOfUIDs, { progress }),
+        listOfUIDs
+      );
+    },
     downloadAndZipSeriesOnViewports({ servers, viewports, progress }) {
       const dicomWebClient = getDicomWebClientFromContext(context, servers);
       const listOfUIDs = getSOPInstanceReferencesFromViewports(viewports);
@@ -57,13 +69,65 @@ export function getCommands(context) {
         listOfUIDs
       );
     },
+    downloadAndUploadStudy({ servers, studies, progress, serverConfig }) {
+      const dicomWebClient = getDicomWebClientFromContext(context, servers);
+      const listOfUIDs = getStudyInstanceUIDFromStudies(studies);
+      return upload(
+        downloadInstances(dicomWebClient, listOfUIDs, { progress }),
+        /**
+         * serverConfig is an object with the values used to create a new
+         * instance of DICOMwebClient.
+         *
+         * Basic Structure:
+         *
+         * const config = {
+         *    url,
+         *    headers,
+         *    errorInterceptor
+         * }
+         *
+         * const dicomWeb = new api.DICOMwebClient(config);
+         */
+        serverConfig
+      );
+    },
+    openDebugInfoModal({ viewports, studies, servers }) {
+      const { UIModalService } = servicesManager.services;
+
+      const WrappedDebugReportModal = function() {
+        return (
+          <DebugReportModal
+            viewports={viewports}
+            studies={studies}
+            servers={servers}
+            extensionManager={extensionManager}
+            mailTo={state.mailTo}
+            debugModalMessage={state.debugModalMessage}
+          />
+        );
+      };
+
+      UIModalService.show({
+        content: WrappedDebugReportModal,
+        title: `Debugging Information`,
+      });
+    },
   };
 
   const definitions = {
+    openDebugInfoModal: {
+      commandFn: actions.openDebugInfoModal,
+      storeContexts: ['viewports', 'servers', 'studies'],
+    },
     downloadAndZip: {
       commandFn: queue.bindSafe(actions.downloadAndZip, error),
       storeContexts: ['servers'],
     },
+    downloadAndZipStudy: {
+      commandFn: queue.bindSafe(actions.downloadAndZipStudy, error),
+      storeContexts: ['servers', 'studies'],
+      options: { progress },
+    },
     downloadAndZipSeriesOnViewports: {
       commandFn: queue.bindSafe(actions.downloadAndZipSeriesOnViewports, error),
       storeContexts: ['servers', 'viewports'],
@@ -77,6 +141,11 @@ export function getCommands(context) {
       storeContexts: ['servers', 'viewports'],
       options: { progress },
     },
+    downloadAndUploadStudy: {
+      commandFn: queue.bindSafe(actions.downloadAndUploadStudy, error),
+      storeContexts: ['servers', 'studies'],
+      options: { progress },
+    },
   };
 
   return {

extensions/debugging/src/downloadAndZip.js

@@ -79,13 +79,7 @@ async function downloadAndZip(dicomWebClient, listOfUIDs, options) {
   if (dicomWebClient instanceof api.DICOMwebClient) {
     const settings = buildSettings(listOfUIDs, options);
     const { compression } = settings.tasks;
-    // Register user-provided progress handler as a task list observer
-    progressUtils.addObserver(settings.taskList, settings.options.progress);
-    const buffers = await downloadAll(dicomWebClient, settings).catch(error => {
-      // Reject promise from compression task on download failure
-      compression.deferred.reject(error);
-      throw error;
-    });
+    const buffers = await downloadBuffers(settings, dicomWebClient);
     compression.deferred.resolve(zipAll(buffers, settings));
     const url = await compression.deferred.promise;
     return url;
@@ -93,6 +87,27 @@ async function downloadAndZip(dicomWebClient, listOfUIDs, options) {
   throw new Error('A valid DICOM Web Client instance is expected');
 }
 
+async function downloadInstances(dicomWebClient, listOfUIDs, options) {
+  if (dicomWebClient instanceof api.DICOMwebClient) {
+    const settings = buildSettings(listOfUIDs, options);
+    const buffers = await downloadBuffers(settings, dicomWebClient);
+    return buffers;
+  }
+  throw new Error('A valid DICOM Web Client instance is expected');
+}
+
+async function downloadBuffers(settings, dicomWebClient) {
+  const { compression } = settings.tasks;
+  // Register user-provided progress handler as a task list observer
+  progressUtils.addObserver(settings.taskList, settings.options.progress);
+  const buffers = await downloadAll(dicomWebClient, settings).catch(error => {
+    // Reject promise from compression task on download failure
+    compression.deferred.reject(error);
+    throw error;
+  });
+  return buffers;
+}
+
 /**
  * Utils
  */
@@ -241,4 +256,4 @@ async function download(
  * Exports
  */
 
-export { downloadAndZip as default, downloadAndZip };
+export { downloadAndZip as default, downloadAndZip, downloadInstances };

extensions/debugging/src/index.js

@@ -0,0 +1,61 @@
+import { getDicomWebClientFromConfig } from './utils';
+import { getCommands } from './commandsModule';
+import { version } from '../package.json';
+import toolbarModule from './toolbarModule';
+import state from './state';
+
+/**
+ * Constants
+ */
+
+/**
+ * Globals
+ */
+
+const sharedContext = {
+  dicomWebClient: null,
+};
+
+/**
+ * Extension
+ */
+export default {
+  /**
+   * Only required property. Should be a unique value across all extensions.
+   */
+  id: 'dicom-p10-downloader',
+  version,
+
+  /**
+   * LIFECYCLE HOOKS
+   */
+
+  preRegistration({ appConfig, configuration }) {
+    const dicomWebClient = getDicomWebClientFromConfig(appConfig);
+    if (dicomWebClient) {
+      sharedContext.dicomWebClient = dicomWebClient;
+    }
+
+    if (configuration) {
+      if (configuration.mailTo) {
+        state.mailTo = configuration.mailTo;
+      }
+
+      if (configuration.debugModalMessage) {
+        state.debugModalMessage = configuration.debugModalMessage;
+      }
+    }
+  },
+
+  /**
+   * MODULE GETTERS
+   */
+
+  getCommandsModule({ servicesManager, extensionManager }) {
+    return getCommands(sharedContext, servicesManager, extensionManager);
+  },
+
+  getToolbarModule() {
+    return toolbarModule;
+  },
+};

extensions/debugging/src/state.js

@@ -0,0 +1,3 @@
+const state = { mailTo: undefined, message: undefined };
+
+export default state;

extensions/debugging/src/toolbarModule.js

@@ -0,0 +1,20 @@
+const TOOLBAR_BUTTON_TYPES = {
+  COMMAND: 'command',
+};
+
+const definitions = [
+  {
+    id: 'Debug Info',
+    label: 'Debug Info',
+    icon: 'cog',
+    //
+    type: TOOLBAR_BUTTON_TYPES.COMMAND,
+    commandName: 'openDebugInfoModal',
+    context: 'VIEWER',
+  },
+];
+
+export default {
+  definitions,
+  defaultContext: 'VIEWER',
+};

extensions/debugging/src/utils.js

@@ -100,11 +100,59 @@ function save(promise, listOfUIDs) {
     });
 }
 
+function upload(promise, serverConfig) {
+  return Promise.resolve(promise)
+    .then(async instances => {
+      const instancesAmount = instances.length;
+      OHIF.log.info(`Uploading study to ${serverConfig.url}`);
+      OHIF.log.info(
+        `${instancesAmount} instances are being uploaded. Don't close your browser.`
+      );
+
+      try {
+        const dicomWeb = new api.DICOMwebClient(serverConfig);
+        let progress = 0;
+
+        const getProgress = () => {
+          return ((progress * 100) / instancesAmount).toFixed();
+        };
+
+        for (const instance of instances) {
+          const options = {
+            datasets: [instance],
+          };
+
+          await dicomWeb.storeInstances(options);
+
+          progress++;
+
+          OHIF.log.info(`Progress: ${getProgress()}%`);
+        }
+
+        OHIF.log.info('Successfully uploaded!');
+      } catch (error) {
+        OHIF.log.error(`Failed to upload: ${error}`);
+      }
+
+      return instances;
+    })
+    .catch(error => {
+      OHIF.log.error(`Failed to upload: ${error}`);
+      return null;
+    });
+}
+
+function getStudyInstanceUIDFromStudies(studies) {
+  return Object.keys(Object(Object(studies).studyData)).slice(0, 1);
+}
+
 export {
   save,
+  upload,
   validDicomUid,
   getDicomWebClientFromConfig,
   getDicomWebClientFromContext,
+  getStudyInstanceUIDFromStudies,
   getSOPInstanceReferenceFromActiveViewport,
   getSOPInstanceReferencesFromViewports,
 };

extensions/dicom-html/CHANGELOG.md

@@ -3,6 +3,57 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [1.2.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.2.7...@ohif/extension-dicom-html@1.2.8) (2020-09-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.2.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.2.6...@ohif/extension-dicom-html@1.2.7) (2020-09-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.2.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.2.5...@ohif/extension-dicom-html@1.2.6) (2020-09-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.2.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.2.4...@ohif/extension-dicom-html@1.2.5) (2020-08-28)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.2.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.2.3...@ohif/extension-dicom-html@1.2.4) (2020-07-13)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.2.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.2.2...@ohif/extension-dicom-html@1.2.3) (2020-06-15)
+
+
+### Bug Fixes
+
+* 🐛 Disable seg panel when data for seg unavailable ([#1732](https://github.com/OHIF/Viewers/issues/1732)) ([698e900](https://github.com/OHIF/Viewers/commit/698e900b85121d3c2a46747c443ef69fb7a8c95b)), closes [#1728](https://github.com/OHIF/Viewers/issues/1728)
+
+
+
+
+
 ## [1.2.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.2.1...@ohif/extension-dicom-html@1.2.2) (2020-05-04)
 
 

extensions/dicom-html/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-html",
-  "version": "1.2.2",
+  "version": "1.2.8",
   "description": "OHIF extension for rendering structured reports to HTML",
   "author": "OHIF",
   "license": "MIT",
@@ -29,7 +29,7 @@
   },
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
-    "dcmjs": "^0.12.3",
+    "dcmjs": "0.16.3",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6"

extensions/dicom-html/src/OHIFDicomHtmlSopClassHandler.js

@@ -22,6 +22,14 @@ const OHIFDicomHtmlSopClassHandler = {
   getDisplaySetFromSeries(series, study, dicomWebClient, authorizationHeaders) {
     const instance = series.getFirstInstance();
 
+    const metadata = instance.getData().metadata;
+    const {
+      SeriesDescription,
+      SeriesNumber,
+      SeriesDate,
+      SeriesTime,
+    } = metadata;
+
     return {
       plugin: 'html',
       Modality: 'SR',
@@ -31,6 +39,11 @@ const OHIFDicomHtmlSopClassHandler = {
       SOPInstanceUID: instance.getSOPInstanceUID(),
       SeriesInstanceUID: series.getSeriesInstanceUID(),
       StudyInstanceUID: study.getStudyInstanceUID(),
+      SeriesDescription,
+      metadata,
+      SeriesDate,
+      SeriesTime,
+      SeriesNumber,
       authorizationHeaders,
     };
   },

extensions/dicom-html/src/index.js

@@ -1,5 +1,6 @@
 import React from 'react';
 import OHIFDicomHtmlSopClassHandler from './OHIFDicomHtmlSopClassHandler.js';
+import { version } from '../package.json';
 
 const Component = React.lazy(() => {
   return import('./OHIFDicomHtmlViewport');
@@ -18,6 +19,7 @@ export default {
    * Only required property. Should be a unique value across all extensions.
    */
   id: 'html',
+  version,
 
   getViewportModule() {
     return OHIFDicomHtmlViewport;

extensions/dicom-microscopy/CHANGELOG.md

@@ -3,6 +3,41 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [0.51.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.51.2...@ohif/extension-dicom-microscopy@0.51.3) (2020-09-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-microscopy
+
+
+
+
+
+## [0.51.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.51.1...@ohif/extension-dicom-microscopy@0.51.2) (2020-09-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-microscopy
+
+
+
+
+
+## [0.51.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.51.0...@ohif/extension-dicom-microscopy@0.51.1) (2020-08-28)
+
+**Note:** Version bump only for package @ohif/extension-dicom-microscopy
+
+
+
+
+
+# [0.51.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.9...@ohif/extension-dicom-microscopy@0.51.0) (2020-06-04)
+
+
+### Features
+
+* 🎸 1729 - error boundary wrapper ([#1764](https://github.com/OHIF/Viewers/issues/1764)) ([c02b232](https://github.com/OHIF/Viewers/commit/c02b232b0cc24f38af5d5e3831d987d048e60ada))
+
+
+
+
+
 ## [0.50.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.8...@ohif/extension-dicom-microscopy@0.50.9) (2020-04-02)
 
 **Note:** Version bump only for package @ohif/extension-dicom-microscopy

extensions/dicom-microscopy/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-microscopy",
-  "version": "0.50.9",
+  "version": "0.51.3",
   "description": "OHIF extension for Dicom Microscopy",
   "author": "OHIF",
   "license": "MIT",

extensions/dicom-microscopy/src/DicomMicroscopySopClassHandler.js

@@ -12,6 +12,14 @@ const DicomMicroscopySopClassHandler = {
   getDisplaySetFromSeries(series, study, dicomWebClient) {
     const instance = series.getFirstInstance();
 
+    const metadata = instance.getData().metadata;
+    const {
+      SeriesDescription,
+      SeriesNumber,
+      ContentDate,
+      ContentTime,
+    } = metadata;
+
     // Note: We are passing the dicomweb client into each viewport!
 
     return {
@@ -22,6 +30,11 @@ const DicomMicroscopySopClassHandler = {
       SOPInstanceUID: instance.getSOPInstanceUID(),
       SeriesInstanceUID: series.getSeriesInstanceUID(),
       StudyInstanceUID: study.getStudyInstanceUID(),
+      SeriesDescription,
+      SeriesDate: ContentDate, // Map ContentDate/Time to SeriesTime for series list sorting.
+      SeriesTime: ContentTime,
+      SeriesNumber,
+      metadata,
     };
   },
 };

extensions/dicom-microscopy/src/DicomMicroscopyViewport.js

@@ -92,8 +92,8 @@ class DicomMicroscopyViewport extends Component {
         {this.state.error ? (
           <h2>{JSON.stringify(this.state.error)}</h2>
         ) : (
-          <div style={style} ref={this.container} />
-        )}
+            <div style={style} ref={this.container} />
+          )}
       </div>
     );
   }

extensions/dicom-microscopy/src/index.js

@@ -1,5 +1,6 @@
 import React from 'react';
 import DicomMicroscopySopClassHandler from './DicomMicroscopySopClassHandler.js';
+import { version } from '../package.json';
 
 const Component = React.lazy(() => {
   return import('./DicomMicroscopyViewport');
@@ -18,6 +19,7 @@ export default {
    * Only required property. Should be a unique value across all extensions.
    */
   id: 'microscopy',
+  version,
 
   getViewportModule() {
     return DicomMicroscopyViewport;

extensions/dicom-p10-downloader/CHANGELOG.md

@@ -1,28 +0,0 @@
-# Change Log
-
-All notable changes to this project will be documented in this file.
-See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
-
-# [0.1.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-p10-downloader@0.0.2...@ohif/extension-dicom-p10-downloader@0.1.0) (2020-04-23)
-
-
-### Features
-
-* configuration to hook into XHR Error handling ([e96205d](https://github.com/OHIF/Viewers/commit/e96205de35e5bec14dc8a9a8509db3dd4e6ecdb6))
-
-
-
-
-
-## 0.0.2 (2020-04-15)
-
-**Note:** Version bump only for package @ohif/extension-dicom-p10-downloader
-
-
-
-
-
-# Change Log
-
-All notable changes to this project will be documented in this file. See
-[Conventional Commits](https://conventionalcommits.org) for commit guidelines.

extensions/dicom-p10-downloader/src/index.js

@@ -1,43 +0,0 @@
-import { getDicomWebClientFromConfig } from './utils';
-import { getCommands } from './commandsModule';
-
-/**
- * Constants
- */
-
-/**
- * Globals
- */
-
-const sharedContext = {
-  dicomWebClient: null,
-};
-
-/**
- * Extension
- */
-export default {
-  /**
-   * Only required property. Should be a unique value across all extensions.
-   */
-  id: 'dicom-p10-downloader',
-
-  /**
-   * LIFECYCLE HOOKS
-   */
-
-  preRegistration({ appConfig }) {
-    const dicomWebClient = getDicomWebClientFromConfig(appConfig);
-    if (dicomWebClient) {
-      sharedContext.dicomWebClient = dicomWebClient;
-    }
-  },
-
-  /**
-   * MODULE GETTERS
-   */
-
-  getCommandsModule() {
-    return getCommands(sharedContext);
-  },
-};

extensions/dicom-pdf/CHANGELOG.md

@@ -3,6 +3,30 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [1.0.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@1.0.5...@ohif/extension-dicom-pdf@1.0.6) (2020-09-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-pdf
+
+
+
+
+
+## [1.0.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@1.0.4...@ohif/extension-dicom-pdf@1.0.5) (2020-09-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-pdf
+
+
+
+
+
+## [1.0.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@1.0.3...@ohif/extension-dicom-pdf@1.0.4) (2020-08-28)
+
+**Note:** Version bump only for package @ohif/extension-dicom-pdf
+
+
+
+
+
 ## [1.0.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@1.0.2...@ohif/extension-dicom-pdf@1.0.3) (2020-04-02)
 
 **Note:** Version bump only for package @ohif/extension-dicom-pdf

extensions/dicom-pdf/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-pdf",
-  "version": "1.0.3",
+  "version": "1.0.6",
   "description": "OHIF extension for Dicom PDF",
   "author": "OHIF",
   "license": "MIT",

extensions/dicom-pdf/src/OHIFDicomPDFSopClassHandler.js

@@ -12,6 +12,14 @@ const OHIFDicomPDFSopClassHandler = {
   getDisplaySetFromSeries(series, study, dicomWebClient, authorizationHeaders) {
     const instance = series.getFirstInstance();
 
