chore(version): Update package versions [skip ci]

Co-authored-by: Joe Boccanfuso <joe.boccanfuso@radicalimaging.com>

.circleci/config.yml

@@ -269,8 +269,7 @@ jobs:
             git config --global user.name "ohif-bot"
       - run:
           name: Authenticate with NPM registry
-          command:
-            echo "//registry.npmjs.org/:_authToken=$NPM_TOKEN" > ~/repo/.npmrc
+          command: echo "//registry.npmjs.org/:_authToken=$NPM_TOKEN" > ~/repo/.npmrc
       - run:
           name: Increase the event emitter limit
           command: |
@@ -289,8 +288,7 @@ jobs:
             node ./publish-version.mjs
       - run:
           name: Again set the NPM registry (was deleted in the version script)
-          command:
-            echo "//registry.npmjs.org/:_authToken=$NPM_TOKEN" > ~/repo/.npmrc
+          command: echo "//registry.npmjs.org/:_authToken=$NPM_TOKEN" > ~/repo/.npmrc
       - run:
           name: publish package dist
           command: |
@@ -337,8 +335,7 @@ jobs:
       - setup_remote_docker:
           docker_layer_caching: false
       - run:
-          name:
-            Build and push Docker image from the master branch (beta releases)
+          name: Build and push Docker image from the master branch (beta releases)
           command: |
             echo $(ls -l)
 
@@ -417,8 +414,8 @@ workflows:
           store_artifacts: false
           working_directory: platform/app
           build:
-            yarn test:data && npx cross-env QUICK_BUILD=true
-            APP_CONFIG=config/dicomweb-server.js yarn run build
+            yarn test:data && npx cross-env QUICK_BUILD=true APP_CONFIG=config/dicomweb-server.js
+            yarn run build
           # start server --> verify running --> percy + chrome + cypress
           command: yarn run test:e2e:dist
           cache-key: 'yarn-packages-{{ checksum "yarn.lock" }}'

.docker/Viewer-v3.x/default.conf.template

@@ -1,5 +1,6 @@
 server {
-  listen ${PORT};
+  listen ${PORT} default_server;
+  listen [::]:${PORT} default_server;
   location / {
     root   /usr/share/nginx/html;
     index  index.html index.htm;

.docker/Viewer-v3.x/default.ssl.conf.template

@@ -0,0 +1,22 @@
+server {
+  listen ${SSL_PORT} ssl http2 default_server;
+  listen [::]:${SSL_PORT} ssl http2 default_server;
+  ssl_certificate /etc/ssl/certs/ssl-certificate.crt;
+  ssl_certificate_key /etc/ssl/private/ssl-private-key.key;
+  location / {
+    root   /usr/share/nginx/html;
+    index  index.html index.htm;
+    try_files $uri $uri/ /index.html;
+    add_header Cross-Origin-Opener-Policy same-origin;
+    add_header Cross-Origin-Embedder-Policy require-corp;
+    add_header Cross-Origin-Resource-Policy same-origin;
+    proxy_set_header Host $host;
+    proxy_set_header X-Real-IP $remote_addr;
+    proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+    proxy_set_header X-Forwarded-Proto $http_x_forwarded_proto;
+  }
+  error_page   500 502 503 504  /50x.html;
+  location = /50x.html {
+    root   /usr/share/nginx/html;
+  }
+}

.docker/Viewer-v3.x/entrypoint.sh

@@ -1,6 +1,16 @@
 #!/bin/sh
 
-envsubst '${PORT}' < /usr/src/default.conf.template > /etc/nginx/conf.d/default.conf
+if [ -n "$SSL_PORT" ]
+  then
+    envsubst '${SSL_PORT}:${PORT}' < /usr/src/default.ssl.conf.template > /etc/nginx/conf.d/default.conf
+  else
+    envsubst '${PORT}' < /usr/src/default.conf.template > /etc/nginx/conf.d/default.conf
+fi
+
+if [ -n "$APP_CONFIG" ]
+  then
+    echo "$APP_CONFIG" > /usr/share/nginx/html/app-config.js
+fi
 
 if [ -n "$CLIENT_ID" ] || [ -n "$HEALTHCARE_API_ENDPOINT" ]
   then

.dockerignore

@@ -1,6 +1,12 @@
 # Reduces size of context and hides
 # files from Docker (can't COPY or ADD these)
 
+# Note that typically the Docker context for various OHIF containers is the
+# directory of this file (i.e. the root of the source). As such, this is
+# the .dockerignore file for ALL Docker containers that are built. For example,
+# the Docker containers built from the recipes in ./platform/app/.recipes will
+# have this file as their .dockerignore.
+
 # Output
 dist/
 build/
@@ -28,3 +34,4 @@ dockerfile
 .vscode/
 coverage/
 docs/
+testdata/

.eslintrc.json

@@ -1,10 +1,5 @@
 {
-  "plugins": [
-    "@typescript-eslint",
-    "import",
-    "eslint-plugin-tsdoc",
-    "prettier"
-  ],
+  "plugins": ["@typescript-eslint", "import", "eslint-plugin-tsdoc", "prettier"],
   "extends": [
     "react-app",
     "eslint:recommended",
@@ -21,6 +16,10 @@
       "version": "detect"
     }
   },
+  "rules": {
+    // Enforce consistent brace style for all control statements for readability
+    "curly": "error"
+  },
   "globals": {
     "cy": true,
     "before": true,

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -39,8 +39,7 @@ body:
     attributes:
       label: The current behavior
       description:
-        'A clear and concise description of what happens instead of the expected
-        behavior.'
+        'A clear and concise description of what happens instead of the expected behavior.'
     validations:
       required: true
 
@@ -48,8 +47,7 @@ body:
     id: expected_behavior
     attributes:
       label: The expected behavior
-      description:
-        'A clear and concise description of what you expected to happen.'
+      description: 'A clear and concise description of what you expected to happen.'
     validations:
       required: true
 
@@ -81,6 +79,6 @@ body:
   - type: markdown
     attributes:
       value: >
-        > :warning: Reports we cannot reproduce are at risk of being marked
-        stale and > closed. The more information you can provide, the more
-        likely we are to look > into and address your issue.
+        > :warning: Reports we cannot reproduce are at risk of being marked stale and > closed. The
+        more information you can provide, the more likely we are to look > into and address your
+        issue.

.github/ISSUE_TEMPLATE/feature-request.yml

@@ -20,17 +20,15 @@ body:
     attributes:
       label: 'What feature or change would you like to see made?'
       description:
-        'Please include as much detail as possible including possibly mock up
-        screen shots, workflow or logic flow diagrams etc.'
+        'Please include as much detail as possible including possibly mock up screen shots, workflow
+        or logic flow diagrams etc.'
       placeholder: '...'
     validations:
       required: true
   - type: textarea
     attributes:
       label: 'Why should we prioritize this feature?'
-      description:
-        'Discuss if and how the requested feature interacts with existing
-        features.'
+      description: 'Discuss if and how the requested feature interacts with existing features.'
       placeholder: '...'
     validations:
       required: true

.github/stale.yml

@@ -19,8 +19,7 @@ exemptLabels:
 staleLabel: 'Stale :baguette_bread:'
 # Comment to post when marking an issue as stale. Set to `false` to disable
 markComment: >
-  This issue has been automatically marked as stale because it has not had
-  recent activity. It will be closed if no further activity occurs. Thank you
-  for your contributions.
+  This issue has been automatically marked as stale because it has not had recent activity. It will
+  be closed if no further activity occurs. Thank you for your contributions.
 # Comment to post when closing a stale issue. Set to `false` to disable
 closeComment: false

.gitmodules

@@ -1,3 +1,4 @@
 [submodule "testdata"]
 	path = testdata
 	url = https://github.com/OHIF/viewer-testdata-dicomweb.git
+	branch = main

.netlify/www/index.html

@@ -1,23 +1,21 @@
 <html>
+  <head>
+    <title>OHIF Viewer: Deploy Preview</title>
+  </head>
 
-<head>
-  <title>OHIF Viewer: Deploy Preview</title>
-</head>
-
-<body>
-  <h1>Index of Previews</h1>
-
-  <ul>
-    <li>
-      <a href="/pwa">OHIF Viewer</a>
-    </li>
-    <li>
-      <a href="/docs">Documentation</a>
-    </li>
-    <li>
-      <a href="/ui">UI: Component Library</a>
-    </li>
-  </ul>
-</body>
+  <body>
+    <h1>Index of Previews</h1>
 
+    <ul>
+      <li>
+        <a href="/pwa">OHIF Viewer</a>
+      </li>
+      <li>
+        <a href="/docs">Documentation</a>
+      </li>
+      <li>
+        <a href="/ui">UI: Component Library</a>
+      </li>
+    </ul>
+  </body>
 </html>

.prettierrc

@@ -1,9 +1,12 @@
 {
+  "plugins": ["prettier-plugin-tailwindcss"],
   "trailingComma": "es5",
-  "printWidth": 80,
+  "printWidth": 100,
   "proseWrap": "always",
   "tabWidth": 2,
   "semi": true,
   "singleQuote": true,
-  "arrowParens": "avoid"
+  "arrowParens": "avoid",
+  "singleAttributePerLine": true,
+  "endOfLine": "auto"
 }

.webpack/helpers/excludeNodeModulesExcept.js

@@ -5,11 +5,11 @@ function excludeNodeModulesExcept(modules) {
   if (pathSep == '\\')
     // must be quoted for use in a regexp:
     pathSep = '\\\\';
-  var moduleRegExps = modules.map(function(modName) {
+  var moduleRegExps = modules.map(function (modName) {
     return new RegExp('node_modules' + pathSep + modName);
   });
 
-  return function(modulePath) {
+  return function (modulePath) {
     if (/node_modules/.test(modulePath)) {
       for (var i = 0; i < moduleRegExps.length; i++)
         if (moduleRegExps[i].test(modulePath)) return false;

.webpack/rules/cssToJavaScript.js

@@ -1,9 +1,7 @@
 const autoprefixer = require('autoprefixer');
 const path = require('path');
 const tailwindcss = require('tailwindcss');
-const tailwindConfigPath = path.resolve(
-  '../../platform/app/tailwind.config.js'
-);
+const tailwindConfigPath = path.resolve('../../platform/app/tailwind.config.js');
 const MiniCssExtractPlugin = require('mini-css-extract-plugin');
 const devMode = process.env.NODE_ENV !== 'production';
 

.webpack/rules/transpileJavaScript.js

@@ -33,7 +33,11 @@ function transpileJavaScript(mode) {
       rootMode: 'upward',
       envName: mode,
       cacheCompression: false,
-      cacheDirectory: true,
+      // Note: This was causing a lot of issues with yarn link of the cornerstone
+      // only set this to true if you don't have a yarn link to external libs
+      // otherwise expect the lib changes not to be reflected in the dev server
+      // as it will be cached
+      cacheDirectory: false,
     },
   };
 }

.webpack/webpack.base.js

@@ -7,8 +7,7 @@ const fs = require('fs');
 const webpack = require('webpack');
 
 // ~~ PLUGINS
-const BundleAnalyzerPlugin = require('webpack-bundle-analyzer')
-  .BundleAnalyzerPlugin;
+const BundleAnalyzerPlugin = require('webpack-bundle-analyzer').BundleAnalyzerPlugin;
 const TerserJSPlugin = require('terser-webpack-plugin');
 
 // ~~ PackageJSON
@@ -26,11 +25,9 @@ const QUICK_BUILD = process.env.QUICK_BUILD;
 const BUILD_NUM = process.env.CIRCLE_BUILD_NUM || '0';
 
 // read from ../version.txt
-const VERSION_NUMBER =
-  fs.readFileSync(path.join(__dirname, '../version.txt'), 'utf8') || '';
+const VERSION_NUMBER = fs.readFileSync(path.join(__dirname, '../version.txt'), 'utf8') || '';
 
-const COMMIT_HASH =
-  fs.readFileSync(path.join(__dirname, '../commit.txt'), 'utf8') || '';
+const COMMIT_HASH = fs.readFileSync(path.join(__dirname, '../commit.txt'), 'utf8') || '';
 
 //
 dotenv.config();
@@ -73,21 +70,17 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
       children: false,
       warnings: true,
     },
-    devServer: {
-      open: true,
-      port: 3000,
-      historyApiFallback: true,
-      headers: {
-        'Cross-Origin-Embedder-Policy': 'require-corp',
-        'Cross-Origin-Opener-Policy': 'same-origin',
-      },
-    },
     cache: {
       type: 'filesystem',
     },
     module: {
       noParse: [/(codec)/, /(dicomicc)/],
       rules: [
+        {
+          test: /\.js$/,
+          enforce: 'pre',
+          use: 'source-map-loader',
+        },
         transpileJavaScriptRule(mode),
         loadWebWorkersRule,
         // loadShadersRule,
@@ -109,10 +102,7 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
       alias: {
         // Viewer project
         '@': path.resolve(__dirname, '../platform/app/src'),
-        '@components': path.resolve(
-          __dirname,
-          '../platform/app/src/components'
-        ),
+        '@components': path.resolve(__dirname, '../platform/app/src/components'),
         '@hooks': path.resolve(__dirname, '../platform/app/src/hooks'),
         '@routes': path.resolve(__dirname, '../platform/app/src/routes'),
         '@state': path.resolve(__dirname, '../platform/app/src/state'),
@@ -135,7 +125,12 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
       extensions: ['.js', '.jsx', '.json', '.ts', '.tsx', '*'],
       // symlinked resources are resolved to their real path, not their symlinked location
       symlinks: true,
-      fallback: { fs: false, path: false, zlib: false },
+      fallback: {
+        fs: false,
+        path: false,
+        zlib: false,
+        buffer: require.resolve('buffer'),
+      },
     },
     plugins: [
       new webpack.DefinePlugin({
@@ -149,15 +144,12 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
         'process.env.COMMIT_HASH': JSON.stringify(COMMIT_HASH),
         /* i18n */
         'process.env.USE_LOCIZE': JSON.stringify(process.env.USE_LOCIZE || ''),
-        'process.env.LOCIZE_PROJECTID': JSON.stringify(
-          process.env.LOCIZE_PROJECTID || ''
-        ),
-        'process.env.LOCIZE_API_KEY': JSON.stringify(
-          process.env.LOCIZE_API_KEY || ''
-        ),
-        'process.env.REACT_APP_I18N_DEBUG': JSON.stringify(
-          process.env.REACT_APP_I18N_DEBUG || ''
-        ),
+        'process.env.LOCIZE_PROJECTID': JSON.stringify(process.env.LOCIZE_PROJECTID || ''),
+        'process.env.LOCIZE_API_KEY': JSON.stringify(process.env.LOCIZE_API_KEY || ''),
+        'process.env.REACT_APP_I18N_DEBUG': JSON.stringify(process.env.REACT_APP_I18N_DEBUG || ''),
+      }),
+      new webpack.ProvidePlugin({
+        Buffer: ['buffer', 'Buffer'],
       }),
       // Uncomment to generate bundle analyzer
       // new BundleAnalyzerPlugin(),

CHANGELOG.md

@@ -0,0 +1,131 @@
+# Change Log
+
+All notable changes to this project will be documented in this file.
+See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+# [3.7.0-beta.69](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.68...v3.7.0-beta.69) (2023-09-11)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
+# [3.7.0-beta.68](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.67...v3.7.0-beta.68) (2023-09-11)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
+# [3.7.0-beta.67](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.66...v3.7.0-beta.67) (2023-09-06)
+
+
+### Bug Fixes
+
+* **hotkeys:** preserve hotkeys if changed, and reduce re-rendering ([#3635](https://github.com/OHIF/Viewers/issues/3635)) ([94f7cfb](https://github.com/OHIF/Viewers/commit/94f7cfb08e3490488394efc42ef089ebe55e86be))
+
+
+
+
+
+# [3.7.0-beta.66](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.65...v3.7.0-beta.66) (2023-09-06)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
+# [3.7.0-beta.65](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.64...v3.7.0-beta.65) (2023-09-06)
+
+
+### Features
+
+* **ImageOverlayViewerTool:** add ImageOverlayViewer tool that can render image overlay (pixel overlay) of the DICOM images ([#3163](https://github.com/OHIF/Viewers/issues/3163)) ([69115da](https://github.com/OHIF/Viewers/commit/69115da06d2d437b57e66608b435bb0bc919a90f))
+
+
+
+
+
+# [3.7.0-beta.64](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.63...v3.7.0-beta.64) (2023-09-05)
+
+
+### Bug Fixes
+
+* **nginx archive recipe:** Fixes to various configuration files. ([#3624](https://github.com/OHIF/Viewers/issues/3624)) ([3ce7225](https://github.com/OHIF/Viewers/commit/3ce72254b390f32c9aa207a0589e688805e2659d))
+
+
+
+
+
+# [3.7.0-beta.63](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.62...v3.7.0-beta.63) (2023-09-01)
+
+
+### Features
+
+* **grid:** remove viewportIndex and only rely on viewportId ([#3591](https://github.com/OHIF/Viewers/issues/3591)) ([4c6ff87](https://github.com/OHIF/Viewers/commit/4c6ff873e887cc30ffc09223f5cb99e5f94c9cdd))
+
+
+
+
+
+# [3.7.0-beta.62](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.61...v3.7.0-beta.62) (2023-08-30)
+
+
+### Features
+
+* **data source UI config:** Popup the configuration dialogue whenever a data source is not fully configured ([#3620](https://github.com/OHIF/Viewers/issues/3620)) ([adedc8c](https://github.com/OHIF/Viewers/commit/adedc8c382e18a2e86a569e3d023cc55a157363f))
+
+
+
+
+
+# [3.7.0-beta.61](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.60...v3.7.0-beta.61) (2023-08-29)
+
+
+### Bug Fixes
+
+* **OpenIdConnectRoutes:** fix handleUnauthenticated ([#3617](https://github.com/OHIF/Viewers/issues/3617)) ([35fc30c](https://github.com/OHIF/Viewers/commit/35fc30c5359d8199cc38ffa670c08687d2672f11))
+
+
+
+
+
+# [3.7.0-beta.60](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.59...v3.7.0-beta.60) (2023-08-29)
+
+
+### Bug Fixes
+
+* **PT Metadata:** Allow for PatientWeight to be missing from the metadata ([#3621](https://github.com/OHIF/Viewers/issues/3621)) ([44f101d](https://github.com/OHIF/Viewers/commit/44f101d3f2b3204b67e31f4e4939062e65a246ee))
+
+
+
+
+
+# [3.7.0-beta.59](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.58...v3.7.0-beta.59) (2023-08-29)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
+# [3.7.0-beta.58](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.57...v3.7.0-beta.58) (2023-08-25)
+
+
+### Features
+
+* **cloud data source config:** GUI and API for configuring a cloud data source with Google cloud healthcare implementation ([#3589](https://github.com/OHIF/Viewers/issues/3589)) ([a336992](https://github.com/OHIF/Viewers/commit/a336992971c07552c9dbb6e1de43169d37762ef1))
+
+
+
+
+
+# [3.7.0-beta.57](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.56...v3.7.0-beta.57) (2023-08-23)
+
+
+### Bug Fixes
+
+* **memory leak:** array buffer was sticking around in volume viewports ([#3611](https://github.com/OHIF/Viewers/issues/3611)) ([65b49ae](https://github.com/OHIF/Viewers/commit/65b49aeb1b5f38224e4892bdf32453500ee351f8))

Dockerfile

@@ -38,6 +38,7 @@ COPY platform /usr/src/app/platform
 
 # Copy Files
 FROM node:16.15.0-slim as builder
+RUN apt-get update && apt-get install -y build-essential python3
 RUN mkdir /usr/src/app
 WORKDIR /usr/src/app
 
@@ -61,7 +62,7 @@ RUN yarn run build
 
 # Stage 3: Bundle the built application into a Docker container
 # which runs Nginx using Alpine Linux
-FROM nginxinc/nginx-unprivileged:1.23.1-alpine as final
+FROM nginxinc/nginx-unprivileged:1.25-alpine as final
 #RUN apk add --no-cache bash
 ENV PORT=80
 RUN rm /etc/nginx/conf.d/default.conf
@@ -69,5 +70,10 @@ USER nginx
 COPY --chown=nginx:nginx .docker/Viewer-v3.x /usr/src
 RUN chmod 777 /usr/src/entrypoint.sh
 COPY --from=builder /usr/src/app/platform/app/dist /usr/share/nginx/html
+# In entrypoint.sh, app-config.js might be overwritten, so chmod it to be writeable.
+# The nginx user cannot chmod it, so change to root.
+USER root
+RUN chmod 666 /usr/share/nginx/html/app-config.js
+USER nginx
 ENTRYPOINT ["/usr/src/entrypoint.sh"]
 CMD ["nginx", "-g", "daemon off;"]

README.md

@@ -3,7 +3,7 @@
 <div align="center">
   <h1>OHIF Medical Imaging Viewer</h1>
   <p><strong>The OHIF Viewer</strong> is a zero-footprint medical image viewer
-provided by the <a href="https://ohif.org/">Open Health Imaging Foundation (OHIF)</a>. It is a configurable and extensible progressive web application with out-of-the-box support for image archives which support <a href="https://www.dicomstandard.org/dicomweb/">DICOMweb</a>.</p>
+provided by the <a href="https://ohif.org/">Open Health Imaging Foundation (OHIF)</a>. It is a configurable and extensible progressive web application with out-of-the-box support for image archives which support <a href="https://www.dicomstandard.org/using/dicomweb/">DICOMweb</a>.</p>
 </div>
 
 
@@ -34,13 +34,15 @@ provided by the <a href="https://ohif.org/">Open Health Imaging Foundation (OHIF
 <!-- [![All Contributors](https://img.shields.io/badge/all_contributors-10-orange.svg?style=flat-square)](#contributors) -->
 <!-- prettier-ignore-end -->
 
-|     |  |
-| :-: | :---  |
-| <img src="platform/docs/docs/assets/img/demo-measurements.jpg" alt="Measurement tracking" width="350"/> | Measurement Tracking |
-| <img src="platform/docs/docs/assets/img/demo-segmentation.png" alt="Segmentations" width="350"/> | Labelmap Segmentations  |
-| <img src="platform/docs/docs/assets/img/demo-ptct.png" alt="Hanging Protocols" width="350"/> | Fusion and Custom Hanging protocols  |
-| <img src="platform/docs/docs/assets/img/demo-microscopy.png" alt="Microscopy" width="350"/> | Slide Microscopy  |
-| <img src="platform/docs/docs/assets/img/demo-volumeRendering.png" alt="Volume Rendering" width="350"/> | Volume Rendering  |
+
+|     |  | |
+| :-: | :---  | :--- |
+| <img src="platform/docs/docs/assets/img/demo-measurements.jpg" alt="Measurement tracking" width="350"/> | Measurement Tracking | [Demo](https://viewer.ohif.org/viewer?StudyInstanceUIDs=1.3.6.1.4.1.25403.345050719074.3824.20170125095438.5) |
+| <img src="platform/docs/docs/assets/img/demo-segmentation.png" alt="Segmentations" width="350"/> | Labelmap Segmentations  | [Demo](https://viewer.ohif.org/viewer?StudyInstanceUIDs=1.3.12.2.1107.5.2.32.35162.30000015050317233592200000046) |
+| <img src="platform/docs/docs/assets/img/demo-ptct.png" alt="Hanging Protocols" width="350"/> | Fusion and Custom Hanging protocols  | [Demo](https://viewer.ohif.org/tmtv?StudyInstanceUIDs=1.3.6.1.4.1.14519.5.2.1.7009.2403.334240657131972136850343327463) |
+| <img src="platform/docs/docs/assets/img/demo-microscopy.png" alt="Microscopy" width="350"/> | Slide Microscopy  | [Demo](https://viewer.ohif.org/microscopy?StudyInstanceUIDs=2.25.275741864483510678566144889372061815320) |
+| <img src="platform/docs/docs/assets/img/demo-volumeRendering.png" alt="Volume Rendering" width="350"/> | Volume Rendering  | [Demo](https://viewer.ohif.org/viewer?StudyInstanceUIDs=1.3.6.1.4.1.25403.345050719074.3824.20170125095438.5&hangingprotocolId=mprAnd3DVolumeViewport) |
+
 
 
 ## About
@@ -161,7 +163,7 @@ yarn install
 
 These commands are available from the root directory. Each project directory
 also supports a number of commands that can be found in their respective
-`README.md` and `project.json` files.
+`README.md` and `package.json` files.
 
 | Yarn Commands                | Description                                                   |
 | ---------------------------- | ------------------------------------------------------------- |
@@ -247,7 +249,7 @@ or, for v1, please cite:
 > [10.1158/0008-5472.CAN-17-0334](https://www.doi.org/10.1158/0008-5472.CAN-17-0334)
 
 **Note:** If you use or find this repository helpful, please take the time to
-star this repository on Github. This is an easy way for us to assess adoption
+star this repository on GitHub. This is an easy way for us to assess adoption
 and it can help us obtain future funding for the project.
 
 This work is supported primarily by the National Institutes of Health, National
@@ -255,7 +257,11 @@ Cancer Institute, Informatics Technology for Cancer Research (ITCR) program,
 under a
 [grant to Dr. Gordon Harris at Massachusetts General Hospital (U24 CA199460)](https://projectreporter.nih.gov/project_info_description.cfm?aid=8971104).
 
-This project is tested with BrowserStack. Thank you for supporting open source
+[NCI Imaging Data Commons (IDC) project](https://imaging.datacommons.cancer.gov/) supported the development of new features and bug fixes marked with ["IDC:priority"](https://github.com/OHIF/Viewers/issues?q=is%3Aissue+is%3Aopen+label%3AIDC%3Apriority),
+["IDC:candidate"](https://github.com/OHIF/Viewers/issues?q=is%3Aissue+is%3Aopen+label%3AIDC%3Acandidate) or ["IDC:collaboration"](https://github.com/OHIF/Viewers/issues?q=is%3Aissue+is%3Aopen+label%3AIDC%3Acollaboration). NCI Imaging Data Commons is supported by contract number 19X037Q from
+Leidos Biomedical Research under Task Order HHSN26100071 from NCI. [IDC Viewer](https://learn.canceridc.dev/portal/visualization) is a customized version of the OHIF Viewer.
+
+This project is tested with BrowserStack. Thank you for supporting open-source!
 
 ## License
 

babel.config.js

@@ -3,22 +3,22 @@ const { extendDefaultPlugins } = require('svgo');
 
 module.exports = {
   babelrcRoots: ['./platform/*', './extensions/*', './modes/*'],
-  presets: [
-    '@babel/preset-env',
-    '@babel/preset-react',
-    '@babel/preset-typescript',
-  ],
+  presets: ['@babel/preset-env', '@babel/preset-react', '@babel/preset-typescript'],
   plugins: [
     [
       'inline-react-svg',
       {
         svgo: {
-          plugins: extendDefaultPlugins([
+          plugins: [
             {
-              name: 'removeViewBox',
-              active: false,
+              name: 'preset-default',
+              params: {
+                overrides: {
+                  removeViewBox: false,
+                },
+              },
             },
-          ]),
+          ],
         },
       },
     ],

commit.txt

@@ -1 +1 @@
-14369414cf0193f00243ae5c9f8415cf7079a753
+de0a74273371ca0f39e8678a098a94db8d88e7a5

extensions/_example/src/index.js

@@ -54,11 +54,7 @@ const getCommandsModule = () => ({
 const ExampleContext = React.createContext();
 
 function ExampleContextProvider({ children }) {
-  return (
-    <ExampleContext.Provider value={{ example: 'value' }}>
-      {children}
-    </ExampleContext.Provider>
-  );
+  return <ExampleContext.Provider value={{ example: 'value' }}>{children}</ExampleContext.Provider>;
 }
 
 const getContextModule = () => [
@@ -121,7 +117,7 @@ const getSopClassHandlerModule = (/* ... */) => {
 
 const getToolbarModule = () => {};
 
-// displaySet, viewportIndex, dataSource
+// displaySet, dataSource
 const getViewportModule = () => {
   const wrappedViewport = props => {
     return (

extensions/cornerstone-dicom-rt/.webpack/webpack.prod.js

@@ -3,8 +3,7 @@ const { merge } = require('webpack-merge');
 const path = require('path');
 const webpackCommon = require('./../../../.webpack/webpack.base.js');
 const pkg = require('./../package.json');
-const BundleAnalyzerPlugin = require('webpack-bundle-analyzer')
-  .BundleAnalyzerPlugin;
+const BundleAnalyzerPlugin = require('webpack-bundle-analyzer').BundleAnalyzerPlugin;
 
 const ROOT_DIR = path.join(__dirname, './..');
 const SRC_DIR = path.join(__dirname, '../src');
@@ -38,13 +37,7 @@ module.exports = (env, argv) => {
       libraryTarget: 'umd',
       filename: pkg.main,
     },
-    externals: [
-      /\b(vtk.js)/,
-      /\b(dcmjs)/,
-      /\b(gl-matrix)/,
-      /^@ohif/,
-      /^@cornerstonejs/,
-    ],
+    externals: [/\b(vtk.js)/, /\b(dcmjs)/, /\b(gl-matrix)/, /^@ohif/, /^@cornerstonejs/],
     plugins: [
       new webpack.optimize.LimitChunkCountPlugin({
         maxChunks: 1,

extensions/cornerstone-dicom-rt/CHANGELOG.md

@@ -0,0 +1,110 @@
+# Change Log
+
+All notable changes to this project will be documented in this file.
+See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+# [3.7.0-beta.69](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.68...v3.7.0-beta.69) (2023-09-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.7.0-beta.68](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.67...v3.7.0-beta.68) (2023-09-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.7.0-beta.67](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.66...v3.7.0-beta.67) (2023-09-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.7.0-beta.66](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.65...v3.7.0-beta.66) (2023-09-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.7.0-beta.65](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.64...v3.7.0-beta.65) (2023-09-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.7.0-beta.64](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.63...v3.7.0-beta.64) (2023-09-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.7.0-beta.63](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.62...v3.7.0-beta.63) (2023-09-01)
+
+
+### Features
+
+* **grid:** remove viewportIndex and only rely on viewportId ([#3591](https://github.com/OHIF/Viewers/issues/3591)) ([4c6ff87](https://github.com/OHIF/Viewers/commit/4c6ff873e887cc30ffc09223f5cb99e5f94c9cdd))
+
+
+
+
+
+# [3.7.0-beta.62](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.61...v3.7.0-beta.62) (2023-08-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.7.0-beta.61](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.60...v3.7.0-beta.61) (2023-08-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.7.0-beta.60](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.59...v3.7.0-beta.60) (2023-08-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.7.0-beta.59](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.58...v3.7.0-beta.59) (2023-08-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.7.0-beta.58](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.57...v3.7.0-beta.58) (2023-08-25)
+
+
+### Features
+
+* **cloud data source config:** GUI and API for configuring a cloud data source with Google cloud healthcare implementation ([#3589](https://github.com/OHIF/Viewers/issues/3589)) ([a336992](https://github.com/OHIF/Viewers/commit/a336992971c07552c9dbb6e1de43169d37762ef1))
+
+
+
+
+
+# [3.7.0-beta.57](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.56...v3.7.0-beta.57) (2023-08-23)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt

extensions/cornerstone-dicom-rt/babel.config.js

@@ -10,7 +10,7 @@ module.exports = {
             modules: 'commonjs',
             debug: false,
           },
-          "@babel/preset-typescript",
+          '@babel/preset-typescript',
         ],
         '@babel/preset-react',
       ],
@@ -26,7 +26,7 @@ module.exports = {
         // WebPack handles ES6 --> Target Syntax
         ['@babel/preset-env', { modules: false }],
         '@babel/preset-react',
-        "@babel/preset-typescript",
+        '@babel/preset-typescript',
       ],
       ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
     },
@@ -35,7 +35,7 @@ module.exports = {
         // WebPack handles ES6 --> Target Syntax
         ['@babel/preset-env', { modules: false }],
         '@babel/preset-react',
-        "@babel/preset-typescript",
+        '@babel/preset-typescript',
       ],
       plugins: ['react-hot-loader/babel'],
       ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],

extensions/cornerstone-dicom-rt/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone-dicom-rt",
-  "version": "3.7.0-beta.2",
+  "version": "3.7.0-beta.69",
   "description": "DICOM RT read workflow",
   "author": "OHIF",
   "license": "MIT",
@@ -31,10 +31,10 @@
     "start": "yarn run dev"
   },
   "peerDependencies": {
-    "@ohif/core": "3.7.0-beta.2",
-    "@ohif/extension-cornerstone": "3.7.0-beta.2",
-    "@ohif/extension-default": "3.7.0-beta.2",
-    "@ohif/i18n": "3.7.0-beta.2",
+    "@ohif/core": "3.7.0-beta.69",
+    "@ohif/extension-cornerstone": "3.7.0-beta.69",
+    "@ohif/extension-default": "3.7.0-beta.69",
+    "@ohif/i18n": "3.7.0-beta.69",
     "prop-types": "^15.6.2",
     "react": "^17.0.2",
     "react-dom": "^17.0.2",

extensions/cornerstone-dicom-rt/src/getSopClassHandlerModule.js

@@ -7,11 +7,7 @@ const sopClassUids = ['1.2.840.10008.5.1.4.1.1.481.3'];
 
 let loadPromises = {};
 
-function _getDisplaySetsFromSeries(
-  instances,
-  servicesManager,
-  extensionManager
-) {
+function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager) {
   const instance = instances[0];
 
   const {
@@ -56,10 +52,7 @@ function _getDisplaySetsFromSeries(
   };
 
   let referencedSeriesSequence = instance.ReferencedSeriesSequence;
-  if (
-    instance.ReferencedFrameOfReferenceSequence &&
-    !instance.ReferencedSeriesSequence
-  ) {
+  if (instance.ReferencedFrameOfReferenceSequence && !instance.ReferencedSeriesSequence) {
     instance.ReferencedSeriesSequence = _deriveReferencedSeriesSequenceFromFrameOfReferenceSequence(
       instance.ReferencedFrameOfReferenceSequence
     );
@@ -72,8 +65,7 @@ function _getDisplaySetsFromSeries(
 
   const referencedSeries = referencedSeriesSequence[0];
 
-  displaySet.referencedImages =
-    instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
+  displaySet.referencedImages = instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
   displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID;
 
   displaySet.getReferenceDisplaySet = () => {
@@ -88,14 +80,12 @@ function _getDisplaySetsFromSeries(
 
     const referencedDisplaySet = referencedDisplaySets[0];
 
-    displaySet.referencedDisplaySetInstanceUID =
-      referencedDisplaySet.displaySetInstanceUID;
+    displaySet.referencedDisplaySetInstanceUID = referencedDisplaySet.displaySetInstanceUID;
 
     return referencedDisplaySet;
   };
 
-  displaySet.load = ({ headers }) =>
-    _load(displaySet, servicesManager, extensionManager, headers);
+  displaySet.load = ({ headers }) => _load(displaySet, servicesManager, extensionManager, headers);
 
   return [displaySet];
 }
@@ -194,11 +184,7 @@ function getSopClassHandlerModule({ servicesManager, extensionManager }) {
       name: 'dicom-rt',
       sopClassUids,
       getDisplaySetsFromSeries: instances => {
-        return _getDisplaySetsFromSeries(
-          instances,
-          servicesManager,
-          extensionManager
-        );
+        return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
       },
     },
   ];

extensions/cornerstone-dicom-rt/src/index.tsx

@@ -2,11 +2,10 @@ import { id } from './id';
 import React from 'react';
 import { Types } from '@ohif/core';
 import getSopClassHandlerModule from './getSopClassHandlerModule';
+import hydrateRTDisplaySet from './utils/_hydrateRT';
 
 const Component = React.lazy(() => {
-  return import(
-    /* webpackPrefetch: true */ './viewports/OHIFCornerstoneRTViewport'
-  );
+  return import(/* webpackPrefetch: true */ './viewports/OHIFCornerstoneRTViewport');
 });
 
 const OHIFCornerstoneRTViewport = props => {
@@ -36,12 +35,14 @@ const extension: Types.Extensions.Extension = {
   getViewportModule({
     servicesManager,
     extensionManager,
+    commandsManager,
   }: Types.Extensions.ExtensionParams) {
     const ExtendedOHIFCornerstoneRTViewport = props => {
       return (
         <OHIFCornerstoneRTViewport
           servicesManager={servicesManager}
           extensionManager={extensionManager}
+          commandsManager={commandsManager}
           {...props}
         />
       );
@@ -59,3 +60,4 @@ const extension: Types.Extensions.Extension = {
 };
 
 export default extension;
+export { hydrateRTDisplaySet };

extensions/cornerstone-dicom-rt/src/loadRTStruct.js

@@ -25,23 +25,13 @@ async function checkAndLoadContourData(instance, datasource) {
 
       if (Array.isArray(contourData)) {
         promisesMap.has(referencedROINumber)
-          ? promisesMap
-              .get(referencedROINumber)
-              .push(Promise.resolve(contourData))
-          : promisesMap.set(referencedROINumber, [
-              Promise.resolve(contourData),
-            ]);
+          ? promisesMap.get(referencedROINumber).push(Promise.resolve(contourData))
+          : promisesMap.set(referencedROINumber, [Promise.resolve(contourData)]);
       } else if (contourData && contourData.BulkDataURI) {
         const bulkDataURI = contourData.BulkDataURI;
 
-        if (
-          !datasource ||
-          !datasource.retrieve ||
-          !datasource.retrieve.bulkDataURI
-        ) {
-          return Promise.reject(
-            'Invalid datasource object or retrieve function'
-          );
+        if (!datasource || !datasource.retrieve || !datasource.retrieve.bulkDataURI) {
+          return Promise.reject('Invalid datasource object or retrieve function');
         }
 
         const bulkDataPromise = datasource.retrieve.bulkDataURI({
@@ -74,10 +64,7 @@ async function checkAndLoadContourData(instance, datasource) {
         ROIContour.ContourSequence.forEach((Contour, index) => {
           const promise = resolvedPromises[index];
           if (promise.status === 'fulfilled') {
-            if (
-              Array.isArray(promise.value) &&
-              promise.value.every(Number.isFinite)
-            ) {
+            if (Array.isArray(promise.value) && promise.value.every(Number.isFinite)) {
               // If promise.value is already an array of numbers, use it directly
               Contour.ContourData = promise.value;
             } else {
@@ -85,13 +72,8 @@ async function checkAndLoadContourData(instance, datasource) {
               const uint8Array = new Uint8Array(promise.value);
               const textDecoder = new TextDecoder();
               const dataUint8Array = textDecoder.decode(uint8Array);
-              if (
-                typeof dataUint8Array === 'string' &&
-                dataUint8Array.includes('\\')
-              ) {
-                Contour.ContourData = dataUint8Array
-                  .split('\\')
-                  .map(parseFloat);
+              if (typeof dataUint8Array === 'string' && dataUint8Array.includes('\\')) {
+                Contour.ContourData = dataUint8Array.split('\\').map(parseFloat);
               } else {
                 Contour.ContourData = [];
               }
@@ -120,9 +102,8 @@ export default async function loadRTStruct(
   const { bulkDataURI } = dataSource.getConfig?.() || {};
 
   const { dicomLoaderService } = utilityModule.exports;
-  const imageIdSopInstanceUidPairs = _getImageIdSopInstanceUidPairsForDisplaySet(
-    referencedDisplaySet
-  );
+  const imageIdSopInstanceUidPairs =
+    _getImageIdSopInstanceUidPairsForDisplaySet(referencedDisplaySet);
 
   // Set here is loading is asynchronous.
   // If this function throws its set back to false.
@@ -137,20 +118,14 @@ export default async function loadRTStruct(
     );
 
     const dicomData = DicomMessage.readFile(segArrayBuffer);
-    const rtStructDataset = DicomMetaDictionary.naturalizeDataset(
-      dicomData.dict
-    );
+    const rtStructDataset = DicomMetaDictionary.naturalizeDataset(dicomData.dict);
     rtStructDataset._meta = DicomMetaDictionary.namifyDataset(dicomData.meta);
     instance = rtStructDataset;
   } else {
     await checkAndLoadContourData(instance, dataSource);
   }
 
-  const {
-    StructureSetROISequence,
-    ROIContourSequence,
-    RTROIObservationsSequence,
-  } = instance;
+  const { StructureSetROISequence, ROIContourSequence, RTROIObservationsSequence } = instance;
 
   // Define our structure set entry and add it to the rtstruct module state.
   const structureSet = {
@@ -174,19 +149,9 @@ export default async function loadRTStruct(
 
     const contourPoints = [];
     for (let c = 0; c < ContourSequenceArray.length; c++) {
-      const {
-        ContourImageSequence,
-        ContourData,
-        NumberOfContourPoints,
-        ContourGeometricType,
-      } = ContourSequenceArray[c];
+      const { ContourImageSequence, ContourData, NumberOfContourPoints, ContourGeometricType } =
+        ContourSequenceArray[c];
 
-      const sopInstanceUID = ContourImageSequence.ReferencedSOPInstanceUID;
-      const imageId = _getImageId(imageIdSopInstanceUidPairs, sopInstanceUID);
-
-      if (!imageId) {
-        continue;
-      }
       let isSupported = false;
 
       const points = [];
@@ -235,9 +200,7 @@ const _getImageId = (imageIdSopInstanceUidPairs, sopInstanceUID) => {
       imageIdSopInstanceUidPairsEntry.sopInstanceUID === sopInstanceUID
   );
 
-  return imageIdSopInstanceUidPairsEntry
-    ? imageIdSopInstanceUidPairsEntry.imageId
-    : null;
+  return imageIdSopInstanceUidPairsEntry ? imageIdSopInstanceUidPairsEntry.imageId : null;
 };
 
 function _getImageIdSopInstanceUidPairsForDisplaySet(referencedDisplaySet) {
@@ -258,8 +221,7 @@ function _setROIContourMetadata(
   isSupported
 ) {
   const StructureSetROI = StructureSetROISequence.find(
-    structureSetROI =>
-      structureSetROI.ROINumber === ROIContour.ReferencedROINumber
+    structureSetROI => structureSetROI.ROINumber === ROIContour.ReferencedROINumber
   );
 
   const ROIContourData = {
@@ -299,23 +261,15 @@ function _setROIContourDataColor(ROIContour, ROIContourData) {
   }
 }
 
-function _setROIContourRTROIObservations(
-  ROIContourData,
-  RTROIObservationsSequence,
-  ROINumber
-) {
+function _setROIContourRTROIObservations(ROIContourData, RTROIObservationsSequence, ROINumber) {
   const RTROIObservations = RTROIObservationsSequence.find(
     RTROIObservations => RTROIObservations.ReferencedROINumber === ROINumber
   );
 
   if (RTROIObservations) {
     // Deep copy so we don't keep the reference to the dcmjs dataset entry.
-    const {
-      ObservationNumber,
-      ROIObservationDescription,
-      RTROIInterpretedType,
-      ROIInterpreter,
-    } = RTROIObservations;
+    const { ObservationNumber, ROIObservationDescription, RTROIInterpretedType, ROIInterpreter } =
+      RTROIObservations;
 
     ROIContourData.RTROIObservations = {
       ObservationNumber,

extensions/cornerstone-dicom-rt/src/utils/_hydrateRT.ts

@@ -1,13 +1,6 @@
-async function _hydrateRTDisplaySet({
-  rtDisplaySet,
-  viewportIndex,
-  servicesManager,
-}) {
-  const {
-    segmentationService,
-    hangingProtocolService,
-    viewportGridService,
-  } = servicesManager.services;
+async function _hydrateRTDisplaySet({ rtDisplaySet, viewportId, servicesManager }) {
+  const { segmentationService, hangingProtocolService, viewportGridService } =
+    servicesManager.services;
 
   const displaySetInstanceUID = rtDisplaySet.referencedDisplaySetInstanceUID;
 
@@ -27,7 +20,7 @@ async function _hydrateRTDisplaySet({
   const { viewports } = viewportGridService.getState();
 
   const updatedViewports = hangingProtocolService.getViewportsRequireUpdate(
-    viewportIndex,
+    viewportId,
     displaySetInstanceUID
   );
 
@@ -39,8 +32,8 @@ async function _hydrateRTDisplaySet({
   // is being displayed, if so we need to update the viewport to use volume viewport
   // (if already is not using it) since Cornerstone3D currently only supports
   // volume viewport for segmentation
-  viewports.forEach((viewport, index) => {
-    if (index === viewportIndex) {
+  viewports.forEach(viewport => {
+    if (viewport.viewportId === viewportId) {
       return;
     }
 
@@ -51,9 +44,16 @@ async function _hydrateRTDisplaySet({
 
     if (shouldDisplaySeg) {
       updatedViewports.push({
-        viewportIndex: index,
+        viewportId: viewport.viewportId,
         displaySetInstanceUIDs: viewport.displaySetInstanceUIDs,
         viewportOptions: {
+          // Note: This is a hack to get the grid to re-render the OHIFCornerstoneViewport component
+          // Used for segmentation hydration right now, since the logic to decide whether
+          // a viewport needs to render a segmentation lives inside the CornerstoneViewportService
+          // so we need to re-render (force update via change of the needsRerendering) so that React
+          // does the diffing and decides we should render this again (although the id and element has not changed)
+          // so that the CornerstoneViewportService can decide whether to render the segmentation or not.
+          needsRerendering: true,
           initialImageOptions: {
             preset: 'middle',
           },

extensions/cornerstone-dicom-rt/src/utils/initRTToolGroup.ts

@@ -1,10 +1,5 @@
-function createRTToolGroupAndAddTools(
-  ToolGroupService,
-  customizationService,
-  toolGroupId
-) {
-  const { tools } =
-    customizationService.get('cornerstone.overlayViewportTools') ?? {};
+function createRTToolGroupAndAddTools(ToolGroupService, customizationService, toolGroupId) {
+  const { tools } = customizationService.get('cornerstone.overlayViewportTools') ?? {};
 
   return ToolGroupService.createToolGroupAndAddTools(toolGroupId, tools, {});
 }

extensions/cornerstone-dicom-rt/src/utils/promptHydrateRT.ts

@@ -1,3 +1,4 @@
+import { ButtonEnums } from '@ohif/ui';
 import hydrateRTDisplaySet from './_hydrateRT';
 
 const RESPONSE = {
@@ -9,21 +10,23 @@ const RESPONSE = {
 function promptHydrateRT({
   servicesManager,
   rtDisplaySet,
-  viewportIndex,
+  viewportId,
   toolGroupId = 'default',
+  preHydrateCallbacks,
 }) {
   const { uiViewportDialogService } = servicesManager.services;
 
-  return new Promise(async function(resolve, reject) {
-    const promptResult = await _askHydrate(
-      uiViewportDialogService,
-      viewportIndex
-    );
+  return new Promise(async function (resolve, reject) {
+    const promptResult = await _askHydrate(uiViewportDialogService, viewportId);
 
     if (promptResult === RESPONSE.HYDRATE_SEG) {
+      preHydrateCallbacks?.forEach(callback => {
+        callback();
+      });
+
       const isHydrated = await hydrateRTDisplaySet({
         rtDisplaySet,
-        viewportIndex,
+        viewportId,
         toolGroupId,
         servicesManager,
       });
@@ -33,17 +36,17 @@ function promptHydrateRT({
   });
 }
 
-function _askHydrate(uiViewportDialogService, viewportIndex) {
-  return new Promise(function(resolve, reject) {
+function _askHydrate(uiViewportDialogService, viewportId) {
+  return new Promise(function (resolve, reject) {
     const message = 'Do you want to open this Segmentation?';
     const actions = [
       {
-        type: 'secondary',
+        type: ButtonEnums.type.secondary,
         text: 'No',
         value: RESPONSE.CANCEL,
       },
       {
-        type: 'primary',
+        type: ButtonEnums.type.primary,
         text: 'Yes',
         value: RESPONSE.HYDRATE_SEG,
       },
@@ -54,7 +57,7 @@ function _askHydrate(uiViewportDialogService, viewportIndex) {
     };
 
     uiViewportDialogService.show({
-      viewportIndex,
+      viewportId,
       type: 'info',
       message,
       actions,

extensions/cornerstone-dicom-rt/src/viewports/OHIFCornerstoneRTViewport.tsx

@@ -1,11 +1,7 @@
 import React, { useCallback, useEffect, useRef, useState } from 'react';
 import PropTypes from 'prop-types';
 import OHIF, { utils } from '@ohif/core';
-import {
-  ViewportActionBar,
-  useViewportGrid,
-  LoadingIndicatorTotalPercent,
-} from '@ohif/ui';
+import { ViewportActionBar, useViewportGrid, LoadingIndicatorTotalPercent } from '@ohif/ui';
 
 import _hydrateRTdisplaySet from '../utils/_hydrateRT';
 import promptHydrateRT from '../utils/promptHydrateRT';
@@ -21,10 +17,10 @@ function OHIFCornerstoneRTViewport(props) {
     children,
     displaySets,
     viewportOptions,
-    viewportIndex,
     viewportLabel,
     servicesManager,
     extensionManager,
+    commandsManager,
   } = props;
 
   const {
@@ -35,7 +31,9 @@ function OHIFCornerstoneRTViewport(props) {
     customizationService,
   } = servicesManager.services;
 
-  const toolGroupId = `${RT_TOOLGROUP_BASE_NAME}-${viewportIndex}`;
+  const viewportId = viewportOptions.viewportId;
+
+  const toolGroupId = `${RT_TOOLGROUP_BASE_NAME}-${viewportId}`;
 
   // RT viewport will always have a single display set
   if (displaySets.length > 1) {
@@ -66,12 +64,10 @@ function OHIFCornerstoneRTViewport(props) {
   // refs
   const referencedDisplaySetRef = useRef(null);
 
-  const { viewports, activeViewportIndex } = viewportGrid;
+  const { viewports, activeViewportId } = viewportGrid;
 
   const referencedDisplaySet = rtDisplaySet.getReferenceDisplaySet();
-  const referencedDisplaySetMetadata = _getReferencedDisplaySetMetadata(
-    referencedDisplaySet
-  );
+  const referencedDisplaySetMetadata = _getReferencedDisplaySetMetadata(referencedDisplaySet);
 
   referencedDisplaySetRef.current = {
     displaySet: referencedDisplaySet,
@@ -91,14 +87,20 @@ function OHIFCornerstoneRTViewport(props) {
     setElement(null);
   };
 
+  const storePresentationState = useCallback(() => {
+    viewportGrid?.viewports.forEach(({ viewportId }) => {
+      commandsManager.runCommand('storePresentation', {
+        viewportId,
+      });
+    });
+  }, [viewportGrid]);
+
   const getCornerstoneViewport = useCallback(() => {
     const { component: Component } = extensionManager.getModuleEntry(
       '@ohif/extension-cornerstone.viewportModule.cornerstone'
     );
 