+    const metadata = instance.getData().metadata;
+    const {
+      ContentDate,
+      ContentTime,
+      SeriesDescription,
+      SeriesNumber,
+    } = metadata;
+
     return {
       plugin: 'pdf',
       Modality: 'DOC',
@@ -21,6 +29,11 @@ const OHIFDicomPDFSopClassHandler = {
       SOPInstanceUID: instance.getSOPInstanceUID(),
       SeriesInstanceUID: series.getSeriesInstanceUID(),
       StudyInstanceUID: study.getStudyInstanceUID(),
+      SeriesDescription,
+      SeriesDate: ContentDate, // Map ContentDate/Time to SeriesTime for series list sorting.
+      SeriesTime: ContentTime,
+      SeriesNumber,
+      metadata,
       authorizationHeaders: authorizationHeaders,
     };
   },

extensions/dicom-pdf/src/index.js

@@ -1,5 +1,6 @@
 import React from 'react';
 import OHIFDicomPDFSopClassHandler from './OHIFDicomPDFSopClassHandler.js';
+import { version } from '../package.json';
 
 const Component = React.lazy(() => {
   return import('./ConnectedOHIFDicomPDFViewer');
@@ -18,6 +19,7 @@ export default {
    * Only required property. Should be a unique value across all extensions.
    */
   id: 'pdf',
+  version,
   getViewportModule() {
     return ConnectedOHIFDicomPDFViewer;
   },

extensions/dicom-rt/CHANGELOG.md

@@ -3,6 +3,182 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [0.4.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.4.6...@ohif/extension-dicom-rt@0.4.7) (2020-10-06)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.4.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.4.5...@ohif/extension-dicom-rt@0.4.6) (2020-09-17)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.4.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.4.4...@ohif/extension-dicom-rt@0.4.5) (2020-09-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.4.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.4.3...@ohif/extension-dicom-rt@0.4.4) (2020-09-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.4.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.4.2...@ohif/extension-dicom-rt@0.4.3) (2020-09-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.4.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.4.1...@ohif/extension-dicom-rt@0.4.2) (2020-09-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.4.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.4.0...@ohif/extension-dicom-rt@0.4.1) (2020-08-28)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+# [0.4.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.3.0...@ohif/extension-dicom-rt@0.4.0) (2020-08-18)
+
+
+### Features
+
+* 🎸 Update react-vtkjs-viewport usage to use requestPool ([#1984](https://github.com/OHIF/Viewers/issues/1984)) ([bb5f30c](https://github.com/OHIF/Viewers/commit/bb5f30ce2a0192d2e021beaaadfff22fd38e17b9))
+
+
+
+
+
+# [0.3.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.2.7...@ohif/extension-dicom-rt@0.3.0) (2020-08-10)
+
+
+### Features
+
+* 🎸 Add support for POINT and OPEN_PLANAR for RT ([0e87ab3](https://github.com/OHIF/Viewers/commit/0e87ab37c29fcf9af74bbcefca854c6e6b8707bc))
+
+
+
+
+
+## [0.2.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.2.6...@ohif/extension-dicom-rt@0.2.7) (2020-08-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.2.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.2.5...@ohif/extension-dicom-rt@0.2.6) (2020-08-05)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.2.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.2.4...@ohif/extension-dicom-rt@0.2.5) (2020-07-13)
+
+
+### Bug Fixes
+
+* 🐛 - Put guards in all places that a cornerstone re-render ([#1899](https://github.com/OHIF/Viewers/issues/1899)) ([451f7ea](https://github.com/OHIF/Viewers/commit/451f7eab9258e7a193eb362e0926b13aedc4b3c9))
+
+
+
+
+
+## [0.2.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.2.3...@ohif/extension-dicom-rt@0.2.4) (2020-07-13)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.2.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.2.2...@ohif/extension-dicom-rt@0.2.3) (2020-07-13)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.2.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.2.1...@ohif/extension-dicom-rt@0.2.2) (2020-07-13)
+
+
+### Bug Fixes
+
+* 🐛 Fix RT Panel hide/show and Fix looping load errors ([#1877](https://github.com/OHIF/Viewers/issues/1877)) ([e7cc735](https://github.com/OHIF/Viewers/commit/e7cc735c03d02eeb0d3af4ba02c15ed4f81bbec2))
+
+
+
+
+
+## [0.2.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.2.0...@ohif/extension-dicom-rt@0.2.1) (2020-06-15)
+
+
+### Bug Fixes
+
+* 🐛 Disable seg panel when data for seg unavailable ([#1732](https://github.com/OHIF/Viewers/issues/1732)) ([698e900](https://github.com/OHIF/Viewers/commit/698e900b85121d3c2a46747c443ef69fb7a8c95b)), closes [#1728](https://github.com/OHIF/Viewers/issues/1728)
+
+
+
+
+
+# [0.2.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.1.4...@ohif/extension-dicom-rt@0.2.0) (2020-06-04)
+
+
+### Features
+
+* 🎸 1729 - error boundary wrapper ([#1764](https://github.com/OHIF/Viewers/issues/1764)) ([c02b232](https://github.com/OHIF/Viewers/commit/c02b232b0cc24f38af5d5e3831d987d048e60ada))
+
+
+
+
+
+## [0.1.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.1.3...@ohif/extension-dicom-rt@0.1.4) (2020-05-14)
+
+
+### Bug Fixes
+
+* 🐛 Load default display set when no time metadata ([#1684](https://github.com/OHIF/Viewers/issues/1684)) ([f7b8b6a](https://github.com/OHIF/Viewers/commit/f7b8b6a41c4626084ef56b0fdf7363e914b143c4)), closes [#1683](https://github.com/OHIF/Viewers/issues/1683)
+
+
+
+
+
+## [0.1.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.1.2...@ohif/extension-dicom-rt@0.1.3) (2020-05-12)
+
+
+### Bug Fixes
+
+* 🐛 Fix seg color load ([#1724](https://github.com/OHIF/Viewers/issues/1724)) ([c4f84b1](https://github.com/OHIF/Viewers/commit/c4f84b1174d04ba84d37ed89b6d7ab541be28181))
+
+
+
+
+
 ## [0.1.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.1.1...@ohif/extension-dicom-rt@0.1.2) (2020-05-04)
 
 

extensions/dicom-rt/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-rt",
-  "version": "0.1.2",
+  "version": "0.4.7",
   "description": "OHIF extension for rendering DICOM RTSTRUCTs on top of cornerstone images.",
   "author": "OHIF",
   "license": "MIT",
@@ -30,11 +30,12 @@
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
     "cornerstone-core": "^2.2.8",
-    "cornerstone-tools": "^4.0.9",
-    "dcmjs": "^0.12.3",
+    "cornerstone-tools": "^4.20.1",
+    "dcmjs": "0.16.3",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
-    "react-dom": "^16.8.6"
+    "react-dom": "^16.8.6",
+    "react-tooltip": "4.2.10"
   },
   "dependencies": {
     "@babel/runtime": "^7.5.5",

extensions/dicom-rt/src/OHIFDicomRTStructSopClassHandler.js

@@ -1,5 +1,6 @@
 import { MODULE_TYPES, utils, DICOMWeb } from '@ohif/core';
 import loadRTStruct from './loadRTStruct';
+import getSourceDisplaySet from './getSourceDisplaySet';
 
 import id from './id';
 
@@ -14,7 +15,7 @@ const OHIFDicomRTStructSopClassHandler = {
   id: 'OHIFDicomRTStructSopClassHandler',
   type: MODULE_TYPES.SOP_CLASS_HANDLER,
   sopClassUIDs,
-  getDisplaySetFromSeries: function (
+  getDisplaySetFromSeries: function(
     series,
     study,
     dicomWebClient,
@@ -26,6 +27,7 @@ const OHIFDicomRTStructSopClassHandler = {
     const {
       SeriesDate,
       SeriesTime,
+      SeriesNumber,
       SeriesDescription,
       FrameOfReferenceUID,
       SOPInstanceUID,
@@ -52,7 +54,9 @@ const OHIFDicomRTStructSopClassHandler = {
       isLoaded: false,
       SeriesDate,
       SeriesTime,
+      SeriesNumber,
       SeriesDescription,
+      metadata,
     };
 
     if (!metadata.ReferencedSeriesSequence) {
@@ -67,13 +71,18 @@ const OHIFDicomRTStructSopClassHandler = {
       }
     }
 
-    rtStructDisplaySet.load = function (referencedDisplaySet, studies) {
+    rtStructDisplaySet.getSourceDisplaySet = function(studies) {
+      return getSourceDisplaySet(studies, rtStructDisplaySet);
+    };
+
+    rtStructDisplaySet.load = function(referencedDisplaySet, studies) {
       return loadRTStruct(
         rtStructDisplaySet,
         referencedDisplaySet,
         studies
       ).catch(error => {
         rtStructDisplaySet.isLoaded = false;
+        rtStructDisplaySet.loadError = true;
         throw new Error(error);
       });
     };

extensions/dicom-rt/src/components/RTPanel/RTPanel.js

@@ -12,12 +12,17 @@ import StructureSetItem from '../StructureSetItem/StructureSetItem';
 import RTPanelSettings from '../RTSettings/RTSettings';
 import PanelSection from '../PanelSection/PanelSection';
 import LoadingIndicator from '../LoadingIndicator/LoadingIndicator';
+import TOOL_NAMES from '../../utils/toolNames';
+
+const { RTSTRUCT_DISPLAY_TOOL } = TOOL_NAMES;
 
 const { studyMetadataManager } = utils;
 
 const refreshViewport = () => {
   cornerstone.getEnabledElements().forEach(enabledElement => {
-    cornerstone.updateImage(enabledElement.element);
+    if (enabledElement.image) {
+      cornerstone.updateImage(enabledElement.element);
+    }
   });
 };
 
@@ -31,7 +36,18 @@ const refreshViewport = () => {
  * @param {number} props.isOpen - isOpen
  * @returns component
  */
-const RTPanel = ({ studies, viewports, activeIndex, isOpen, onContourItemClick }) => {
+const RTPanel = ({
+  studies,
+  viewports,
+  activeIndex,
+  isOpen,
+  onContourItemClick,
+  activeContexts = [],
+  contexts = {},
+}) => {
+  const isVTK = () => activeContexts.includes(contexts.VTK);
+  const isCornerstone = () => activeContexts.includes(contexts.CORNERSTONE);
+
   const [selectedContour, setSelectedContour] = useState();
   const DEFAULT_SET_INDEX = 0;
   const DEFAULT_STATE = {
@@ -65,7 +81,10 @@ const RTPanel = ({ studies, viewports, activeIndex, isOpen, onContourItemClick }
     document.addEventListener('extensiondicomrtrtloaded', updateStructureSets);
 
     return () => {
-      document.removeEventListener('extensiondicomrtrtloaded', updateStructureSets);
+      document.removeEventListener(
+        'extensiondicomrtrtloaded',
+        updateStructureSets
+      );
     };
   }, []);
 
@@ -78,7 +97,9 @@ const RTPanel = ({ studies, viewports, activeIndex, isOpen, onContourItemClick }
         activeViewport.SeriesInstanceUID
       );
 
-      const studyMetadata = studyMetadataManager.get(activeViewport.StudyInstanceUID);
+      const studyMetadata = studyMetadataManager.get(
+        activeViewport.StudyInstanceUID
+      );
       const referencedDisplaysets = studyMetadata.getDerivedDatasets({
         referencedSeriesInstanceUID: activeViewport.SeriesInstanceUID,
         Modality: 'RTSTRUCT',
@@ -89,7 +110,7 @@ const RTPanel = ({ studies, viewports, activeIndex, isOpen, onContourItemClick }
         setState({
           referencedDisplaysets,
           selectedSet: defaultSet,
-          sets: viewportSets
+          sets: viewportSets,
         });
       } else {
         setState(DEFAULT_STATE);
@@ -105,7 +126,10 @@ const RTPanel = ({ studies, viewports, activeIndex, isOpen, onContourItemClick }
     setShowSettings(showSettings && !isOpen);
   }, [isOpen]);
 
-  const toContourItem = ({ ROINumber, ROIName, RTROIObservations, colorArray, visible }, loadedSet) => {
+  const toContourItem = (
+    { ROINumber, ROIName, RTROIObservations, colorArray, visible, isSupported },
+    loadedSet
+  ) => {
     let interpretedType = '';
     if (RTROIObservations && RTROIObservations.RTROIInterpretedType) {
       interpretedType = `(${RTROIObservations.RTROIInterpretedType})`;
@@ -116,36 +140,60 @@ const RTPanel = ({ studies, viewports, activeIndex, isOpen, onContourItemClick }
       <StructureSetItem
         key={ROINumber}
         selected={isSameContour}
+        isDisabled={!isSupported}
         onClick={() => {
           setSelectedContour(isSameContour ? null : ROINumber);
 
-          const enabledElements = cornerstone.getEnabledElements();
-          const element = enabledElements[activeIndex].element;
-          const toolState = cornerstoneTools.getToolState(element, 'stack');
+          if (isCornerstone()) {
+            const enabledElements = cornerstone.getEnabledElements();
+            const element = enabledElements[activeIndex].element;
+            const stackToolState = cornerstoneTools.getToolState(
+              element,
+              'stack'
+            );
 
-          if (!toolState) {
-            return;
+            if (!stackToolState) {
+              return;
+            }
+
+            const imageIds = stackToolState.data[0].imageIds;
+
+            const module = cornerstoneTools.getModule('rtstruct');
+            const imageId = module.getters.imageIdOfCenterFrameOfROIContour(
+              state.selectedSet.SeriesInstanceUID,
+              ROINumber,
+              imageIds
+            );
+
+            const toolState = cornerstoneTools.globalImageIdSpecificToolStateManager.saveToolState();
+            const imageIdSpecificToolState = toolState[imageId];
+
+            const rtstructData =
+              imageIdSpecificToolState[RTSTRUCT_DISPLAY_TOOL];
+
+            const specificData = rtstructData.data.find(
+              rtData => rtData.ROINumber === ROINumber
+            );
+
+            specificData.highlight = true;
+
+            const frameIndex = imageIds.indexOf(imageId);
+            const SOPInstanceUID = cornerstone.metaData.get(
+              'SOPInstanceUID',
+              imageId
+            );
+            const StudyInstanceUID = cornerstone.metaData.get(
+              'StudyInstanceUID',
+              imageId
+            );
+
+            onContourItemClick({
+              StudyInstanceUID,
+              SOPInstanceUID,
+              frameIndex,
+              activeViewportIndex: activeIndex,
+            });
           }
-
-          const imageIds = toolState.data[0].imageIds;
-
-          const module = cornerstoneTools.getModule('rtstruct');
-          const imageId = module.getters.imageIdOfCenterFrameOfROIContour(
-            state.selectedSet.SeriesInstanceUID,
-            ROINumber,
-            imageIds
-          );
-
-          const frameIndex = imageIds.indexOf(imageId);
-          const SOPInstanceUID = cornerstone.metaData.get('SOPInstanceUID', imageId);
-          const StudyInstanceUID = cornerstone.metaData.get('StudyInstanceUID', imageId);
-
-          onContourItemClick({
-            StudyInstanceUID,
-            SOPInstanceUID,
-            frameIndex,
-            activeViewportIndex: activeIndex
-          });
         }}
         label={`${ROIName} ${interpretedType}`}
         index={ROINumber}
@@ -153,7 +201,10 @@ const RTPanel = ({ studies, viewports, activeIndex, isOpen, onContourItemClick }
         visible={visible}
         onVisibilityChange={() => {
           const module = cornerstoneTools.getModule('rtstruct');
-          module.setters.toggleROIContour(state.selectedSet.SeriesInstanceUID, ROINumber);
+          module.setters.toggleROIContour(
+            state.selectedSet.SeriesInstanceUID,
+            ROINumber
+          );
         }}
       />
     );
@@ -189,44 +240,70 @@ const RTPanel = ({ studies, viewports, activeIndex, isOpen, onContourItemClick }
           onClick={() => setShowSettings(true)}
         />
       </div>
-      {!state.referencedDisplaysets.length && <LoadingIndicator expand height="70px" width="70px" />}
-      {state.referencedDisplaysets.map(displaySet => {
-        const { SeriesInstanceUID, metadata, isLoaded } = displaySet;
+      {!state.referencedDisplaysets.length && (
+        <LoadingIndicator expand height="70px" width="70px" />
+      )}
+      {state.sets &&
+        state.referencedDisplaysets.map(displaySet => {
+          const { SeriesInstanceUID, metadata, isLoaded } = displaySet;
 
-        const module = cornerstoneTools.getModule('rtstruct');
-        const sets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(viewports[activeIndex].SeriesInstanceUID);
+          const module = cornerstoneTools.getModule('rtstruct');
+          const sets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(
+            viewports[activeIndex].SeriesInstanceUID
+          );
 
-        const loadedSet = sets.find(set => set.SeriesInstanceUID === SeriesInstanceUID);
-        return (
-          <PanelSection
-            key={SeriesInstanceUID}
-            title={metadata.StructureSetLabel}
-            loading={!isLoaded || !loadedSet}
-            visible={isLoaded && loadedSet.visible}
-            hideVisibleButton={!isLoaded}
-            expanded={isLoaded && loadedSet.SeriesInstanceUID === state.selectedSet.SeriesInstanceUID}
-            onVisibilityChange={() => {
-              const module = cornerstoneTools.getModule('rtstruct');
-              module.setters.toggleStructureSet(SeriesInstanceUID);
-            }}
-            onExpandChange={async () => {
-              if (!isLoaded) {
-                await displaySet.load(viewports[activeIndex], studies);
-                const module = cornerstoneTools.getModule('rtstruct');
-                const sets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(viewports[activeIndex].SeriesInstanceUID);
-                const selectedSet = sets.find(set => set.SeriesInstanceUID === SeriesInstanceUID);
-                setState(state => ({ ...state, selectedSet, sets }));
+          const loadedSet = sets.find(
+            set => set.SeriesInstanceUID === SeriesInstanceUID
+          );
+          return (
+            <PanelSection
+              key={SeriesInstanceUID}
+              title={metadata.StructureSetLabel}
+              loading={!isLoaded || !loadedSet}
+              visible={isLoaded && loadedSet && loadedSet.visible}
+              hideVisibleButton={!isLoaded}
+              expanded={
+                isLoaded &&
+                loadedSet.SeriesInstanceUID ===
+                  state.selectedSet.SeriesInstanceUID
               }
-            }}
-          >
-            <ScrollableArea>
-              <TableList headless>
-                {isLoaded && loadedSet.ROIContours.map(c => toContourItem(c, loadedSet))}
-              </TableList>
-            </ScrollableArea>
-          </PanelSection>
-        );
-      })}
+              onVisibilityChange={newVisibility => {
+                const module = cornerstoneTools.getModule('rtstruct');
+
+                if (newVisibility) {
+                  module.setters.showStructureSet(loadedSet.SeriesInstanceUID);
+                } else {
+                  module.setters.hideStructureSet(loadedSet.SeriesInstanceUID);
+                }
+                const sets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(
+                  viewports[activeIndex].SeriesInstanceUID
+                );
+                setState(state => ({ ...state, sets }));
+                refreshViewport();
+              }}
+              onExpandChange={async () => {
+                if (!isLoaded) {
+                  await displaySet.load(viewports[activeIndex], studies);
+                  const module = cornerstoneTools.getModule('rtstruct');
+                  const sets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(
+                    viewports[activeIndex].SeriesInstanceUID
+                  );
+                  const selectedSet = sets.find(
+                    set => set.SeriesInstanceUID === SeriesInstanceUID
+                  );
+                  setState(state => ({ ...state, selectedSet, sets }));
+                }
+              }}
+            >
+              <ScrollableArea>
+                <TableList headless>
+                  {isLoaded &&
+                    loadedSet.ROIContours.map(c => toContourItem(c, loadedSet))}
+                </TableList>
+              </ScrollableArea>
+            </PanelSection>
+          );
+        })}
     </div>
   );
 };

extensions/dicom-rt/src/components/StructureSetItem/StructureSetItem.css

@@ -22,11 +22,6 @@
   width: 100%;
 }
 
-.dcmrt-structure-set-item.selected .item-actions {
-  height: 35px;
-  visibility: visible;
-}
-
 .dcmrt-structure-set-item .item-actions {
   margin-left: -1px;
   background-color: var(--ui-gray-darker);
@@ -47,7 +42,8 @@
   transition: all 0.3s ease;
 }
 
-.dcmrt-structure-set-item .item-actions .btnAction:hover, .dcmrt-structure-set-item .item-actions .btnAction:active {
+.dcmrt-structure-set-item .item-actions .btnAction:hover,
+.dcmrt-structure-set-item .item-actions .btnAction:active {
   color: var(--text-primary-color);
 }
 
@@ -86,3 +82,12 @@
 .dcmrt-structure-set-item .item-label .eye-icon.--visible {
   color: var(--default-color);
 }
+
+.dcmrt-structure-set-item.isDisabled .item-color-section {
+  background-color: #e29e4a;
+  color: #fff;
+}
+
+.dcmrt-structure-set-item.isDisabled .item-label {
+  color: var(--text-disabled-color);
+}

extensions/dicom-rt/src/components/StructureSetItem/StructureSetItem.js

@@ -1,6 +1,7 @@
-import React, { useState } from 'react';
+import React, { useState, useEffect } from 'react';
 import PropTypes from 'prop-types';
-import { TableListItem, Icon } from '@ohif/ui';
+import { TableListItem, Icon, Tooltip, OverlayTrigger } from '@ohif/ui';
+import ReactTooltip from 'react-tooltip';
 
 import './StructureSetItem.css';
 
@@ -20,6 +21,7 @@ ColoredCircle.propTypes = {
 const StructureSetItem = ({
   index,
   label,
+  isDisabled,
   onClick,
   itemClass,
   color,
@@ -28,20 +30,58 @@ const StructureSetItem = ({
   selected = false,
 }) => {
   const [isVisible, setIsVisible] = useState(visible);
-  return (
-    <div className={`dcmrt-structure-set-item ${selected && 'selected'}`}>
-      <TableListItem
-        key={index}
-        itemKey={index}
-        itemIndex={index}
-        itemClass={itemClass}
-        itemMeta={<ColoredCircle color={color} />}
-        itemMetaClass="item-color-section"
-        onItemClick={onClick}
-      >
-        <div>
-          <div className="item-label" style={{ marginBottom: 4 }}>
+
+  useEffect(() => {
+    setIsVisible(visible);
+  }, [visible]);
+
+  let dcmrtClassNames = `dcmrt-structure-set-item`;
+
+  if (selected) {
+    dcmrtClassNames += ' selected';
+  }
+
+  if (isDisabled) {
+    dcmrtClassNames += ' isDisabled';
+  }
+
+  const warningIcon = (
+    <span>
+      <Icon name="exclamation-triangle" />
+    </span>
+  );
+
+  const tableListItem = (
+    <TableListItem
+      key={index}
+      itemKey={index}
+      itemIndex={index}
+      itemClass={itemClass}
+      itemMeta={isDisabled ? warningIcon : <ColoredCircle color={color} />}
+      itemMetaClass="item-color-section"
+      onItemClick={() => {
+        if (isDisabled) {
+          return;
+        }
+
+        onClick();
+      }}
+    >
+      <div>
+        <div className="item-label" style={{ marginBottom: 4 }}>
+          <a data-tip data-for={`StructureHover${index}`}>
             <span>{label}</span>
+          </a>
+          <ReactTooltip
+            id={`StructureHover${index}`}
+            delayShow={250}
+            place="right"
+            border={true}
+            type="light"
+          >
+            <span>{label}</span>
+          </ReactTooltip>
+          {!isDisabled && (
             <Icon
               className={`eye-icon ${isVisible && '--visible'}`}
               name={isVisible ? 'eye' : 'eye-closed'}
@@ -49,37 +89,72 @@ const StructureSetItem = ({
               height="20px"
               onClick={event => {
                 event.stopPropagation();
+
+                if (isDisabled) {
+                  return;
+                }
+
                 const newVisibility = !isVisible;
                 setIsVisible(newVisibility);
                 onVisibilityChange(newVisibility);
               }}
             />
-          </div>
-          {false && <div className="item-info">{'...'}</div>}
-          {false && (
-            <div className="item-actions">
-              <button
-                className="btnAction"
-                onClick={() => console.log('Relabelling...')}
-              >
-                <span style={{ marginRight: '4px' }}>
-                  <Icon name="edit" width="14px" height="14px" />
-                </span>
-                Relabel
-              </button>
-              <button
-                className="btnAction"
-                onClick={() => console.log('Editing description...')}
-              >
-                <span style={{ marginRight: '4px' }}>
-                  <Icon name="edit" width="14px" height="14px" />
-                </span>
-                Description
-              </button>
-            </div>
           )}
         </div>
-      </TableListItem>
+
+        {false && <div className="item-info">{'...'}</div>}
+        {false && (
+          <div className="item-actions">
+            <button
+              className="btnAction"
+              onClick={() => console.log('Relabelling...')}
+            >
+              <span style={{ marginRight: '4px' }}>
+                <Icon name="edit" width="14px" height="14px" />
+              </span>
+              Relabel
+            </button>
+            <button
+              className="btnAction"
+              onClick={() => console.log('Editing description...')}
+            >
+              <span style={{ marginRight: '4px' }}>
+                <Icon name="edit" width="14px" height="14px" />
+              </span>
+              Description
+            </button>
+          </div>
+        )}
+      </div>
+    </TableListItem>
+  );
+
+  return (
+    <div className={dcmrtClassNames}>
+      <React.Fragment>
+        {isDisabled ? (
+          <OverlayTrigger
+            key={index}
+            placement="left"
+            overlay={
+              <Tooltip
+                placement="left"
+                className="in tooltip-warning"
+                id="tooltip-left"
+              >
+                <div className="warningTitle">Unsupported Region</div>
+                <div className="warningContent">
+                  Contour type currently unsupported.
+                </div>
+              </Tooltip>
+            }
+          >
+            <div>{tableListItem}</div>
+          </OverlayTrigger>
+        ) : (
+          <React.Fragment>{tableListItem} </React.Fragment>
+        )}
+      </React.Fragment>
     </div>
   );
 };
@@ -94,7 +169,7 @@ StructureSetItem.propTypes = {
 