-    const {
-      displaySet: referencedDisplaySet,
-    } = referencedDisplaySetRef.current;
+    const { displaySet: referencedDisplaySet } = referencedDisplaySetRef.current;
 
     // Todo: jump to the center of the first segment
     return (
@@ -115,7 +117,7 @@ function OHIFCornerstoneRTViewport(props) {
         onElementDisabled={onElementDisabled}
       ></Component>
     );
-  }, [viewportIndex, rtDisplaySet, toolGroupId]);
+  }, [viewportId, rtDisplaySet, toolGroupId]);
 
   const onSegmentChange = useCallback(
     direction => {
@@ -136,11 +138,7 @@ function OHIFCornerstoneRTViewport(props) {
         newSelectedSegmentIndex = numberOfSegments - 1;
       }
 
-      segmentationService.jumpToSegmentCenter(
-        segmentationId,
-        newSelectedSegmentIndex,
-        toolGroupId
-      );
+      segmentationService.jumpToSegmentCenter(segmentationId, newSelectedSegmentIndex, toolGroupId);
       setSelectedSegment(newSelectedSegmentIndex);
     },
     [selectedSegment]
@@ -153,31 +151,28 @@ function OHIFCornerstoneRTViewport(props) {
 
     promptHydrateRT({
       servicesManager,
-      viewportIndex,
+      viewportId,
       rtDisplaySet,
+      preHydrateCallbacks: [storePresentationState],
     }).then(isHydrated => {
       if (isHydrated) {
         setIsHydrated(true);
       }
     });
-  }, [servicesManager, viewportIndex, rtDisplaySet, rtIsLoading]);
+  }, [servicesManager, viewportId, rtDisplaySet, rtIsLoading]);
 
   useEffect(() => {
     const { unsubscribe } = segmentationService.subscribe(
       segmentationService.EVENTS.SEGMENTATION_LOADING_COMPLETE,
       evt => {
-        if (
-          evt.rtDisplaySet.displaySetInstanceUID ===
-          rtDisplaySet.displaySetInstanceUID
-        ) {
+        if (evt.rtDisplaySet.displaySetInstanceUID === rtDisplaySet.displaySetInstanceUID) {
           setRtIsLoading(false);
         }
 
         if (evt.overlappingSegments) {
           uiNotificationService.show({
             title: 'Overlapping Segments',
-            message:
-              'Overlapping segments detected which is not currently supported',
+            message: 'Overlapping segments detected which is not currently supported',
             type: 'warning',
           });
         }
@@ -212,12 +207,10 @@ function OHIFCornerstoneRTViewport(props) {
     const onDisplaySetsRemovedSubscription = displaySetService.subscribe(
       displaySetService.EVENTS.DISPLAY_SETS_REMOVED,
       ({ displaySetInstanceUIDs }) => {
-        const activeViewport = viewports[activeViewportIndex];
-        if (
-          displaySetInstanceUIDs.includes(activeViewport.displaySetInstanceUID)
-        ) {
+        const activeViewport = viewports.get(activeViewportId);
+        if (displaySetInstanceUIDs.includes(activeViewport.displaySetInstanceUID)) {
           viewportGridService.setDisplaySetsForViewport({
-            viewportIndex: activeViewportIndex,
+            viewportId: activeViewportId,
             displaySetInstanceUIDs: [],
           });
         }
@@ -236,19 +229,13 @@ function OHIFCornerstoneRTViewport(props) {
       return;
     }
 
-    toolGroup = createRTToolGroupAndAddTools(
-      toolGroupService,
-      customizationService,
-      toolGroupId
-    );
+    toolGroup = createRTToolGroupAndAddTools(toolGroupService, customizationService, toolGroupId);
 
     setToolGroupCreated(true);
 
     return () => {
       // remove the segmentation representations if seg displayset changed
-      segmentationService.removeSegmentationRepresentationFromToolGroup(
-        toolGroupId
-      );
+      segmentationService.removeSegmentationRepresentationFromToolGroup(toolGroupId);
 
       toolGroupService.destroyToolGroup(toolGroupId);
     };
@@ -259,9 +246,7 @@ function OHIFCornerstoneRTViewport(props) {
 
     return () => {
       // remove the segmentation representations if seg displayset changed
-      segmentationService.removeSegmentationRepresentationFromToolGroup(
-        toolGroupId
-      );
+      segmentationService.removeSegmentationRepresentationFromToolGroup(toolGroupId);
       referencedDisplaySetRef.current = null;
     };
   }, [rtDisplaySet]);
@@ -282,7 +267,7 @@ function OHIFCornerstoneRTViewport(props) {
       return (
         child &&
         React.cloneElement(child, {
-          viewportIndex,
+          viewportId,
           key: index,
         })
       );
@@ -303,9 +288,16 @@ function OHIFCornerstoneRTViewport(props) {
   } = referencedDisplaySetRef.current.metadata;
 
   const onStatusClick = async () => {
+    // Before hydrating a RT and make it added to all viewports in the grid
+    // that share the same frameOfReferenceUID, we need to store the viewport grid
+    // presentation state, so that we can restore it after hydrating the RT. This is
+    // required if the user has changed the viewport (other viewport than RT viewport)
+    // presentation state (w/l and invert) and then opens the RT. If we don't store
+    // the presentation state, the viewport will be reset to the default presentation
+    storePresentationState();
     const isHydrated = await _hydrateRTDisplaySet({
       rtDisplaySet,
-      viewportIndex,
+      viewportId,
       servicesManager,
     });
 
@@ -333,26 +325,22 @@ function OHIFCornerstoneRTViewport(props) {
           currentSeries: SeriesNumber,
           seriesDescription: `RT Viewport ${SeriesDescription}`,
           patientInformation: {
-            patientName: PatientName
-              ? OHIF.utils.formatPN(PatientName.Alphabetic)
-              : '',
+            patientName: PatientName ? OHIF.utils.formatPN(PatientName.Alphabetic) : '',
             patientSex: PatientSex || '',
             patientAge: PatientAge || '',
             MRN: PatientID || '',
             thickness: SliceThickness ? `${SliceThickness.toFixed(2)}mm` : '',
             spacing:
-              SpacingBetweenSlices !== undefined
-                ? `${SpacingBetweenSlices.toFixed(2)}mm`
-                : '',
+              SpacingBetweenSlices !== undefined ? `${SpacingBetweenSlices.toFixed(2)}mm` : '',
             scanner: ManufacturerModelName || '',
           },
         }}
       />
 
-      <div className="relative flex flex-row w-full h-full overflow-hidden">
+      <div className="relative flex h-full w-full flex-row overflow-hidden">
         {rtIsLoading && (
           <LoadingIndicatorTotalPercent
-            className="w-full h-full"
+            className="h-full w-full"
             totalNumbers={processingProgress.totalSegments}
             percentComplete={processingProgress.percentComplete}
             loadingText="Loading RTSTRUCT..."
@@ -367,7 +355,7 @@ function OHIFCornerstoneRTViewport(props) {
 
 OHIFCornerstoneRTViewport.propTypes = {
   displaySets: PropTypes.arrayOf(PropTypes.object),
-  viewportIndex: PropTypes.number.isRequired,
+  viewportId: PropTypes.string.isRequired,
   dataSource: PropTypes.object,
   children: PropTypes.node,
   customProps: PropTypes.object,

extensions/cornerstone-dicom-rt/src/viewports/_getStatusComponent.tsx

@@ -13,25 +13,28 @@ export default function _getStatusComponent({ isHydrated, onStatusClick }) {
     case true:
       StatusIcon = () => <Icon name="status-alert" />;
 
-      ToolTipMessage = () => (
-        <div>This Segmentation is loaded in the segmentation panel</div>
-      );
+      ToolTipMessage = () => <div>This Segmentation is loaded in the segmentation panel</div>;
       break;
     case false:
-      StatusIcon = () => <Icon name="status-untracked" />;
+      StatusIcon = () => (
+        <Icon
+          className="text-aqua-pale"
+          name="status-untracked"
+        />
+      );
 
       ToolTipMessage = () => <div>Click LOAD to load RTSTRUCT.</div>;
   }
 
   const StatusArea = () => (
-    <div className="flex h-6 leading-6 cursor-default text-sm text-white">
-      <div className="min-w-[45px] flex items-center p-1 rounded-l-xl rounded-r bg-customgray-100">
+    <div className="flex h-6 cursor-default text-sm leading-6 text-white">
+      <div className="bg-customgray-100 flex min-w-[45px] items-center rounded-l-xl rounded-r p-1">
         <StatusIcon />
         <span className="ml-1">RTSTRUCT</span>
       </div>
       {!isHydrated && (
         <div
-          className="ml-1 px-1.5 rounded cursor-pointer hover:text-black bg-primary-main hover:bg-primary-light"
+          className="bg-primary-main hover:bg-primary-light ml-1 cursor-pointer rounded px-1.5 hover:text-black"
           // Using onMouseUp here because onClick is not working when the viewport is not active and is styled with pointer-events:none
           onMouseUp={onStatusClick}
         >
@@ -44,7 +47,10 @@ export default function _getStatusComponent({ isHydrated, onStatusClick }) {
   return (
     <>
       {ToolTipMessage && (
-        <Tooltip content={<ToolTipMessage />} position="bottom-left">
+        <Tooltip
+          content={<ToolTipMessage />}
+          position="bottom-left"
+        >
           <StatusArea />
         </Tooltip>
       )}

extensions/cornerstone-dicom-seg/.webpack/webpack.prod.js

@@ -40,13 +40,7 @@ module.exports = (env, argv) => {
       libraryTarget: 'umd',
       filename: pkg.main,
     },
-    externals: [
-      /\b(vtk.js)/,
-      /\b(dcmjs)/,
-      /\b(gl-matrix)/,
-      /^@ohif/,
-      /^@cornerstonejs/,
-    ],
+    externals: [/\b(vtk.js)/, /\b(dcmjs)/, /\b(gl-matrix)/, /^@ohif/, /^@cornerstonejs/],
     plugins: [
       new webpack.optimize.LimitChunkCountPlugin({
         maxChunks: 1,

extensions/cornerstone-dicom-seg/CHANGELOG.md

@@ -0,0 +1,110 @@
+# Change Log
+
+All notable changes to this project will be documented in this file.
+See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+# [3.7.0-beta.69](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.68...v3.7.0-beta.69) (2023-09-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.7.0-beta.68](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.67...v3.7.0-beta.68) (2023-09-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.7.0-beta.67](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.66...v3.7.0-beta.67) (2023-09-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.7.0-beta.66](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.65...v3.7.0-beta.66) (2023-09-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.7.0-beta.65](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.64...v3.7.0-beta.65) (2023-09-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.7.0-beta.64](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.63...v3.7.0-beta.64) (2023-09-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.7.0-beta.63](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.62...v3.7.0-beta.63) (2023-09-01)
+
+
+### Features
+
+* **grid:** remove viewportIndex and only rely on viewportId ([#3591](https://github.com/OHIF/Viewers/issues/3591)) ([4c6ff87](https://github.com/OHIF/Viewers/commit/4c6ff873e887cc30ffc09223f5cb99e5f94c9cdd))
+
+
+
+
+
+# [3.7.0-beta.62](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.61...v3.7.0-beta.62) (2023-08-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.7.0-beta.61](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.60...v3.7.0-beta.61) (2023-08-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.7.0-beta.60](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.59...v3.7.0-beta.60) (2023-08-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.7.0-beta.59](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.58...v3.7.0-beta.59) (2023-08-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.7.0-beta.58](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.57...v3.7.0-beta.58) (2023-08-25)
+
+
+### Features
+
+* **cloud data source config:** GUI and API for configuring a cloud data source with Google cloud healthcare implementation ([#3589](https://github.com/OHIF/Viewers/issues/3589)) ([a336992](https://github.com/OHIF/Viewers/commit/a336992971c07552c9dbb6e1de43169d37762ef1))
+
+
+
+
+
+# [3.7.0-beta.57](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.56...v3.7.0-beta.57) (2023-08-23)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg

extensions/cornerstone-dicom-seg/babel.config.js

@@ -10,7 +10,7 @@ module.exports = {
             modules: 'commonjs',
             debug: false,
           },
-          "@babel/preset-typescript",
+          '@babel/preset-typescript',
         ],
         '@babel/preset-react',
       ],
@@ -26,7 +26,7 @@ module.exports = {
         // WebPack handles ES6 --> Target Syntax
         ['@babel/preset-env', { modules: false }],
         '@babel/preset-react',
-        "@babel/preset-typescript",
+        '@babel/preset-typescript',
       ],
       ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
     },
@@ -35,7 +35,7 @@ module.exports = {
         // WebPack handles ES6 --> Target Syntax
         ['@babel/preset-env', { modules: false }],
         '@babel/preset-react',
-        "@babel/preset-typescript",
+        '@babel/preset-typescript',
       ],
       plugins: ['react-hot-loader/babel'],
       ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],

extensions/cornerstone-dicom-seg/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone-dicom-seg",
-  "version": "3.7.0-beta.2",
+  "version": "3.7.0-beta.69",
   "description": "DICOM SEG read workflow",
   "author": "OHIF",
   "license": "MIT",
@@ -31,10 +31,10 @@
     "start": "yarn run dev"
   },
   "peerDependencies": {
-    "@ohif/core": "3.7.0-beta.2",
-    "@ohif/extension-cornerstone": "3.7.0-beta.2",
-    "@ohif/extension-default": "3.7.0-beta.2",
-    "@ohif/i18n": "3.7.0-beta.2",
+    "@ohif/core": "3.7.0-beta.69",
+    "@ohif/extension-cornerstone": "3.7.0-beta.69",
+    "@ohif/extension-default": "3.7.0-beta.69",
+    "@ohif/i18n": "3.7.0-beta.69",
     "prop-types": "^15.6.2",
     "react": "^17.0.2",
     "react-dom": "^17.0.2",

extensions/cornerstone-dicom-seg/src/getHangingProtocolModule.ts

@@ -5,7 +5,6 @@ const segProtocol: Types.HangingProtocol.Protocol = {
   // Don't store this hanging protocol as it applies to the currently active
   // display set by default
   // cacheId: null,
-  hasUpdatedPriorsInformation: false,
   name: 'Segmentations',
   // Just apply this one when specifically listed
   protocolMatchingRules: [],

extensions/cornerstone-dicom-seg/src/getSopClassHandlerModule.js

@@ -1,21 +1,15 @@
-import vtkMath from '@kitware/vtk.js/Common/Core/Math';
-
 import { utils } from '@ohif/core';
+import { metaData, cache, triggerEvent, eventTarget } from '@cornerstonejs/core';
+import { adaptersSEG, Enums } from '@cornerstonejs/adapters';
 
 import { SOPClassHandlerId } from './id';
-import dcmjs from 'dcmjs';
-
-const { DicomMessage, DicomMetaDictionary } = dcmjs.data;
+import { dicomlabToRGB } from './utils/dicomlabToRGB';
 
 const sopClassUids = ['1.2.840.10008.5.1.4.1.1.66.4'];
 
 let loadPromises = {};
 
-function _getDisplaySetsFromSeries(
-  instances,
-  servicesManager,
-  extensionManager
-) {
+function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager) {
   const instance = instances[0];
 
   const {
@@ -68,8 +62,7 @@ function _getDisplaySetsFromSeries(
 
   const referencedSeries = referencedSeriesSequence[0];
 
-  displaySet.referencedImages =
-    instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
+  displaySet.referencedImages = instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
   displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID;
 
   displaySet.getReferenceDisplaySet = () => {
@@ -84,8 +77,7 @@ function _getDisplaySetsFromSeries(
 
     const referencedDisplaySet = referencedDisplaySets[0];
 
-    displaySet.referencedDisplaySetInstanceUID =
-      referencedDisplaySet.displaySetInstanceUID;
+    displaySet.referencedDisplaySetInstanceUID = referencedDisplaySet.displaySetInstanceUID;
 
     // Todo: this needs to be able to work with other reference volumes (other than streaming) such as nifti, etc.
     displaySet.referencedVolumeURI = referencedDisplaySet.displaySetInstanceUID;
@@ -118,17 +110,13 @@ function _load(segDisplaySet, servicesManager, extensionManager, headers) {
   // We don't want to fire multiple loads, so we'll wait for the first to finish
   // and also return the same promise to any other callers.
   loadPromises[SOPInstanceUID] = new Promise(async (resolve, reject) => {
-    if (
-      !segDisplaySet.segments ||
-      Object.keys(segDisplaySet.segments).length === 0
-    ) {
-      const segments = await _loadSegments(
+    if (!segDisplaySet.segments || Object.keys(segDisplaySet.segments).length === 0) {
+      await _loadSegments({
         extensionManager,
+        servicesManager,
         segDisplaySet,
-        headers
-      );
-
-      segDisplaySet.segments = segments;
+        headers,
+      });
     }
 
     const suppressEvents = true;
@@ -147,152 +135,61 @@ function _load(segDisplaySet, servicesManager, extensionManager, headers) {
   return loadPromises[SOPInstanceUID];
 }
 
-async function _loadSegments(extensionManager, segDisplaySet, headers) {
+async function _loadSegments({ extensionManager, servicesManager, segDisplaySet, headers }) {
   const utilityModule = extensionManager.getModuleEntry(
     '@ohif/extension-cornerstone.utilityModule.common'
   );
 
+  const { segmentationService } = servicesManager.services;
+
   const { dicomLoaderService } = utilityModule.exports;
-  const segArrayBuffer = await dicomLoaderService.findDicomDataPromise(
-    segDisplaySet,
-    null,
-    headers
-  );
+  const arrayBuffer = await dicomLoaderService.findDicomDataPromise(segDisplaySet, null, headers);
 
-  const dicomData = DicomMessage.readFile(segArrayBuffer);
-  const dataset = DicomMetaDictionary.naturalizeDataset(dicomData.dict);
-  dataset._meta = DicomMetaDictionary.namifyDataset(dicomData.meta);
+  const cachedReferencedVolume = cache.getVolume(segDisplaySet.referencedVolumeId);
 
-  if (!Array.isArray(dataset.SegmentSequence)) {
-    dataset.SegmentSequence = [dataset.SegmentSequence];
+  if (!cachedReferencedVolume) {
+    throw new Error(
+      'Referenced Volume is missing for the SEG, and stack viewport SEG is not supported yet'
+    );
   }
 
-  const segments = _getSegments(dataset);
-  return segments;
+  const { imageIds } = cachedReferencedVolume;
+
+  // Todo: what should be defaults here
+  const tolerance = 0.001;
+  const skipOverlapping = true;
+
+  eventTarget.addEventListener(Enums.Events.SEGMENTATION_LOAD_PROGRESS, evt => {
+    const { percentComplete } = evt.detail;
+    segmentationService._broadcastEvent(segmentationService.EVENTS.SEGMENT_LOADING_COMPLETE, {
+      percentComplete,
+    });
+  });
+
+  const results = await adaptersSEG.Cornerstone3D.Segmentation.generateToolState(
+    imageIds,
+    arrayBuffer,
+    metaData,
+    { skipOverlapping, tolerance, eventTarget, triggerEvent }
+  );
+
+  results.segMetadata.data.forEach((data, i) => {
+    if (i > 0) {
+      data.rgba = dicomlabToRGB(data.RecommendedDisplayCIELabValue);
+    }
+  });
+
+  Object.assign(segDisplaySet, results);
 }
 
 function _segmentationExists(segDisplaySet, segmentationService) {
   // This should be abstracted with the CornerstoneCacheService
-  return segmentationService.getSegmentation(
-    segDisplaySet.displaySetInstanceUID
-  );
-}
-
-function _getPixelData(dataset, segments) {
-  let frameSize = Math.ceil((dataset.Rows * dataset.Columns) / 8);
-  let nextOffset = 0;
-
-  Object.keys(segments).forEach(segmentKey => {
-    const segment = segments[segmentKey];
-    segment.numberOfFrames = segment.functionalGroups.length;
-    segment.size = segment.numberOfFrames * frameSize;
-    segment.offset = nextOffset;
-    nextOffset = segment.offset + segment.size;
-    const packedSegment = dataset.PixelData[0].slice(
-      segment.offset,
-      nextOffset
-    );
-
-    segment.pixelData = dcmjs.data.BitArray.unpack(packedSegment);
-    segment.geometry = geometryFromFunctionalGroups(
-      dataset,
-      segment.functionalGroups
-    );
-  });
-
-  return segments;
-}
-
-function geometryFromFunctionalGroups(dataset, perFrame) {
-  let pixelMeasures =
-    dataset.SharedFunctionalGroupsSequence.PixelMeasuresSequence;
-  let planeOrientation =
-    dataset.SharedFunctionalGroupsSequence.PlaneOrientationSequence;
-  let planePosition = perFrame[0].PlanePositionSequence; // TODO: assume sorted frames!
-
-  const geometry = {};
-
-  // NB: DICOM PixelSpacing is defined as Row then Column,
-  // unlike ImageOrientationPatient
-  let spacingBetweenSlices = pixelMeasures.SpacingBetweenSlices;
-  if (!spacingBetweenSlices) {
-    if (pixelMeasures.SliceThickness) {
-      console.log('Using SliceThickness as SpacingBetweenSlices');
-      spacingBetweenSlices = pixelMeasures.SliceThickness;
-    }
-  }
-  geometry.spacing = [
-    pixelMeasures.PixelSpacing[1],
-    pixelMeasures.PixelSpacing[0],
-    spacingBetweenSlices,
-  ].map(Number);
-
-  geometry.dimensions = [dataset.Columns, dataset.Rows, perFrame.length].map(
-    Number
-  );
-
-  let orientation = planeOrientation.ImageOrientationPatient.map(Number);
-  const columnStepToPatient = orientation.slice(0, 3);
-  const rowStepToPatient = orientation.slice(3, 6);
-  geometry.planeNormal = [];
-  vtkMath.cross(columnStepToPatient, rowStepToPatient, geometry.planeNormal);
-
-  let firstPosition = perFrame[0].PlanePositionSequence.ImagePositionPatient.map(
-    Number
-  );
-  let lastPosition = perFrame[
-    perFrame.length - 1
-  ].PlanePositionSequence.ImagePositionPatient.map(Number);
-  geometry.sliceStep = [];
-  vtkMath.subtract(lastPosition, firstPosition, geometry.sliceStep);
-  vtkMath.normalize(geometry.sliceStep);
-  geometry.direction = columnStepToPatient
-    .concat(rowStepToPatient)
-    .concat(geometry.sliceStep);
-  geometry.origin = planePosition.ImagePositionPatient.map(Number);
-
-  return geometry;
-}
-
-function _getSegments(dataset) {
-  const segments = {};
-
-  dataset.SegmentSequence.forEach(segment => {
-    const cielab = segment.RecommendedDisplayCIELabValue;
-    const rgba = dcmjs.data.Colors.dicomlab2RGB(cielab).map(x =>
-      Math.round(x * 255)
-    );
-
-    rgba.push(255);
-    const segmentNumber = segment.SegmentNumber;
-
-    segments[segmentNumber] = {
-      color: rgba,
-      functionalGroups: [],
-      offset: null,
-      size: null,
-      pixelData: null,
-      label: segment.SegmentLabel,
-    };
-  });
-
-  // make a list of functional groups per segment
-  dataset.PerFrameFunctionalGroupsSequence.forEach(functionalGroup => {
-    const segmentNumber =
-      functionalGroup.SegmentIdentificationSequence.ReferencedSegmentNumber;
-    segments[segmentNumber].functionalGroups.push(functionalGroup);
-  });
-
-  return _getPixelData(dataset, segments);
+  return segmentationService.getSegmentation(segDisplaySet.displaySetInstanceUID);
 }
 
 function getSopClassHandlerModule({ servicesManager, extensionManager }) {
   const getDisplaySetsFromSeries = instances => {
-    return _getDisplaySetsFromSeries(
-      instances,
-      servicesManager,
-      extensionManager
-    );
+    return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
   };
 
   return [

extensions/cornerstone-dicom-seg/src/index.tsx

@@ -6,11 +6,10 @@ import { Types } from '@ohif/core';
 import getSopClassHandlerModule from './getSopClassHandlerModule';
 import PanelSegmentation from './panels/PanelSegmentation';
 import getHangingProtocolModule from './getHangingProtocolModule';
+import hydrateSEGDisplaySet from './utils/_hydrateSEG';
 
 const Component = React.lazy(() => {
-  return import(
-    /* webpackPrefetch: true */ './viewports/OHIFCornerstoneSEGViewport'
-  );
+  return import(/* webpackPrefetch: true */ './viewports/OHIFCornerstoneSEGViewport');
 });
 
 const OHIFCornerstoneSEGViewport = props => {
@@ -37,11 +36,7 @@ const extension = {
    * iconName, iconLabel, label, component} object. Example of a panel module
    * is the StudyBrowserPanel that is provided by the default extension in OHIF.
    */
-  getPanelModule: ({
-    servicesManager,
-    commandsManager,
-    extensionManager,
-  }): Types.Panel[] => {
+  getPanelModule: ({ servicesManager, commandsManager, extensionManager }): Types.Panel[] => {
     const wrappedPanelSegmentation = () => {
       return (
         <PanelSegmentation
@@ -69,14 +64,13 @@ const extension = {
         <OHIFCornerstoneSEGViewport
           servicesManager={servicesManager}
           extensionManager={extensionManager}
+          commandsManager={commandsManager}
           {...props}
         />
       );
     };
 
-    return [
-      { name: 'dicom-seg', component: ExtendedOHIFCornerstoneSEGViewport },
-    ];
+    return [{ name: 'dicom-seg', component: ExtendedOHIFCornerstoneSEGViewport }];
   },
   /**
    * SopClassHandlerModule should provide a list of sop class handlers that will be
@@ -88,4 +82,5 @@ const extension = {
   getHangingProtocolModule,
 };
 
-export default extension;
+export default extension;
+export { hydrateSEGDisplaySet };

extensions/cornerstone-dicom-seg/src/panels/PanelSegmentation.tsx

@@ -2,14 +2,13 @@ import React, { useEffect, useState, useCallback } from 'react';
 import PropTypes from 'prop-types';
 import { SegmentationGroupTable } from '@ohif/ui';
 import callInputDialog from './callInputDialog';
-
+import { useAppConfig } from '@state';
 import { useTranslation } from 'react-i18next';
 
-export default function PanelSegmentation({
-  servicesManager,
-  commandsManager,
-}) {
+export default function PanelSegmentation({ servicesManager, commandsManager }) {
   const { segmentationService, uiDialogService } = servicesManager.services;
+  const [appConfig] = useAppConfig();
+  const disableEditing = appConfig?.disableEditing;
 
   const { t } = useTranslation('PanelSegmentation');
   const [selectedSegmentationId, setSelectedSegmentationId] = useState(null);
@@ -17,9 +16,7 @@ export default function PanelSegmentation({
     segmentationService.getConfiguration()
   );
 
-  const [segmentations, setSegmentations] = useState(() =>
-    segmentationService.getSegmentations()
-  );
+  const [segmentations, setSegmentations] = useState(() => segmentationService.getSegmentations());
 
   const [isMinimized, setIsMinimized] = useState({});
 
@@ -76,32 +73,20 @@ export default function PanelSegmentation({
   };
 
   const getToolGroupIds = segmentationId => {
-    const toolGroupIds = segmentationService.getToolGroupIdsWithSegmentation(
-      segmentationId
-    );
+    const toolGroupIds = segmentationService.getToolGroupIdsWithSegmentation(segmentationId);
 
     return toolGroupIds;
   };
 
   const onSegmentClick = (segmentationId, segmentIndex) => {
-    segmentationService.setActiveSegmentForSegmentation(
-      segmentationId,
-      segmentIndex
-    );
+    segmentationService.setActiveSegmentForSegmentation(segmentationId, segmentIndex);
 
     const toolGroupIds = getToolGroupIds(segmentationId);
 
     toolGroupIds.forEach(toolGroupId => {
       // const toolGroupId =
-      segmentationService.setActiveSegmentationForToolGroup(
-        segmentationId,
-        toolGroupId
-      );
-      segmentationService.jumpToSegmentCenter(
-        segmentationId,
-        segmentIndex,
-        toolGroupId
-      );
+      segmentationService.setActiveSegmentationForToolGroup(segmentationId, toolGroupId);
+      segmentationService.jumpToSegmentCenter(segmentationId, segmentIndex, toolGroupId);
     });
   };
 
@@ -116,11 +101,7 @@ export default function PanelSegmentation({
         return;
       }
 
-      segmentationService.setSegmentLabelForSegmentation(
-        segmentationId,
-        segmentIndex,
-        label
-      );
+      segmentationService.setSegmentLabelForSegmentation(segmentationId, segmentIndex, label);
     });
   };
 
@@ -189,7 +170,7 @@ export default function PanelSegmentation({
   );
 
   return (
-    <div className="flex flex-col flex-auto min-h-0 justify-between mt-1">
+    <div className="mt-1 flex min-h-0 flex-auto flex-col justify-between">
       {/* show segmentation table */}
       {segmentations?.length ? (
         <SegmentationGroupTable
@@ -203,6 +184,7 @@ export default function PanelSegmentation({
           onSegmentationEdit={onSegmentationEdit}
           onSegmentClick={onSegmentClick}
           onSegmentEdit={onSegmentEdit}
+          disableEditing={disableEditing}
           onSegmentColorClick={onSegmentColorClick}
           onSegmentDelete={onSegmentDelete}
           onToggleSegmentVisibility={onToggleSegmentVisibility}
@@ -210,25 +192,13 @@ export default function PanelSegmentation({
           onToggleMinimizeSegmentation={onToggleMinimizeSegmentation}
           segmentationConfig={{ initialConfig: segmentationConfiguration }}
           setRenderOutline={value =>
-            _setSegmentationConfiguration(
-              selectedSegmentationId,
-              'renderOutline',
-              value
-            )
+            _setSegmentationConfiguration(selectedSegmentationId, 'renderOutline', value)
           }
           setOutlineOpacityActive={value =>
-            _setSegmentationConfiguration(
-              selectedSegmentationId,
-              'outlineOpacity',
-              value
-            )
+            _setSegmentationConfiguration(selectedSegmentationId, 'outlineOpacity', value)
           }
           setRenderFill={value =>
-            _setSegmentationConfiguration(
-              selectedSegmentationId,
-              'renderFill',
-              value
-            )
+            _setSegmentationConfiguration(selectedSegmentationId, 'renderFill', value)
           }
           setRenderInactiveSegmentations={value =>
             _setSegmentationConfiguration(
@@ -238,25 +208,13 @@ export default function PanelSegmentation({
             )
           }
           setOutlineWidthActive={value =>
-            _setSegmentationConfiguration(
-              selectedSegmentationId,
-              'outlineWidthActive',
-              value
-            )
+            _setSegmentationConfiguration(selectedSegmentationId, 'outlineWidthActive', value)
           }
           setFillAlpha={value =>
-            _setSegmentationConfiguration(
-              selectedSegmentationId,
-              'fillAlpha',
-              value
-            )
+            _setSegmentationConfiguration(selectedSegmentationId, 'fillAlpha', value)
           }
           setFillAlphaInactive={value =>
-            _setSegmentationConfiguration(
-              selectedSegmentationId,
-              'fillAlphaInactive',
-              value
-            )
+            _setSegmentationConfiguration(selectedSegmentationId, 'fillAlphaInactive', value)
           }
         />
       ) : null}

extensions/cornerstone-dicom-seg/src/panels/callInputDialog.tsx

@@ -1,5 +1,5 @@
 import React from 'react';
-import { Input, Dialog } from '@ohif/ui';
+import { Input, Dialog, ButtonEnums } from '@ohif/ui';
 
 function callInputDialog(uiDialogService, label, callback) {
   const dialogId = 'enter-segment-label';
@@ -29,8 +29,8 @@ function callInputDialog(uiDialogService, label, callback) {
         noCloseButton: true,
         onClose: () => uiDialogService.dismiss({ id: dialogId }),
         actions: [
-          { id: 'cancel', text: 'Cancel', type: 'primary' },
-          { id: 'save', text: 'Confirm', type: 'secondary' },
+          { id: 'cancel', text: 'Cancel', type: ButtonEnums.type.secondary },
+          { id: 'save', text: 'Confirm', type: ButtonEnums.type.primary },
         ],
         onSubmit: onSubmitHandler,
         body: ({ value, setValue }) => {
@@ -39,7 +39,7 @@ function callInputDialog(uiDialogService, label, callback) {
               label="Enter the segment label"
               labelClassName="text-white text-[14px] leading-[1.2]"
               autoFocus
-              className="bg-black border-primary-main"
+              className="border-primary-main bg-black"
               type="text"
               value={value.label}
               onChange={event => {

extensions/cornerstone-dicom-seg/src/utils/_hydrateSEG.ts

@@ -1,13 +1,10 @@
 async function _hydrateSEGDisplaySet({
   segDisplaySet,
-  viewportIndex,
+  viewportId: targetViewportId,
   servicesManager,
 }) {
-  const {
-    segmentationService,
-    hangingProtocolService,
-    viewportGridService,
-  } = servicesManager.services;
+  const { segmentationService, hangingProtocolService, viewportGridService } =
+    servicesManager.services;
 
   const displaySetInstanceUID = segDisplaySet.referencedDisplaySetInstanceUID;
 
@@ -27,7 +24,7 @@ async function _hydrateSEGDisplaySet({
   const { viewports } = viewportGridService.getState();
 
   const updatedViewports = hangingProtocolService.getViewportsRequireUpdate(
-    viewportIndex,
+    targetViewportId,
     displaySetInstanceUID
   );
 
@@ -37,8 +34,8 @@ async function _hydrateSEGDisplaySet({
   // is being displayed, if so we need to update the viewport to use volume viewport
   // (if already is not using it) since Cornerstone3D currently only supports
   // volume viewport for segmentation
-  viewports.forEach((viewport, index) => {
-    if (index === viewportIndex) {
+  viewports.forEach((viewport, viewportId) => {
+    if (targetViewportId === viewportId) {
       return;
     }
 
@@ -49,9 +46,16 @@ async function _hydrateSEGDisplaySet({
 
     if (shouldDisplaySeg) {
       updatedViewports.push({
-        viewportIndex: index,
+        viewportId,
         displaySetInstanceUIDs: viewport.displaySetInstanceUIDs,
         viewportOptions: {
+          // Note: This is a hack to get the grid to re-render the OHIFCornerstoneViewport component
+          // Used for segmentation hydration right now, since the logic to decide whether
+          // a viewport needs to render a segmentation lives inside the CornerstoneViewportService
+          // so we need to re-render (force update via change of the needsRerendering) so that React
+          // does the diffing and decides we should render this again (although the id and element has not changed)
+          // so that the CornerstoneViewportService can decide whether to render the segmentation or not.
+          needsRerendering: true,
           initialImageOptions: {
             preset: 'middle',
           },

extensions/cornerstone-dicom-seg/src/utils/dicomlabToRGB.ts

@@ -0,0 +1,14 @@
+import dcmjs from 'dcmjs';
+
+/**
+ * Converts a CIELAB color to an RGB color using the dcmjs library.
+ * @param cielab - The CIELAB color to convert.
+ * @returns The RGB color as an array of three integers between 0 and 255.
+ */
+function dicomlabToRGB(cielab: number[]): number[] {
+  const rgb = dcmjs.data.Colors.dicomlab2RGB(cielab).map(x => Math.round(x * 255));
+
+  return rgb;
+}
+
+export { dicomlabToRGB };

extensions/cornerstone-dicom-seg/src/utils/initSEGToolGroup.ts

@@ -1,10 +1,5 @@
-function createSEGToolGroupAndAddTools(
-  ToolGroupService,
-  customizationService,
-  toolGroupId
-) {
-  const { tools } =
-    customizationService.get('cornerstone.overlayViewportTools') ?? {};
+function createSEGToolGroupAndAddTools(ToolGroupService, customizationService, toolGroupId) {
+  const { tools } = customizationService.get('cornerstone.overlayViewportTools') ?? {};
 
   return ToolGroupService.createToolGroupAndAddTools(toolGroupId, tools, {});
 }

extensions/cornerstone-dicom-seg/src/utils/promptHydrateSEG.ts

@@ -1,3 +1,4 @@
+import { ButtonEnums } from '@ohif/ui';
 import hydrateSEGDisplaySet from './_hydrateSEG';
 
 const RESPONSE = {
@@ -6,23 +7,20 @@ const RESPONSE = {
   HYDRATE_SEG: 5,
 };
 
-function promptHydrateSEG({
-  servicesManager,
-  segDisplaySet,
-  viewportIndex,
-}) {
+function promptHydrateSEG({ servicesManager, segDisplaySet, viewportId, preHydrateCallbacks }) {
   const { uiViewportDialogService } = servicesManager.services;
 
-  return new Promise(async function(resolve, reject) {
-    const promptResult = await _askHydrate(
-      uiViewportDialogService,
-      viewportIndex
-    );
+  return new Promise(async function (resolve, reject) {
+    const promptResult = await _askHydrate(uiViewportDialogService, viewportId);
 
     if (promptResult === RESPONSE.HYDRATE_SEG) {
+      preHydrateCallbacks?.forEach(callback => {
+        callback();
+      });
+
       const isHydrated = await hydrateSEGDisplaySet({
         segDisplaySet,
-        viewportIndex,
+        viewportId,
         servicesManager,
       });
 
@@ -31,17 +29,17 @@ function promptHydrateSEG({
   });
 }
 
-function _askHydrate(uiViewportDialogService, viewportIndex) {
-  return new Promise(function(resolve, reject) {
+function _askHydrate(uiViewportDialogService, viewportId) {
+  return new Promise(function (resolve, reject) {
     const message = 'Do you want to open this Segmentation?';
     const actions = [
       {
-        type: 'secondary',
+        type: ButtonEnums.type.secondary,
         text: 'No',
         value: RESPONSE.CANCEL,
       },
       {
-        type: 'primary',
+        type: ButtonEnums.type.primary,
         text: 'Yes',
         value: RESPONSE.HYDRATE_SEG,
       },
@@ -52,7 +50,7 @@ function _askHydrate(uiViewportDialogService, viewportIndex) {
     };
 
     uiViewportDialogService.show({
-      viewportIndex,
+      viewportId,
       type: 'info',
       message,
       actions,

extensions/cornerstone-dicom-seg/src/viewports/OHIFCornerstoneSEGViewport.tsx

@@ -2,11 +2,7 @@ import PropTypes from 'prop-types';
 import React, { useCallback, useEffect, useRef, useState } from 'react';
 import { useTranslation } from 'react-i18next';
 import OHIF, { utils } from '@ohif/core';
-import {
-  LoadingIndicatorTotalPercent,
-  useViewportGrid,
-  ViewportActionBar,
-} from '@ohif/ui';
+import { LoadingIndicatorTotalPercent, useViewportGrid, ViewportActionBar } from '@ohif/ui';
 import createSEGToolGroupAndAddTools from '../utils/initSEGToolGroup';
 import promptHydrateSEG from '../utils/promptHydrateSEG';
 import hydrateSEGDisplaySet from '../utils/_hydrateSEG';
@@ -20,13 +16,14 @@ function OHIFCornerstoneSEGViewport(props) {
     children,
     displaySets,
     viewportOptions,
-    viewportIndex,
     viewportLabel,
     servicesManager,
     extensionManager,
+    commandsManager,
   } = props;
 
   const { t } = useTranslation('SEGViewport');
+  const viewportId = viewportOptions.viewportId;
 
   const {
     displaySetService,
@@ -36,7 +33,7 @@ function OHIFCornerstoneSEGViewport(props) {
     customizationService,
   } = servicesManager.services;
 
-  const toolGroupId = `${SEG_TOOLGROUP_BASE_NAME}-${viewportIndex}`;
+  const toolGroupId = `${SEG_TOOLGROUP_BASE_NAME}-${viewportId}`;
 
   // SEG viewport will always have a single display set
   if (displaySets.length > 1) {
@@ -48,7 +45,6 @@ function OHIFCornerstoneSEGViewport(props) {
   const [viewportGrid, viewportGridService] = useViewportGrid();
 
   // States
-  const [isToolGroupCreated, setToolGroupCreated] = useState(false);
   const [selectedSegment, setSelectedSegment] = useState(1);
 
   // Hydration means that the SEG is opened and segments are loaded into the
@@ -67,11 +63,12 @@ function OHIFCornerstoneSEGViewport(props) {
   // refs
   const referencedDisplaySetRef = useRef(null);
 
-  const { viewports, activeViewportIndex } = viewportGrid;
+  const { viewports, activeViewportId } = viewportGrid;
 
   const referencedDisplaySet = segDisplaySet.getReferenceDisplaySet();
   const referencedDisplaySetMetadata = _getReferencedDisplaySetMetadata(
-    referencedDisplaySet
+    referencedDisplaySet,
+    segDisplaySet
   );
 
   referencedDisplaySetRef.current = {
@@ -92,14 +89,20 @@ function OHIFCornerstoneSEGViewport(props) {
     setElement(null);
   };
 
+  const storePresentationState = useCallback(() => {
+    viewportGrid?.viewports.forEach(({ viewportId }) => {
+      commandsManager.runCommand('storePresentation', {
+        viewportId,
+      });
+    });
+  }, [viewportGrid]);
+
   const getCornerstoneViewport = useCallback(() => {
     const { component: Component } = extensionManager.getModuleEntry(
       '@ohif/extension-cornerstone.viewportModule.cornerstone'
     );
 
-    const {
-      displaySet: referencedDisplaySet,
-    } = referencedDisplaySetRef.current;
+    const { displaySet: referencedDisplaySet } = referencedDisplaySetRef.current;
 
     // Todo: jump to the center of the first segment
     return (
@@ -117,7 +120,7 @@ function OHIFCornerstoneSEGViewport(props) {
         // initialImageIndex={initialImageIndex}
       ></Component>
     );
-  }, [viewportIndex, segDisplaySet, toolGroupId]);
+  }, [viewportId, segDisplaySet, toolGroupId]);
 
   const onSegmentChange = useCallback(
     direction => {
@@ -139,11 +142,7 @@ function OHIFCornerstoneSEGViewport(props) {
         newSelectedSegmentIndex = numberOfSegments - 1;
       }
 
-      segmentationService.jumpToSegmentCenter(
-        segmentationId,
-        newSelectedSegmentIndex,
-        toolGroupId
-      );
+      segmentationService.jumpToSegmentCenter(segmentationId, newSelectedSegmentIndex, toolGroupId);
       setSelectedSegment(newSelectedSegmentIndex);
     },
     [selectedSegment]
@@ -156,31 +155,28 @@ function OHIFCornerstoneSEGViewport(props) {
 
     promptHydrateSEG({
       servicesManager,
-      viewportIndex,
+      viewportId,
       segDisplaySet,
+      preHydrateCallbacks: [storePresentationState],
     }).then(isHydrated => {
       if (isHydrated) {
         setIsHydrated(true);
       }
     });
-  }, [servicesManager, viewportIndex, segDisplaySet, segIsLoading]);
+  }, [servicesManager, viewportId, segDisplaySet, segIsLoading]);
 
   useEffect(() => {
     const { unsubscribe } = segmentationService.subscribe(
       segmentationService.EVENTS.SEGMENTATION_LOADING_COMPLETE,
       evt => {
-        if (
-          evt.segDisplaySet.displaySetInstanceUID ===
-          segDisplaySet.displaySetInstanceUID
-        ) {
+        if (evt.segDisplaySet.displaySetInstanceUID === segDisplaySet.displaySetInstanceUID) {
           setSegIsLoading(false);
         }
 
         if (evt.overlappingSegments) {
           uiNotificationService.show({
             title: 'Overlapping Segments',
-            message:
-              'Overlapping segments detected which is not currently supported',
+            message: 'Overlapping segments detected which is not currently supported',
             type: 'warning',
           });
         }
@@ -215,12 +211,10 @@ function OHIFCornerstoneSEGViewport(props) {
     const onDisplaySetsRemovedSubscription = displaySetService.subscribe(
       displaySetService.EVENTS.DISPLAY_SETS_REMOVED,
       ({ displaySetInstanceUIDs }) => {
-        const activeViewport = viewports[activeViewportIndex];
-        if (
-          displaySetInstanceUIDs.includes(activeViewport.displaySetInstanceUID)
-        ) {
+        const activeViewport = viewports.get(activeViewportId);
+        if (displaySetInstanceUIDs.includes(activeViewport.displaySetInstanceUID)) {
           viewportGridService.setDisplaySetsForViewport({
-            viewportIndex: activeViewportIndex,
+            viewportId: activeViewportId,
             displaySetInstanceUIDs: [],
           });
         }
@@ -241,19 +235,11 @@ function OHIFCornerstoneSEGViewport(props) {
 
     // This creates a custom tool group which has the lifetime of this view
     // only, and does NOT interfere with currently displayed segmentations.
-    toolGroup = createSEGToolGroupAndAddTools(
-      toolGroupService,
-      customizationService,
-      toolGroupId
-    );
-
-    setToolGroupCreated(true);
+    toolGroup = createSEGToolGroupAndAddTools(toolGroupService, customizationService, toolGroupId);
 
     return () => {
       // remove the segmentation representations if seg displayset changed
-      segmentationService.removeSegmentationRepresentationFromToolGroup(
-        toolGroupId
-      );
+      segmentationService.removeSegmentationRepresentationFromToolGroup(toolGroupId);
 
       // Only destroy the viewport specific implementation
       toolGroupService.destroyToolGroup(toolGroupId);
@@ -265,9 +251,7 @@ function OHIFCornerstoneSEGViewport(props) {
 
     return () => {
       // remove the segmentation representations if seg displayset changed
-      segmentationService.removeSegmentationRepresentationFromToolGroup(
-        toolGroupId
-      );
+      segmentationService.removeSegmentationRepresentationFromToolGroup(toolGroupId);
       referencedDisplaySetRef.current = null;
     };
   }, [segDisplaySet]);
@@ -288,7 +272,7 @@ function OHIFCornerstoneSEGViewport(props) {
       return (
         child &&
         React.cloneElement(child, {
-          viewportIndex,
+          viewportId,
           key: index,
         })
       );
@@ -308,15 +292,21 @@ function OHIFCornerstoneSEGViewport(props) {
   } = referencedDisplaySetRef.current.metadata;
 
   const onStatusClick = async () => {
+    // Before hydrating a SEG and make it added to all viewports in the grid
+    // that share the same frameOfReferenceUID, we need to store the viewport grid
+    // presentation state, so that we can restore it after hydrating the SEG. This is
+    // required if the user has changed the viewport (other viewport than SEG viewport)
+    // presentation state (w/l and invert) and then opens the SEG. If we don't store
+    // the presentation state, the viewport will be reset to the default presentation
+    storePresentationState();
     const isHydrated = await hydrateSEGDisplaySet({
       segDisplaySet,
-      viewportIndex,
+      viewportId,
       servicesManager,
     });
 
     setIsHydrated(isHydrated);
   };
-
   return (
     <>
       <ViewportActionBar
@@ -337,26 +327,23 @@ function OHIFCornerstoneSEGViewport(props) {
           studyDate: formatDate(StudyDate),
           seriesDescription: `SEG Viewport ${SeriesDescription}`,
           patientInformation: {
-            patientName: PatientName
-              ? OHIF.utils.formatPN(PatientName.Alphabetic)
-              : '',
+            patientName: PatientName ? OHIF.utils.formatPN(PatientName.Alphabetic) : '',
             patientSex: PatientSex || '',
             patientAge: PatientAge || '',
             MRN: PatientID || '',
-            thickness: SliceThickness ? `${SliceThickness.toFixed(2)}mm` : '',
+            thickness: SliceThickness ? utils.roundNumber(SliceThickness, 2) : '',
+            thicknessUnits: SliceThickness !== undefined ? 'mm' : '',
             spacing:
-              SpacingBetweenSlices !== undefined
-                ? `${SpacingBetweenSlices.toFixed(2)}mm`
-                : '',
+              SpacingBetweenSlices !== undefined ? utils.roundNumber(SpacingBetweenSlices, 2) : '',
             scanner: ManufacturerModelName || '',
           },
         }}
       />
 
-      <div className="relative flex flex-row w-full h-full overflow-hidden">
+      <div className="relative flex h-full w-full flex-row overflow-hidden">
         {segIsLoading && (
           <LoadingIndicatorTotalPercent
-            className="w-full h-full"
+            className="h-full w-full"
             totalNumbers={processingProgress.totalSegments}
             percentComplete={processingProgress.percentComplete}
             loadingText="Loading SEG..."
@@ -371,7 +358,7 @@ function OHIFCornerstoneSEGViewport(props) {
 
 OHIFCornerstoneSEGViewport.propTypes = {
   displaySets: PropTypes.arrayOf(PropTypes.object),
-  viewportIndex: PropTypes.number.isRequired,
+  viewportId: PropTypes.string.isRequired,
   dataSource: PropTypes.object,
   children: PropTypes.node,
   customProps: PropTypes.object,
@@ -381,20 +368,28 @@ OHIFCornerstoneSEGViewport.defaultProps = {
   customProps: {},
 };
 
-function _getReferencedDisplaySetMetadata(referencedDisplaySet) {
+function _getReferencedDisplaySetMetadata(referencedDisplaySet, segDisplaySet) {
+  const {
+    SharedFunctionalGroupsSequence: [SharedFunctionalGroup],
+  } = segDisplaySet.instance;
+  const {
+    PixelMeasuresSequence: [PixelMeasures],
+  } = SharedFunctionalGroup;
+  const { SpacingBetweenSlices, SliceThickness } = PixelMeasures;
+
   const image0 = referencedDisplaySet.images[0];
   const referencedDisplaySetMetadata = {
     PatientID: image0.PatientID,
     PatientName: image0.PatientName,
     PatientSex: image0.PatientSex,
     PatientAge: image0.PatientAge,
-    SliceThickness: image0.SliceThickness,
+    SliceThickness: image0.SliceThickness || SliceThickness,
     StudyDate: image0.StudyDate,
     SeriesDescription: image0.SeriesDescription,
     SeriesInstanceUID: image0.SeriesInstanceUID,
     SeriesNumber: image0.SeriesNumber,
     ManufacturerModelName: image0.ManufacturerModelName,
-    SpacingBetweenSlices: image0.SpacingBetweenSlices,
+    SpacingBetweenSlices: image0.SpacingBetweenSlices || SpacingBetweenSlices,
   };
 
   return referencedDisplaySetMetadata;

extensions/cornerstone-dicom-seg/src/viewports/_getStatusComponent.tsx

@@ -2,37 +2,39 @@ import React from 'react';
 import { useTranslation } from 'react-i18next';
 import { Icon, Tooltip } from '@ohif/ui';
 