 StructureSetItem.defaultProps = {
   itemClass: '',
-  onClick: () => { },
+  onClick: () => {},
 };
 
 export default StructureSetItem;

extensions/dicom-rt/src/getSourceDisplaySet.js

@@ -0,0 +1,38 @@
+export default function getSourceDisplaySet(studies, rtStructDisplaySet) {
+  const referencedDisplaySet = _getReferencedDisplaySet(
+    rtStructDisplaySet,
+    studies
+  );
+
+  rtStructDisplaySet.load(referencedDisplaySet, studies);
+
+  return referencedDisplaySet;
+}
+
+const _getReferencedDisplaySet = (rtStructDisplaySet, studies) => {
+  let allDisplaySets = [];
+
+  studies.forEach(study => {
+    allDisplaySets = allDisplaySets.concat(study.displaySets);
+  });
+
+  const otherDisplaySets = allDisplaySets.filter(
+    ds => ds.displaySetInstanceUID !== rtStructDisplaySet.displaySetInstanceUID
+  );
+
+  const ReferencedSeriesSequence = Array.isArray(
+    rtStructDisplaySet.metadata.ReferencedSeriesSequence
+  )
+    ? rtStructDisplaySet.metadata.ReferencedSeriesSequence
+    : [rtStructDisplaySet.metadata.ReferencedSeriesSequence];
+
+  const referencedSeriesInstanceUIDs = ReferencedSeriesSequence.map(
+    ReferencedSeries => ReferencedSeries.SeriesInstanceUID
+  );
+
+  const referencedDisplaySet = otherDisplaySets.find(ds =>
+    referencedSeriesInstanceUIDs.includes(ds.SeriesInstanceUID)
+  );
+
+  return referencedDisplaySet;
+};

extensions/dicom-rt/src/index.js

@@ -1,15 +1,16 @@
 import React from 'react';
-
 import init from './init.js';
 import sopClassHandlerModule from './OHIFDicomRTStructSopClassHandler';
 import id from './id.js';
 import RTPanel from './components/RTPanel/RTPanel';
+import { version } from '../package.json';
 
 export default {
   /**
    * Only required property. Should be a unique value across all extensions.
    */
   id,
+  version,
 
   /**
    *
@@ -20,14 +21,21 @@ export default {
   preRegistration({ servicesManager, configuration = {} }) {
     init({ servicesManager, configuration });
   },
-  getPanelModule({ commandsManager }) {
+  getPanelModule({ commandsManager, servicesManager, api }) {
     const ExtendedRTPanel = props => {
+      const { activeContexts } = api.hooks.useAppContext();
+
       const contourItemClickHandler = contourData => {
         commandsManager.runCommand('jumpToImage', contourData);
       };
 
       return (
-        <RTPanel {...props} onContourItemClick={contourItemClickHandler} />
+        <RTPanel
+          {...props}
+          onContourItemClick={contourItemClickHandler}
+          activeContexts={activeContexts}
+          contexts={api.contexts}
+        />
       );
     };
 

extensions/dicom-rt/src/loadRTStruct.js

@@ -16,7 +16,6 @@ export default async function loadRTStruct(
   studies
 ) {
   const rtStructModule = cornerstoneTools.getModule('rtstruct');
-
   // Set here is loading is asynchronous.
   // If this function throws its set back to false.
   rtStructDisplaySet.isLoaded = true;
@@ -67,8 +66,9 @@ export default async function loadRTStruct(
 
   const rtStructDisplayToolName = TOOL_NAMES.RTSTRUCT_DISPLAY_TOOL;
 
-  for (let i = 0; i < ROIContourSequence.length; i++) {
+  debugger;
 
+  for (let i = 0; i < ROIContourSequence.length; i++) {
     const ROIContour = ROIContourSequence[i];
     const { ReferencedROINumber, ContourSequence } = ROIContour;
 
@@ -76,26 +76,17 @@ export default async function loadRTStruct(
       continue;
     }
 
-    _setROIContourMetadata(
-      structureSet,
-      StructureSetROISequence,
-      RTROIObservationsSequence,
-      ROIContour
-    );
+    const isSupported = false;
 
-    for (let c = 0; c < ContourSequence.length; c++) {
+    const ContourSequenceArray = _toArray(ContourSequence);
+
+    for (let c = 0; c < ContourSequenceArray.length; c++) {
       const {
         ContourImageSequence,
         ContourData,
         NumberOfContourPoints,
         ContourGeometricType,
-      } = ContourSequence[c];
-
-      if (ContourGeometricType !== 'CLOSED_PLANAR') {
-        // TODO: Do we want to visualise types other than closed planar?
-        // We could easily do open planar.
-        continue;
-      }
+      } = ContourSequenceArray[c];
 
       const sopInstanceUID = ContourImageSequence.ReferencedSOPInstanceUID;
       const imageId = _getImageId(imageIdSopInstanceUidPairs, sopInstanceUID);
@@ -107,27 +98,47 @@ export default async function loadRTStruct(
 
       const imagePlane = cornerstone.metaData.get('imagePlaneModule', imageId);
       const points = [];
+      let measurementData;
 
-      for (let p = 0; p < NumberOfContourPoints * 3; p += 3) {
-        points.push({
-          x: ContourData[p],
-          y: ContourData[p + 1],
-          z: ContourData[p + 2],
-        });
+      switch (ContourGeometricType) {
+        case 'CLOSED_PLANAR':
+        case 'OPEN_PLANAR':
+        case 'POINT':
+          isSupported = true;
+
+          for (let p = 0; p < NumberOfContourPoints * 3; p += 3) {
+            points.push({
+              x: ContourData[p],
+              y: ContourData[p + 1],
+              z: ContourData[p + 2],
+            });
+          }
+
+          transformPointsToImagePlane(points, imagePlane);
+
+          measurementData = {
+            handles: {
+              points,
+            },
+            type: ContourGeometricType,
+            structureSetSeriesInstanceUid: rtStructDataset.SeriesInstanceUID,
+            ROINumber: ReferencedROINumber,
+          };
+
+          imageIdSpecificToolData.push(measurementData);
+          break;
+        default:
+          continue;
       }
-
-      transformPointsToImagePlane(points, imagePlane);
-
-      const measurementData = {
-        handles: {
-          points,
-        },
-        structureSetSeriesInstanceUid: rtStructDataset.SeriesInstanceUID,
-        ROINumber: ReferencedROINumber,
-      };
-
-      imageIdSpecificToolData.push(measurementData);
     }
+
+    _setROIContourMetadata(
+      structureSet,
+      StructureSetROISequence,
+      RTROIObservationsSequence,
+      ROIContour,
+      isSupported
+    );
   }
 
   _setToolEnabledIfNotEnabled(rtStructDisplayToolName);
@@ -157,7 +168,8 @@ function _setROIContourMetadata(
   structureSet,
   StructureSetROISequence,
   RTROIObservationsSequence,
-  ROIContour
+  ROIContour,
+  isSupported
 ) {
   const StructureSetROI = StructureSetROISequence.find(
     structureSetROI =>
@@ -169,6 +181,7 @@ function _setROIContourMetadata(
     ROIName: StructureSetROI.ROIName,
     ROIGenerationAlgorithm: StructureSetROI.ROIGenerationAlgorithm,
     ROIDescription: StructureSetROI.ROIDescription,
+    isSupported,
     visible: true,
   };
 
@@ -238,7 +251,7 @@ function _setROIContourRTROIObservations(
 
 function _setToolEnabledIfNotEnabled(toolName) {
   cornerstone.getEnabledElements().forEach(enabledElement => {
-    const { element } = enabledElement;
+    const { element, image } = enabledElement;
     const tool = cornerstoneTools.getToolForElement(element, toolName);
 
     if (tool.mode !== 'enabled') {
@@ -246,7 +259,9 @@ function _setToolEnabledIfNotEnabled(toolName) {
       cornerstoneTools.setToolEnabled(toolName);
     }
 
-    cornerstone.updateImage(element);
+    if (image) {
+      cornerstone.updateImage(element);
+    }
   });
 }
 
@@ -307,3 +322,7 @@ function _getImageIdSopInstanceUidPairsForDisplaySet(
     };
   });
 }
+
+function _toArray(objOrArray) {
+  return Array.isArray(objOrArray) ? objOrArray : [objOrArray];
+}

extensions/dicom-rt/src/tools/RTStructDisplayTool.js

@@ -1,9 +1,10 @@
 import { importInternal, getToolState, toolColors } from 'cornerstone-tools';
-
 import TOOL_NAMES from '../utils/toolNames';
+import drawCanvasCrosshairs from '../utils/drawCanvasCrosshairs';
 
 // Cornerstone 3rd party dev kit imports
 const draw = importInternal('drawing/draw');
+const drawCircle = importInternal('drawing/drawCircle');
 const drawJoinedLines = importInternal('drawing/drawJoinedLines');
 const getNewContext = importInternal('drawing/getNewContext');
 const BaseTool = importInternal('base/BaseTool');
@@ -36,11 +37,17 @@ export default class RTStructDisplayTool extends BaseTool {
       return;
     }
 
-    const { lineWidth, opacity } = rtstructModule.configuration;
+    const {
+      lineWidth,
+      opacity,
+      highlightOpacity,
+    } = rtstructModule.configuration;
 
     // We have tool data for this element - iterate over each one and draw it
     const context = getNewContext(eventData.canvasContext.canvas);
 
+    let crossHairCenter;
+
     for (let i = 0; i < toolState.data.length; i++) {
       const data = toolState.data[i];
 
@@ -72,22 +79,76 @@ export default class RTStructDisplayTool extends BaseTool {
       const colorArray = ROIContourData.colorArray;
       const color = `rgba(${colorArray[0]},${colorArray[1]},${
         colorArray[2]
-        },${opacity})`;
+      },${opacity})`;
 
-      lineWidth;
+      let highlight = data.highlight;
+      const options = { color, lineWidth };
 
-      draw(context, context => {
-        drawJoinedLines(
-          context,
-          eventData.element,
-          points[points.length - 1],
-          points,
-          {
-            color,
-            lineWidth,
-          }
-        );
+      if (highlight) {
+        crossHairCenter = { x: 0, y: 0 };
+
+        points.forEach(point => {
+          crossHairCenter.x += point.x;
+          crossHairCenter.y += point.y;
+        });
+
+        crossHairCenter.x /= points.length;
+        crossHairCenter.y /= points.length;
+
+        // TODO: Disabling hightlight for now, it'd be good to bring it back
+        // when we have a good way of doing this for SEG.
+
+        // options.fillStyle = color = `rgba(${colorArray[0]},${colorArray[1]},${
+        //   colorArray[2]
+        // },${highlightOpacity})`;
+
+        // Draw highlight lines.
+
+        delete data.highlight; // Don't highlight on next render.
+      }
+
+      switch (data.type) {
+        case 'CLOSED_PLANAR':
+          this._renderClosedPlanar(context, eventData.element, points, options);
+          break;
+        case 'POINT':
+          this._renderPoint(context, eventData.element, points, options);
+          break;
+        case 'OPEN_PLANAR':
+          this._renderOpenPlanar(context, eventData.element, points, options);
+          break;
+      }
+    }
+
+    if (crossHairCenter) {
+      drawCanvasCrosshairs(eventData, crossHairCenter, {
+        color: toolColors.getActiveColor(),
+        lineWidth: 1,
       });
     }
   }
+
+  _renderClosedPlanar(context, element, points, options) {
+    draw(context, context => {
+      drawJoinedLines(
+        context,
+        element,
+        points[points.length - 1],
+        points,
+        options
+      );
+    });
+  }
+
+  _renderPoint(context, element, points, options) {
+    draw(context, context => {
+      drawCircle(context, element, points[0], 3, options);
+    });
+  }
+
+  _renderOpenPlanar(context, element, points, options) {
+    draw(context, context => {
+      drawJoinedLines(context, element, points[0], points, options);
+    });
+  }
 }

extensions/dicom-rt/src/tools/modules/rtStructModule.js

@@ -5,13 +5,16 @@ import structureSetReferencesSeriesInstanceUid from './lib/structureSetReference
 // We should put this as a helper somewhere as we are using it in mutliple places.
 function refreshViewport() {
   cornerstone.getEnabledElements().forEach(enabledElement => {
-    cornerstone.updateImage(enabledElement.element);
+    if (enabledElement.image) {
+      cornerstone.updateImage(enabledElement.element);
+    }
   });
 }
 
 const configuration = {
   lineWidth: 3,
-  opacity: 1.0,
+  opacity: 0.75,
+  highlightOpacity: 0.5,
 };
 
 const state = {
@@ -81,7 +84,9 @@ function _setStructureSetVisible(SeriesInstanceUID, visible = true) {
   const StructureSet = getStructureSet(SeriesInstanceUID);
 
   if (StructureSet) {
-    StructureSet.visible = visible;
+    StructureSet.ROIContours.forEach(ROIContour => {
+      ROIContour.visible = visible;
+    });
 
     refreshViewport();
   }
@@ -154,15 +159,10 @@ function setToggleROIContour(SeriesInstanceUID, ROINumber) {
  * Returns an array of StructureSets which reference the given SeriesInstanceUID.
  * @param {string} SeriesInstanceUID The SeriesInstanceUID to check.
  */
-function getStructuresSetsWhichReferenceSeriesInstanceUid(
-  SeriesInstanceUID
-) {
+function getStructuresSetsWhichReferenceSeriesInstanceUid(SeriesInstanceUID) {
   const { StructureSets } = state;
   return StructureSets.filter(StructureSet =>
-    structureSetReferencesSeriesInstanceUid(
-      StructureSet,
-      SeriesInstanceUID
-    )
+    structureSetReferencesSeriesInstanceUid(StructureSet, SeriesInstanceUID)
   );
 }
 

extensions/dicom-rt/src/utils/drawCanvasCrosshairs.js

@@ -0,0 +1,56 @@
+import cornerstone from 'cornerstone-core';
+import cornerstoneTools from 'cornerstone-tools';
+
+const { importInternal } = cornerstoneTools;
+const draw = importInternal('drawing/draw');
+const drawLine = importInternal('drawing/drawLine');
+const getNewContext = importInternal('drawing/getNewContext');
+
+export default function _drawCanvasCrosshairs(eventData, center, options) {
+  const context = getNewContext(eventData.canvasContext.canvas);
+  const { element } = eventData;
+
+  const centerCanvas = cornerstone.pixelToCanvas(element, center);
+
+  const { clientWidth: width, clientHeight: height } = element;
+
+  const offset = 10;
+
+  draw(context, context => {
+    drawLine(
+      context,
+      element,
+      { x: centerCanvas.x + offset, y: centerCanvas.y },
+      { x: width, y: centerCanvas.y },
+      options,
+      'canvas'
+    );
+
+    drawLine(
+      context,
+      element,
+      { x: centerCanvas.x - offset, y: centerCanvas.y },
+      { x: 0, y: centerCanvas.y },
+      options,
+      'canvas'
+    );
+
+    drawLine(
+      context,
+      element,
+      { x: centerCanvas.x, y: centerCanvas.y + offset },
+      { x: centerCanvas.x, y: height },
+      options,
+      'canvas'
+    );
+
+    drawLine(
+      context,
+      element,
+      { x: centerCanvas.x, y: centerCanvas.y - offset },
+      { x: centerCanvas.x, y: 0 },
+      options,
+      'canvas'
+    );
+  });
+}

extensions/dicom-segmentation/CHANGELOG.md

@@ -3,6 +3,133 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [0.4.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.4.5...@ohif/extension-dicom-segmentation@0.4.6) (2020-09-17)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.4.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.4.4...@ohif/extension-dicom-segmentation@0.4.5) (2020-09-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.4.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.4.3...@ohif/extension-dicom-segmentation@0.4.4) (2020-09-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.4.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.4.2...@ohif/extension-dicom-segmentation@0.4.3) (2020-09-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.4.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.4.1...@ohif/extension-dicom-segmentation@0.4.2) (2020-09-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.4.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.4.0...@ohif/extension-dicom-segmentation@0.4.1) (2020-08-28)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+# [0.4.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.3.4...@ohif/extension-dicom-segmentation@0.4.0) (2020-08-18)
+
+
+### Features
+
+* 🎸 Update react-vtkjs-viewport usage to use requestPool ([#1984](https://github.com/OHIF/Viewers/issues/1984)) ([bb5f30c](https://github.com/OHIF/Viewers/commit/bb5f30ce2a0192d2e021beaaadfff22fd38e17b9))
+
+
+
+
+
+## [0.3.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.3.3...@ohif/extension-dicom-segmentation@0.3.4) (2020-08-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.3.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.3.2...@ohif/extension-dicom-segmentation@0.3.3) (2020-07-13)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.3.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.3.1...@ohif/extension-dicom-segmentation@0.3.2) (2020-07-13)
+
+
+### Bug Fixes
+
+* 🐛 Fix RT Panel hide/show and Fix looping load errors ([#1877](https://github.com/OHIF/Viewers/issues/1877)) ([e7cc735](https://github.com/OHIF/Viewers/commit/e7cc735c03d02eeb0d3af4ba02c15ed4f81bbec2))
+
+
+
+
+
+## [0.3.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.3.0...@ohif/extension-dicom-segmentation@0.3.1) (2020-06-15)
+
+
+### Bug Fixes
+
+* 🐛 Disable seg panel when data for seg unavailable ([#1732](https://github.com/OHIF/Viewers/issues/1732)) ([698e900](https://github.com/OHIF/Viewers/commit/698e900b85121d3c2a46747c443ef69fb7a8c95b)), closes [#1728](https://github.com/OHIF/Viewers/issues/1728)
+
+
+
+
+
+# [0.3.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.2.6...@ohif/extension-dicom-segmentation@0.3.0) (2020-06-04)
+
+
+### Features
+
+* 🎸 1729 - error boundary wrapper ([#1764](https://github.com/OHIF/Viewers/issues/1764)) ([c02b232](https://github.com/OHIF/Viewers/commit/c02b232b0cc24f38af5d5e3831d987d048e60ada))
+
+
+
+
+
+## [0.2.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.2.5...@ohif/extension-dicom-segmentation@0.2.6) (2020-05-12)
+
+
+### Bug Fixes
+
+* 🐛 Fix seg color load ([#1724](https://github.com/OHIF/Viewers/issues/1724)) ([c4f84b1](https://github.com/OHIF/Viewers/commit/c4f84b1174d04ba84d37ed89b6d7ab541be28181))
+
+
+
+
+
+## [0.2.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.2.4...@ohif/extension-dicom-segmentation@0.2.5) (2020-05-06)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
 ## [0.2.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.2.3...@ohif/extension-dicom-segmentation@0.2.4) (2020-05-04)
 
 **Note:** Version bump only for package @ohif/extension-dicom-segmentation

extensions/dicom-segmentation/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-segmentation",
-  "version": "0.2.4",
+  "version": "0.4.6",
   "description": "OHIF extension for viewing segmentations in the 2D MPR view",
   "author": "OHIF",
   "license": "MIT",
@@ -30,14 +30,16 @@
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
     "cornerstone-core": "^2.2.8",
-    "cornerstone-tools": "4.12.5",
-    "dcmjs": "^0.12.2",
+    "cornerstone-tools": "^4.20.1",
+    "dcmjs": "0.16.3",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6"
   },
   "dependencies": {
     "@babel/runtime": "^7.5.5",
-    "react-select": "^3.0.8"
+    "gl-matrix": "^3.3.0",
+    "react-select": "^3.0.8",
+    "react-tooltip": "4.2.10"
   }
 }

extensions/dicom-segmentation/src/components/SegmentItem/SegmentItem.js

@@ -1,6 +1,7 @@
-import React, { useState } from 'react';
+import React, { useState, useEffect } from 'react';
 import PropTypes from 'prop-types';
 import { TableListItem, Icon } from '@ohif/ui';
+import ReactTooltip from 'react-tooltip';
 
 import './SegmentItem.css';
 
@@ -17,8 +18,21 @@ ColoredCircle.propTypes = {
   color: PropTypes.array.isRequired,
 };
 
-const SegmentItem = ({ index, label, onClick, itemClass, color, visible = true, onVisibilityChange }) => {
+const SegmentItem = ({
+  index,
+  label,
+  onClick,
+  itemClass,
+  color,
+  visible = true,
+  onVisibilityChange,
+}) => {
   const [isVisible, setIsVisible] = useState(visible);
+
+  useEffect(() => {
+    setIsVisible(visible);
+  }, [visible]);
+
   return (
     <div className="dcmseg-segment-item">
       <TableListItem
@@ -32,7 +46,18 @@ const SegmentItem = ({ index, label, onClick, itemClass, color, visible = true,
       >
         <div>
           <div className="segment-label" style={{ marginBottom: 4 }}>
-            <span>{label}</span>
+            <a data-tip data-for={`SegmentHover${index}`}>
+              <span>{label}</span>
+            </a>
+            <ReactTooltip
+              id={`SegmentHover${index}`}
+              delayShow={250}
+              place="right"
+              border={true}
+              type="light"
+            >
+              <span>{label}</span>
+            </ReactTooltip>
             <Icon
               className={`eye-icon ${isVisible && '--visible'}`}
               name={isVisible ? 'eye' : 'eye-closed'}
@@ -56,7 +81,7 @@ const SegmentItem = ({ index, label, onClick, itemClass, color, visible = true,
                 <span style={{ marginRight: '4px' }}>
                   <Icon name="edit" width="14px" height="14px" />
                 </span>
-              Relabel
+                Relabel
               </button>
               <button
                 className="btnAction"
@@ -65,7 +90,7 @@ const SegmentItem = ({ index, label, onClick, itemClass, color, visible = true,
                 <span style={{ marginRight: '4px' }}>
                   <Icon name="edit" width="14px" height="14px" />
                 </span>
-              Description
+                Description
               </button>
             </div>
           )}
@@ -85,7 +110,7 @@ SegmentItem.propTypes = {
 
 SegmentItem.defaultProps = {
   itemClass: '',
-  onClick: () => { }
+  onClick: () => {},
 };
 
 export default SegmentItem;

extensions/dicom-segmentation/src/components/SegmentationPanel/SegmentationPanel.css

@@ -8,6 +8,11 @@
   flex-direction: column;
 }
 
+.dcmseg-segmentation-panel.disabled {
+  opacity: 0.6;
+  pointer-events: none;
+}
+
 .dcmseg-segmentation-panel h3 {
   padding-left: 20px;
   margin-top: 0;

extensions/dicom-segmentation/src/components/SegmentationPanel/SegmentationPanel.js

@@ -5,6 +5,10 @@ import cornerstone from 'cornerstone-core';
 import moment from 'moment';
 import { utils, log } from '@ohif/core';
 import { ScrollableArea, TableList, Icon } from '@ohif/ui';
+import DICOMSegTempCrosshairsTool from '../../tools/DICOMSegTempCrosshairsTool';
+
+import setActiveLabelmap from '../../utils/setActiveLabelMap';
+import refreshViewports from '../../utils/refreshViewports';
 
 import {
   BrushColorSelector,
@@ -19,12 +23,6 @@ import SegmentationSettings from '../SegmentationSettings/SegmentationSettings';
 
 const { studyMetadataManager } = utils;
 
-const refreshViewport = () => {
-  cornerstone.getEnabledElements().forEach(enabledElement => {
-    cornerstone.updateImage(enabledElement.element);
-  });
-};
-
 /**
  * SegmentationPanel component
  *
@@ -32,7 +30,11 @@ const refreshViewport = () => {
  * @param {Array} props.viewports - Viewports data (viewportSpecificData)
  * @param {number} props.activeIndex - Active viewport index
  * @param {boolean} props.isOpen - Boolean that indicates if the panel is expanded
- * @param {Function} props.onSegItemClick - Segment click handler
+ * @param {Function} props.onSegmentItemClick - Segment click handler
+ * @param {Function} props.onSegmentVisibilityChange - Segment visibiliy change handler
+ * @param {Function} props.onConfigurationChange - Configuration change handler
+ * @param {Function} props.activeContexts - List of active application contexts
+ * @param {Function} props.contexts - List of available application contexts
  * @returns component
  */
 const SegmentationPanel = ({
@@ -40,25 +42,40 @@ const SegmentationPanel = ({
   viewports,
   activeIndex,
   isOpen,
-  onSegItemClick,
-  UINotificationService,
+  onSegmentItemClick,
+  onSegmentVisibilityChange,
+  onConfigurationChange,
+  onDisplaySetLoadFailure,
+  onSelectedSegmentationChange,
+  activeContexts = [],
+  contexts = {},
 }) => {
+  const isVTK = () => activeContexts.includes(contexts.VTK);
+  const isCornerstone = () => activeContexts.includes(contexts.CORNERSTONE);
+
   /*
    * TODO: wrap get/set interactions with the cornerstoneTools
    * store with context to make these kind of things less blurry.
    */
   const { configuration } = cornerstoneTools.getModule('segmentation');
   const DEFAULT_BRUSH_RADIUS = configuration.radius || 10;
+
+  /*
+   * TODO: We shouldn't hardcode brushColor color, in the future
+   * the SEG may set the colorLUT to whatever it wants.
+   */
   const [state, setState] = useState({
     brushRadius: DEFAULT_BRUSH_RADIUS,
-    brushColor:
-      'rgba(221, 85, 85, 1)' /* TODO: We shouldn't hardcode this color, in the future the SEG may set the colorLUT to whatever it wants. */,
+    brushColor: 'rgba(221, 85, 85, 1)',
     selectedSegment: null,
     selectedSegmentation: null,
-    showSegSettings: false,
+    showSegmentationSettings: false,
     brushStackState: null,
     labelmapList: [],
     segmentList: [],
+    cachedSegmentsProperties: [],
+    isLoading: false,
+    isDisabled: true,
   });
 
   useEffect(() => {
@@ -75,6 +92,28 @@ const SegmentationPanel = ({
       updateState('brushStackState', module.state.series[firstImageId]);
     };
 
+    /*
+     * TODO: Improve the way we notify parts of the app that depends on segs to be loaded.
+     *
+     * Currently we are using a non-ideal implementation through a custom event to notify the segmentation panel
+     * or other components that could rely on loaded segmentations that
+     * the segments were loaded so that e.g. when the user opens the panel
+     * before the segments are fully loaded, the panel can subscribe to this custom event
+     * and update itself with the new segments.
+     *
+     * This limitation is due to the fact that the cs segmentation module is an object (which will be
+     * updated after the segments are loaded) that React its not aware of its changes
+     * because the module object its not passed in to the panel component as prop but accessed externally.
+     *
+     * Improving this event approach to something reactive that can be tracked inside the react lifecycle,
+     * allows us to easily watch the module or the segmentations loading process in any other component
+     * without subscribing to external events.
+     */
+    document.addEventListener(
+      'extensiondicomsegmentationsegloaded',
+      refreshSegmentations
+    );
+
     /*
      * These are specific to each element;
      * Need to iterate cornerstone-tools tracked enabled elements?
@@ -88,6 +127,10 @@ const SegmentationPanel = ({
     );
 
     return () => {
+      document.removeEventListener(
+        'extensiondicomsegmentationsegloaded',
+        refreshSegmentations
+      );
       cornerstoneTools.store.state.enabledElements.forEach(enabledElement =>
         enabledElement.removeEventListener(
           'cornerstonetoolslabelmapmodified',
@@ -95,60 +138,69 @@ const SegmentationPanel = ({
         )
       );
     };
-  });
+  }, [activeIndex, viewports]);
 
-  useEffect(() => {
+  const refreshSegmentations = useCallback(() => {
     const module = cornerstoneTools.getModule('segmentation');
     const activeViewport = viewports[activeIndex];
-    const studyMetadata = studyMetadataManager.get(
-      activeViewport.StudyInstanceUID
-    );
-    const firstImageId = studyMetadata.getFirstImageId(
-      activeViewport.displaySetInstanceUID
-    );
-    const brushStackState = module.state.series[firstImageId];
 
-    if (brushStackState) {
-      const labelmap3D =
-        brushStackState.labelmaps3D[brushStackState.activeLabelmapIndex];
-      const labelmapList = getLabelmapList(
-        brushStackState,
-        firstImageId,
-        activeViewport
+    const isDisabled = !activeViewport || !activeViewport.StudyInstanceUID;
+    if (!isDisabled) {
+      const studyMetadata = studyMetadataManager.get(
+        activeViewport.StudyInstanceUID
       );
-      const segmentList = getSegmentList(
-        labelmap3D,
-        firstImageId,
-        brushStackState
+      const firstImageId = studyMetadata.getFirstImageId(
+        activeViewport.displaySetInstanceUID
       );
-      setState(state => ({
-        ...state,
-        brushStackState,
-        selectedSegmentation: brushStackState.activeLabelmapIndex,
-        labelmapList,
-        segmentList,
-      }));
-    } else {
-      setState(state => ({
-        ...state,
-        labelmapList: [],
-        segmentList: [],
-      }));
+      const brushStackState = module.state.series[firstImageId];
+      if (brushStackState) {
+        const labelmap3D =
+          brushStackState.labelmaps3D[brushStackState.activeLabelmapIndex];
+        const labelmapList = getLabelmapList(
+          brushStackState,
+          firstImageId,
+          activeViewport
+        );
+        const segmentList = getSegmentList(
+          labelmap3D,
+          firstImageId,
+          brushStackState
+        );
+        setState(state => ({
+          ...state,
+          brushStackState,
+          selectedSegmentation: brushStackState.activeLabelmapIndex,
+          labelmapList,
+          segmentList,
+          isDisabled,
+        }));
+      } else {
+        setState(state => ({
+          ...state,
+          labelmapList: [],
+          segmentList: [],
+          isDisabled,
+        }));
+      }
     }
+  }, [viewports, activeIndex, state.isLoading]);
+
+  useEffect(() => {
+    refreshSegmentations();
   }, [
-    studies,
     viewports,
     activeIndex,
-    getLabelmapList,
-    getSegmentList,
+    isOpen,
     state.selectedSegmentation,
+    activeContexts,
+    state.isLoading,
   ]);
 
   /* Handle open/closed panel behaviour */
   useEffect(() => {
     setState(state => ({
       ...state,
-      showSegSettings: state.showSegSettings && !isOpen,
+      showSegmentationSettings: state.showSegmentationSettings && !isOpen,
     }));
   }, [isOpen]);
 
@@ -177,13 +229,12 @@ const SegmentationPanel = ({
           title: displayDescription,
           description: displayDate,
           onClick: async () => {
-            const activatedLabelmapIndex = await _setActiveLabelmap(
+            const activatedLabelmapIndex = await setActiveLabelmap(
               activeViewport,
               studies,
               displaySet,
-              firstImageId,
-              brushStackState.activeLabelmapIndex,
-              UINotificationService
+              () => onSelectedSegmentationChange(),
+              onDisplaySetLoadFailure
             );
             updateState('selectedSegmentation', activatedLabelmapIndex);
           },
@@ -262,66 +313,117 @@ const SegmentationPanel = ({
               : prev;
           });
 
-          const enabledElements = cornerstone.getEnabledElements();
-          const element = enabledElements[activeIndex].element;
-          const toolState = cornerstoneTools.getToolState(element, 'stack');
+          if (isCornerstone()) {
+            const enabledElements = cornerstone.getEnabledElements();
+            const element = enabledElements[activeIndex].element;
+            const toolState = cornerstoneTools.getToolState(element, 'stack');
 
-          if (!toolState) {
-            return;
+            if (!toolState) {
+              return;
+            }
+
+            const imageIds = toolState.data[0].imageIds;
+            const imageId = imageIds[closest];
+            const frameIndex = imageIds.indexOf(imageId);
+
+            const SOPInstanceUID = cornerstone.metaData.get(
+              'SOPInstanceUID',
+              imageId
+            );
+            const StudyInstanceUID = cornerstone.metaData.get(
+              'StudyInstanceUID',
+              imageId
+            );
+
+            DICOMSegTempCrosshairsTool.addCrosshair(
+              element,
+              imageId,
+              segmentNumber
+            );
+
+            onSegmentItemClick({
+              StudyInstanceUID,
+              SOPInstanceUID,
+              frameIndex,
+              activeViewportIndex: activeIndex,
+            });
           }
 
-          const imageIds = toolState.data[0].imageIds;
-          const imageId = imageIds[closest];
-          const frameIndex = imageIds.indexOf(imageId);
+          if (isVTK()) {
+            const activeViewport = viewports[activeIndex];
+            const studyMetadata = studyMetadataManager.get(
+              activeViewport.StudyInstanceUID
+            );
+            const allDisplaySets = studyMetadata.getDisplaySets();
+            const currentDisplaySet = allDisplaySets.find(
+              displaySet =>
+                displaySet.displaySetInstanceUID ===
+                activeViewport.displaySetInstanceUID
+            );
 
-          const SOPInstanceUID = cornerstone.metaData.get(
-            'SOPInstanceUID',
-            imageId
-          );
-          const StudyInstanceUID = cornerstone.metaData.get(
-            'StudyInstanceUID',
-            imageId
-          );
+            const frame = labelmap3D.labelmaps2D[closest];
 
-          onSegItemClick({
-            StudyInstanceUID,
-            SOPInstanceUID,
-            frameIndex,
-            activeViewportIndex: activeIndex,
-          });
+            onSegmentItemClick({
+              studies,
+              StudyInstanceUID: currentDisplaySet.StudyInstanceUID,
+              displaySetInstanceUID: currentDisplaySet.displaySetInstanceUID,
+              SOPClassUID: viewports[activeIndex].sopClassUIDs[0],
+              SOPInstanceUID: currentDisplaySet.SOPInstanceUID,
+              segmentNumber,
+              frameIndex: closest,
+              frame,
+            });
+          }
         };
 
-        const enabledElements = cornerstone.getEnabledElements();
-        const enabledElementViewport = enabledElements[activeIndex];
+        const isSegmentVisible = () => {
+          return !labelmap3D.segmentsHidden[segmentIndex];
+        };
 
-        let isVisible = true;
-        if (enabledElementViewport) {
-          const element = enabledElementViewport.element;
-          const module = cornerstoneTools.getModule('segmentation');
-          isVisible = module.getters.isSegmentVisible(
-            element,
-            segmentNumber,
-            brushStackState.activeLabelmapIndex
-          );
+        const toggleSegmentVisibility = () => {
+          const segmentsHidden = labelmap3D.segmentsHidden;
+          segmentsHidden[segmentIndex] = !segmentsHidden[segmentIndex];
+          return !segmentsHidden[segmentIndex];
+        };
+
+        const cachedSegmentProperties =
+          state.cachedSegmentsProperties[segmentNumber];
+        let visible = isSegmentVisible();
+        if (
+          cachedSegmentProperties &&
+          cachedSegmentProperties.visible !== visible
+        ) {
+          toggleSegmentVisibility();
         }
 
         segmentList.push(
           <SegmentItem
             key={segmentNumber}
             itemClass={`segment-item ${sameSegment && 'selected'}`}
-            onClick={setCurrentSelectedSegment}
+            onClick={() => setCurrentSelectedSegment()}
             label={segmentLabel}
             index={segmentNumber}
             color={color}
-            visible={isVisible}
-            onVisibilityChange={() => {
-              const element = enabledElements[activeIndex].element;
-              module.setters.toggleSegmentVisibility(
-                element,
-                segmentNumber,
-                brushStackState.activeLabelmapIndex
-              );
-              refreshViewport();
+            visible={visible}
+            onVisibilityChange={newVisibility => {
+              if (isCornerstone()) {
+                const enabledElements = cornerstone.getEnabledElements();
+                const element = enabledElements[activeIndex].element;
+                module.setters.toggleSegmentVisibility(
+                  element,
+                  segmentNumber,
+                  brushStackState.activeLabelmapIndex
+                );
+              }
+
+              if (isVTK()) {
+                onSegmentVisibilityChange(segmentNumber, newVisibility);
+              }
+
+              updateCachedSegmentsProperties(segmentNumber, {
+                visible: newVisibility,
+              });
+              refreshViewports();
             }}
           />
         );
@@ -336,9 +438,24 @@ const SegmentationPanel = ({
        * Show default name
        */
     },
-    [activeIndex, onSegItemClick, state.selectedSegment]
+    [activeIndex, onSegmentItemClick, state.selectedSegment, state.isLoading]
   );
 
+  const updateCachedSegmentsProperties = (segmentNumber, properties) => {
+    const segmentsProperties = state.cachedSegmentsProperties;
+    const segmentProperties = state.cachedSegmentsProperties[segmentNumber];
+
+    segmentsProperties[segmentNumber] = segmentProperties
+      ? { ...segmentProperties, ...properties }
+      : properties;
+
+    updateState('cachedSegmentsProperties', segmentsProperties);
+  };
+
+  useEffect(() => {
+    updateState('cachedSegmentsProperties', []);
+  }, [activeContexts]);
+
   const updateState = (field, value) => {
     setState(state => ({ ...state, [field]: value }));
   };
@@ -387,7 +504,6 @@ const SegmentationPanel = ({
   };
 
   const updateConfiguration = newConfiguration => {
-    /* Supported configuration */
     configuration.renderFill = newConfiguration.renderFill;
     configuration.renderOutline = newConfiguration.renderOutline;
     configuration.shouldRenderInactiveLabelmaps =
@@ -397,26 +513,35 @@ const SegmentationPanel = ({
     configuration.outlineWidth = newConfiguration.outlineWidth;
     configuration.fillAlphaInactive = newConfiguration.fillAlphaInactive;
     configuration.outlineAlphaInactive = newConfiguration.outlineAlphaInactive;
-    refreshViewport();
+    onConfigurationChange(newConfiguration);
+    refreshViewports();
   };
 
-  if (state.showSegSettings) {
+  const disabledConfigurationFields = [
+    'outlineAlpha',
+    'shouldRenderInactiveLabelmaps',
+  ];
+  if (state.showSegmentationSettings) {
     return (
       <SegmentationSettings
+        disabledFields={isVTK() ? disabledConfigurationFields : []}
         configuration={configuration}
-        onBack={() => updateState('showSegSettings', false)}
+        onBack={() => updateState('showSegmentationSettings', false)}
         onChange={updateConfiguration}
       />
     );
   } else {
     return (
-      <div className="dcmseg-segmentation-panel">
+      <div
+        className={`dcmseg-segmentation-panel ${state.isDisabled &&
+          'disabled'}`}
+      >
         <Icon
           className="cog-icon"
           name="cog"
           width="25px"
           height="25px"
-          onClick={() => updateState('showSegSettings', true)}
+          onClick={() => updateState('showSegmentationSettings', true)}
         />
         {false && (
           <form className="selector-form">
@@ -509,59 +634,6 @@ const _getReferencedSegDisplaysets = (StudyInstanceUID, SeriesInstanceUID) => {
   return referencedDisplaysets;
 };
 