-
 export default function _getStatusComponent({ isHydrated, onStatusClick }) {
   let ToolTipMessage = null;
   let StatusIcon = null;
 
-  const {t} = useTranslation("Common");
-  const loadStr = t("LOAD");
+  const { t } = useTranslation('Common');
+  const loadStr = t('LOAD');
 
   switch (isHydrated) {
     case true:
       StatusIcon = () => <Icon name="status-alert" />;
 
-      ToolTipMessage = () => (
-        <div>This Segmentation is loaded in the segmentation panel</div>
-      );
+      ToolTipMessage = () => <div>This Segmentation is loaded in the segmentation panel</div>;
       break;
-  case false:
-      StatusIcon = () => <Icon name="status-untracked" />;
+    case false:
+      StatusIcon = () => (
+        <Icon
+          className="text-aqua-pale"
+          name="status-untracked"
+        />
+      );
 
       ToolTipMessage = () => <div>Click LOAD to load segmentation.</div>;
   }
 
   const StatusArea = () => (
-    <div className="flex h-6 leading-6 cursor-default text-sm text-white">
-      <div className="min-w-[45px] flex items-center p-1 rounded-l-xl rounded-r bg-customgray-100">
+    <div className="flex h-6 cursor-default text-sm leading-6 text-white">
+      <div className="bg-customgray-100 flex min-w-[45px] items-center rounded-l-xl rounded-r p-1">
         <StatusIcon />
         <span className="ml-1">SEG</span>
       </div>
       {!isHydrated && (
         <div
-          className="ml-1 px-1.5 rounded cursor-pointer hover:text-black bg-primary-main hover:bg-primary-light"
+          className="bg-primary-main hover:bg-primary-light ml-1 cursor-pointer rounded px-1.5 hover:text-black"
           // Using onMouseUp here because onClick is not working when the viewport is not active and is styled with pointer-events:none
           onMouseUp={onStatusClick}
         >
@@ -42,11 +44,13 @@ export default function _getStatusComponent({ isHydrated, onStatusClick }) {
     </div>
   );
 
-
   return (
     <>
       {ToolTipMessage && (
-        <Tooltip content={<ToolTipMessage />} position="bottom-left">
+        <Tooltip
+          content={<ToolTipMessage />}
+          position="bottom-left"
+        >
           <StatusArea />
         </Tooltip>
       )}

extensions/cornerstone-dicom-sr/.webpack/webpack.prod.js

@@ -41,13 +41,7 @@ module.exports = (env, argv) => {
       libraryTarget: 'umd',
       filename: pkg.main,
     },
-    externals: [
-      /\b(vtk.js)/,
-      /\b(dcmjs)/,
-      /\b(gl-matrix)/,
-      /^@ohif/,
-      /^@cornerstonejs/,
-    ],
+    externals: [/\b(vtk.js)/, /\b(dcmjs)/, /\b(gl-matrix)/, /^@ohif/, /^@cornerstonejs/],
     plugins: [
       new webpack.optimize.LimitChunkCountPlugin({
         maxChunks: 1,

extensions/cornerstone-dicom-sr/CHANGELOG.md

@@ -0,0 +1,119 @@
+# Change Log
+
+All notable changes to this project will be documented in this file.
+See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+# [3.7.0-beta.69](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.68...v3.7.0-beta.69) (2023-09-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.7.0-beta.68](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.67...v3.7.0-beta.68) (2023-09-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.7.0-beta.67](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.66...v3.7.0-beta.67) (2023-09-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.7.0-beta.66](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.65...v3.7.0-beta.66) (2023-09-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.7.0-beta.65](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.64...v3.7.0-beta.65) (2023-09-06)
+
+
+### Features
+
+* **ImageOverlayViewerTool:** add ImageOverlayViewer tool that can render image overlay (pixel overlay) of the DICOM images ([#3163](https://github.com/OHIF/Viewers/issues/3163)) ([69115da](https://github.com/OHIF/Viewers/commit/69115da06d2d437b57e66608b435bb0bc919a90f))
+
+
+
+
+
+# [3.7.0-beta.64](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.63...v3.7.0-beta.64) (2023-09-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.7.0-beta.63](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.62...v3.7.0-beta.63) (2023-09-01)
+
+
+### Features
+
+* **grid:** remove viewportIndex and only rely on viewportId ([#3591](https://github.com/OHIF/Viewers/issues/3591)) ([4c6ff87](https://github.com/OHIF/Viewers/commit/4c6ff873e887cc30ffc09223f5cb99e5f94c9cdd))
+
+
+
+
+
+# [3.7.0-beta.62](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.61...v3.7.0-beta.62) (2023-08-30)
+
+
+### Features
+
+* **data source UI config:** Popup the configuration dialogue whenever a data source is not fully configured ([#3620](https://github.com/OHIF/Viewers/issues/3620)) ([adedc8c](https://github.com/OHIF/Viewers/commit/adedc8c382e18a2e86a569e3d023cc55a157363f))
+
+
+
+
+
+# [3.7.0-beta.61](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.60...v3.7.0-beta.61) (2023-08-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.7.0-beta.60](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.59...v3.7.0-beta.60) (2023-08-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.7.0-beta.59](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.58...v3.7.0-beta.59) (2023-08-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.7.0-beta.58](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.57...v3.7.0-beta.58) (2023-08-25)
+
+
+### Features
+
+* **cloud data source config:** GUI and API for configuring a cloud data source with Google cloud healthcare implementation ([#3589](https://github.com/OHIF/Viewers/issues/3589)) ([a336992](https://github.com/OHIF/Viewers/commit/a336992971c07552c9dbb6e1de43169d37762ef1))
+
+
+
+
+
+# [3.7.0-beta.57](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.56...v3.7.0-beta.57) (2023-08-23)
+
+
+### Bug Fixes
+
+* **memory leak:** array buffer was sticking around in volume viewports ([#3611](https://github.com/OHIF/Viewers/issues/3611)) ([65b49ae](https://github.com/OHIF/Viewers/commit/65b49aeb1b5f38224e4892bdf32453500ee351f8))

extensions/cornerstone-dicom-sr/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone-dicom-sr",
-  "version": "3.7.0-beta.2",
+  "version": "3.7.0-beta.69",
   "description": "OHIF extension for an SR Cornerstone Viewport",
   "author": "OHIF",
   "license": "MIT",
@@ -32,10 +32,10 @@
     "test:unit:ci": "jest --ci --runInBand --collectCoverage --passWithNoTests"
   },
   "peerDependencies": {
-    "@ohif/core": "3.7.0-beta.2",
-    "@ohif/extension-cornerstone": "3.7.0-beta.2",
-    "@ohif/extension-measurement-tracking": "3.7.0-beta.2",
-    "@ohif/ui": "3.7.0-beta.2",
+    "@ohif/core": "3.7.0-beta.69",
+    "@ohif/extension-cornerstone": "3.7.0-beta.69",
+    "@ohif/extension-measurement-tracking": "3.7.0-beta.69",
+    "@ohif/ui": "3.7.0-beta.69",
     "dcmjs": "^0.29.5",
     "dicom-parser": "^1.8.9",
     "hammerjs": "^2.0.8",
@@ -44,9 +44,9 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/adapters": "^1.1.8",
-    "@cornerstonejs/core": "^1.1.8",
-    "@cornerstonejs/tools": "^1.1.8",
+    "@cornerstonejs/adapters": "^1.13.2",
+    "@cornerstonejs/core": "^1.13.2",
+    "@cornerstonejs/tools": "^1.13.2",
     "classnames": "^2.3.2"
   }
 }

extensions/cornerstone-dicom-sr/src/commandsModule.js

@@ -17,11 +17,7 @@ const { log } = OHIF;
  * @param options Naturalized DICOM JSON headers to merge into the displaySet.
  *
  */
-const _generateReport = (
-  measurementData,
-  additionalFindingTypes,
-  options = {}
-) => {
+const _generateReport = (measurementData, additionalFindingTypes, options = {}) => {
   const filteredToolState = getFilteredCornerstoneToolState(
     measurementData,
     additionalFindingTypes
@@ -54,16 +50,8 @@ const commandsModule = ({}) => {
      * as opposed to Finding Sites.
      * that you wish to serialize.
      */
-    downloadReport: ({
-      measurementData,
-      additionalFindingTypes,
-      options = {},
-    }) => {
-      const srDataset = actions.generateReport(
-        measurementData,
-        additionalFindingTypes,
-        options
-      );
+    downloadReport: ({ measurementData, additionalFindingTypes, options = {} }) => {
+      const srDataset = actions.generateReport(measurementData, additionalFindingTypes, options);
       const reportBlob = dcmjs.data.datasetToBlob(srDataset);
 
       //Create a URL for the binary.
@@ -91,28 +79,19 @@ const commandsModule = ({}) => {
       log.info('[DICOMSR] storeMeasurements');
 
       if (!dataSource || !dataSource.store || !dataSource.store.dicom) {
-        log.error(
-          '[DICOMSR] datasource has no dataSource.store.dicom endpoint!'
-        );
+        log.error('[DICOMSR] datasource has no dataSource.store.dicom endpoint!');
         return Promise.reject({});
       }
 
       try {
-        const naturalizedReport = _generateReport(
-          measurementData,
-          additionalFindingTypes,
-          options
-        );
+        const naturalizedReport = _generateReport(measurementData, additionalFindingTypes, options);
 
         const { StudyInstanceUID, ContentSequence } = naturalizedReport;
         // The content sequence has 5 or more elements, of which
         // the `[4]` element contains the annotation data, so this is
         // checking that there is some annotation data present.
         if (!ContentSequence?.[4].ContentSequence?.length) {
-          console.log(
-            'naturalizedReport missing imaging content',
-            naturalizedReport
-          );
+          console.log('naturalizedReport missing imaging content', naturalizedReport);
           throw new Error('Invalid report, no content');
         }
 
@@ -130,12 +109,8 @@ const commandsModule = ({}) => {
         return naturalizedReport;
       } catch (error) {
         console.warn(error);
-        log.error(
-          `[DICOMSR] Error while saving the measurements: ${error.message}`
-        );
-        throw new Error(
-          error.message || 'Error while saving the measurements.'
-        );
+        log.error(`[DICOMSR] Error while saving the measurements: ${error.message}`);
+        throw new Error(error.message || 'Error while saving the measurements.');
       }
     },
   };

extensions/cornerstone-dicom-sr/src/getHangingProtocolModule.ts

@@ -5,7 +5,6 @@ const srProtocol: Types.HangingProtocol.Protocol = {
   // Don't store this hanging protocol as it applies to the currently active
   // display set by default
   // cacheId: null,
-  hasUpdatedPriorsInformation: false,
   name: 'SR Key Images',
   // Just apply this one when specifically listed
   protocolMatchingRules: [],

extensions/cornerstone-dicom-sr/src/getSopClassHandlerModule.ts

@@ -29,9 +29,7 @@ const validateSameStudyUID = (uid: string, instances): void => {
   instances.forEach(it => {
     if (it.StudyInstanceUID !== uid) {
       console.warn('Not all instances have the same UID', uid, it);
-      throw new Error(
-        `Instances ${it.SOPInstanceUID} does not belong to ${uid}`
-      );
+      throw new Error(`Instances ${it.SOPInstanceUID} does not belong to ${uid}`);
     }
   });
 };
@@ -51,10 +49,7 @@ const CodeNameCodeSequenceValues = {
 
 const CodingSchemeDesignators = {
   SRT: 'SRT',
-  CornerstoneCodeSchemes: [
-    Cornerstone3DCodeScheme.CodingSchemeDesignator,
-    'CST4',
-  ],
+  CornerstoneCodeSchemes: [Cornerstone3DCodeScheme.CodingSchemeDesignator, 'CST4'],
 };
 
 const RELATIONSHIP_TYPE = {
@@ -71,10 +66,7 @@ const CORNERSTONE_FREETEXT_CODE_VALUE = 'CORNERSTONEFREETEXT';
  * @param instances is a list of instances from THIS series that are not
  *     in this DICOM SR Display Set already.
  */
-function addInstances(
-  instances: InstanceMetadata[],
-  displaySetService: DisplaySetService
-) {
+function addInstances(instances: InstanceMetadata[], displaySetService: DisplaySetService) {
   this.instances.push(...instances);
   utils.sortStudyInstances(this.instances);
   // The last instance is the newest one, so is the one most interesting.
@@ -93,11 +85,7 @@ function addInstances(
  * @param servicesManager is the services that can be used for creating
  * @returns The list of display sets created for the given instances object
  */
-function _getDisplaySetsFromSeries(
-  instances,
-  servicesManager,
-  extensionManager
-) {
+function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager) {
   // If the series has no instances, stop here
   if (!instances || !instances.length) {
     throw new Error('No instances were provided');
@@ -123,8 +111,7 @@ function _getDisplaySetsFromSeries(
 
   if (
     !ConceptNameCodeSequence ||
-    ConceptNameCodeSequence.CodeValue !==
-      CodeNameCodeSequenceValues.ImagingMeasurementReport
+    ConceptNameCodeSequence.CodeValue !== CodeNameCodeSequenceValues.ImagingMeasurementReport
   ) {
     servicesManager.services.uiNotificationService.show({
       title: 'DICOM SR',
@@ -184,36 +171,21 @@ function _load(displaySet, servicesManager, extensionManager) {
 
   // Check currently added displaySets and add measurements if the sources exist.
   displaySetService.activeDisplaySets.forEach(activeDisplaySet => {
-    _checkIfCanAddMeasurementsToDisplaySet(
-      displaySet,
-      activeDisplaySet,
-      dataSource
-    );
+    _checkIfCanAddMeasurementsToDisplaySet(displaySet, activeDisplaySet, dataSource);
   });
 
   // Subscribe to new displaySets as the source may come in after.
-  displaySetService.subscribe(
-    displaySetService.EVENTS.DISPLAY_SETS_ADDED,
-    data => {
-      const { displaySetsAdded } = data;
-      // If there are still some measurements that have not yet been loaded into cornerstone,
-      // See if we can load them onto any of the new displaySets.
-      displaySetsAdded.forEach(newDisplaySet => {
-        _checkIfCanAddMeasurementsToDisplaySet(
-          displaySet,
-          newDisplaySet,
-          dataSource
-        );
-      });
-    }
-  );
+  displaySetService.subscribe(displaySetService.EVENTS.DISPLAY_SETS_ADDED, data => {
+    const { displaySetsAdded } = data;
+    // If there are still some measurements that have not yet been loaded into cornerstone,
+    // See if we can load them onto any of the new displaySets.
+    displaySetsAdded.forEach(newDisplaySet => {
+      _checkIfCanAddMeasurementsToDisplaySet(displaySet, newDisplaySet, dataSource);
+    });
+  });
 }
 
-function _checkIfCanAddMeasurementsToDisplaySet(
-  srDisplaySet,
-  newDisplaySet,
-  dataSource
-) {
+function _checkIfCanAddMeasurementsToDisplaySet(srDisplaySet, newDisplaySet, dataSource) {
   let unloadedMeasurements = srDisplaySet.measurements.filter(
     measurement => measurement.loaded === false
   );
@@ -248,8 +220,7 @@ function _checkIfCanAddMeasurementsToDisplaySet(
     const { coords } = measurement;
 
     coords.forEach(coord => {
-      const SOPInstanceUID =
-        coord.ReferencedSOPSequence.ReferencedSOPInstanceUID;
+      const SOPInstanceUID = coord.ReferencedSOPSequence.ReferencedSOPInstanceUID;
 
       if (!SOPInstanceUIDs.includes(SOPInstanceUID)) {
         SOPInstanceUIDs.push(SOPInstanceUID);
@@ -257,9 +228,7 @@ function _checkIfCanAddMeasurementsToDisplaySet(
     });
   });
 
-  const imageIdsForDisplaySet = dataSource.getImageIdsForDisplaySet(
-    newDisplaySet
-  );
+  const imageIdsForDisplaySet = dataSource.getImageIdsForDisplaySet(newDisplaySet);
 
   for (const imageId of imageIdsForDisplaySet) {
     if (!unloadedMeasurements.length) {
@@ -267,25 +236,13 @@ function _checkIfCanAddMeasurementsToDisplaySet(
       return;
     }
 
-    const { SOPInstanceUID, frameNumber } = metadataProvider.getUIDsFromImageID(
-      imageId
-    );
+    const { SOPInstanceUID, frameNumber } = metadataProvider.getUIDsFromImageID(imageId);
 
     if (SOPInstanceUIDs.includes(SOPInstanceUID)) {
       for (let j = unloadedMeasurements.length - 1; j >= 0; j--) {
         const measurement = unloadedMeasurements[j];
-        if (
-          _measurementReferencesSOPInstanceUID(
-            measurement,
-            SOPInstanceUID,
-            frameNumber
-          )
-        ) {
-          addMeasurement(
-            measurement,
-            imageId,
-            newDisplaySet.displaySetInstanceUID
-          );
+        if (_measurementReferencesSOPInstanceUID(measurement, SOPInstanceUID, frameNumber)) {
+          addMeasurement(measurement, imageId, newDisplaySet.displaySetInstanceUID);
 
           unloadedMeasurements.splice(j, 1);
         }
@@ -294,11 +251,7 @@ function _checkIfCanAddMeasurementsToDisplaySet(
   }
 }
 
-function _measurementReferencesSOPInstanceUID(
-  measurement,
-  SOPInstanceUID,
-  frameNumber
-) {
+function _measurementReferencesSOPInstanceUID(measurement, SOPInstanceUID, frameNumber) {
   const { coords } = measurement;
 
   // NOTE: The ReferencedFrameNumber can be multiple values according to the DICOM
@@ -308,8 +261,9 @@ function _measurementReferencesSOPInstanceUID(
       measurement.coords[0].ReferencedSOPSequence[0]?.ReferencedFrameNumber) ||
     1;
 
-  if (frameNumber && Number(frameNumber) !== Number(ReferencedFrameNumber))
+  if (frameNumber && Number(frameNumber) !== Number(ReferencedFrameNumber)) {
     return false;
+  }
 
   for (let j = 0; j < coords.length; j++) {
     const coord = coords[j];
@@ -323,11 +277,7 @@ function _measurementReferencesSOPInstanceUID(
 
 function getSopClassHandlerModule({ servicesManager, extensionManager }) {
   const getDisplaySetsFromSeries = instances => {
-    return _getDisplaySetsFromSeries(
-      instances,
-      servicesManager,
-      extensionManager
-    );
+    return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
   };
 
   return [
@@ -342,30 +292,22 @@ function getSopClassHandlerModule({ servicesManager, extensionManager }) {
 function _getMeasurements(ImagingMeasurementReportContentSequence) {
   const ImagingMeasurements = ImagingMeasurementReportContentSequence.find(
     item =>
-      item.ConceptNameCodeSequence.CodeValue ===
-      CodeNameCodeSequenceValues.ImagingMeasurements
+      item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.ImagingMeasurements
   );
 
-  const MeasurementGroups = _getSequenceAsArray(
-    ImagingMeasurements.ContentSequence
-  ).filter(
-    item =>
-      item.ConceptNameCodeSequence.CodeValue ===
-      CodeNameCodeSequenceValues.MeasurementGroup
+  const MeasurementGroups = _getSequenceAsArray(ImagingMeasurements.ContentSequence).filter(
+    item => item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.MeasurementGroup
   );
 
-  const mergedContentSequencesByTrackingUniqueIdentifiers = _getMergedContentSequencesByTrackingUniqueIdentifiers(
-    MeasurementGroups
-  );
+  const mergedContentSequencesByTrackingUniqueIdentifiers =
+    _getMergedContentSequencesByTrackingUniqueIdentifiers(MeasurementGroups);
 
   const measurements = [];
 
   Object.keys(mergedContentSequencesByTrackingUniqueIdentifiers).forEach(
     trackingUniqueIdentifier => {
       const mergedContentSequence =
-        mergedContentSequencesByTrackingUniqueIdentifiers[
-          trackingUniqueIdentifier
-        ];
+        mergedContentSequencesByTrackingUniqueIdentifiers[trackingUniqueIdentifier];
 
       const measurement = _processMeasurement(mergedContentSequence);
 
@@ -378,15 +320,11 @@ function _getMeasurements(ImagingMeasurementReportContentSequence) {
   return measurements;
 }
 
-function _getMergedContentSequencesByTrackingUniqueIdentifiers(
-  MeasurementGroups
-) {
+function _getMergedContentSequencesByTrackingUniqueIdentifiers(MeasurementGroups) {
   const mergedContentSequencesByTrackingUniqueIdentifiers = {};
 
   MeasurementGroups.forEach(MeasurementGroup => {
-    const ContentSequence = _getSequenceAsArray(
-      MeasurementGroup.ContentSequence
-    );
+    const ContentSequence = _getSequenceAsArray(MeasurementGroup.ContentSequence);
 
     const TrackingUniqueIdentifierItem = ContentSequence.find(
       item =>
@@ -395,22 +333,16 @@ function _getMergedContentSequencesByTrackingUniqueIdentifiers(
     );
 
     if (!TrackingUniqueIdentifierItem) {
-      console.warn(
-        'No Tracking Unique Identifier, skipping ambiguous measurement.'
-      );
+      console.warn('No Tracking Unique Identifier, skipping ambiguous measurement.');
     }
 
     const trackingUniqueIdentifier = TrackingUniqueIdentifierItem.UID;
 
-    if (
-      mergedContentSequencesByTrackingUniqueIdentifiers[
-        trackingUniqueIdentifier
-      ] === undefined
-    ) {
+    if (mergedContentSequencesByTrackingUniqueIdentifiers[trackingUniqueIdentifier] === undefined) {
       // Add the full ContentSequence
-      mergedContentSequencesByTrackingUniqueIdentifiers[
-        trackingUniqueIdentifier
-      ] = [...ContentSequence];
+      mergedContentSequencesByTrackingUniqueIdentifiers[trackingUniqueIdentifier] = [
+        ...ContentSequence,
+      ];
     } else {
       // Add the ContentSequence minus the tracking identifier, as we have this
       // Information in the merged ContentSequence anyway.
@@ -419,9 +351,7 @@ function _getMergedContentSequencesByTrackingUniqueIdentifiers(
           item.ConceptNameCodeSequence.CodeValue !==
           CodeNameCodeSequenceValues.TrackingUniqueIdentifier
         ) {
-          mergedContentSequencesByTrackingUniqueIdentifiers[
-            trackingUniqueIdentifier
-          ].push(item);
+          mergedContentSequencesByTrackingUniqueIdentifiers[trackingUniqueIdentifier].push(item);
         }
       });
     }
@@ -446,18 +376,12 @@ function _processTID1410Measurement(mergedContentSequence) {
   // Need to deal with TID 1410 style measurements, which will have a SCOORD or SCOORD3D at the top level,
   // And non-geometric representations where each NUM has "INFERRED FROM" SCOORD/SCOORD3D
 
-  const graphicItem = mergedContentSequence.find(
-    group => group.ValueType === 'SCOORD'
-  );
+  const graphicItem = mergedContentSequence.find(group => group.ValueType === 'SCOORD');
 
-  const UIDREFContentItem = mergedContentSequence.find(
-    group => group.ValueType === 'UIDREF'
-  );
+  const UIDREFContentItem = mergedContentSequence.find(group => group.ValueType === 'UIDREF');
 
   const TrackingIdentifierContentItem = mergedContentSequence.find(
-    item =>
-      item.ConceptNameCodeSequence.CodeValue ===
-      CodeNameCodeSequenceValues.TrackingIdentifier
+    item => item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.TrackingIdentifier
   );
 
   if (!graphicItem) {
@@ -467,9 +391,7 @@ function _processTID1410Measurement(mergedContentSequence) {
     return;
   }
 
-  const NUMContentItems = mergedContentSequence.filter(
-    group => group.ValueType === 'NUM'
-  );
+  const NUMContentItems = mergedContentSequence.filter(group => group.ValueType === 'NUM');
 
   const measurement = {
     loaded: false,
@@ -484,10 +406,7 @@ function _processTID1410Measurement(mergedContentSequence) {
 
     if (MeasuredValueSequence) {
       measurement.labels.push(
-        _getLabelFromMeasuredValueSequence(
-          ConceptNameCodeSequence,
-          MeasuredValueSequence
-        )
+        _getLabelFromMeasuredValueSequence(ConceptNameCodeSequence, MeasuredValueSequence)
       );
     }
   });
@@ -496,32 +415,22 @@ function _processTID1410Measurement(mergedContentSequence) {
 }
 
 function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
-  const NUMContentItems = mergedContentSequence.filter(
-    group => group.ValueType === 'NUM'
-  );
+  const NUMContentItems = mergedContentSequence.filter(group => group.ValueType === 'NUM');
 