-/**
- *
- *
- * @param {*} viewportSpecificData
- * @param {*} studies
- * @param {*} displaySet
- * @param {*} firstImageId
- * @param {*} activeLabelmapIndex
- * @returns
- */
-const _setActiveLabelmap = async (
-  viewportSpecificData,
-  studies,
-  displaySet,
-  firstImageId,
-  activeLabelmapIndex,
-  UINotificationService
-) => {
-  if (displaySet.labelmapIndex === activeLabelmapIndex) {
-    log.warn(`${activeLabelmapIndex} is already the active labelmap`);
-    return displaySet.labelmapIndex;
-  }
-
-  if (!displaySet.isLoaded) {
-    // What props does this expect `viewportSpecificData` to have?
-    // TODO: Should this return the `labelmapIndex`?
-
-    const loadPromise = displaySet.load(viewportSpecificData, studies);
-
-    loadPromise.catch(error => {
-      UINotificationService.show({
-        title: 'DICOM Segmentation Loader',
-        message: error.message,
-        type: 'error',
-        autoClose: false,
-      });
-
-      // Return old index.
-      return activeLabelmapIndex;
-    });
-
-    await loadPromise;
-  }
-
-  const { state } = cornerstoneTools.getModule('segmentation');
-  const brushStackState = state.series[firstImageId];
-  brushStackState.activeLabelmapIndex = displaySet.labelmapIndex;
-
-  refreshViewport();
-
-  return displaySet.labelmapIndex;
-};
-
 /**
  *
  * @param {*} firstImageId
@@ -581,7 +653,7 @@ const _setActiveSegment = (firstImageId, segmentIndex, activeSegmentIndex) => {
     brushStackState.labelmaps3D[brushStackState.activeLabelmapIndex];
   labelmap3D.activeSegmentIndex = segmentIndex;
 
-  refreshViewport();
+  refreshViewports();
 
   return segmentIndex;
 };

extensions/dicom-segmentation/src/components/SegmentationSettings/SegmentationSettings.js

@@ -4,7 +4,7 @@ import { Range } from '@ohif/ui';
 
 import './SegmentationSettings.css';
 
-const SegmentationSettings = ({ configuration, onBack, onChange }) => {
+const SegmentationSettings = ({ configuration, onBack, onChange, disabledFields = [] }) => {
   const [state, setState] = useState({
     renderFill: configuration.renderFill,
     renderOutline: configuration.renderOutline,
@@ -70,28 +70,32 @@ const SegmentationSettings = ({ configuration, onBack, onChange }) => {
         />
         {state.renderOutline && (
           <>
-            <CustomRange
-              value={state.outlineAlpha * 100}
-              label="Opacity"
-              showPercentage
-              step={1}
-              min={0}
-              max={100}
-              onChange={event => save('outlineAlpha', toFloat(event.target.value))}
-            />
-            <CustomRange
-              value={state.outlineWidth}
-              label="Width"
-              showValue
-              step={1}
-              min={0}
-              max={5}
-              onChange={event => save('outlineWidth', parseInt(event.target.value))}
-            />
+            {!disabledFields.includes('outlineAlpha') && (
+              <CustomRange
+                value={state.outlineAlpha * 100}
+                label="Opacity"
+                showPercentage
+                step={1}
+                min={0}
+                max={100}
+                onChange={event => save('outlineAlpha', toFloat(event.target.value))}
+              />
+            )}
+            {!disabledFields.includes('outlineWidth') && (
+              <CustomRange
+                value={state.outlineWidth}
+                label="Width"
+                showValue
+                step={1}
+                min={0}
+                max={5}
+                onChange={event => save('outlineWidth', parseInt(event.target.value))}
+              />
+            )}
           </>
         )}
       </div>
-      {(state.renderFill || state.renderOutline) && (
+      {(state.renderFill || state.renderOutline) && !disabledFields.includes('shouldRenderInactiveLabelmaps') && (
         <div
           className="settings-group"
           style={{ marginBottom: state.shouldRenderInactiveLabelmaps ? 15 : 0 }}
@@ -103,7 +107,7 @@ const SegmentationSettings = ({ configuration, onBack, onChange }) => {
           />
           {state.shouldRenderInactiveLabelmaps && (
             <>
-              {state.renderFill && (
+              {state.renderFill && !disabledFields.includes('fillAlphaInactive') && (
                 <CustomRange
                   label="Fill Opacity"
                   showPercentage
@@ -114,7 +118,7 @@ const SegmentationSettings = ({ configuration, onBack, onChange }) => {
                   onChange={event => save('fillAlphaInactive', toFloat(event.target.value))}
                 />
               )}
-              {state.renderOutline && (
+              {state.renderOutline && !disabledFields.includes('outlineAlphaInactive') && (
                 <CustomRange
                   label="Outline Opacity"
                   showPercentage

extensions/dicom-segmentation/src/getOHIFDicomSegSopClassHandler.js

@@ -1,5 +1,6 @@
 import { MODULE_TYPES, utils } from '@ohif/core';
 import loadSegmentation from './loadSegmentation';
+import getSourceDisplaySet from './getSourceDisplaySet';
 
 // TODO: Should probably use dcmjs for this
 const SOP_CLASS_UIDS = {
@@ -32,6 +33,7 @@ export default function getSopClassHandlerModule({ servicesManager }) {
         SOPInstanceUID,
         SeriesInstanceUID,
         StudyInstanceUID,
+        SeriesNumber,
       } = metadata;
 
       const segDisplaySet = {
@@ -51,7 +53,13 @@ export default function getSopClassHandlerModule({ servicesManager }) {
         isLoaded: false,
         SeriesDate,
         SeriesTime,
+        SeriesNumber,
         SeriesDescription,
+        metadata,
+      };
+
+      segDisplaySet.getSourceDisplaySet = function(studies) {
+        return getSourceDisplaySet(studies, segDisplaySet);
       };
 
       segDisplaySet.load = function(referencedDisplaySet, studies) {

extensions/dicom-segmentation/src/getSourceDisplaySet.js

@@ -0,0 +1,88 @@
+import setActiveLabelmap from './utils/setActiveLabelMap';
+import { classes } from '@ohif/core';
+
+const { ImageSet } = classes;
+
+export default function getSourceDisplaySet(studies, segDisplaySet) {
+  const referencedDisplaySet = _getReferencedDisplaySet(segDisplaySet, studies);
+
+  setActiveLabelmap(referencedDisplaySet, studies, segDisplaySet);
+
+  return referencedDisplaySet;
+}
+
+const _getReferencedDisplaySet = (segDisplaySet, studies) => {
+  let allDisplaySets = [];
+
+  studies.forEach(study => {
+    allDisplaySets = allDisplaySets.concat(study.displaySets);
+  });
+
+  const otherDisplaySets = allDisplaySets.filter(
+    ds => ds.displaySetInstanceUID !== segDisplaySet.displaySetInstanceUID
+  );
+
+  const { metadata } = segDisplaySet;
+
+  let referencedSeriesInstanceUIDs;
+
+  if (metadata.ReferencedSeriesSequence) {
+    const ReferencedSeriesSequence = _toArray(
+      metadata.ReferencedSeriesSequence
+    );
+
+    referencedSeriesInstanceUIDs = ReferencedSeriesSequence.map(
+      ReferencedSeries => ReferencedSeries.SeriesInstanceUID
+    );
+  } else {
+    const { PerFrameFunctionalGroupsSequence } = metadata;
+
+    let SourceImageSequence;
+
+    if (metadata.SourceImageSequence) {
+      SourceImageSequence = metadata.SourceImageSequence;
+    } else {
+      const firstFunctionalGroups = _toArray(
+        PerFrameFunctionalGroupsSequence
+      )[0];
+      const { DerivationImageSequence } = firstFunctionalGroups;
+
+      SourceImageSequence = DerivationImageSequence;
+    }
+
+    const firstSourceImage = _toArray(SourceImageSequence)[0];
+
+    const { ReferencedSOPInstanceUID } = firstSourceImage;
+
+    referencedSeriesInstanceUIDs = _findReferencedSeriesInstanceUIDsFromSOPInstanceUID(
+      otherDisplaySets,
+      ReferencedSOPInstanceUID
+    );
+  }
+
+  const referencedDisplaySet = otherDisplaySets.find(ds =>
+    referencedSeriesInstanceUIDs.includes(ds.SeriesInstanceUID)
+  );
+
+  return referencedDisplaySet;
+};
+
+const _findReferencedSeriesInstanceUIDsFromSOPInstanceUID = (
+  displaySets,
+  SOPInstanceUID
+) => {
+  const imageSets = displaySets.filter(ds => ds instanceof ImageSet);
+
+  for (let i = 0; i < imageSets.length; i++) {
+    const { images } = imageSets[i];
+    for (let j = 0; j < images.length; j++) {
+      if (images[j].SOPInstanceUID === SOPInstanceUID) {
+        return [images[j].getData().metadata.SeriesInstanceUID];
+      }
+    }
+  }
+};
+
+function _toArray(arrayOrObject) {
+  return Array.isArray(arrayOrObject) ? arrayOrObject : [arrayOrObject];
+}

extensions/dicom-segmentation/src/index.js

@@ -1,15 +1,16 @@
 import React from 'react';
-
 import init from './init.js';
 import toolbarModule from './toolbarModule.js';
 import getSopClassHandlerModule from './getOHIFDicomSegSopClassHandler.js';
 import SegmentationPanel from './components/SegmentationPanel/SegmentationPanel.js';
+import { version } from '../package.json';
 
 export default {
   /**
    * Only required property. Should be a unique value across all extensions.
    */
   id: 'com.ohif.dicom-segmentation',
+  version,
 
   /**
    *
@@ -23,19 +24,56 @@ export default {
   getToolbarModule({ servicesManager }) {
     return toolbarModule;
   },
-  getPanelModule({ commandsManager, servicesManager }) {
+  getPanelModule({ commandsManager, api, servicesManager }) {
+    const { UINotificationService } = servicesManager.services;
+
     const ExtendedSegmentationPanel = props => {
-      const segItemClickHandler = segData => {
-        commandsManager.runCommand('jumpToImage', segData);
+      const { activeContexts } = api.hooks.useAppContext();
+
+      const onDisplaySetLoadFailureHandler = error => {
+        UINotificationService.show({
+          title: 'DICOM Segmentation Loader',
+          message: error.message,
+          type: 'error',
+          autoClose: false,
+        });
       };
 
-      const { UINotificationService } = servicesManager.services;
+      const segmentItemClickHandler = data => {
+        commandsManager.runCommand('jumpToImage', data);
+        commandsManager.runCommand('jumpToSlice', data);
+      };
+
+      const onSegmentVisibilityChangeHandler = (segmentNumber, visible) => {
+        commandsManager.runCommand('setSegmentConfiguration', {
+          segmentNumber,
+          visible,
+        });
+      };
+
+      const onConfigurationChangeHandler = configuration => {
+        commandsManager.runCommand('setSegmentationConfiguration', {
+          globalOpacity: configuration.fillAlpha,
+          outlineThickness: configuration.outlineWidth,
+          renderOutline: configuration.renderOutline,
+          visible: configuration.renderFill,
+        });
+      };
+
+      const onSelectedSegmentationChangeHandler = () => {
+        commandsManager.runCommand('requestNewSegmentation');
+      };
 
       return (
         <SegmentationPanel
           {...props}
-          onSegItemClick={segItemClickHandler}
-          UINotificationService={UINotificationService}
+          activeContexts={activeContexts}
+          contexts={api.contexts}
+          onSegmentItemClick={segmentItemClickHandler}
+          onSegmentVisibilityChange={onSegmentVisibilityChangeHandler}
+          onConfigurationChange={onConfigurationChangeHandler}
+          onSelectedSegmentationChange={onSelectedSegmentationChangeHandler}
+          onDisplaySetLoadFailure={onDisplaySetLoadFailureHandler}
         />
       );
     };

extensions/dicom-segmentation/src/init.js

@@ -1,4 +1,5 @@
 import csTools from 'cornerstone-tools';
+import DICOMSegTempCrosshairsTool from './tools/DICOMSegTempCrosshairsTool';
 
 /**
  *
@@ -17,4 +18,6 @@ export default function init({ servicesManager, configuration = {} }) {
       alwaysEraseOnClick: true,
     },
   });
+
+  csTools.addTool(DICOMSegTempCrosshairsTool);
 }

extensions/dicom-segmentation/src/loadSegmentation.js

@@ -41,6 +41,7 @@ export default async function loadSegmentation(
       results = _parseSeg(segArrayBuffer, imageIds);
     } catch (error) {
       segDisplaySet.isLoaded = false;
+      segDisplaySet.loadError = true;
       reject(error);
     }
 
@@ -63,6 +64,27 @@ export default async function loadSegmentation(
 
     segDisplaySet.labelmapIndex = labelmapIndex;
 
+    /*
+     * TODO: Improve the way we notify parts of the app that depends on segs to be loaded.
+     *
+     * Currently we are using a non-ideal implementation through a custom event to notify the segmentation panel
+     * or other components that could rely on loaded segmentations that
+     * the segments were loaded so that e.g. when the user opens the panel
+     * before the segments are fully loaded, the panel can subscribe to this custom event
+     * and update itself with the new segments.
+     *
+     * This limitation is due to the fact that the cs segmentation module is an object (which will be
+     * updated after the segments are loaded) that React its not aware of its changes
+     * because the module object its not passed in to the panel component as prop but accessed externally.
+     *
+     * Improving this event approach to something reactive that can be tracked inside the react lifecycle,
+     * allows us to easily watch the module or the segmentations loading process in any other component
+     * without subscribing to external events.
+     */
+    console.log('Segmentation loaded.');
+    const event = new CustomEvent('extensiondicomsegmentationsegloaded');
+    document.dispatchEvent(event);
+
     resolve(labelmapIndex);
   });
 }

extensions/dicom-segmentation/src/tools/DICOMSegTempCrosshairsTool.js

@@ -0,0 +1,127 @@
+import cornerstoneTools, {
+  importInternal,
+  getToolState,
+  toolColors,
+  getModule,
+  globalImageIdSpecificToolStateManager,
+} from 'cornerstone-tools';
+import cornerstone from 'cornerstone-core';
+import drawCanvasCrosshairs from '../utils/drawCanvasCrosshairs';
+import TOOL_NAMES from './TOOL_NAMES';
+
+const { DICOM_SEG_TEMP_CROSSHAIRS_TOOL } = TOOL_NAMES;
+const { getters } = getModule('segmentation');
+
+// Cornerstone 3rd party dev kit imports
+const BaseTool = importInternal('base/BaseTool');
+
+/**
+ * @class RTStructDisplayTool - Renders RTSTRUCT data in a read only manner (i.e. as an overlay).
+ * @extends cornerstoneTools.BaseTool
+ */
+export default class DICOMSegTempCrosshairsTool extends BaseTool {
+  constructor(props = {}) {
+    const defaultProps = {
+      mixins: ['enabledOrDisabledBinaryTool'],
+      name: DICOM_SEG_TEMP_CROSSHAIRS_TOOL,
+    };
+
+    const initialProps = Object.assign(defaultProps, props);
+
+    super(initialProps);
+
+    this._rtStructModule = cornerstoneTools.getModule('rtstruct');
+  }
+
+  renderToolData(evt) {
+    const eventData = evt.detail;
+    const { element } = eventData;
+    const toolState = getToolState(evt.currentTarget, this.name);
+
+    if (!toolState) {
+      return;
+    }
+
+    // We have tool data for this element - iterate over each one and draw it
+
+    for (let i = 0; i < toolState.data.length; i++) {
+      const data = toolState.data[i];
+      const crossHairCenter = data.center;
+
+      drawCanvasCrosshairs(eventData, crossHairCenter, {
+        color: toolColors.getActiveColor(),
+        lineWidth: 1,
+      });
+
+      // Remove the crosshairs, we only render them for one redraw.
+      toolState.data.pop();
+    }
+  }
+}
+
+DICOMSegTempCrosshairsTool.addCrosshair = (element, imageId, segmentNumber) => {
+  const labelmap3D = getters.labelmap3D(element);
+  const stackToolState = cornerstoneTools.getToolState(element, 'stack');
+  const enabledElement = cornerstone.getEnabledElement(element);
+
+  const { rows, columns } = enabledElement.image;
+
+  if (!stackToolState) {
+    return;
+  }
+
+  const imageIds = stackToolState.data[0].imageIds;
+  const imageIdIndex = imageIds.findIndex(imgId => imgId === imageId);
+
+  const labelmap2D = labelmap3D.labelmaps2D[imageIdIndex];
+  const { pixelData } = labelmap2D;
+
+  let xCenter = 0;
+  let yCenter = 0;
+
+  let count = 0;
+
+  for (let y = 0; y < rows; y++) {
+    for (let x = 0; x < columns; x++) {
+      if (pixelData[y * columns + x] === segmentNumber) {
+        count++;
+        xCenter += x + 0.5;
+        yCenter += y + 0.5;
+      }
+    }
+  }
+
+  xCenter /= count;
+  yCenter /= count;
+
+  const globalToolState = globalImageIdSpecificToolStateManager.saveToolState();
+
+  if (!globalToolState[imageId]) {
+    globalToolState[imageId] = {};
+  }
+
+  const imageIdSpecificToolState = globalToolState[imageId];
+
+  if (!imageIdSpecificToolState[DICOM_SEG_TEMP_CROSSHAIRS_TOOL]) {
+    imageIdSpecificToolState[DICOM_SEG_TEMP_CROSSHAIRS_TOOL] = { data: [] };
+  } else if (!imageIdSpecificToolState[DICOM_SEG_TEMP_CROSSHAIRS_TOOL].data) {
+    imageIdSpecificToolState[DICOM_SEG_TEMP_CROSSHAIRS_TOOL].data = [];
+  }
+
+  const toolSpecificData =
+    imageIdSpecificToolState[DICOM_SEG_TEMP_CROSSHAIRS_TOOL].data;
+
+  toolSpecificData.push({ center: { x: xCenter, y: yCenter }, segmentNumber });
+
+  // Enable the tool if not enabled for the element.
+
+  const tool = cornerstoneTools.getToolForElement(
+    element,
+    DICOM_SEG_TEMP_CROSSHAIRS_TOOL
+  );
+
+  if (tool.mode !== 'enabled') {
+    // If not already active or passive, set passive so contours render.
+    cornerstoneTools.setToolEnabled(DICOM_SEG_TEMP_CROSSHAIRS_TOOL);
+  }
+};

extensions/dicom-segmentation/src/tools/TOOL_NAMES.js

@@ -0,0 +1,5 @@
+const TOOL_NAMES = {
+  DICOM_SEG_TEMP_CROSSHAIRS_TOOL: 'DICOMSegTempCrosshairsTool',
+};
+
+export default TOOL_NAMES;

extensions/dicom-segmentation/src/utils/drawCanvasCrosshairs.js

@@ -0,0 +1,56 @@
+import cornerstone from 'cornerstone-core';
+import cornerstoneTools from 'cornerstone-tools';
+
+const { importInternal } = cornerstoneTools;
+const draw = importInternal('drawing/draw');
+const drawLine = importInternal('drawing/drawLine');
+const getNewContext = importInternal('drawing/getNewContext');
+
+export default function _drawCanvasCrosshairs(eventData, center, options) {
+  const context = getNewContext(eventData.canvasContext.canvas);
+  const { element } = eventData;
+
+  const centerCanvas = cornerstone.pixelToCanvas(element, center);
+
+  const { clientWidth: width, clientHeight: height } = element;
+
+  const offset = 10;
+
+  draw(context, context => {
+    drawLine(
+      context,
+      element,
+      { x: centerCanvas.x + offset, y: centerCanvas.y },
+      { x: width, y: centerCanvas.y },
+      options,
+      'canvas'
+    );
+
+    drawLine(
+      context,
+      element,
+      { x: centerCanvas.x - offset, y: centerCanvas.y },
+      { x: 0, y: centerCanvas.y },
+      options,
+      'canvas'
+    );
+
+    drawLine(
+      context,
+      element,
+      { x: centerCanvas.x, y: centerCanvas.y + offset },
+      { x: centerCanvas.x, y: height },
+      options,
+      'canvas'
+    );
+
+    drawLine(
+      context,
+      element,
+      { x: centerCanvas.x, y: centerCanvas.y - offset },
+      { x: centerCanvas.x, y: 0 },
+      options,
+      'canvas'
+    );
+  });
+}

extensions/dicom-segmentation/src/utils/refreshViewports.js

@@ -0,0 +1,5 @@
+export default function refreshViewports() {
+  cornerstone.getEnabledElements().forEach(enabledElement => {
+    cornerstone.updateImage(enabledElement.element);
+  });
+}

extensions/dicom-segmentation/src/utils/setActiveLabelMap.js

@@ -0,0 +1,67 @@
+import { utils, log } from '@ohif/core';
+import cornerstoneTools from 'cornerstone-tools';
+import refreshViewports from './refreshViewports';
+
+const { studyMetadataManager } = utils;
+
+/**
+ *
+ *
+ * @param {*} viewportSpecificData
+ * @param {*} studies
+ * @param {*} displaySet
+ * @param {*} firstImageId
+ * @param {*} activeLabelmapIndex
+ * @returns
+ */
+export default async function setActiveLabelmap(
+  referencedDisplaySet,
+  studies,
+  displaySet,
+  callback = () => {},
+  onDisplaySetLoadFailure = err => {
+    throw new Error(err.message);
+  }
+) {
+  const studyMetadata = studyMetadataManager.get(
+    referencedDisplaySet.StudyInstanceUID
+  );
+  const firstImageId = studyMetadata.getFirstImageId(
+    referencedDisplaySet.displaySetInstanceUID
+  );
+
+  let { state } = cornerstoneTools.getModule('segmentation');
+
+  let brushStackState = state.series[firstImageId];
+  const activeLabelmapIndex = brushStackState
+    ? brushStackState.activeLabelmapIndex
+    : undefined;
+
+  if (displaySet.labelmapIndex === activeLabelmapIndex) {
+    log.warn(`${activeLabelmapIndex} is already the active labelmap`);
+    return displaySet.labelmapIndex;
+  }
+
+  if (!displaySet.isLoaded) {
+    const loadPromise = displaySet.load(referencedDisplaySet, studies);
+
+    loadPromise.catch(error => {
+      onDisplaySetLoadFailure(error);
+
+      // Return old index.
+      return activeLabelmapIndex;
+    });
+
+    await loadPromise;
+  }
+
+  // This might have just been created, so need to use the non-cached value.
+  state = cornerstoneTools.getModule('segmentation').state;
+  brushStackState = state.series[firstImageId];
+  brushStackState.activeLabelmapIndex = displaySet.labelmapIndex;
+
+  refreshViewports();
+  callback();
+
+  return displaySet.labelmapIndex;
+}

extensions/dicom-tag-browser/.webpack/webpack.dev.js

@@ -0,0 +1,8 @@
+const path = require('path');
+const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+
+module.exports = (env, argv) => {
+  return webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
+};

extensions/dicom-tag-browser/.webpack/webpack.prod.js

@@ -0,0 +1,38 @@
+const merge = require('webpack-merge');
+const path = require('path');
+const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
+const pkg = require('./../package.json');
+
+const ROOT_DIR = path.join(__dirname, './..');
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+
+module.exports = (env, argv) => {
+  const commonConfig = webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
+
+  return merge(commonConfig, {
+    devtool: 'source-map',
+    stats: {
+      colors: true,
+      hash: true,
+      timings: true,
+      assets: true,
+      chunks: false,
+      chunkModules: false,
+      modules: false,
+      children: false,
+      warnings: true,
+    },
+    optimization: {
+      minimize: true,
+      sideEffects: true,
+    },
+    output: {
+      path: ROOT_DIR,
+      library: 'OHIFExtDicomP10Downloader',
+      libraryTarget: 'umd',
+      libraryExport: 'default',
+      filename: pkg.main,
+    },
+  });
+};

extensions/dicom-tag-browser/CHANGELOG.md

@@ -0,0 +1,16 @@
+# Change Log
+
+All notable changes to this project will be documented in this file.
+See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+## [0.0.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.0.2...@ohif/extension-dicom-tag-browser@0.0.3) (2020-09-24)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
+## 0.0.2 (2020-09-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser

extensions/dicom-tag-browser/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-tag-browser/README.md