-  const UIDREFContentItem = mergedContentSequence.find(
-    group => group.ValueType === 'UIDREF'
-  );
+  const UIDREFContentItem = mergedContentSequence.find(group => group.ValueType === 'UIDREF');
 
   const TrackingIdentifierContentItem = mergedContentSequence.find(
-    item =>
-      item.ConceptNameCodeSequence.CodeValue ===
-      CodeNameCodeSequenceValues.TrackingIdentifier
+    item => item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.TrackingIdentifier
   );
 
   const finding = mergedContentSequence.find(
-    item =>
-      item.ConceptNameCodeSequence.CodeValue ===
-      CodeNameCodeSequenceValues.Finding
+    item => item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.Finding
   );
 
   const findingSites = mergedContentSequence.filter(
     item =>
-      item.ConceptNameCodeSequence.CodingSchemeDesignator ===
-        CodingSchemeDesignators.SRT &&
-      item.ConceptNameCodeSequence.CodeValue ===
-        CodeNameCodeSequenceValues.FindingSite
+      item.ConceptNameCodeSequence.CodingSchemeDesignator === CodingSchemeDesignators.SRT &&
+      item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.FindingSite
   );
 
   const measurement = {
@@ -537,8 +446,7 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
     CodingSchemeDesignators.CornerstoneCodeSchemes.includes(
       finding.ConceptCodeSequence.CodingSchemeDesignator
     ) &&
-    finding.ConceptCodeSequence.CodeValue ===
-      CodeNameCodeSequenceValues.CornerstoneFreeText
+    finding.ConceptCodeSequence.CodeValue === CodeNameCodeSequenceValues.CornerstoneFreeText
   ) {
     measurement.labels.push({
       label: CORNERSTONE_FREETEXT_CODE_VALUE,
@@ -553,8 +461,7 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
         CodingSchemeDesignators.CornerstoneCodeSchemes.includes(
           FindingSite.ConceptCodeSequence.CodingSchemeDesignator
         ) &&
-        FindingSite.ConceptCodeSequence.CodeValue ===
-          CodeNameCodeSequenceValues.CornerstoneFreeText
+        FindingSite.ConceptCodeSequence.CodeValue === CodeNameCodeSequenceValues.CornerstoneFreeText
     );
 
     if (cornerstoneFreeTextFindingSite) {
@@ -566,18 +473,12 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
   }
 
   NUMContentItems.forEach(item => {
-    const {
-      ConceptNameCodeSequence,
-      ContentSequence,
-      MeasuredValueSequence,
-    } = item;
+    const { ConceptNameCodeSequence, ContentSequence, MeasuredValueSequence } = item;
 
     const { ValueType } = ContentSequence;
 
     if (!ValueType === 'SCOORD') {
-      console.warn(
-        `Graphic ${ValueType} not currently supported, skipping annotation.`
-      );
+      console.warn(`Graphic ${ValueType} not currently supported, skipping annotation.`);
 
       return;
     }
@@ -590,10 +491,7 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
 
     if (MeasuredValueSequence) {
       measurement.labels.push(
-        _getLabelFromMeasuredValueSequence(
-          ConceptNameCodeSequence,
-          MeasuredValueSequence
-        )
+        _getLabelFromMeasuredValueSequence(ConceptNameCodeSequence, MeasuredValueSequence)
       );
     }
   });
@@ -633,17 +531,12 @@ function _getCoordsFromSCOORDOrSCOORD3D(item) {
   return coords;
 }
 
-function _getLabelFromMeasuredValueSequence(
-  ConceptNameCodeSequence,
-  MeasuredValueSequence
-) {
+function _getLabelFromMeasuredValueSequence(ConceptNameCodeSequence, MeasuredValueSequence) {
   const { CodeMeaning } = ConceptNameCodeSequence;
   const { NumericValue, MeasurementUnitsCodeSequence } = MeasuredValueSequence;
   const { CodeValue } = MeasurementUnitsCodeSequence;
 
-  const formatedNumericValue = NumericValue
-    ? Number(NumericValue).toFixed(2)
-    : '';
+  const formatedNumericValue = NumericValue ? Number(NumericValue).toFixed(2) : '';
 
   return {
     label: CodeMeaning,
@@ -653,24 +546,20 @@ function _getLabelFromMeasuredValueSequence(
 
 function _getReferencedImagesList(ImagingMeasurementReportContentSequence) {
   const ImageLibrary = ImagingMeasurementReportContentSequence.find(
-    item =>
-      item.ConceptNameCodeSequence.CodeValue ===
-      CodeNameCodeSequenceValues.ImageLibrary
+    item => item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.ImageLibrary
   );
 
-  const ImageLibraryGroup = _getSequenceAsArray(
-    ImageLibrary.ContentSequence
-  ).find(
-    item =>
-      item.ConceptNameCodeSequence.CodeValue ===
-      CodeNameCodeSequenceValues.ImageLibraryGroup
+  const ImageLibraryGroup = _getSequenceAsArray(ImageLibrary.ContentSequence).find(
+    item => item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.ImageLibraryGroup
   );
 
   const referencedImages = [];
 
   _getSequenceAsArray(ImageLibraryGroup.ContentSequence).forEach(item => {
     const { ReferencedSOPSequence } = item;
-    if (!ReferencedSOPSequence) return;
+    if (!ReferencedSOPSequence) {
+      return;
+    }
     for (const ref of _getSequenceAsArray(ReferencedSOPSequence)) {
       if (ref.ReferencedSOPClassUID) {
         const { ReferencedSOPClassUID, ReferencedSOPInstanceUID } = ref;
@@ -687,7 +576,9 @@ function _getReferencedImagesList(ImagingMeasurementReportContentSequence) {
 }
 
 function _getSequenceAsArray(sequence) {
-  if (!sequence) return [];
+  if (!sequence) {
+    return [];
+  }
   return Array.isArray(sequence) ? sequence : [sequence];
 }
 

extensions/cornerstone-dicom-sr/src/index.tsx

@@ -1,8 +1,6 @@
 import React from 'react';
 import getSopClassHandlerModule from './getSopClassHandlerModule';
-import getHangingProtocolModule, {
-  srProtocol,
-} from './getHangingProtocolModule';
+import getHangingProtocolModule, { srProtocol } from './getHangingProtocolModule';
 import onModeEnter from './onModeEnter';
 import getCommandsModule from './commandsModule';
 import preRegistration from './init';
@@ -12,9 +10,7 @@ import hydrateStructuredReport from './utils/hydrateStructuredReport';
 import createReferencedImageDisplaySet from './utils/createReferencedImageDisplaySet';
 
 const Component = React.lazy(() => {
-  return import(
-    /* webpackPrefetch: true */ './viewports/OHIFCornerstoneSRViewport'
-  );
+  return import(/* webpackPrefetch: true */ './viewports/OHIFCornerstoneSRViewport');
 });
 
 const OHIFCornerstoneSRViewport = props => {

extensions/cornerstone-dicom-sr/src/init.ts

@@ -18,9 +18,7 @@ import toolNames from './tools/toolNames';
 /**
  * @param {object} configuration
  */
-export default function init({
-  configuration = {},
-}: Types.Extensions.ExtensionParams): void {
+export default function init({ configuration = {} }: Types.Extensions.ExtensionParams): void {
   addTool(DICOMSRDisplayTool);
   addToolInstance(toolNames.SRLength, LengthTool, {});
   addToolInstance(toolNames.SRBidirectional, BidirectionalTool);

extensions/cornerstone-dicom-sr/src/tools/DICOMSRDisplayTool.ts

@@ -40,49 +40,32 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
   isPointNearTool = () => null;
   getHandleNearImagePoint = () => null;
 
-  renderAnnotation = (
-    enabledElement: Types.IEnabledElement,
-    svgDrawingHelper: any
-  ): void => {
+  renderAnnotation = (enabledElement: Types.IEnabledElement, svgDrawingHelper: any): void => {
     const { viewport } = enabledElement;
     const { element } = viewport;
 
-    let annotations = annotation.state.getAnnotations(
-      this.getToolName(),
-      element
-    );
+    let annotations = annotation.state.getAnnotations(this.getToolName(), element);
 
     // Todo: We don't need this anymore, filtering happens in triggerAnnotationRender
     if (!annotations?.length) {
       return;
     }
 
-    annotations = this.filterInteractableAnnotationsForElement(
-      element,
-      annotations
-    );
+    annotations = this.filterInteractableAnnotationsForElement(element, annotations);
 
     if (!annotations?.length) {
       return;
     }
 
-    const trackingUniqueIdentifiersForElement = getTrackingUniqueIdentifiersForElement(
-      element
-    );
+    const trackingUniqueIdentifiersForElement = getTrackingUniqueIdentifiersForElement(element);
 
-    const {
-      activeIndex,
-      trackingUniqueIdentifiers,
-    } = trackingUniqueIdentifiersForElement;
+    const { activeIndex, trackingUniqueIdentifiers } = trackingUniqueIdentifiersForElement;
 
-    const activeTrackingUniqueIdentifier =
-      trackingUniqueIdentifiers[activeIndex];
+    const activeTrackingUniqueIdentifier = trackingUniqueIdentifiers[activeIndex];
 
     // Filter toolData to only render the data for the active SR.
     const filteredAnnotations = annotations.filter(annotation =>
-      trackingUniqueIdentifiers.includes(
-        annotation.data?.cachedStats?.TrackingUniqueIdentifier
-      )
+      trackingUniqueIdentifiers.includes(annotation.data?.cachedStats?.TrackingUniqueIdentifier)
     );
 
     if (!viewport._actors?.size) {
@@ -138,8 +121,7 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
             break;
           case SCOORD_TYPES.ELLIPSE:
             renderMethod = this.renderEllipse;
-            canvasCoordinatesAdapter =
-              utilities.math.ellipse.getCanvasEllipseCorners;
+            canvasCoordinatesAdapter = utilities.math.ellipse.getCanvasEllipseCorners;
             break;
           default:
             throw new Error(`Unsupported GraphicType: ${GraphicType}`);
@@ -221,15 +203,9 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
     renderableData.map((data, index) => {
       canvasCoordinates = data.map(p => viewport.worldToCanvas(p));
       const handleGroupUID = '0';
-      drawing.drawHandles(
-        svgDrawingHelper,
-        annotationUID,
-        handleGroupUID,
-        canvasCoordinates,
-        {
-          color: options.color,
-        }
-      );
+      drawing.drawHandles(svgDrawingHelper, annotationUID, handleGroupUID, canvasCoordinates, {
+        color: options.color,
+      });
     });
   }
 
@@ -248,10 +224,7 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
       canvasCoordinates.push(viewport.worldToCanvas(point));
 
       // We get the other point for the arrow by using the image size
-      const imagePixelModule = metaData.get(
-        'imagePixelModule',
-        referencedImageId
-      );
+      const imagePixelModule = metaData.get('imagePixelModule', referencedImageId);
 
       let xOffset = 10;
       let yOffset = 10;
@@ -309,23 +282,19 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
 
       const rotation = viewport.getRotation();
 
-      canvasCoordinates = ellipsePointsWorld.map(p =>
-        viewport.worldToCanvas(p)
-      );
+      canvasCoordinates = ellipsePointsWorld.map(p => viewport.worldToCanvas(p));
       let canvasCorners;
       if (rotation == 90 || rotation == 270) {
-        canvasCorners = <Array<Types.Point2>>(
-          utilities.math.ellipse.getCanvasEllipseCorners([
-            canvasCoordinates[2],
-            canvasCoordinates[3],
-            canvasCoordinates[0],
-            canvasCoordinates[1],
-          ])
-        );
+        canvasCorners = utilities.math.ellipse.getCanvasEllipseCorners([
+          canvasCoordinates[2],
+          canvasCoordinates[3],
+          canvasCoordinates[0],
+          canvasCoordinates[1],
+        ]) as Array<Types.Point2>;
       } else {
-        canvasCorners = <Array<Types.Point2>>(
-          utilities.math.ellipse.getCanvasEllipseCorners(canvasCoordinates)
-        );
+        canvasCorners = utilities.math.ellipse.getCanvasEllipseCorners(
+          canvasCoordinates
+        ) as Array<Types.Point2>;
       }
 
       const lineUID = `${index}`;
@@ -368,23 +337,14 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
       adaptedCanvasCoordinates = canvasCoordinatesAdapter(canvasCoordinates);
     }
     const textLines = this._getTextBoxLinesFromLabels(label);
-    const canvasTextBoxCoords = utilities.drawing.getTextBoxCoordsCanvas(
-      adaptedCanvasCoordinates
-    );
+    const canvasTextBoxCoords = utilities.drawing.getTextBoxCoordsCanvas(adaptedCanvasCoordinates);
 
-    annotation.data.handles.textBox.worldPosition = viewport.canvasToWorld(
-      canvasTextBoxCoords
-    );
+    annotation.data.handles.textBox.worldPosition = viewport.canvasToWorld(canvasTextBoxCoords);
 
-    const textBoxPosition = viewport.worldToCanvas(
-      annotation.data.handles.textBox.worldPosition
-    );
+    const textBoxPosition = viewport.worldToCanvas(annotation.data.handles.textBox.worldPosition);
 
     const textBoxUID = '1';
-    const textBoxOptions = this.getLinkedTextBoxStyle(
-      styleSpecifier,
-      annotation
-    );
+    const textBoxOptions = this.getLinkedTextBoxStyle(styleSpecifier, annotation);
 
     const boundingBox = drawing.drawLinkedTextBox(
       svgDrawingHelper,

extensions/cornerstone-dicom-sr/src/tools/modules/dicomSRModule.js

@@ -27,15 +27,11 @@ function setTrackingUniqueIdentifiersForElement(
   };
 }
 
-function setActiveTrackingUniqueIdentifierForElement(
-  element,
-  TrackingUniqueIdentifier
-) {
+function setActiveTrackingUniqueIdentifierForElement(element, TrackingUniqueIdentifier) {
   const enabledElement = getEnabledElement(element);
   const { viewport } = enabledElement;
 
-  const trackingIdentifiersForElement =
-    state.trackingIdentifiersByViewportId[viewport.id];
+  const trackingIdentifiersForElement = state.trackingIdentifiersByViewportId[viewport.id];
 
   if (trackingIdentifiersForElement) {
     const activeIndex = trackingIdentifiersForElement.trackingUniqueIdentifiers.findIndex(

extensions/cornerstone-dicom-sr/src/utils/addMeasurement.ts

@@ -8,11 +8,7 @@ const EPSILON = 1e-4;
 
 const supportedLegacyCornerstoneTags = ['cornerstoneTools@^4.0.0'];
 
-export default function addMeasurement(
-  measurement,
-  imageId,
-  displaySetInstanceUID
-) {
+export default function addMeasurement(measurement, imageId, displaySetInstanceUID) {
   // TODO -> Render rotated ellipse .
   const toolName = toolNames.DICOMSRDisplay;
 
@@ -31,12 +27,7 @@ export default function addMeasurement(
     }
 
     measurementData.renderableData[GraphicType].push(
-      _getRenderableData(
-        GraphicType,
-        GraphicData,
-        imageId,
-        measurement.TrackingIdentifier
-      )
+      _getRenderableData(GraphicType, GraphicData, imageId, measurement.TrackingIdentifier)
     );
   });
 
@@ -86,12 +77,7 @@ export default function addMeasurement(
   delete measurement.coords;
 }
 
-function _getRenderableData(
-  GraphicType,
-  GraphicData,
-  imageId,
-  TrackingIdentifier
-) {
+function _getRenderableData(GraphicType, GraphicData, imageId, TrackingIdentifier) {
   const [cornerstoneTag, toolName] = TrackingIdentifier.split(':');
 
   let renderableData: csTypes.Point3[];
@@ -207,38 +193,22 @@ function _getRenderableData(
         throw new Error('imageId does not have imagePlaneModule metadata');
       }
 
-      const {
-        columnCosines,
-      }: { columnCosines: csTypes.Point3 } = imagePlaneModule;
+      const { columnCosines }: { columnCosines: csTypes.Point3 } = imagePlaneModule;
 
       // find which axis is parallel to the columnCosines
       const columnCosinesVec = vec3.fromValues(...columnCosines);
 
-      const projectedMajorAxisOnColVec = Math.abs(
-        vec3.dot(columnCosinesVec, majorAxisVec)
-      );
-      const projectedMinorAxisOnColVec = Math.abs(
-        vec3.dot(columnCosinesVec, minorAxisVec)
-      );
+      const projectedMajorAxisOnColVec = Math.abs(vec3.dot(columnCosinesVec, majorAxisVec));
+      const projectedMinorAxisOnColVec = Math.abs(vec3.dot(columnCosinesVec, minorAxisVec));
 
       const absoluteOfMajorDotProduct = Math.abs(projectedMajorAxisOnColVec);
       const absoluteOfMinorDotProduct = Math.abs(projectedMinorAxisOnColVec);
 
       renderableData = [];
       if (Math.abs(absoluteOfMajorDotProduct - 1) < EPSILON) {
-        renderableData = [
-          pointsWorld[0],
-          pointsWorld[1],
-          pointsWorld[2],
-          pointsWorld[3],
-        ];
+        renderableData = [pointsWorld[0], pointsWorld[1], pointsWorld[2], pointsWorld[3]];
       } else if (Math.abs(absoluteOfMinorDotProduct - 1) < EPSILON) {
-        renderableData = [
-          pointsWorld[2],
-          pointsWorld[3],
-          pointsWorld[0],
-          pointsWorld[1],
-        ];
+        renderableData = [pointsWorld[2], pointsWorld[3], pointsWorld[0], pointsWorld[1]];
       } else {
         console.warn('OBLIQUE ELLIPSE NOT YET SUPPORTED');
       }

extensions/cornerstone-dicom-sr/src/utils/addToolInstance.ts

@@ -1,10 +1,6 @@
 import { addTool } from '@cornerstonejs/tools';
 
-export default function addToolInstance(
-  name: string,
-  toolClass,
-  configuration?
-): void {
+export default function addToolInstance(name: string, toolClass, configuration?): void {
   class InstanceClass extends toolClass {
     static toolName = name;
   }

extensions/cornerstone-dicom-sr/src/utils/createReferencedImageDisplaySet.ts

@@ -3,12 +3,11 @@ import { DisplaySetService, classes } from '@ohif/core';
 const ImageSet = classes.ImageSet;
 
 const findInstance = (measurement, displaySetService: DisplaySetService) => {
-  const { displaySetInstanceUID, ReferencedSOPInstanceUID: sopUid } =
-    measurement;
-  const referencedDisplaySet = displaySetService.getDisplaySetByUID(
-    displaySetInstanceUID
-  );
-  if (!referencedDisplaySet.images) return;
+  const { displaySetInstanceUID, ReferencedSOPInstanceUID: sopUid } = measurement;
+  const referencedDisplaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
+  if (!referencedDisplaySet.images) {
+    return;
+  }
   return referencedDisplaySet.images.find(it => it.SOPInstanceUID === sopUid);
 };
 
@@ -16,16 +15,17 @@ const findInstance = (measurement, displaySetService: DisplaySetService) => {
  * contained within the provided display set.
  * @return an array of instances referenced.
  */
-const findReferencedInstances = (
-  displaySetService: DisplaySetService,
-  displaySet
-) => {
+const findReferencedInstances = (displaySetService: DisplaySetService, displaySet) => {
   const instances = [];
   const instanceById = {};
   for (const measurement of displaySet.measurements) {
     const { imageId } = measurement;
-    if (!imageId) continue;
-    if (instanceById[imageId]) continue;
+    if (!imageId) {
+      continue;
+    }
+    if (instanceById[imageId]) {
+      continue;
+    }
 
     const instance = findInstance(measurement, displaySetService);
     if (!instance) {
@@ -50,7 +50,7 @@ const findReferencedInstances = (
 const createReferencedImageDisplaySet = (displaySetService, displaySet) => {
   const instances = findReferencedInstances(displaySetService, displaySet);
   // This will be a  member function of the created image set
-  const updateInstances = function() {
+  const updateInstances = function () {
     this.images.splice(
       0,
       this.images.length,

extensions/cornerstone-dicom-sr/src/utils/findInstanceMetadataBySopInstanceUid.js

@@ -9,11 +9,12 @@ const findInstanceMetadataBySopInstanceUID = (displaySets, SOPInstanceUID) => {
   let instanceFound;
 
   displaySets.find(displaySet => {
-    if (!displaySet.images) return false;
+    if (!displaySet.images) {
+      return false;
+    }
 
     instanceFound = displaySet.images.find(
-      instanceMetadata =>
-        instanceMetadata.getSOPInstanceUID() === SOPInstanceUID
+      instanceMetadata => instanceMetadata.getSOPInstanceUID() === SOPInstanceUID
     );
 
     return !!instanceFound;

extensions/cornerstone-dicom-sr/src/utils/findMostRecentStructuredReport.js

@@ -18,10 +18,7 @@ const findMostRecentStructuredReport = studies => {
       }
 
       if (isStructuredReportSeries(series)) {
-        if (
-          !mostRecentStructuredReport ||
-          compareSeriesDate(series, mostRecentStructuredReport)
-        ) {
+        if (!mostRecentStructuredReport || compareSeriesDate(series, mostRecentStructuredReport)) {
           mostRecentStructuredReport = series;
         }
       }
@@ -38,10 +35,7 @@ const findMostRecentStructuredReport = studies => {
  * @returns {boolean}
  */
 const isStructuredReportSeries = series => {
-  const supportedSopClassUIDs = [
-    '1.2.840.10008.5.1.4.1.1.88.22',
-    '1.2.840.10008.5.1.4.1.1.11.1',
-  ];
+  const supportedSopClassUIDs = ['1.2.840.10008.5.1.4.1.1.88.22', '1.2.840.10008.5.1.4.1.1.11.1'];
 
   const firstInstance = series.getFirstInstance();
   const SOPClassUID = firstInstance.getData().metadata.SOPClassUID;

extensions/cornerstone-dicom-sr/src/utils/getFilteredCornerstoneToolState.ts

@@ -2,17 +2,12 @@ import OHIF from '@ohif/core';
 import { annotation } from '@cornerstonejs/tools';
 const { log } = OHIF;
 
-function getFilteredCornerstoneToolState(
-  measurementData,
-  additionalFindingTypes
-) {
+function getFilteredCornerstoneToolState(measurementData, additionalFindingTypes) {
   const filteredToolState = {};
 
   function addToFilteredToolState(annotation, toolType) {
     if (!annotation.metadata?.referencedImageId) {
-      log.warn(
-        `[DICOMSR] No referencedImageId found for ${toolType} ${annotation.id}`
-      );
+      log.warn(`[DICOMSR] No referencedImageId found for ${toolType} ${annotation.id}`);
       return;
     }
 
@@ -30,9 +25,7 @@ function getFilteredCornerstoneToolState(
       };
     }
 
-    const measurementDataI = measurementData.find(
-      md => md.uid === annotation.annotationUID
-    );
+    const measurementDataI = measurementData.find(md => md.uid === annotation.annotationUID);
     const toolData = imageIdSpecificToolState[toolType].data;
 
     let { finding } = measurementDataI;
@@ -77,9 +70,7 @@ function getFilteredCornerstoneToolState(
   for (let i = 0; i < framesOfReference.length; i++) {
     const frameOfReference = framesOfReference[i];
 
-    const frameOfReferenceAnnotations = annotationManager.getAnnotations(
-      frameOfReference
-    );
+    const frameOfReferenceAnnotations = annotationManager.getAnnotations(frameOfReference);
 
     const toolTypes = Object.keys(frameOfReferenceAnnotations);
 
@@ -91,9 +82,7 @@ function getFilteredCornerstoneToolState(
       if (annotations) {
         for (let k = 0; k < annotations.length; k++) {
           const annotation = annotations[k];
-          const uidIndex = uids.findIndex(
-            uid => uid === annotation.annotationUID
-          );
+          const uidIndex = uids.findIndex(uid => uid === annotation.annotationUID);
 
           if (uidIndex !== -1) {
             addToFilteredToolState(annotation, toolType);

extensions/cornerstone-dicom-sr/src/utils/getLabelFromDCMJSImportedToolData.js

@@ -9,9 +9,7 @@
 export default function getLabelFromDCMJSImportedToolData(toolData) {
   const { findingSites = [], finding } = toolData;
 
-  let freeTextLabel = findingSites.find(
-    fs => fs.CodeValue === 'CORNERSTONEFREETEXT'
-  );
+  let freeTextLabel = findingSites.find(fs => fs.CodeValue === 'CORNERSTONEFREETEXT');
 
   if (freeTextLabel) {
     return freeTextLabel.CodeMeaning;

extensions/cornerstone-dicom-sr/src/utils/hydrateStructuredReport.js

@@ -2,6 +2,8 @@ import { utilities, metaData } from '@cornerstonejs/core';
 import OHIF, { DicomMetadataStore } from '@ohif/core';
 import getLabelFromDCMJSImportedToolData from './getLabelFromDCMJSImportedToolData';
 import { adaptersSR } from '@cornerstonejs/adapters';
+import { annotation as CsAnnotation } from '@cornerstonejs/tools';
+const { locking } = CsAnnotation;
 
 const { guid } = OHIF.utils;
 const { MeasurementReport, CORNERSTONE_3D_TAG } = adaptersSR.Cornerstone3D;
@@ -12,20 +14,26 @@ const CORNERSTONE_3D_TOOLS_SOURCE_VERSION = '0.1';
 const supportedLegacyCornerstoneTags = ['cornerstoneTools@^4.0.0'];
 
 const convertCode = (codingValues, code) => {
-  if (!code || code.CodingSchemeDesignator === 'CORNERSTONEJS') return;
+  if (!code || code.CodingSchemeDesignator === 'CORNERSTONEJS') {
+    return;
+  }
   const ref = `${code.CodingSchemeDesignator}:${code.CodeValue}`;
   const ret = { ...codingValues[ref], ref, ...code, text: code.CodeMeaning };
   return ret;
 };
 
 const convertSites = (codingValues, sites) => {
-  if (!sites || !sites.length) return;
+  if (!sites || !sites.length) {
+    return;
+  }
   const ret = [];
   // Do as a loop to convert away from Proxy instances
   for (let i = 0; i < sites.length; i++) {
     // Deal with irregular conversion from dcmjs
     const site = convertCode(codingValues, sites[i][0] || sites[i]);
-    if (site) ret.push(site);
+    if (site) {
+      ret.push(site);
+    }
   }
   return (ret.length && ret) || undefined;
 };
@@ -35,23 +43,16 @@ const convertSites = (codingValues, sites) => {
  *
  */
 export default function hydrateStructuredReport(
-  { servicesManager, extensionManager },
+  { servicesManager, extensionManager, appConfig },
   displaySetInstanceUID
 ) {
+  const annotationManager = CsAnnotation.state.getAnnotationManager();
+  const disableEditing = appConfig?.disableEditing;
   const dataSource = extensionManager.getActiveDataSource()[0];
-  const {
-    measurementService,
-    displaySetService,
-    customizationService,
-  } = servicesManager.services;
+  const { measurementService, displaySetService, customizationService } = servicesManager.services;
 