@@ -0,0 +1 @@
+# @ohif/extension-dicom-tag-browser

extensions/dicom-tag-browser/package.json

@@ -0,0 +1,40 @@
+{
+  "name": "@ohif/extension-dicom-tag-browser",
+  "version": "0.0.3",
+  "description": "OHIF extension for checking DICOM headers.",
+  "author": "OHIF",
+  "license": "MIT",
+  "repository": "OHIF/Viewers",
+  "main": "dist/index.umd.js",
+  "module": "src/index.js",
+  "publishConfig": {
+    "access": "public"
+  },
+  "engines": {
+    "node": ">=10",
+    "npm": ">=6",
+    "yarn": ">=1.16.0"
+  },
+  "files": [
+    "dist",
+    "README.md"
+  ],
+  "scripts": {
+    "dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --debug --output-pathinfo",
+    "build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
+    "build:package": "yarn run build",
+    "prepublishOnly": "yarn run build",
+    "start": "yarn run dev"
+  },
+  "peerDependencies": {
+    "@ohif/core": "^2.6.0",
+    "dcmjs": "0.16.0",
+    "react": "^16.8.6"
+  },
+  "dependencies": {
+    "@babel/runtime": "^7.5.5",
+    "dicomweb-client": "^0.6.0",
+    "moment": "2.24.0",
+    "react-select": "^3.0.8"
+  }
+}

extensions/dicom-tag-browser/src/components/DicomBrowserSelect.js

@@ -0,0 +1,59 @@
+import React from 'react';
+import Select from 'react-select';
+
+const DicomBrowserSelect = ({ value, formatOptionLabel, options }) => (
+  <Select
+    value={value}
+    formatOptionLabel={formatOptionLabel}
+    styles={dicomBrowserSelectStyles}
+    options={options}
+  />
+);
+
+const computedstyle = getComputedStyle(document.body);
+const uiGrayDarker = computedstyle.getPropertyValue('--ui-gray-darker');
+const activeColor = computedstyle.getPropertyValue('--active-color');
+const defaultColor = computedstyle.getPropertyValue('--default-color');
+const uiGrayDark = computedstyle.getPropertyValue('--ui-gray-dark');
+
+const dicomBrowserSelectStyles = {
+  singleValue: (base, state) => ({
+    ...base,
+    width: '100%',
+  }),
+  control: (base, state) => ({
+    ...base,
+    cursor: 'pointer',
+    background: uiGrayDarker,
+    borderRadius: state.isFocused ? '5px 5px 5px 5px' : 5,
+    borderColor: state.isFocused ? activeColor : defaultColor,
+    minHeight: '50px',
+    '&:hover': {
+      borderColor: activeColor,
+    },
+  }),
+  menu: base => ({
+    ...base,
+    borderRadius: 5,
+    background: uiGrayDarker,
+  }),
+  option: (base, state) => ({
+    ...base,
+    width: '100%',
+    cursor: 'pointer',
+    '&:first-of-type': {
+      borderTopLeftRadius: 5,
+      borderTopRightRadius: 5,
+    },
+    '&:last-of-type': {
+      borderBottomLeftRadius: 5,
+      borderBottomRightRadius: 5,
+    },
+    background: state.isSelected ? uiGrayDark : uiGrayDarker,
+    '&:hover': {
+      background: uiGrayDark,
+    },
+  }),
+};
+
+export default DicomBrowserSelect;

extensions/dicom-tag-browser/src/components/DicomBrowserSelectItem.css

@@ -0,0 +1,26 @@
+.dcmseg-segmentation-item {
+  display: flex;
+  justify-content: start;
+  margin: 0;
+  width: 100%;
+}
+
+.dcmseg-segmentation-item .segmentation-meta {
+  display: flex;
+  flex-direction: column;
+  flex-grow: 1;
+  overflow: hidden;
+}
+
+.dcmseg-segmentation-item .segmentation-meta-title {
+  text-overflow: ellipsis;
+  overflow: hidden;
+  white-space: nowrap;
+  color: white;
+  max-width: calc(100% - 30px);
+}
+
+.dcmseg-segmentation-item .segmentation-meta-description {
+  font-size: 12px;
+  color: var(--text-secondary-color);
+}

extensions/dicom-tag-browser/src/components/DicomBrowserSelectItem.js

@@ -0,0 +1,27 @@
+import React from 'react';
+import PropTypes from 'prop-types';
+
+import './DicomBrowserSelectItem.css';
+
+const DicomBrowserSelectItem = ({ onClick, title, description }) => {
+  return (
+    <li className="dcmseg-segmentation-item" onClick={onClick}>
+      <div className="segmentation-meta">
+        <div className="segmentation-meta-title">{title}</div>
+        <div className="segmentation-meta-description">{description}</div>
+      </div>
+    </li>
+  );
+};
+
+DicomBrowserSelectItem.propTypes = {
+  onClick: PropTypes.func.isRequired,
+  title: PropTypes.string.isRequired,
+  description: PropTypes.string.isRequired,
+};
+
+DicomBrowserSelectItem.defaultProps = {
+  description: '',
+};
+
+export default DicomBrowserSelectItem;

extensions/dicom-tag-browser/src/components/DicomTagBrowser.css

@@ -0,0 +1,27 @@
+.dicom-tag-browser-table {
+  margin-right: auto;
+  margin-left: auto;
+}
+
+.dicom-tag-browser-table tr {
+  padding-left: 10px;
+  padding-right: 10px;
+  color: var(--table-text-primary-color);
+  border-top: 1px solid #ddd;
+  white-space: nowrap;
+}
+
+.dicom-tag-browser-table td.dicom-tag-browser-table-center {
+  text-align: center;
+}
+
+.dicom-tag-browser-table th {
+  padding-left: 10px;
+  padding-right: 10px;
+  text-align: center;
+  color: var(--active-color);
+}
+
+.dicom-tag-browser-table th.dicom-tag-browser-table-left {
+  text-align: left;
+}

extensions/dicom-tag-browser/src/components/DicomTagBrowser.js

@@ -0,0 +1,335 @@
+import React, { useState, useEffect } from 'react';
+import { classes } from '@ohif/core';
+import dcmjs from 'dcmjs';
+import DicomBrowserSelect from './DicomBrowserSelect';
+import moment from 'moment';
+import './DicomTagBrowser.css';
+import DicomBrowserSelectItem from './DicomBrowserSelectItem';
+
+const { ImageSet } = classes;
+const { DicomMetaDictionary } = dcmjs.data;
+const { nameMap } = DicomMetaDictionary;
+
+const DicomTagBrowser = ({ displaySets, displaySetInstanceUID }) => {
+  const [
+    activeDisplaySetInstanceUID,
+    setActiveDisplaySetInstanceUID,
+  ] = useState(displaySetInstanceUID);
+  const [activeInstance, setActiveInstance] = useState(0);
+  const [tags, setTags] = useState([]);
+  const [instanceList, setInstanceList] = useState([]);
+  const [displaySetList, setDisplaySetList] = useState([]);
+  const [isImageStack, setIsImageStack] = useState(false);
+
+  useEffect(() => {
+    const activeDisplaySet = displaySets.find(
+      ds => ds.displaySetInstanceUID === activeDisplaySetInstanceUID
+    );
+
+    const newDisplaySetList = displaySets.map(displaySet => {
+      const {
+        displaySetInstanceUID,
+        SeriesDate,
+        SeriesTime,
+        SeriesNumber,
+        SeriesDescription,
+        Modality,
+      } = displaySet;
+
+      /* Map to display representation */
+      const dateStr = `${SeriesDate}:${SeriesTime}`.split('.')[0];
+      const date = moment(dateStr, 'YYYYMMDD:HHmmss');
+      const displayDate = date.format('ddd, MMM Do YYYY');
+
+      return {
+        value: displaySetInstanceUID,
+        title: `${SeriesNumber} (${Modality}): ${SeriesDescription}`,
+        description: displayDate,
+        onClick: () => {
+          setActiveDisplaySetInstanceUID(displaySetInstanceUID);
+          setActiveInstance(0);
+        },
+      };
+    });
+
+    let metadata;
+    const isImageStack = activeDisplaySet instanceof ImageSet;
+
+    let selectedInstanceValue;
+    let instanceList;
+
+    if (isImageStack) {
+      const { images } = activeDisplaySet;
+      const image = images[activeInstance];
+
+      instanceList = images.map((image, index) => {
+        const metadata = image.getData().metadata;
+
+        const { InstanceNumber } = metadata;
+
+        return {
+          value: index,
+          title: `Instance Number: ${InstanceNumber}`,
+          description: '',
+          onClick: () => {
+            setActiveInstance(index);
+          },
+        };
+      });
+
+      metadata = image.getData().metadata;
+    } else {
+      metadata = activeDisplaySet.metadata;
+    }
+
+    setTags(getSortedTags(metadata));
+    setInstanceList(instanceList);
+    setDisplaySetList(newDisplaySetList);
+    setIsImageStack(isImageStack);
+  }, [activeDisplaySetInstanceUID, activeInstance]);
+
+  const selectedDisplaySetValue = displaySetList.find(
+    ds => ds.value === activeDisplaySetInstanceUID
+  );
+
+  let instanceSelectList = null;
+
+  if (isImageStack) {
+    const selectedInstanceValue = instanceList[activeInstance];
+
+    instanceSelectList = (
+      <DicomBrowserSelect
+        value={selectedInstanceValue}
+        formatOptionLabel={DicomBrowserSelectItem}
+        options={instanceList}
+      />
+    );
+  }
+
+  return (
+    <div>
+      <DicomBrowserSelect
+        value={selectedDisplaySetValue}
+        formatOptionLabel={DicomBrowserSelectItem}
+        options={displaySetList}
+      />
+      {instanceSelectList}
+      <DicomTagTable tags={tags}></DicomTagTable>
+    </div>
+  );
+};
+
+function DicomTagTable({ tags }) {
+  const rows = getFormattedRowsFromTags(tags);
+
+  return (
+    <div>
+      <table className="dicom-tag-browser-table">
+        <tr>
+          <th className="dicom-tag-browser-table-left">Tag</th>
+          <th className="dicom-tag-browser-table-left">Value Representation</th>
+          <th className="dicom-tag-browser-table-left">Keyword</th>
+          <th className="dicom-tag-browser-table-left">Value</th>
+        </tr>
+        {rows.map(row => {
+          const className = row.className ? row.className : null;
+
+          return (
+            <tr className={className}>
+              <td>{row[0]}</td>
+              <td className="dicom-tag-browser-table-center">{row[1]}</td>
+              <td>{row[2]}</td>
+              <td>{row[3]}</td>
+            </tr>
+          );
+        })}
+      </table>
+    </div>
+  );
+}
+
+function getFormattedRowsFromTags(tags) {
+  const rows = [];
+
+  tags.forEach(tagInfo => {
+    if (tagInfo.vr === 'SQ') {
+      rows.push([
+        `${tagInfo.tagIndent}${tagInfo.tag}`,
+        tagInfo.vr,
+        tagInfo.keyword,
+        '',
+      ]);
+
+      const { values } = tagInfo;
+
+      values.forEach((item, index) => {
+        const formatedRowsFromTags = getFormattedRowsFromTags(item);
+
+        rows.push([
+          `${item[0].tagIndent}(FFFE,E000)`,
+          '',
+          `Item #${index}`,
+          '',
+        ]);
+
+        rows.push(...formatedRowsFromTags);
+      });
+    } else {
+      rows.push([
+        `${tagInfo.tagIndent}${tagInfo.tag}`,
+        tagInfo.vr,
+        tagInfo.keyword,
+        tagInfo.value,
+      ]);
+    }
+  });
+
+  return rows;
+}
+
+function getSortedTags(metadata) {
+  const tagList = getRows(metadata);
+
+  // Sort top level tags, sequence groups are sorted when created.
+  _sortTagList(tagList);
+
+  return tagList;
+}
+
+function getRows(metadata, depth = 0) {
+  // Tag, Type, Value, Keyword
+
+  const keywords = Object.keys(metadata);
+
+  let tagIndent = '';
+
+  for (let i = 0; i < depth; i++) {
+    tagIndent += '>';
+  }
+
+  if (depth > 0) {
+    tagIndent += ' '; // If indented, add a space after the indents.
+  }
+
+  const rows = [];
+
+  for (let i = 0; i < keywords.length; i++) {
+    let keyword = keywords[i];
+
+    if (keyword === '_vrMap') {
+      continue;
+    }
+
+    const tagInfo = nameMap[keyword];
+
+    let value = metadata[keyword];
+
+    if (tagInfo && tagInfo.vr === 'SQ') {
+      const sequenceAsArray = toArray(value);
+
+      // Push line defining the sequence
+
+      const sequence = {
+        tag: tagInfo.tag,
+        tagIndent,
+        vr: tagInfo.vr,
+        keyword,
+        values: [],
+      };
+
+      rows.push(sequence);
+
+      if (value === null) {
+        // Type 2 Sequence
+        continue;
+      }
+
+      sequenceAsArray.forEach(item => {
+        const sequenceRows = getRows(item, depth + 1);
+
+        // Sort the sequence group.
+        _sortTagList(sequenceRows);
+
+        sequence.values.push(sequenceRows);
+      });
+
+      continue;
+    }
+
+    if (Array.isArray(value)) {
+      value = value.join('\\');
+    }
+
+    if (typeof value === 'number') {
+      value = value.toString();
+    }
+
+    if (typeof value !== 'string') {
+      if (value === null) {
+        value = ' ';
+      } else {
+        if (typeof value === 'object') {
+          if (value.InlineBinary) {
+            value = 'Inline Binary';
+          } else if (value.BulkDataURI) {
+            value = `Bulk Data URI`; //: ${value.BulkDataURI}`;
+          } else if (value.Alphabetic) {
+            value = value.Alphabetic;
+          } else {
+            console.error('Unrecognised Value for element:');
+            console.error(value);
+            value = ' ';
+          }
+        } else {
+          console.error('Unrecognised Value for element:');
+          console.error(value);
+          value = ' ';
+        }
+      }
+    }
+
+    // tag / vr/ keyword/ value
+
+    // Remove retired tags
+    keyword = keyword.replace('RETIRED_', '');
+
+    if (tagInfo) {
+      rows.push({
+        tag: tagInfo.tag,
+        tagIndent,
+        vr: tagInfo.vr,
+        keyword,
+        value,
+      });
+    } else {
+      // Private tag
+      const tag = `(${keyword.substring(0, 4)},${keyword.substring(4, 8)})`;
+
+      rows.push({
+        tag,
+        tagIndent,
+        vr: '',
+        keyword: 'Private Tag',
+        value,
+      });
+    }
+  }
+
+  return rows;
+}
+
+function toArray(objectOrArray) {
+  return Array.isArray(objectOrArray) ? objectOrArray : [objectOrArray];
+}
+
+function _sortTagList(tagList) {
+  tagList.sort((a, b) => {
+    if (a.tag < b.tag) {
+      return -1;
+    }
+
+    return 1;
+  });
+}
+
+export default DicomTagBrowser;

extensions/dicom-tag-browser/src/getCommandsModule.js

@@ -0,0 +1,52 @@
+import { utils } from '@ohif/core';
+import React from 'react';
+import DicomTagBrowser from './components/DicomTagBrowser';
+
+const { studyMetadataManager } = utils;
+
+export default function getCommandsModule(servicesManager) {
+  const actions = {
+    openDICOMTagViewer({ viewports }) {
+      const { activeViewportIndex, viewportSpecificData } = viewports;
+      const activeViewportSpecificData =
+        viewportSpecificData[activeViewportIndex];
+
+      const {
+        StudyInstanceUID,
+        displaySetInstanceUID,
+      } = activeViewportSpecificData;
+
+      const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
+      const displaySets = studyMetadata.getDisplaySets();
+
+      const { UIModalService } = servicesManager.services;
+
+      const WrappedDicomTagBrowser = function() {
+        return (
+          <DicomTagBrowser
+            displaySets={displaySets}
+            displaySetInstanceUID={displaySetInstanceUID}
+          />
+        );
+      };
+
+      UIModalService.show({
+        content: WrappedDicomTagBrowser,
+        title: `DICOM Tag Browser`,
+        fullscreen: true,
+      });
+    },
+  };
+
+  const definitions = {
+    openDICOMTagViewer: {
+      commandFn: actions.openDICOMTagViewer,
+      storeContexts: ['servers', 'viewports'],
+    },
+  };
+
+  return {
+    actions,
+    definitions,
+  };
+}

extensions/dicom-tag-browser/src/index.js

@@ -0,0 +1,26 @@
+import getCommandsModule from './getCommandsModule';
+import toolbarModule from './toolbarModule';
+
+/**
+ * Constants
+ */
+
+/**
+ * Extension
+ */
+export default {
+  /**
+   * Only required property. Should be a unique value across all extensions.
+   */
+  id: 'dicom-tag-browser',
+
+  /**
+   * MODULE GETTERS
+   */
+  getCommandsModule({ servicesManager }) {
+    return getCommandsModule(servicesManager);
+  },
+  getToolbarModule() {
+    return toolbarModule;
+  },
+};

extensions/dicom-tag-browser/src/toolbarModule.js

@@ -0,0 +1,20 @@
+const TOOLBAR_BUTTON_TYPES = {
+  COMMAND: 'command',
+};
+
+const definitions = [
+  {
+    id: 'TagBrowser',
+    label: 'Tag Browser',
+    icon: 'list',
+    //
+    type: TOOLBAR_BUTTON_TYPES.COMMAND,
+    commandName: 'openDICOMTagViewer',
+    context: 'VIEWER',
+  },
+];
+
+export default {
+  definitions,
+  defaultContext: 'VIEWER',
+};

extensions/lesion-tracker/CHANGELOG.md

@@ -3,6 +3,14 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [0.2.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-lesion-tracker@0.2.0...@ohif/extension-lesion-tracker@0.2.1) (2020-09-03)
+
+**Note:** Version bump only for package @ohif/extension-lesion-tracker
+
+
+
+
+
 # [0.2.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-lesion-tracker@0.1.0...@ohif/extension-lesion-tracker@0.2.0) (2020-02-10)
 
 

extensions/lesion-tracker/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-lesion-tracker",
-  "version": "0.2.0",
+  "version": "0.2.1",
   "description": "OHIF extension for Lesion Tracker",
   "author": "OHIF",
   "license": "MIT",

extensions/lesion-tracker/src/index.js

@@ -1,10 +1,12 @@
 import MeasurementComparisonTable from './components/MeasurementComparisonTable';
+import { version } from '../package.json';
 
 export default {
   /**
    * Only required property. Should be a unique value across all extensions.
    */
   id: 'lesion-tracker',
+  version,
 
   /**
    * @param {object} params
@@ -26,7 +28,7 @@ export default {
           component: MeasurementComparisonTable,
         },
       ],
-      defaultContext: ['VIEWER']
+      defaultContext: ['VIEWER'],
     };
   },
 

extensions/vtk/CHANGELOG.md

@@ -3,6 +3,213 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [1.7.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.7.8...@ohif/extension-vtk@1.7.9) (2020-10-06)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.7.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.7.7...@ohif/extension-vtk@1.7.8) (2020-09-30)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.7.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.7.6...@ohif/extension-vtk@1.7.7) (2020-09-17)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.7.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.7.5...@ohif/extension-vtk@1.7.6) (2020-09-10)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.7.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.7.4...@ohif/extension-vtk@1.7.5) (2020-09-03)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.7.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.7.3...@ohif/extension-vtk@1.7.4) (2020-09-03)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.7.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.7.2...@ohif/extension-vtk@1.7.3) (2020-09-02)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.7.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.7.1...@ohif/extension-vtk@1.7.2) (2020-08-28)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.7.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.7.0...@ohif/extension-vtk@1.7.1) (2020-08-24)
+
+
+### Bug Fixes
+
+* 🐛 Fail gracefully on an MPR load error ([#1992](https://github.com/OHIF/Viewers/issues/1992)) ([779a7e0](https://github.com/OHIF/Viewers/commit/779a7e0976aa3a2d2bf1dc8f056950f0545c9fff))
+
+
+
+
+
+# [1.7.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.6.10...@ohif/extension-vtk@1.7.0) (2020-08-18)
+
+
+### Features
+
+* 🎸 Update react-vtkjs-viewport usage to use requestPool ([#1984](https://github.com/OHIF/Viewers/issues/1984)) ([bb5f30c](https://github.com/OHIF/Viewers/commit/bb5f30ce2a0192d2e021beaaadfff22fd38e17b9))
+
+
+
+
+
+## [1.6.10](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.6.9...@ohif/extension-vtk@1.6.10) (2020-08-10)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.6.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.6.8...@ohif/extension-vtk@1.6.9) (2020-07-23)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.6.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.6.7...@ohif/extension-vtk@1.6.8) (2020-07-22)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.6.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.6.6...@ohif/extension-vtk@1.6.7) (2020-07-13)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.6.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.6.5...@ohif/extension-vtk@1.6.6) (2020-07-13)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.6.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.6.4...@ohif/extension-vtk@1.6.5) (2020-07-13)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.6.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.6.3...@ohif/extension-vtk@1.6.4) (2020-06-18)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.6.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.6.2...@ohif/extension-vtk@1.6.3) (2020-06-15)
+
+
+### Bug Fixes
+
+* 🐛 Disable seg panel when data for seg unavailable ([#1732](https://github.com/OHIF/Viewers/issues/1732)) ([698e900](https://github.com/OHIF/Viewers/commit/698e900b85121d3c2a46747c443ef69fb7a8c95b)), closes [#1728](https://github.com/OHIF/Viewers/issues/1728)
+
+
+
+
+
+## [1.6.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.6.1...@ohif/extension-vtk@1.6.2) (2020-06-05)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.6.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.6.0...@ohif/extension-vtk@1.6.1) (2020-06-04)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+# [1.6.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.5.6...@ohif/extension-vtk@1.6.0) (2020-06-04)
+
+
+### Features
+
+* 🎸 1729 - error boundary wrapper ([#1764](https://github.com/OHIF/Viewers/issues/1764)) ([c02b232](https://github.com/OHIF/Viewers/commit/c02b232b0cc24f38af5d5e3831d987d048e60ada))
+
+
+
+
+
+## [1.5.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.5.5...@ohif/extension-vtk@1.5.6) (2020-05-14)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.5.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.5.4...@ohif/extension-vtk@1.5.5) (2020-05-12)
+
+
+### Bug Fixes
+
+* 🐛 Fix seg color load ([#1724](https://github.com/OHIF/Viewers/issues/1724)) ([c4f84b1](https://github.com/OHIF/Viewers/commit/c4f84b1174d04ba84d37ed89b6d7ab541be28181))
+
+
+
+
+
+## [1.5.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.5.3...@ohif/extension-vtk@1.5.4) (2020-05-06)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
 ## [1.5.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.5.2...@ohif/extension-vtk@1.5.3) (2020-05-04)
 
 **Note:** Version bump only for package @ohif/extension-vtk

extensions/vtk/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-vtk",
-  "version": "1.5.3",
+  "version": "1.7.9",
   "description": "OHIF extension for VTK.js",
   "author": "OHIF",
   "license": "MIT",
@@ -33,9 +33,9 @@
     "@ohif/i18n": "^0.50.0",
     "@ohif/ui": "^0.50.0",
     "cornerstone-core": "^2.2.8",
-    "cornerstone-tools": "4.12.5",
+    "cornerstone-tools": "^4.20.1",
     "cornerstone-wado-image-loader": "^3.1.0",
-    "dcmjs": "^0.12.2",
+    "dcmjs": "0.16.3",
     "dicom-parser": "^1.8.3",
     "i18next": "^17.0.3",
     "i18next-browser-languagedetector": "^3.0.1",
@@ -50,12 +50,12 @@
   "dependencies": {
     "@babel/runtime": "^7.5.5",
     "lodash.throttle": "^4.1.1",
-    "react-vtkjs-viewport": "^0.8.3"
+    "react-vtkjs-viewport": "^0.10.4"
   },
   "devDependencies": {
-    "@ohif/core": "^2.9.3",
-    "@ohif/ui": "^1.4.4",
-    "cornerstone-tools": "4.12.5",
+    "@ohif/core": "^2.10.6",
+    "@ohif/ui": "^1.5.6",
+    "cornerstone-tools": "^4.20.1",
     "cornerstone-wado-image-loader": "^3.1.0",
     "dicom-parser": "^1.8.3",
     "gh-pages": "^2.0.1",

extensions/vtk/src/LoadingIndicator.js

@@ -35,7 +35,7 @@ class LoadingIndicator extends PureComponent {
           <div className="imageViewerLoadingIndicator loadingIndicator">
             <div className="indicatorContents">
               <p>
-                {this.props.t('Reformatting')}...
+                {this.props.t('Loading...')}
                 <i className="fa fa-spin fa-circle-o-notch fa-fw" />
                 {percComplete}
               </p>

extensions/vtk/src/OHIFVTKViewport.js

@@ -50,22 +50,25 @@ class OHIFVTKViewport extends Component {
     volumes: null,
     paintFilterLabelMapImageData: null,
     paintFilterBackgroundImageData: null,
+    percentComplete: 0,
+    isLoaded: false,
   };
 
   static propTypes = {
     viewportData: PropTypes.shape({
-      studies: PropTypes.array,
+      studies: PropTypes.array.isRequired,
       displaySet: PropTypes.shape({
-        StudyInstanceUID: PropTypes.string,
-        displaySetInstanceUID: PropTypes.string,
+        StudyInstanceUID: PropTypes.string.isRequired,
+        displaySetInstanceUID: PropTypes.string.isRequired,
         sopClassUIDs: PropTypes.arrayOf(PropTypes.string),
         SOPInstanceUID: PropTypes.string,
         frameIndex: PropTypes.number,
       }),
     }),
-    viewportIndex: PropTypes.number,
+    viewportIndex: PropTypes.number.isRequired,
     children: PropTypes.node,
     onScroll: PropTypes.func,
+    servicesManager: PropTypes.object.isRequired,
   };
 
   static defaultProps = {
@@ -156,6 +159,12 @@ class OHIFVTKViewport extends Component {
       const { activeLabelmapIndex } = brushStackState;
       const labelmap3D = brushStackState.labelmaps3D[activeLabelmapIndex];
 
+      this.segmentsDefaultProperties = labelmap3D.segmentsHidden.map(
+        isHidden => {
+          return { visible: !isHidden };
+        }
+      );
+
       const vtkLabelmapID = `${firstImageId}_${activeLabelmapIndex}`;
 
       if (labelmapCache[vtkLabelmapID]) {
@@ -339,7 +348,7 @@ class OHIFVTKViewport extends Component {
     this.setStateFromProps();
   }
 
-  componentDidUpdate(prevProps) {
+  componentDidUpdate(prevProps, prevState) {
     const { displaySet } = this.props.viewportData;
     const prevDisplaySet = prevProps.viewportData.displaySet;
 
@@ -356,34 +365,54 @@ class OHIFVTKViewport extends Component {
   loadProgressively(imageDataObject) {
     loadImageData(imageDataObject);
 
-    const { isLoading, insertPixelDataPromises } = imageDataObject;
-
-    const NumberOfFrames = insertPixelDataPromises.length;
+    const { isLoading, imageIds } = imageDataObject;
 
     if (!isLoading) {
       this.setState({ isLoaded: true });
       return;
     }
 
-    insertPixelDataPromises.forEach(promise => {
-      promise.then(numberProcessed => {
-        const percentComplete = Math.floor(
-          (numberProcessed * 100) / NumberOfFrames
-        );
+    const NumberOfFrames = imageIds.length;
 
-        if (percentComplete !== this.state.percentComplete) {
-          this.setState({
-            percentComplete,
+    const onPixelDataInsertedCallback = numberProcessed => {
+      const percentComplete = Math.floor(
+        (numberProcessed * 100) / NumberOfFrames
+      );
+
+      if (percentComplete !== this.state.percentComplete) {
+        this.setState({
+          percentComplete,
+        });
+      }
+    };
+
+    const onPixelDataInsertedErrorCallback = error => {
+      const { UINotificationService } = this.props.servicesManager.services;
+
+      if (!this.hasError) {
+        if (this.props.viewportIndex === 0) {
+          // Only show the notification from one viewport 1 in MPR2D.
+          UINotificationService.show({
+            title: 'MPR Load Error',
+            message: error.message,
+            type: 'error',
+            autoClose: false,
           });
         }
-      });
-    });
 
-    Promise.all(insertPixelDataPromises).then(() => {
+        this.hasError = true;
+      }
+    };
+
+    const onAllPixelDataInsertedCallback = () => {
       this.setState({
         isLoaded: true,
       });
-    });
+    };
+
+    imageDataObject.onPixelDataInserted(onPixelDataInsertedCallback);
+    imageDataObject.onAllPixelDataInserted(onAllPixelDataInsertedCallback);
+    imageDataObject.onPixelDataInsertedError(onPixelDataInsertedErrorCallback);
   }
 
   render() {
@@ -405,10 +434,6 @@ class OHIFVTKViewport extends Component {
 
     const style = { width: '100%', height: '100%', position: 'relative' };
 
-    const visible = configuration.renderFill || configuration.renderOutline;
-    const opacity = configuration.fillAlpha;
-    const outlineThickness = configuration.outlineThickness;
-
     return (
       <>
         <div style={style}>
@@ -428,10 +453,14 @@ class OHIFVTKViewport extends Component {
               dataDetails={this.state.dataDetails}
               labelmapRenderingOptions={{
                 colorLUT: this.state.labelmapColorLUT,
-                globalOpacity: opacity,
-                visible,
-                outlineThickness,
-                renderOutline: true,
+                globalOpacity: configuration.fillAlpha,
+                visible: configuration.renderFill,
+                outlineThickness: configuration.outlineWidth,
+                renderOutline: configuration.renderOutline,
+                segmentsDefaultProperties: this.segmentsDefaultProperties,
+                onNewSegmentationRequested: () => {
+                  this.setStateFromProps();
+                },
               }}
               onScroll={this.props.onScroll}
             />

extensions/vtk/src/commandsModule.js

@@ -5,10 +5,13 @@ import {
   vtkInteractorStyleMPRRotate,
   vtkSVGCrosshairsWidget,
 } from 'react-vtkjs-viewport';
-
+import { getImageData } from 'react-vtkjs-viewport';
+import { vec3 } from 'gl-matrix';
 import setMPRLayout from './utils/setMPRLayout.js';
 import setViewportToVTK from './utils/setViewportToVTK.js';
 import Constants from 'vtk.js/Sources/Rendering/Core/VolumeMapper/Constants.js';
+import OHIFVTKViewport from './OHIFVTKViewport';
+import vtkCoordinate from 'vtk.js/Sources/Rendering/Core/Coordinate';
 
 const { BlendMode } = Constants;
 
@@ -34,7 +37,6 @@ const commandsModule = ({ commandsManager }) => {
     }
 
     const displaySet = viewportSpecificData[activeViewportIndex];
-
     let api;
     if (!api) {
       try {
@@ -99,6 +101,20 @@ const commandsModule = ({ commandsManager }) => {
     });
   }
 
+  const _convertModelToWorldSpace = (position, vtkImageData) => {
+    const indexToWorld = vtkImageData.getIndexToWorld();
+    const pos = vec3.create();
+
+    position[0] += 0.5; /* Move to the centre of the voxel. */
+    position[1] += 0.5; /* Move to the centre of the voxel. */
+    position[2] += 0.5; /* Move to the centre of the voxel. */
+
+    vec3.set(pos, position[0], position[1], position[2]);
+    vec3.transformMat4(pos, pos, indexToWorld);
+
+    return pos;
+  };
+
   const actions = {
     getVtkApis: ({ index }) => {
       return apis[index];
@@ -124,6 +140,119 @@ const commandsModule = ({ commandsManager }) => {
 
       _setView(api, [0, 1, 0], [0, 0, 1]);
     },
+    requestNewSegmentation: async ({ viewports }) => {
+      const allViewports = Object.values(viewports.viewportSpecificData);
+      const promises = allViewports.map(async (viewport, viewportIndex) => {
+        let api = apis[viewportIndex];
+
+        if (!api) {
+          api = await _getActiveViewportVTKApi(viewports);
+          apis[viewportIndex] = api;
+        }
+
+        api.requestNewSegmentation();
+        api.updateImage();
+      });
+      await Promise.all(promises);
+    },
+    jumpToSlice: async ({
+      viewports,
+      studies,
+      StudyInstanceUID,
+      displaySetInstanceUID,
+      SOPClassUID,
+      SOPInstanceUID,
+      segmentNumber,
+      frameIndex,
+      frame,
+      done = () => { }
+    }) => {
+      let api = apis[viewports.activeViewportIndex];
+
+      if (!api) {
+        api = await _getActiveViewportVTKApi(viewports);
+        apis[viewports.activeViewportIndex] = api;
+      }
+
+      const stack = OHIFVTKViewport.getCornerstoneStack(
+        studies,
+        StudyInstanceUID,
+        displaySetInstanceUID,
+        SOPClassUID,
+        SOPInstanceUID,
+        frameIndex,
+      );
+
+      const imageDataObject = getImageData(stack.imageIds, displaySetInstanceUID);
+
+      let pixelIndex = 0;
+      let x = 0;
+      let y = 0;
+      let count = 0;
+
+      const rows = imageDataObject.dimensions[1];
+      const cols = imageDataObject.dimensions[0];
+
+      for (let j = 0; j < rows; j++) {
+        for (let i = 0; i < cols; i++) {
+          // [i, j] =
+          const pixel = frame.pixelData[pixelIndex];
+          if (pixel === segmentNumber) {
+            x += i;
+            y += j;
+            count++;
+          }
+          pixelIndex++;
+        }
+      }
+      x /= count;
+      y /= count;
+
+      const position = [x, y, frameIndex];
+      const worldPos = _convertModelToWorldSpace(position, imageDataObject.vtkImageData);
+
+      api.svgWidgets.crosshairsWidget.moveCrosshairs(worldPos, apis);
+      done();
+    },
+    setSegmentationConfiguration: async ({
+      viewports,
+      globalOpacity,
+      visible,
+      renderOutline,
+      outlineThickness,
+    }) => {
+      const allViewports = Object.values(viewports.viewportSpecificData);
+      const promises = allViewports.map(async (viewport, viewportIndex) => {
+        let api = apis[viewportIndex];
+
+        if (!api) {
+          api = await _getActiveViewportVTKApi(viewports);
+          apis[viewportIndex] = api;
+        }
+
+        api.setGlobalOpacity(globalOpacity);
+        api.setVisibility(visible);
+        api.setOutlineThickness(outlineThickness);
+        api.setOutlineRendering(renderOutline);
+        api.updateImage();
+      });
+      await Promise.all(promises);
+    },
+    setSegmentConfiguration: async ({ viewports, visible, segmentNumber }) => {
+      const allViewports = Object.values(viewports.viewportSpecificData);
+      const promises = allViewports.map(async (viewport, viewportIndex) => {
+        let api = apis[viewportIndex];
+
+        if (!api) {
+          api = await _getActiveViewportVTKApi(viewports);
+          apis[viewportIndex] = api;
+        }
+
+        api.setSegmentVisibility(segmentNumber, visible);
+        api.updateImage();
+      });
+      await Promise.all(promises);
+    },
     enableRotateTool: () => {
       apis.forEach(api => {
         const istyle = vtkInteractorStyleMPRRotate.newInstance();
@@ -280,6 +409,26 @@ const commandsModule = ({ commandsManager }) => {
   window.vtkActions = actions;
 
   const definitions = {
+    requestNewSegmentation: {
+      commandFn: actions.requestNewSegmentation,
+      storeContexts: ['viewports'],
+      options: {},
+    },
+    jumpToSlice: {
+      commandFn: actions.jumpToSlice,
+      storeContexts: ['viewports'],
+      options: {},
+    },
+    setSegmentationConfiguration: {
+      commandFn: actions.setSegmentationConfiguration,
+      storeContexts: ['viewports'],
+      options: {},
+    },
+    setSegmentConfiguration: {
+      commandFn: actions.setSegmentConfiguration,
+      storeContexts: ['viewports'],
+      options: {},
+    },
     axial: {
       commandFn: actions.axial,
       storeContexts: ['viewports'],

extensions/vtk/src/index.js

@@ -1,7 +1,9 @@
+import React from 'react';
 import asyncComponent from './asyncComponent.js';
 import commandsModule from './commandsModule.js';
 import toolbarModule from './toolbarModule.js';
 import withCommandsManager from './withCommandsManager.js';
+import { version } from '../package.json';
 // This feels weird
 // import loadLocales from './loadLocales';
 
@@ -14,9 +16,13 @@ const vtkExtension = {
    * Only required property. Should be a unique value across all extensions.
    */
   id: 'vtk',
+  version,
 
-  getViewportModule({ commandsManager }) {
-    return withCommandsManager(OHIFVTKViewport, commandsManager);
+  getViewportModule({ commandsManager, servicesManager }) {
+    const ExtendedVTKViewport = props => (
+      <OHIFVTKViewport {...props} servicesManager={servicesManager} />
+    );
+    return withCommandsManager(ExtendedVTKViewport, commandsManager);
   },
   getToolbarModule() {
     return toolbarModule;

netlify-lerna-cache.sh

@@ -0,0 +1,26 @@
+#!/bin/sh
+NODE_MODULES_CACHE="./node_modules"
+LERNA_CACHE="$NODE_MODULES_CACHE/lerna-cache"
+
+echo "Running netlify-lerna-cache.sh"
+mkdir -p "$NODE_MODULES_CACHE/lerna-cache"
+
+cache_deps() {
+    PACKAGES=$(ls -1 $1)
+
+    for PKG in $PACKAGES
+    do
+        PKG_NODE_MODULES="$1/$PKG/node_modules"
+        if [ -d $PKG_NODE_MODULES ];
+        then
+            mv $PKG_NODE_MODULES $LERNA_CACHE/$PKG
+            echo "Cached node modules for $PKG"
+        else
+            echo "Unable to cache node modules for $PKG"
+        fi
+    done
+}
+
+cache_deps platform
+cache_deps extensions
+cache_deps modes

netlify-lerna-restore.sh

@@ -0,0 +1,27 @@
+#!/bin/sh
+NODE_MODULES_CACHE="./node_modules"
+LERNA_CACHE="$NODE_MODULES_CACHE/lerna-cache"
+
+echo "Running netlify-lerna-restore.sh"
+mkdir -p "$NODE_MODULES_CACHE/lerna-cache"
+echo "$NODE_MODULES_CACHE/lerna-cache/*"
+
+restore_deps() {
+    PACKAGES=$(ls -1 $1)
+
+    for PKG in $PACKAGES
+    do
+        PKG_CACHE="$LERNA_CACHE/$PKG"
+        if [ -d $PKG_CACHE ];
+        then
+            mv $PKG_CACHE $1/$PKG/node_modules
+            echo "Restored node modules for $PKG"
+        else
+            echo "Unable to restore cache for $PKG"
+        fi
+    done
+}
+
+restore_deps platform
+restore_deps extensions
+restore_deps modes

netlify.toml

@@ -8,6 +8,11 @@
 # managed by CircleCI and deployed to our Google Hosting
 #
 
+[build]
+  base = ""
+  publish = ".netlify/www/"
+  command = "chmod +x .netlify/build-deploy-preview.sh && .netlify/build-deploy-preview.sh"
+
 # NODE_VERSION in root `.nvmrc` takes priority
 # YARN_FLAGS: https://www.netlify.com/docs/build-gotchas/#yarn
 [build.environment]
@@ -16,19 +21,13 @@
   YARN_VERSION = "1.17.3"
   RUBY_VERSION = "2.6.2"
   YARN_FLAGS = "--no-ignore-optional --pure-lockfile"
+  NETLIFY_RESTORE = "1"
 