-  const codingValues = customizationService.getCustomization(
-    'codingValues',
-    {}
-  );
-  const displaySet = displaySetService.getDisplaySetByUID(
-    displaySetInstanceUID
-  );
+  const codingValues = customizationService.getCustomization('codingValues', {});
+  const displaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
 
   // TODO -> We should define a strict versioning somewhere.
   const mappings = measurementService.getSourceMappings(
@@ -115,16 +116,14 @@ export default function hydrateStructuredReport(
 
   // TODO: notification if no hydratable?
   Object.keys(hydratableMeasurementsInSR).forEach(annotationType => {
-    const toolDataForAnnotationType =
-      hydratableMeasurementsInSR[annotationType];
+    const toolDataForAnnotationType = hydratableMeasurementsInSR[annotationType];
 
     toolDataForAnnotationType.forEach(toolData => {
       // Add the measurement to toolState
       // dcmjs and Cornerstone3D has structural defect in supporting multi-frame
       // files, and looking up the imageId from sopInstanceUIDToImageId results
       // in the wrong value.
-      const frameNumber =
-        (toolData.annotation.data && toolData.annotation.data.frameNumber) || 1;
+      const frameNumber = (toolData.annotation.data && toolData.annotation.data.frameNumber) || 1;
       const imageId =
         imageIdsForToolState[toolData.sopInstanceUid][frameNumber] ||
         sopInstanceUIDToImageId[toolData.sopInstanceUid];
@@ -140,10 +139,7 @@ export default function hydrateStructuredReport(
 
   for (let i = 0; i < imageIds.length; i++) {
     const imageId = imageIds[i];
-    const { SeriesInstanceUID, StudyInstanceUID } = metaData.get(
-      'instance',
-      imageId
-    );
+    const { SeriesInstanceUID, StudyInstanceUID } = metaData.get('instance', imageId);
 
     if (!SeriesInstanceUIDs.includes(SeriesInstanceUID)) {
       SeriesInstanceUIDs.push(SeriesInstanceUID);
@@ -152,23 +148,19 @@ export default function hydrateStructuredReport(
     if (!targetStudyInstanceUID) {
       targetStudyInstanceUID = StudyInstanceUID;
     } else if (targetStudyInstanceUID !== StudyInstanceUID) {
-      console.warn(
-        'NO SUPPORT FOR SRs THAT HAVE MEASUREMENTS FROM MULTIPLE STUDIES.'
-      );
+      console.warn('NO SUPPORT FOR SRs THAT HAVE MEASUREMENTS FROM MULTIPLE STUDIES.');
     }
   }
 
   Object.keys(hydratableMeasurementsInSR).forEach(annotationType => {
-    const toolDataForAnnotationType =
-      hydratableMeasurementsInSR[annotationType];
+    const toolDataForAnnotationType = hydratableMeasurementsInSR[annotationType];
 
     toolDataForAnnotationType.forEach(toolData => {
       // Add the measurement to toolState
       // dcmjs and Cornerstone3D has structural defect in supporting multi-frame
       // files, and looking up the imageId from sopInstanceUIDToImageId results
       // in the wrong value.
-      const frameNumber =
-        (toolData.annotation.data && toolData.annotation.data.frameNumber) || 1;
+      const frameNumber = (toolData.annotation.data && toolData.annotation.data.frameNumber) || 1;
       const imageId =
         imageIdsForToolState[toolData.sopInstanceUid][frameNumber] ||
         sopInstanceUIDToImageId[toolData.sopInstanceUid];
@@ -198,21 +190,13 @@ export default function hydrateStructuredReport(
         CORNERSTONE_3D_TOOLS_SOURCE_VERSION
       );
       annotation.data.label = getLabelFromDCMJSImportedToolData(toolData);
-      annotation.data.finding = convertCode(
-        codingValues,
-        toolData.finding?.[0]
-      );
-      annotation.data.findingSites = convertSites(
-        codingValues,
-        toolData.findingSites
-      );
+      annotation.data.finding = convertCode(codingValues, toolData.finding?.[0]);
+      annotation.data.findingSites = convertSites(codingValues, toolData.findingSites);
       annotation.data.site = annotation.data.findingSites?.[0];
 
-      const matchingMapping = mappings.find(
-        m => m.annotationType === annotationType
-      );
+      const matchingMapping = mappings.find(m => m.annotationType === annotationType);
 
-      measurementService.addRawMeasurement(
+      const newAnnotationUID = measurementService.addRawMeasurement(
         source,
         annotationType,
         { annotation },
@@ -220,6 +204,11 @@ export default function hydrateStructuredReport(
         dataSource
       );
 
+      if (disableEditing) {
+        const addedAnnotation = annotationManager.getAnnotation(newAnnotationUID);
+        locking.setAnnotationLocked(addedAnnotation, true);
+      }
+
       if (!imageIds.includes(imageId)) {
         imageIds.push(imageId);
       }
@@ -245,15 +234,14 @@ function _mapLegacyDataSet(dataset) {
   );
 
   // Retrieve the Measurements themselves
-  const measurementGroups = toArray(
-    imagingMeasurementContent.ContentSequence
-  ).filter(codeMeaningEquals(GROUP));
+  const measurementGroups = toArray(imagingMeasurementContent.ContentSequence).filter(
+    codeMeaningEquals(GROUP)
+  );
 
   // For each of the supported measurement types, compute the measurement data
   const measurementData = {};
 
-  const cornerstoneToolClasses =
-    MeasurementReport.CORNERSTONE_TOOL_CLASSES_BY_UTILITY_TYPE;
+  const cornerstoneToolClasses = MeasurementReport.CORNERSTONE_TOOL_CLASSES_BY_UTILITY_TYPE;
 
   const registeredToolClasses = [];
 
@@ -263,13 +251,10 @@ function _mapLegacyDataSet(dataset) {
   });
 
   measurementGroups.forEach((measurementGroup, index) => {
-    const measurementGroupContentSequence = toArray(
-      measurementGroup.ContentSequence
-    );
+    const measurementGroupContentSequence = toArray(measurementGroup.ContentSequence);
 
     const TrackingIdentifierGroup = measurementGroupContentSequence.find(
-      contentItem =>
-        contentItem.ConceptNameCodeSequence.CodeMeaning === TRACKING_IDENTIFIER
+      contentItem => contentItem.ConceptNameCodeSequence.CodeMeaning === TRACKING_IDENTIFIER
     );
 
     const TrackingIdentifier = TrackingIdentifierGroup.TextValue;

extensions/cornerstone-dicom-sr/src/utils/isRehydratable.js

@@ -1,8 +1,7 @@
 import { adaptersSR } from '@cornerstonejs/adapters';
 
 const cornerstoneAdapters =
-  adaptersSR.Cornerstone3D.MeasurementReport
-    .CORNERSTONE_TOOL_CLASSES_BY_UTILITY_TYPE;
+  adaptersSR.Cornerstone3D.MeasurementReport.CORNERSTONE_TOOL_CLASSES_BY_UTILITY_TYPE;
 
 const supportedLegacyCornerstoneTags = ['cornerstoneTools@^4.0.0'];
 const CORNERSTONE_3D_TAG = cornerstoneAdapters.CORNERSTONE_3D_TAG;
@@ -24,8 +23,7 @@ export default function isRehydratable(displaySet, mappings) {
 
   const adapterKeys = Object.keys(cornerstoneAdapters).filter(
     adapterKey =>
-      typeof cornerstoneAdapters[adapterKey]
-        .isValidCornerstoneTrackingIdentifier === 'function'
+      typeof cornerstoneAdapters[adapterKey].isValidCornerstoneTrackingIdentifier === 'function'
   );
 
   const adapters = [];
@@ -48,19 +46,13 @@ export default function isRehydratable(displaySet, mappings) {
 
       const mappedTrackingIdentifier = `${cornerstoneTag}:${toolName}`;
 
-      return adapter.isValidCornerstoneTrackingIdentifier(
-        mappedTrackingIdentifier
-      );
+      return adapter.isValidCornerstoneTrackingIdentifier(mappedTrackingIdentifier);
     });
 
     if (hydratable) {
       return true;
     }
-    console.log(
-      'Measurement is not rehydratable',
-      TrackingIdentifier,
-      measurements[i]
-    );
+    console.log('Measurement is not rehydratable', TrackingIdentifier, measurements[i]);
   }
 
   console.log('No measurements found which were rehydratable');

extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx

@@ -7,11 +7,11 @@ import { setTrackingUniqueIdentifiersForElement } from '../tools/modules/dicomSR
 
 import { Icon, Tooltip, useViewportGrid, ViewportActionBar } from '@ohif/ui';
 import hydrateStructuredReport from '../utils/hydrateStructuredReport';
+import { useAppConfig } from '@state';
 
 const { formatDate } = utils;
 
-const MEASUREMENT_TRACKING_EXTENSION_ID =
-  '@ohif/extension-measurement-tracking';
+const MEASUREMENT_TRACKING_EXTENSION_ID = '@ohif/extension-measurement-tracking';
 
 const SR_TOOLGROUP_BASE_NAME = 'SRToolGroup';
 
@@ -20,18 +20,18 @@ function OHIFCornerstoneSRViewport(props) {
     children,
     dataSource,
     displaySets,
-    viewportIndex,
     viewportLabel,
     viewportOptions,
     servicesManager,
     extensionManager,
   } = props;
 
-  const {
-    displaySetService,
-    cornerstoneViewportService,
-    measurementService,
-  } = servicesManager.services;
+  const [appConfig] = useAppConfig();
+
+  const { displaySetService, cornerstoneViewportService, measurementService } =
+    servicesManager.services;
+
+  const viewportId = viewportOptions.viewportId;
 
   // SR viewport will always have a single display set
   if (displaySets.length > 1) {
@@ -43,15 +43,10 @@ function OHIFCornerstoneSRViewport(props) {
   const [viewportGrid, viewportGridService] = useViewportGrid();
   const [measurementSelected, setMeasurementSelected] = useState(0);
   const [measurementCount, setMeasurementCount] = useState(1);
-  const [activeImageDisplaySetData, setActiveImageDisplaySetData] = useState(
-    null
-  );
-  const [
-    referencedDisplaySetMetadata,
-    setReferencedDisplaySetMetadata,
-  ] = useState(null);
+  const [activeImageDisplaySetData, setActiveImageDisplaySetData] = useState(null);
+  const [referencedDisplaySetMetadata, setReferencedDisplaySetMetadata] = useState(null);
   const [element, setElement] = useState(null);
-  const { viewports, activeViewportIndex } = viewportGrid;
+  const { viewports, activeViewportId } = viewportGrid;
 
   // Optional hook into tracking extension, if present.
   let trackedMeasurements;
@@ -76,16 +71,14 @@ function OHIFCornerstoneSRViewport(props) {
     sendTrackedMeasurementsEvent = (eventName, { displaySetInstanceUID }) => {
       measurementService.clearMeasurements();
       const { SeriesInstanceUIDs } = hydrateStructuredReport(
-        { servicesManager, extensionManager },
+        { servicesManager, extensionManager, appConfig },
         displaySetInstanceUID
       );
-      const displaySets = displaySetService.getDisplaySetsForSeries(
-        SeriesInstanceUIDs[0]
-      );
+      const displaySets = displaySetService.getDisplaySetsForSeries(SeriesInstanceUIDs[0]);
       if (displaySets.length) {
         viewportGridService.setDisplaySetsForViewports([
           {
-            viewportIndex: activeViewportIndex,
+            viewportId: activeViewportId,
             displaySetInstanceUIDs: [displaySets[0].displaySetInstanceUID],
           },
         ]);
@@ -123,11 +116,7 @@ function OHIFCornerstoneSRViewport(props) {
 
   const updateViewport = useCallback(
     newMeasurementSelected => {
-      const {
-        StudyInstanceUID,
-        displaySetInstanceUID,
-        sopClassUids,
-      } = srDisplaySet;
+      const { StudyInstanceUID, displaySetInstanceUID, sopClassUids } = srDisplaySet;
 
       if (!StudyInstanceUID || !displaySetInstanceUID) {
         return;
@@ -136,9 +125,7 @@ function OHIFCornerstoneSRViewport(props) {
       if (sopClassUids && sopClassUids.length > 1) {
         // Todo: what happens if there are multiple SOP Classes? Why we are
         // not throwing an error?
-        console.warn(
-          'More than one SOPClassUID in the same series is not yet supported.'
-        );
+        console.warn('More than one SOPClassUID in the same series is not yet supported.');
       }
 
       _getViewportReferencedDisplaySetData(
@@ -160,19 +147,11 @@ function OHIFCornerstoneSRViewport(props) {
           // imageIdIndex will handle it by updating the viewport, but if they
           // are the same we just need to use measurementService to jump to the
           // new measurement
-          const viewportInfo = cornerstoneViewportService.getViewportInfoByIndex(
-            viewportIndex
-          );
-
-          const csViewport = cornerstoneViewportService.getCornerstoneViewport(
-            viewportInfo.getViewportId()
-          );
+          const csViewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
 
           const imageIds = csViewport.getImageIds();
 
-          const imageIdIndex = imageIds.indexOf(
-            measurements[newMeasurementSelected].imageId
-          );
+          const imageIdIndex = imageIds.indexOf(measurements[newMeasurementSelected].imageId);
 
           if (imageIdIndex !== -1) {
             csViewport.setImageIdIndex(imageIdIndex);
@@ -180,7 +159,7 @@ function OHIFCornerstoneSRViewport(props) {
         }
       });
     },
-    [dataSource, srDisplaySet, activeImageDisplaySetData, viewportIndex]
+    [dataSource, srDisplaySet, activeImageDisplaySetData, viewportId]
   );
 
   const getCornerstoneViewport = useCallback(() => {
@@ -225,9 +204,10 @@ function OHIFCornerstoneSRViewport(props) {
         }}
         onElementEnabled={onElementEnabled}
         initialImageIndex={initialImageIndex}
+        isJumpToMeasurementDisabled={true}
       ></Component>
     );
-  }, [activeImageDisplaySetData, viewportIndex, measurementSelected]);
+  }, [activeImageDisplaySetData, viewportId, measurementSelected]);
 
   const onMeasurementChange = useCallback(
     direction => {
@@ -250,12 +230,7 @@ function OHIFCornerstoneSRViewport(props) {
       setTrackingIdentifiers(newMeasurementSelected);
       updateViewport(newMeasurementSelected);
     },
-    [
-      measurementSelected,
-      measurementCount,
-      updateViewport,
-      setTrackingIdentifiers,
-    ]
+    [measurementSelected, measurementCount, updateViewport, setTrackingIdentifiers]
   );
 
   /**
@@ -265,12 +240,10 @@ function OHIFCornerstoneSRViewport(props) {
     const onDisplaySetsRemovedSubscription = displaySetService.subscribe(
       displaySetService.EVENTS.DISPLAY_SETS_REMOVED,
       ({ displaySetInstanceUIDs }) => {
-        const activeViewport = viewports[activeViewportIndex];
-        if (
-          displaySetInstanceUIDs.includes(activeViewport.displaySetInstanceUID)
-        ) {
+        const activeViewport = viewports[activeViewportId];
+        if (displaySetInstanceUIDs.includes(activeViewport.displaySetInstanceUID)) {
           viewportGridService.setDisplaySetsForViewport({
-            viewportIndex: activeViewportIndex,
+            viewportId: activeViewportId,
             displaySetInstanceUIDs: [],
           });
         }
@@ -337,7 +310,7 @@ function OHIFCornerstoneSRViewport(props) {
       return (
         child &&
         React.cloneElement(child, {
-          viewportIndex,
+          viewportId,
           key: index,
         })
       );
@@ -369,7 +342,7 @@ function OHIFCornerstoneSRViewport(props) {
         getStatusComponent={() =>
           _getStatusComponent({
             srDisplaySet,
-            viewportIndex,
+            viewportId,
             isTracked: false,
             isRehydratable: srDisplaySet.isRehydratable,
             isLocked,
@@ -383,23 +356,19 @@ function OHIFCornerstoneSRViewport(props) {
           currentSeries: SeriesNumber,
           seriesDescription: SeriesDescription || '',
           patientInformation: {
-            patientName: PatientName
-              ? OHIF.utils.formatPN(PatientName.Alphabetic)
-              : '',
+            patientName: PatientName ? OHIF.utils.formatPN(PatientName.Alphabetic) : '',
             patientSex: PatientSex || '',
             patientAge: PatientAge || '',
             MRN: PatientID || '',
             thickness: SliceThickness ? `${SliceThickness.toFixed(2)}mm` : '',
             spacing:
-              SpacingBetweenSlices !== undefined
-                ? `${SpacingBetweenSlices.toFixed(2)}mm`
-                : '',
+              SpacingBetweenSlices !== undefined ? `${SpacingBetweenSlices.toFixed(2)}mm` : '',
             scanner: ManufacturerModelName || '',
           },
         }}
       />
 
-      <div className="relative flex flex-row w-full h-full overflow-hidden">
+      <div className="relative flex h-full w-full flex-row overflow-hidden">
         {getCornerstoneViewport()}
         {childrenWithProps}
       </div>
@@ -409,7 +378,7 @@ function OHIFCornerstoneSRViewport(props) {
 
 OHIFCornerstoneSRViewport.propTypes = {
   displaySets: PropTypes.arrayOf(PropTypes.object),
-  viewportIndex: PropTypes.number.isRequired,
+  viewportId: PropTypes.string.isRequired,
   dataSource: PropTypes.object,
   children: PropTypes.node,
   viewportLabel: PropTypes.string,
@@ -434,9 +403,7 @@ async function _getViewportReferencedDisplaySetData(
 
   const { displaySetInstanceUID } = measurement;
 
-  const referencedDisplaySet = displaySetService.getDisplaySetByUID(
-    displaySetInstanceUID
-  );
+  const referencedDisplaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
 
   const image0 = referencedDisplaySet.images[0];
   const referencedDisplaySetMetadata = {
@@ -458,7 +425,7 @@ async function _getViewportReferencedDisplaySetData(
 
 function _getStatusComponent({
   srDisplaySet,
-  viewportIndex,
+  viewportId,
   isRehydratable,
   isLocked,
   sendTrackedMeasurementsEvent,
@@ -466,7 +433,7 @@ function _getStatusComponent({
   const handleMouseUp = () => {
     sendTrackedMeasurementsEvent('HYDRATE_SR', {
       displaySetInstanceUID: srDisplaySet.displaySetInstanceUID,
-      viewportIndex,
+      viewportId,
     });
   };
 
@@ -476,8 +443,7 @@ function _getStatusComponent({
   // 1 - Incompatible
   // 2 - Locked
   // 3 - Rehydratable / Open
-  const state =
-    isRehydratable && !isLocked ? 3 : isRehydratable && isLocked ? 2 : 1;
+  const state = isRehydratable && !isLocked ? 3 : isRehydratable && isLocked ? 2 : 1;
   let ToolTipMessage = null;
   let StatusIcon = null;
 
@@ -507,22 +473,25 @@ function _getStatusComponent({
       );
       break;
     case 3:
-      StatusIcon = () => <Icon name="status-untracked" />;
-
-      ToolTipMessage = () => (
-        <div>{`Click ${loadStr} to restore measurements.`}</div>
+      StatusIcon = () => (
+        <Icon
+          className="text-aqua-pale"
+          name="status-untracked"
+        />
       );
+
+      ToolTipMessage = () => <div>{`Click ${loadStr} to restore measurements.`}</div>;
   }
 
   const StatusArea = () => (
-    <div className="flex h-6 leading-6 cursor-default text-sm text-white">
-      <div className="min-w-[45px] flex items-center p-1 rounded-l-xl rounded-r bg-customgray-100">
+    <div className="flex h-6 cursor-default text-sm leading-6 text-white">
+      <div className="bg-customgray-100 flex min-w-[45px] items-center rounded-l-xl rounded-r p-1">
         <StatusIcon />
         <span className="ml-1">SR</span>
       </div>
       {state === 3 && (
         <div
-          className="ml-1 px-1.5 rounded cursor-pointer hover:text-black bg-primary-main hover:bg-primary-light"
+          className="bg-primary-main hover:bg-primary-light ml-1 cursor-pointer rounded px-1.5 hover:text-black"
           // Using onMouseUp here because onClick is not working when the viewport is not active and is styled with pointer-events:none
           onMouseUp={handleMouseUp}
         >
@@ -535,7 +504,10 @@ function _getStatusComponent({
   return (
     <>
       {ToolTipMessage && (
-        <Tooltip content={<ToolTipMessage />} position="bottom-left">
+        <Tooltip
+          content={<ToolTipMessage />}
+          position="bottom-left"
+        >
           <StatusArea />
         </Tooltip>
       )}

extensions/cornerstone/.webpack/webpack.prod.js

@@ -40,13 +40,7 @@ module.exports = (env, argv) => {
       libraryTarget: 'umd',
       filename: pkg.main,
     },
-    externals: [
-      /\b(vtk.js)/,
-      /\b(dcmjs)/,
-      /\b(gl-matrix)/,
-      /^@ohif/,
-      /^@cornerstonejs/,
-    ],
+    externals: [/\b(vtk.js)/, /\b(dcmjs)/, /\b(gl-matrix)/, /^@ohif/, /^@cornerstonejs/],
     plugins: [
       new webpack.optimize.LimitChunkCountPlugin({
         maxChunks: 1,

extensions/cornerstone/CHANGELOG.md

@@ -0,0 +1,116 @@
+# Change Log
+
+All notable changes to this project will be documented in this file.
+See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+# [3.7.0-beta.69](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.68...v3.7.0-beta.69) (2023-09-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.7.0-beta.68](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.67...v3.7.0-beta.68) (2023-09-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.7.0-beta.67](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.66...v3.7.0-beta.67) (2023-09-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.7.0-beta.66](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.65...v3.7.0-beta.66) (2023-09-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.7.0-beta.65](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.64...v3.7.0-beta.65) (2023-09-06)
+
+
+### Features
+
+* **ImageOverlayViewerTool:** add ImageOverlayViewer tool that can render image overlay (pixel overlay) of the DICOM images ([#3163](https://github.com/OHIF/Viewers/issues/3163)) ([69115da](https://github.com/OHIF/Viewers/commit/69115da06d2d437b57e66608b435bb0bc919a90f))
+
+
+
+
+
+# [3.7.0-beta.64](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.63...v3.7.0-beta.64) (2023-09-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.7.0-beta.63](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.62...v3.7.0-beta.63) (2023-09-01)
+
+
+### Features
+
+* **grid:** remove viewportIndex and only rely on viewportId ([#3591](https://github.com/OHIF/Viewers/issues/3591)) ([4c6ff87](https://github.com/OHIF/Viewers/commit/4c6ff873e887cc30ffc09223f5cb99e5f94c9cdd))
+
+
+
+
+
+# [3.7.0-beta.62](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.61...v3.7.0-beta.62) (2023-08-30)
+
+
+### Features
+
+* **data source UI config:** Popup the configuration dialogue whenever a data source is not fully configured ([#3620](https://github.com/OHIF/Viewers/issues/3620)) ([adedc8c](https://github.com/OHIF/Viewers/commit/adedc8c382e18a2e86a569e3d023cc55a157363f))
+
+
+
+
+
+# [3.7.0-beta.61](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.60...v3.7.0-beta.61) (2023-08-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.7.0-beta.60](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.59...v3.7.0-beta.60) (2023-08-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.7.0-beta.59](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.58...v3.7.0-beta.59) (2023-08-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.7.0-beta.58](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.57...v3.7.0-beta.58) (2023-08-25)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.7.0-beta.57](https://github.com/OHIF/Viewers/compare/v3.7.0-beta.56...v3.7.0-beta.57) (2023-08-23)
+
+
+### Bug Fixes
+
+* **memory leak:** array buffer was sticking around in volume viewports ([#3611](https://github.com/OHIF/Viewers/issues/3611)) ([65b49ae](https://github.com/OHIF/Viewers/commit/65b49aeb1b5f38224e4892bdf32453500ee351f8))

extensions/cornerstone/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone",
-  "version": "3.7.0-beta.2",
+  "version": "3.7.0-beta.69",
   "description": "OHIF extension for Cornerstone",
   "author": "OHIF",
   "license": "MIT",
@@ -36,9 +36,9 @@
     "@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2",
     "@cornerstonejs/codec-openjpeg": "^1.2.2",
     "@cornerstonejs/codec-openjph": "^2.4.2",
-    "@cornerstonejs/dicom-image-loader": "^1.1.8",
-    "@ohif/core": "3.7.0-beta.2",
-    "@ohif/ui": "3.7.0-beta.2",
+    "@cornerstonejs/dicom-image-loader": "^1.13.2",
+    "@ohif/core": "3.7.0-beta.69",
+    "@ohif/ui": "3.7.0-beta.69",
     "dcmjs": "^0.29.6",
     "dicom-parser": "^1.8.21",
     "hammerjs": "^2.0.8",
@@ -52,10 +52,10 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/adapters": "^1.1.8",
-    "@cornerstonejs/core": "^1.1.8",
-    "@cornerstonejs/streaming-image-volume-loader": "^1.1.8",
-    "@cornerstonejs/tools": "^1.1.8",
+    "@cornerstonejs/adapters": "^1.13.2",
+    "@cornerstonejs/core": "^1.13.2",
+    "@cornerstonejs/streaming-image-volume-loader": "^1.13.2",
+    "@cornerstonejs/tools": "^1.13.2",
     "@kitware/vtk.js": "27.3.1",
     "html2canvas": "^1.4.1",
     "lodash.debounce": "4.0.8",

extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx

@@ -10,17 +10,8 @@ import {
   utilities as csUtils,
 } from '@cornerstonejs/core';
 import { MeasurementService } from '@ohif/core';
-import {
-  CinePlayer,
-  useCine,
-  useViewportGrid,
-  Notification,
-  useViewportDialog,
-} from '@ohif/ui';
-import {
-  IStackViewport,
-  IVolumeViewport,
-} from '@cornerstonejs/core/dist/esm/types';
+import { Notification, useViewportDialog } from '@ohif/ui';
+import { IStackViewport, IVolumeViewport } from '@cornerstonejs/core/dist/esm/types';
 
 import { setEnabledElement } from '../state';
 