 # Production context: all deploys from the Production branch set in your site's
 # deploy contexts will inherit these settings.
 [context.production]
   ignore = "exit 0" # Never build production; We'll let our CI do that
 
-# Deploy Preview context: all deploys generated from a pull/merge request will
-# inherit these settings.
-[context.deploy-preview]
-  base = ""
-  publish = ".netlify/www/"
-  command = "chmod +x .netlify/build-deploy-preview.sh && .netlify/build-deploy-preview.sh"
-
 [[headers]]
   # Define which paths this specific [[headers]] block will cover.
   for = "/*"

package.json

@@ -34,6 +34,8 @@
     "see-changed": "lerna changed",
     "docs:publish": "chmod +x ./build-and-publish-docs.sh && ./build-and-publish-docs.sh",
     "release": "yarn run lerna:version && yarn run lerna:publish",
+    "lerna:cache": "./netlify-lerna-cache.sh",
+    "lerna:restore": "./netlify-lerna-restore.sh",
     "lerna:version": "npx lerna version prerelease --force-publish",
     "lerna:publish": "lerna publish from-package --canary --dist-tag canary",
     "link-list": "npm ls --depth=0 --link=true"

platform/core/CHANGELOG.md

@@ -3,6 +3,174 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [2.10.6](https://github.com/OHIF/Viewers/compare/@ohif/core@2.10.5...@ohif/core@2.10.6) (2020-09-30)
+
+
+### Bug Fixes
+
+* use SeriesMetadata method instead of property in findMostRecentStructuredReport ([#2038](https://github.com/OHIF/Viewers/issues/2038)) ([91364db](https://github.com/OHIF/Viewers/commit/91364db8820efc86665db258d0044c16fb3e2c87)), closes [#1714](https://github.com/OHIF/Viewers/issues/1714)
+
+
+
+
+
+## [2.10.5](https://github.com/OHIF/Viewers/compare/@ohif/core@2.10.4...@ohif/core@2.10.5) (2020-09-10)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.10.4](https://github.com/OHIF/Viewers/compare/@ohif/core@2.10.3...@ohif/core@2.10.4) (2020-09-03)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.10.3](https://github.com/OHIF/Viewers/compare/@ohif/core@2.10.2...@ohif/core@2.10.3) (2020-09-03)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.10.2](https://github.com/OHIF/Viewers/compare/@ohif/core@2.10.1...@ohif/core@2.10.2) (2020-09-02)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.10.1](https://github.com/OHIF/Viewers/compare/@ohif/core@2.10.0...@ohif/core@2.10.1) (2020-08-28)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+# [2.10.0](https://github.com/OHIF/Viewers/compare/@ohif/core@2.9.14...@ohif/core@2.10.0) (2020-08-18)
+
+
+### Features
+
+* 🎸 Update react-vtkjs-viewport usage to use requestPool ([#1984](https://github.com/OHIF/Viewers/issues/1984)) ([bb5f30c](https://github.com/OHIF/Viewers/commit/bb5f30ce2a0192d2e021beaaadfff22fd38e17b9))
+
+
+
+
+
+## [2.9.14](https://github.com/OHIF/Viewers/compare/@ohif/core@2.9.13...@ohif/core@2.9.14) (2020-08-10)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.9.13](https://github.com/OHIF/Viewers/compare/@ohif/core@2.9.12...@ohif/core@2.9.13) (2020-07-22)
+
+
+### Bug Fixes
+
+* Switch DICOMFileUploader to use the UIModalService ([#1904](https://github.com/OHIF/Viewers/issues/1904)) ([7772fee](https://github.com/OHIF/Viewers/commit/7772fee21ae6a65994e1251e2f1d2554b47781be))
+
+
+
+
+
+## [2.9.12](https://github.com/OHIF/Viewers/compare/@ohif/core@2.9.11...@ohif/core@2.9.12) (2020-07-13)
+
+
+### Bug Fixes
+
+* 🐛 - Put guards in all places that a cornerstone re-render ([#1899](https://github.com/OHIF/Viewers/issues/1899)) ([451f7ea](https://github.com/OHIF/Viewers/commit/451f7eab9258e7a193eb362e0926b13aedc4b3c9))
+
+
+
+
+
+## [2.9.11](https://github.com/OHIF/Viewers/compare/@ohif/core@2.9.10...@ohif/core@2.9.11) (2020-07-13)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.9.10](https://github.com/OHIF/Viewers/compare/@ohif/core@2.9.9...@ohif/core@2.9.10) (2020-07-13)
+
+
+### Bug Fixes
+
+* 🐛 Fix RT Panel hide/show and Fix looping load errors ([#1877](https://github.com/OHIF/Viewers/issues/1877)) ([e7cc735](https://github.com/OHIF/Viewers/commit/e7cc735c03d02eeb0d3af4ba02c15ed4f81bbec2))
+
+
+
+
+
+## [2.9.9](https://github.com/OHIF/Viewers/compare/@ohif/core@2.9.8...@ohif/core@2.9.9) (2020-06-18)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.9.8](https://github.com/OHIF/Viewers/compare/@ohif/core@2.9.7...@ohif/core@2.9.8) (2020-06-15)
+
+
+### Bug Fixes
+
+* 🐛 Disable seg panel when data for seg unavailable ([#1732](https://github.com/OHIF/Viewers/issues/1732)) ([698e900](https://github.com/OHIF/Viewers/commit/698e900b85121d3c2a46747c443ef69fb7a8c95b)), closes [#1728](https://github.com/OHIF/Viewers/issues/1728)
+
+
+
+
+
+## [2.9.7](https://github.com/OHIF/Viewers/compare/@ohif/core@2.9.6...@ohif/core@2.9.7) (2020-06-04)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.9.6](https://github.com/OHIF/Viewers/compare/@ohif/core@2.9.5...@ohif/core@2.9.6) (2020-05-14)
+
+
+### Bug Fixes
+
+* 🐛 Load default display set when no time metadata ([#1684](https://github.com/OHIF/Viewers/issues/1684)) ([f7b8b6a](https://github.com/OHIF/Viewers/commit/f7b8b6a41c4626084ef56b0fdf7363e914b143c4)), closes [#1683](https://github.com/OHIF/Viewers/issues/1683)
+
+
+
+
+
+## [2.9.5](https://github.com/OHIF/Viewers/compare/@ohif/core@2.9.4...@ohif/core@2.9.5) (2020-05-12)
+
+
+### Bug Fixes
+
+* 🐛 Fix seg color load ([#1724](https://github.com/OHIF/Viewers/issues/1724)) ([c4f84b1](https://github.com/OHIF/Viewers/commit/c4f84b1174d04ba84d37ed89b6d7ab541be28181))
+
+
+
+
+
+## [2.9.4](https://github.com/OHIF/Viewers/compare/@ohif/core@2.9.3...@ohif/core@2.9.4) (2020-05-06)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
 ## [2.9.3](https://github.com/OHIF/Viewers/compare/@ohif/core@2.9.2...@ohif/core@2.9.3) (2020-05-04)
 
 

platform/core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/core",
-  "version": "2.9.3",
+  "version": "2.10.6",
   "description": "Generic business logic for web-based medical imaging applications",
   "author": "OHIF Core Team",
   "license": "MIT",
@@ -32,14 +32,14 @@
   },
   "peerDependencies": {
     "cornerstone-core": "^2.2.8",
-    "cornerstone-tools": "4.12.5",
+    "cornerstone-tools": "^4.20.1",
     "cornerstone-wado-image-loader": "^3.1.0",
     "dicom-parser": "^1.8.3"
   },
   "dependencies": {
     "@babel/runtime": "^7.5.5",
     "ajv": "^6.10.0",
-    "dcmjs": "^0.12.2",
+    "dcmjs": "0.16.3",
     "dicomweb-client": "^0.6.0",
     "immer": "6.0.2",
     "isomorphic-base64": "^1.0.2",

platform/core/src/DICOMSR/utils/findMostRecentStructuredReport.js

@@ -13,7 +13,7 @@ const findMostRecentStructuredReport = studies => {
       // Skip series that may not have instances yet
       // This can happen if we have retrieved just the initial
       // details about the series via QIDO-RS, but not the full metadata
-      if (!series.instances.length) {
+      if (!series || series.getInstanceCount() === 0) {
         return;
       }
 

platform/core/src/classes/OHIFStudyMetadataSource.js

@@ -54,9 +54,6 @@ export class OHIFStudyMetadataSource extends StudyMetadataSource {
           // Get Study display sets
           const displaySets = studyMetadata.createDisplaySets();
 
-          // Set studyMetadata display sets
-          studyMetadata.setDisplaySets(displaySets);
-
           OHIFStudyMetadataSource._updateStudyCollections(studyMetadata);
           resolve(studyMetadata);
         })

platform/core/src/classes/metadata/StudyMetadata.js

@@ -10,8 +10,8 @@ import { api } from 'dicomweb-client';
 // - createStacks
 import { isImage } from '../../utils/isImage';
 import isDisplaySetReconstructable from '../../utils/isDisplaySetReconstructable';
-import isLowPriorityModality from '../../utils/isLowPriorityModality';
 import errorHandler from '../../errorHandler';
+import isLowPriorityModality from '../../utils/isLowPriorityModality';
 
 export class StudyMetadata extends Metadata {
   constructor(data, uid) {
@@ -135,12 +135,15 @@ export class StudyMetadata extends Metadata {
         study,
         sopClassUIDs
       );
+
       if (displaySet) {
         displaySet.sopClassModule = true;
 
-        displaySet.isDerived
-          ? this._addDerivedDisplaySet(displaySet)
-          : displaySets.push(displaySet);
+        if (displaySet.isDerived) {
+          this._addDerivedDisplaySet(displaySet);
+        }
+
+        displaySets.push(displaySet);
 
         return displaySets;
       }
@@ -215,6 +218,14 @@ export class StudyMetadata extends Metadata {
     // TODO -> Get x Modality by referencedSeriesInstanceUid, FoR, etc.
   }
 
+  /**
+   * Adds the displaySets to the studies list of derived displaySets.
+   * @param {array} displaySets The displaySets array to append to the derived displaysets list.
+   */
+  _addDerivedDisplaySets(displaySets) {
+    displaySets.map(displaySet => this._derivedDisplaySets.push(displaySet));
+  }
+
   /**
    * Returns a list of derived datasets in the study, filtered by the given filter.
    * @param {object} filter An object containing search filters
@@ -263,7 +274,7 @@ export class StudyMetadata extends Metadata {
       filteredDerivedDisplaySets = filteredDerivedDisplaySets.filter(
         displaySet =>
           displaySet.ReferencedFrameOfReferenceUID ===
-          ReferencedFrameOfReferenceUID
+          referencedFrameOfReferenceUID
       );
     }
 
@@ -297,14 +308,10 @@ export class StudyMetadata extends Metadata {
         series
       );
 
-      displaySets.push(...displaySetsForSeries);
+      displaySetsForSeries.forEach(ds => this._insertDisplaySet(ds));
     });
 
-    return sortDisplaySetList(displaySets);
-  }
-
-  sortDisplaySets() {
-    sortDisplaySetList(this._displaySets);
+    return this._displaySets;
   }
 
   /**
@@ -335,25 +342,9 @@ export class StudyMetadata extends Metadata {
       this.addDisplaySet(displaySet);
     });
 
-    this.sortDisplaySets();
-
     return true;
   }
 
-  /**
-   * Set display sets
-   * @param {Array} displaySets Array of display sets (ImageSet[])
-   */
-  setDisplaySets(displaySets) {
-    if (Array.isArray(displaySets) && displaySets.length > 0) {
-      // TODO: This is weird, can we just switch it to writable: true?
-      this._displaySets.splice(0);
-
-      displaySets.forEach(displaySet => this.addDisplaySet(displaySet));
-      this.sortDisplaySets();
-    }
-  }
-
   /**
    * Add a single display set to the list
    * @param {Object} displaySet Display set object
@@ -361,7 +352,7 @@ export class StudyMetadata extends Metadata {
    */
   addDisplaySet(displaySet) {
     if (displaySet instanceof ImageSet || displaySet.sopClassModule) {
-      this._displaySets.push(displaySet);
+      this._insertDisplaySet(displaySet);
       return true;
     }
     return false;
@@ -382,6 +373,96 @@ export class StudyMetadata extends Metadata {
     }
   }
 
+  /**
+   * Insert the displaySet so that the list has an increasing SeriesNumber,
+   * with the most recent series first for displaySets with the same SeriesNumber.
+   *
+   * If the displaySet is low priority, the same logic is applied, but is sorted within a sub list
+   * At the end of the list, where all low priority data is found.
+   */
+  _insertDisplaySet(displaySet) {
+    const { SeriesNumber } = displaySet;
+    const displaySets = this._displaySets;
+    let insertIndex = displaySets.length;
+    let firstIndexWithSameSeriesNumber;
+
+    // If low priority, start search from next low priority.
+    if (isLowPriorityModality(displaySet.Modality)) {
+      let startingIndex;
+
+      // Find where the first low priority displaySet is.
+      for (let i = 0; i < displaySets.length; i++) {
+        if (isLowPriorityModality(displaySets[i].Modality)) {
+          startingIndex = i;
+          break;
+        }
+      }
+
+      if (!startingIndex) {
+        startingIndex = displaySets.length;
+      }
+
+      // Find the correct SeriesNumber location to insert within the low priority
+      // Modality displaySets
+      for (let i = startingIndex; i < displaySets.length; i++) {
+        if (
+          displaySets[i].SeriesNumber === SeriesNumber &&
+          !firstIndexWithSameSeriesNumber
+        ) {
+          firstIndexWithSameSeriesNumber = i;
+        }
+
+        if (displaySets[i].SeriesNumber > SeriesNumber) {
+          insertIndex = i;
+          break;
+        }
+      }
+    } else {
+      // Find correct SeriesNumber to insert or where the low priority modalities start.
+      for (let i = 0; i < displaySets.length; i++) {
+        if (
+          displaySets[i].SeriesNumber === SeriesNumber &&
+          !firstIndexWithSameSeriesNumber
+        ) {
+          firstIndexWithSameSeriesNumber = i;
+        }
+
+        if (
+          displaySets[i].SeriesNumber > SeriesNumber ||
+          isLowPriorityModality(displaySets[i].Modality)
+        ) {
+          insertIndex = i;
+          break;
+        }
+      }
+    }
+
+    // If we have multiple displaySets with the same series number, find the insert position based on
+    // SeriesDate and SeriesTime.
+    if (firstIndexWithSameSeriesNumber !== undefined) {
+      // If no SeriesDate, is just a placeholder displaySet, just insert anywhere, it will be re-added later.
+      if (displaySet.SeriesDate) {
+        const seriesDateTime = `${displaySet.SeriesDate}${displaySet.SeriesTime}`;
+
+        for (let i = firstIndexWithSameSeriesNumber; i < insertIndex; i++) {
+          const displaySetI = displaySets[i];
+
+          if (
+            displaySetI.SeriesDate &&
+            `${displaySetI.SeriesDate}${displaySetI.SeriesTime}` <
+              seriesDateTime
+          ) {
+            insertIndex = i;
+            break;
+          }
+        }
+      }
+    }
+
+    this._displaySets.splice(insertIndex, 0, displaySet);
+    this.displaySets = this._displaySets;
+  }
+
   /**
    * Search the associated display sets using the supplied callback as criteria. The callback is passed
    * two arguments: display set (an ImageSet instance) and index (the integer
@@ -537,49 +618,6 @@ export class StudyMetadata extends Metadata {
     return this._series.indexOf(series);
   }
 
-  /**
-   * It sorts the series based on display sets order. Each series must be an instance
-   * of SeriesMetadata and each display sets must be an instance of ImageSet.
-   * Useful example of usage:
-   *     Study data provided by backend does not sort series at all and client-side
-   *     needs series sorted by the same criteria used for sorting display sets.
-   */
-  sortSeriesByDisplaySets() {
-    // Object for mapping display sets' index by SeriesInstanceUID
-    const displaySetsMapping = {};
-
-    // Loop through each display set to create the mapping
-    this.forEachDisplaySet((displaySet, index) => {
-      if (!(displaySet instanceof ImageSet)) {
-        throw new OHIFError(
-          `StudyMetadata::sortSeriesByDisplaySets display set at index ${index} is not an instance of ImageSet`
-        );
-      }
-
-      // In case of multiframe studies, just get the first index occurence
-      if (displaySetsMapping[displaySet.SeriesInstanceUID] === void 0) {
-        displaySetsMapping[displaySet.SeriesInstanceUID] = index;
-      }
-    });
-
-    // Clone of actual series
-    const actualSeries = this.getSeries();
-
-    actualSeries.forEach((series, index) => {
-      if (!(series instanceof SeriesMetadata)) {
-        throw new OHIFError(
-          `StudyMetadata::sortSeriesByDisplaySets series at index ${index} is not an instance of SeriesMetadata`
-        );
-      }
-
-      // Get the new series index
-      const seriesIndex = displaySetsMapping[series.getSeriesInstanceUID()];
-
-      // Update the series object with the new series position
-      this._series[seriesIndex] = series;
-    });
-  }
-
   /**
    * Compares the current study instance with another one.
    * @param {StudyMetadata} study An instance of the StudyMetadata class.
@@ -854,53 +892,3 @@ function _getDisplaySetFromSopClassModule(
   }
   return displaySet;
 }
-
-/**
- * Sort series primarily by Modality (i.e., series with references to other
- * series like SEG, KO or PR are grouped in the end of the list) and then by
- * series number:
- *
- *  --------
- * | CT #3  |
- * | CT #4  |
- * | CT #5  |
- *  --------
- * | SEG #1 |
- * | SEG #2 |
- *  --------
- *
- * @param {*} a - DisplaySet
- * @param {*} b - DisplaySet
- */
-
-function seriesSortingCriteria(a, b) {
-  const isLowPriorityA = isLowPriorityModality(a.Modality);
-  const isLowPriorityB = isLowPriorityModality(b.Modality);
-  if (!isLowPriorityA && isLowPriorityB) {
-    return -1;
-  }
-  if (isLowPriorityA && !isLowPriorityB) {
-    return 1;
-  }
-  return sortBySeriesNumber(a, b);
-}
-
-/**
- * Sort series by series number. Series with low
- * @param {*} a - DisplaySet
- * @param {*} b - DisplaySet
- */
-function sortBySeriesNumber(a, b) {
-  const seriesNumberAIsGreaterOrUndefined =
-    a.SeriesNumber > b.SeriesNumber || (!a.SeriesNumber && b.SeriesNumber);
-
-  return seriesNumberAIsGreaterOrUndefined ? 1 : -1;
-}
-
-/**
- * Sorts a list of display set objects
- * @param {Array} list A list of display sets to be sorted
- */
-function sortDisplaySetList(list) {
-  return list.sort(seriesSortingCriteria);
-}

platform/core/src/extensions/ExtensionManager.js

@@ -2,14 +2,16 @@ import MODULE_TYPES from './MODULE_TYPES.js';
 import log from './../log.js';
 
 export default class ExtensionManager {
-  constructor({ commandsManager, servicesManager, appConfig = {} }) {
+  constructor({ commandsManager, servicesManager, api, appConfig = {} }) {
     this.modules = {};
     this.registeredExtensionIds = [];
+    this.registeredExtensionVesions = {};
     this.moduleTypeNames = Object.values(MODULE_TYPES);
     //
     this._commandsManager = commandsManager;
     this._servicesManager = servicesManager;
     this._appConfig = appConfig;
+    this._api = api;
 
     this.moduleTypeNames.forEach(moduleType => {
       this.modules[moduleType] = [];
@@ -50,6 +52,7 @@ export default class ExtensionManager {
     }
 
     let extensionId = extension.id;
+    const version = extension.version;
 
     if (!extensionId) {
       extensionId = Math.random()
@@ -97,6 +100,8 @@ export default class ExtensionManager {
 
     // Track extension registration
     this.registeredExtensionIds.push(extensionId);
+
+    this.registeredExtensionVesions[extensionId] = version;
   }
 
   /**
@@ -119,6 +124,8 @@ export default class ExtensionManager {
         commandsManager: this._commandsManager,
         appConfig: this._appConfig,
         configuration,
+        api: this._api,
+        extensionManager: this,
       });
 
       if (!extensionModule) {

platform/core/src/extensions/ExtensionManager.test.js

@@ -184,6 +184,8 @@ describe('ExtensionManager.js', () => {
             commandsManager,
             appConfig,
             configuration: extensionConfiguration,
+            api: undefined,
+            extensionManager,
           });
         }
       });
@@ -226,7 +228,7 @@ describe('ExtensionManager.js', () => {
           return {
             definitions: {
               exampleDefinition: {
-                commandFn: () => { },
+                commandFn: () => {},
                 storeContexts: [],
                 options: {},
               },