@@ -28,6 +19,8 @@ import './OHIFCornerstoneViewport.css';
 import CornerstoneOverlays from './Overlays/CornerstoneOverlays';
 import getSOPInstanceAttributes from '../utils/measurementServiceMappings/utils/getSOPInstanceAttributes';
 import CornerstoneServices from '../types/CornerstoneServices';
+import CinePlayer from '../components/CinePlayer';
+import { Types } from '@ohif/core';
 
 const STACK = 'stack';
 
@@ -46,24 +39,19 @@ function areEqual(prevProps, nextProps) {
     return false;
   }
 
-  if (
-    prevProps.viewportOptions.orientation !==
-    nextProps.viewportOptions.orientation
-  ) {
+  if (prevProps.viewportOptions.orientation !== nextProps.viewportOptions.orientation) {
     return false;
   }
 
-  if (
-    prevProps.viewportOptions.toolGroupId !==
-    nextProps.viewportOptions.toolGroupId
-  ) {
+  if (prevProps.viewportOptions.toolGroupId !== nextProps.viewportOptions.toolGroupId) {
     return false;
   }
 
-  if (
-    prevProps.viewportOptions.viewportType !==
-    nextProps.viewportOptions.viewportType
-  ) {
+  if (prevProps.viewportOptions.viewportType !== nextProps.viewportOptions.viewportType) {
+    return false;
+  }
+
+  if (nextProps.viewportOptions.needsRerendering) {
     return false;
   }
 
@@ -79,8 +67,7 @@ function areEqual(prevProps, nextProps) {
 
     const foundDisplaySet = nextDisplaySets.find(
       nextDisplaySet =>
-        nextDisplaySet.displaySetInstanceUID ===
-        prevDisplaySet.displaySetInstanceUID
+        nextDisplaySet.displaySetInstanceUID === prevDisplaySet.displaySetInstanceUID
     );
 
     if (!foundDisplaySet) {
@@ -95,9 +82,7 @@ function areEqual(prevProps, nextProps) {
     // check if their imageIds are the same
     if (foundDisplaySet.images?.length) {
       for (let j = 0; j < foundDisplaySet.images.length; j++) {
-        if (
-          foundDisplaySet.images[j].imageId !== prevDisplaySet.images[j].imageId
-        ) {
+        if (foundDisplaySet.images[j].imageId !== prevDisplaySet.images[j].imageId) {
           return false;
         }
       }
@@ -111,25 +96,24 @@ function areEqual(prevProps, nextProps) {
 // Then we don't need to worry about the re-renders if the props change.
 const OHIFCornerstoneViewport = React.memo(props => {
   const {
-    viewportIndex,
     displaySets,
     dataSource,
     viewportOptions,
     displaySetOptions,
     servicesManager,
+    commandsManager,
     onElementEnabled,
     onElementDisabled,
+    isJumpToMeasurementDisabled,
     // Note: you SHOULD NOT use the initialImageIdOrIndex for manipulation
     // of the imageData in the OHIFCornerstoneViewport. This prop is used
     // to set the initial state of the viewport's first image to render
     initialImageIndex,
   } = props;
 
+  const viewportId = viewportOptions.viewportId;
   const [scrollbarHeight, setScrollbarHeight] = useState('100px');
-  const [{ isCineEnabled, cines }, cineService] = useCine();
-  const [{ activeViewportIndex }] = useViewportGrid();
   const [enabledVPElement, setEnabledVPElement] = useState(null);
-
   const elementRef = useRef();
 
   const {
@@ -145,74 +129,6 @@ const OHIFCornerstoneViewport = React.memo(props => {
   } = servicesManager.services as CornerstoneServices;
 
   const [viewportDialogState] = useViewportDialog();
-
-  const cineHandler = () => {
-    if (!cines || !cines[viewportIndex] || !enabledVPElement) {
-      return;
-    }
-
-    const cine = cines[viewportIndex];
-    const isPlaying = cine.isPlaying || false;
-    const frameRate = cine.frameRate || 24;
-
-    const validFrameRate = Math.max(frameRate, 1);
-
-    if (isPlaying) {
-      cineService.playClip(enabledVPElement, {
-        framesPerSecond: validFrameRate,
-      });
-    } else {
-      cineService.stopClip(enabledVPElement);
-    }
-  };
-
-  useEffect(() => {
-    eventTarget.addEventListener(
-      Enums.Events.STACK_VIEWPORT_NEW_STACK,
-      cineHandler
-    );
-
-    return () => {
-      cineService.setCine({ id: viewportIndex, isPlaying: false });
-      eventTarget.removeEventListener(
-        Enums.Events.STACK_VIEWPORT_NEW_STACK,
-        cineHandler
-      );
-    };
-  }, [enabledVPElement]);
-
-  useEffect(() => {
-    if (!cines || !cines[viewportIndex] || !enabledVPElement) {
-      return;
-    }
-
-    cineHandler();
-
-    return () => {
-      if (enabledVPElement && cines?.[viewportIndex]?.isPlaying) {
-        cineService.stopClip(enabledVPElement);
-      }
-    };
-  }, [cines, viewportIndex, cineService, enabledVPElement, cineHandler]);
-
-  const cine = cines[viewportIndex];
-  const isPlaying = (cine && cine.isPlaying) || false;
-
-  const handleCineClose = () => {
-    toolbarService.recordInteraction({
-      groupId: 'MoreTools',
-      itemId: 'cine',
-      interactionType: 'toggle',
-      commands: [
-        {
-          commandName: 'toggleCine',
-          commandOptions: {},
-          context: 'CORNERSTONE',
-        },
-      ],
-    });
-  };
-
   // useCallback for scroll bar height calculation
   const setImageScrollBarHeight = useCallback(() => {
     const scrollbarHeight = `${elementRef.current.clientHeight - 20}px`;
@@ -227,54 +143,17 @@ const OHIFCornerstoneViewport = React.memo(props => {
     }
   }, [elementRef]);
 
-  const storePresentation = () => {
-    const currentPresentation = cornerstoneViewportService.getPresentation(
-      viewportIndex
-    );
-    if (!currentPresentation || !currentPresentation.presentationIds) return;
-    const {
-      lutPresentationStore,
-      positionPresentationStore,
-    } = stateSyncService.getState();
-    const { presentationIds } = currentPresentation;
-    const { lutPresentationId, positionPresentationId } = presentationIds || {};
-    const storeState = {};
-    if (lutPresentationId) {
-      storeState.lutPresentationStore = {
-        ...lutPresentationStore,
-        [lutPresentationId]: currentPresentation,
-      };
-    }
-    if (positionPresentationId) {
-      storeState.positionPresentationStore = {
-        ...positionPresentationStore,
-        [positionPresentationId]: currentPresentation,
-      };
-    }
-    stateSyncService.store(storeState);
-  };
+  const cleanUpServices = useCallback(
+    viewportInfo => {
+      const renderingEngineId = viewportInfo.getRenderingEngineId();
+      const syncGroups = viewportInfo.getSyncGroups();
 
-  const cleanUpServices = useCallback(() => {
-    const viewportInfo = cornerstoneViewportService.getViewportInfoByIndex(
-      viewportIndex
-    );
+      toolGroupService.removeViewportFromToolGroup(viewportId, renderingEngineId);
 
-    if (!viewportInfo) {
-      return;
-    }
-
-    const viewportId = viewportInfo.getViewportId();
-    const renderingEngineId = viewportInfo.getRenderingEngineId();
-    const syncGroups = viewportInfo.getSyncGroups();
-
-    toolGroupService.removeViewportFromToolGroup(viewportId, renderingEngineId);
-
-    syncGroupService.removeViewportFromSyncGroup(
-      viewportId,
-      renderingEngineId,
-      syncGroups
-    );
-  }, [viewportIndex, viewportOptions.viewportId]);
+      syncGroupService.removeViewportFromSyncGroup(viewportId, renderingEngineId, syncGroups);
+    },
+    [viewportId]
+  );
 
   const elementEnabledHandler = useCallback(
     evt => {
@@ -284,71 +163,48 @@ const OHIFCornerstoneViewport = React.memo(props => {
       }
 
       const { viewportId, element } = evt.detail;
-      const viewportInfo = cornerstoneViewportService.getViewportInfo(
-        viewportId
-      );
-      const viewportIndex = viewportInfo.getViewportIndex();
-
-      setEnabledElement(viewportIndex, element);
+      const viewportInfo = cornerstoneViewportService.getViewportInfo(viewportId);
+      setEnabledElement(viewportId, element);
       setEnabledVPElement(element);
 
       const renderingEngineId = viewportInfo.getRenderingEngineId();
       const toolGroupId = viewportInfo.getToolGroupId();
       const syncGroups = viewportInfo.getSyncGroups();
 
-      toolGroupService.addViewportToToolGroup(
-        viewportId,
-        renderingEngineId,
-        toolGroupId
-      );
+      toolGroupService.addViewportToToolGroup(viewportId, renderingEngineId, toolGroupId);
 
-      syncGroupService.addViewportToSyncGroup(
-        viewportId,
-        renderingEngineId,
-        syncGroups
-      );
+      syncGroupService.addViewportToSyncGroup(viewportId, renderingEngineId, syncGroups);
 
       if (onElementEnabled) {
         onElementEnabled(evt);
       }
     },
-    [viewportIndex, onElementEnabled, toolGroupService]
+    [viewportId, onElementEnabled, toolGroupService]
   );
 
   // disable the element upon unmounting
   useEffect(() => {
-    cornerstoneViewportService.enableViewport(
-      viewportIndex,
-      viewportOptions,
-      elementRef.current
-    );
+    cornerstoneViewportService.enableViewport(viewportId, elementRef.current);
 
-    eventTarget.addEventListener(
-      Enums.Events.ELEMENT_ENABLED,
-      elementEnabledHandler
-    );
+    eventTarget.addEventListener(Enums.Events.ELEMENT_ENABLED, elementEnabledHandler);
 
     setImageScrollBarHeight();
 
     return () => {
-      storePresentation();
+      const viewportInfo = cornerstoneViewportService.getViewportInfo(viewportId);
 
-      cleanUpServices();
+      if (!viewportInfo) {
+        return;
+      }
 
-      const viewportInfo = cornerstoneViewportService.getViewportInfoByIndex(
-        viewportIndex
-      );
-
-      cornerstoneViewportService.disableElement(viewportIndex);
+      cleanUpServices(viewportInfo);
+      cornerstoneViewportService.storePresentation({ viewportId });
 
       if (onElementDisabled) {
         onElementDisabled(viewportInfo);
       }
 
-      eventTarget.removeEventListener(
-        Enums.Events.ELEMENT_ENABLED,
-        elementEnabledHandler
-      );
+      eventTarget.removeEventListener(Enums.Events.ELEMENT_ENABLED, elementEnabledHandler);
     };
   }, []);
 
@@ -363,10 +219,15 @@ const OHIFCornerstoneViewport = React.memo(props => {
   useEffect(() => {
     const { unsubscribe } = displaySetService.subscribe(
       displaySetService.EVENTS.DISPLAY_SET_SERIES_METADATA_INVALIDATED,
-      async invalidatedDisplaySetInstanceUID => {
-        const viewportInfo = cornerstoneViewportService.getViewportInfoByIndex(
-          viewportIndex
-        );
+      async ({
+        displaySetInstanceUID: invalidatedDisplaySetInstanceUID,
+        invalidateData,
+      }: Types.DisplaySetSeriesMetadataInvalidatedEvent) => {
+        if (!invalidateData) {
+          return;
+        }
+
+        const viewportInfo = cornerstoneViewportService.getViewportInfo(viewportId);
 
         if (viewportInfo.hasDisplaySet(invalidatedDisplaySetInstanceUID)) {
           const viewportData = viewportInfo.getViewportData();
@@ -378,18 +239,14 @@ const OHIFCornerstoneViewport = React.memo(props => {
           );
 
           const keepCamera = true;
-          cornerstoneViewportService.updateViewport(
-            viewportIndex,
-            newViewportData,
-            keepCamera
-          );
+          cornerstoneViewportService.updateViewport(viewportId, newViewportData, keepCamera);
         }
       }
     );
     return () => {
       unsubscribe();
     };
-  }, [viewportIndex]);
+  }, [viewportId]);
 
   useEffect(() => {
     // handle the default viewportType to be stack
@@ -408,33 +265,37 @@ const OHIFCornerstoneViewport = React.memo(props => {
       // The presentation state will have been stored previously by closing
       // a viewport.  Otherwise, this viewport will be unchanged and the
       // presentation information will be directly carried over.
-      const {
-        lutPresentationStore,
-        positionPresentationStore,
-      } = stateSyncService.getState();
+      const { lutPresentationStore, positionPresentationStore } = stateSyncService.getState();
       const { presentationIds } = viewportOptions;
       const presentations = {
-        positionPresentation:
-          positionPresentationStore[presentationIds?.positionPresentationId],
-        lutPresentation:
-          lutPresentationStore[presentationIds?.lutPresentationId],
+        positionPresentation: positionPresentationStore[presentationIds?.positionPresentationId],
+        lutPresentation: lutPresentationStore[presentationIds?.lutPresentationId],
       };
       let measurement;
-      if (cacheJumpToMeasurementEvent?.viewportIndex === viewportIndex) {
+      if (cacheJumpToMeasurementEvent?.viewportId === viewportId) {
         measurement = cacheJumpToMeasurementEvent.measurement;
         // Delete the position presentation so that viewport navigates direct
         presentations.positionPresentation = null;
         cacheJumpToMeasurementEvent = null;
       }
 
+      // Note: This is a hack to get the grid to re-render the OHIFCornerstoneViewport component
+      // Used for segmentation hydration right now, since the logic to decide whether
+      // a viewport needs to render a segmentation lives inside the CornerstoneViewportService
+      // so we need to re-render (force update via change of the needsRerendering) so that React
+      // does the diffing and decides we should render this again (although the id and element has not changed)
+      // so that the CornerstoneViewportService can decide whether to render the segmentation or not. Not that we reached here we can turn it off.
+      if (viewportOptions.needsRerendering) {
+        viewportOptions.needsRerendering = false;
+      }
+
       cornerstoneViewportService.setViewportData(
-        viewportIndex,
+        viewportId,
         viewportData,
         viewportOptions,
         displaySetOptions,
         presentations
       );
-
       if (measurement) {
         cs3DTools.annotation.selection.setAnnotationSelected(measurement.uid);
       }
@@ -454,11 +315,15 @@ const OHIFCornerstoneViewport = React.memo(props => {
    * the cache for jumping to see if there is any jump queued, then we jump to the correct slice.
    */
   useEffect(() => {
+    if (isJumpToMeasurementDisabled) {
+      return;
+    }
+
     const unsubscribeFromJumpToMeasurementEvents = _subscribeToJumpToMeasurementEvents(
       measurementService,
       displaySetService,
       elementRef,
-      viewportIndex,
+      viewportId,
       displaySets,
       viewportGridService,
       cornerstoneViewportService
@@ -468,7 +333,7 @@ const OHIFCornerstoneViewport = React.memo(props => {
       measurementService,
       displaySetService,
       elementRef,
-      viewportIndex,
+      viewportId,
       displaySets,
       viewportGridService,
       cornerstoneViewportService
@@ -477,17 +342,14 @@ const OHIFCornerstoneViewport = React.memo(props => {
     return () => {
       unsubscribeFromJumpToMeasurementEvents();
     };
-  }, [displaySets, elementRef, viewportIndex]);
+  }, [displaySets, elementRef, viewportId]);
 
   return (
     <React.Fragment>
       <div className="viewport-wrapper">
         <ReactResizeDetector
-          handleWidth
-          handleHeight
-          skipOnMount={true} // Todo: make these configurable
-          refreshMode={'debounce'}
-          refreshRate={200} // transition amount in side panel
+          refreshMode="debounce"
+          refreshRate={50} // Wait 50 ms after last move to render
           onResize={onResize}
           targetRef={elementRef.current}
         />
@@ -499,34 +361,20 @@ const OHIFCornerstoneViewport = React.memo(props => {
           ref={elementRef}
         ></div>
         <CornerstoneOverlays
-          viewportIndex={viewportIndex}
+          viewportId={viewportId}
           toolBarService={toolbarService}
           element={elementRef.current}
           scrollbarHeight={scrollbarHeight}
           servicesManager={servicesManager}
         />
-        {isCineEnabled && (
-          <CinePlayer
-            className="absolute left-1/2 -translate-x-1/2 bottom-3"
-            isPlaying={isPlaying}
-            onClose={handleCineClose}
-            onPlayPauseChange={isPlaying =>
-              cineService.setCine({
-                id: activeViewportIndex,
-                isPlaying,
-              })
-            }
-            onFrameRateChange={frameRate =>
-              cineService.setCine({
-                id: activeViewportIndex,
-                frameRate,
-              })
-            }
-          />
-        )}
+        <CinePlayer
+          enabledVPElement={enabledVPElement}
+          viewportId={viewportId}
+          servicesManager={servicesManager}
+        />
       </div>
       <div className="absolute w-full">
-        {viewportDialogState.viewportIndex === viewportIndex && (
+        {viewportDialogState.viewportId === viewportId && (
           <Notification
             id="viewport-notification"
             message={viewportDialogState.message}
@@ -545,35 +393,35 @@ function _subscribeToJumpToMeasurementEvents(
   measurementService,
   displaySetService,
   elementRef,
-  viewportIndex,
+  viewportId,
   displaySets,
   viewportGridService,
   cornerstoneViewportService
 ) {
-  const displaysUIDs = displaySets.map(
-    displaySet => displaySet.displaySetInstanceUID
-  );
   const { unsubscribe } = measurementService.subscribe(
     MeasurementService.EVENTS.JUMP_TO_MEASUREMENT_VIEWPORT,
     props => {
       cacheJumpToMeasurementEvent = props;
-      const { viewportIndex: jumpIndex, measurement, isConsumed } = props;
-      if (!measurement || isConsumed) return;
+      const { viewportId: jumpId, measurement, isConsumed } = props;
+      if (!measurement || isConsumed) {
+        return;
+      }
       if (cacheJumpToMeasurementEvent.cornerstoneViewport === undefined) {
         // Decide on which viewport should handle this
-        cacheJumpToMeasurementEvent.cornerstoneViewport = cornerstoneViewportService.getViewportIndexToJump(
-          jumpIndex,
-          measurement.displaySetInstanceUID,
-          { referencedImageId: measurement.referencedImageId }
-        );
+        cacheJumpToMeasurementEvent.cornerstoneViewport =
+          cornerstoneViewportService.getViewportIdToJump(
+            jumpId,
+            measurement.displaySetInstanceUID,
+            { referencedImageId: measurement.referencedImageId }
+          );
       }
-      if (cacheJumpToMeasurementEvent.cornerstoneViewport !== viewportIndex) {
+      if (cacheJumpToMeasurementEvent.cornerstoneViewport !== viewportId) {
         return;
       }
       _jumpToMeasurement(
         measurement,
         elementRef,
-        viewportIndex,
+        viewportId,
         measurementService,
         displaySetService,
         viewportGridService,
@@ -590,20 +438,22 @@ function _checkForCachedJumpToMeasurementEvents(
   measurementService,
   displaySetService,
   elementRef,
-  viewportIndex,
+  viewportId,
   displaySets,
   viewportGridService,
   cornerstoneViewportService
 ) {
-  if (!cacheJumpToMeasurementEvent) return;
+  if (!cacheJumpToMeasurementEvent) {
+    return;
+  }
   if (cacheJumpToMeasurementEvent.isConsumed) {
     cacheJumpToMeasurementEvent = null;
     return;
   }
-  const displaysUIDs = displaySets.map(
-    displaySet => displaySet.displaySetInstanceUID
-  );
-  if (!displaysUIDs?.length) return;
+  const displaysUIDs = displaySets.map(displaySet => displaySet.displaySetInstanceUID);
+  if (!displaysUIDs?.length) {
+    return;
+  }
 
   // Jump to measurement if the measurement exists
   const { measurement } = cacheJumpToMeasurementEvent;
@@ -612,7 +462,7 @@ function _checkForCachedJumpToMeasurementEvents(
       _jumpToMeasurement(
         measurement,
         elementRef,
-        viewportIndex,
+        viewportId,
         measurementService,
         displaySetService,
         viewportGridService,
@@ -625,7 +475,7 @@ function _checkForCachedJumpToMeasurementEvents(
 function _jumpToMeasurement(
   measurement,
   targetElementRef,
-  viewportIndex,
+  viewportId,
   measurementService,
   displaySetService,
   viewportGridService,
@@ -639,27 +489,19 @@ function _jumpToMeasurement(
     return;
   }
 
-  const referencedDisplaySet = displaySetService.getDisplaySetByUID(
-    displaySetInstanceUID
-  );
+  const referencedDisplaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
 
   // Todo: setCornerstoneMeasurementActive should be handled by the toolGroupManager
   //  to set it properly
   // setCornerstoneMeasurementActive(measurement);
 
-  viewportGridService.setActiveViewportIndex(viewportIndex);
+  viewportGridService.setActiveViewportId(viewportId);
 
   const enabledElement = getEnabledElement(targetElement);
 
-  const viewportInfo = cornerstoneViewportService.getViewportInfoByIndex(
-    viewportIndex
-  );
-
   if (enabledElement) {
     // See how the jumpToSlice() of Cornerstone3D deals with imageIdx param.
-    const viewport = enabledElement.viewport as
-      | IStackViewport
-      | IVolumeViewport;
+    const viewport = enabledElement.viewport as IStackViewport | IVolumeViewport;
 
     let imageIdIndex = 0;
     let viewportCameraDirectionMatch = true;
@@ -667,14 +509,9 @@ function _jumpToMeasurement(
     if (viewport instanceof StackViewport) {
       const imageIds = viewport.getImageIds();
       imageIdIndex = imageIds.findIndex(imageId => {
-        const {
-          SOPInstanceUID: aSOPInstanceUID,
-          frameNumber: aFrameNumber,
-        } = getSOPInstanceAttributes(imageId);
-        return (
-          aSOPInstanceUID === SOPInstanceUID &&
-          (!frameNumber || frameNumber === aFrameNumber)
-        );
+        const { SOPInstanceUID: aSOPInstanceUID, frameNumber: aFrameNumber } =
+          getSOPInstanceAttributes(imageId);
+        return aSOPInstanceUID === SOPInstanceUID && (!frameNumber || frameNumber === aFrameNumber);
       });
     } else {
       // for volume viewport we can't rely on the imageIdIndex since it can be
@@ -689,10 +526,7 @@ function _jumpToMeasurement(
       // should compare abs for both planes since the direction can be flipped
       if (
         measurementViewPlane &&
-        !csUtils.isEqual(
-          measurementViewPlane.map(Math.abs),
-          viewportViewPlane.map(Math.abs)
-        )
+        !csUtils.isEqual(measurementViewPlane.map(Math.abs), viewportViewPlane.map(Math.abs))
       ) {
         viewportCameraDirectionMatch = false;
       }
@@ -716,21 +550,22 @@ function _jumpToMeasurement(
 // Component displayName
 OHIFCornerstoneViewport.displayName = 'OHIFCornerstoneViewport';
 
+OHIFCornerstoneViewport.defaultProps = {
+  isJumpToMeasurementDisabled: false,
+};
+
 OHIFCornerstoneViewport.propTypes = {
-  viewportIndex: PropTypes.number.isRequired,
   displaySets: PropTypes.array.isRequired,
   dataSource: PropTypes.object.isRequired,
   viewportOptions: PropTypes.object,
   displaySetOptions: PropTypes.arrayOf(PropTypes.any),
   servicesManager: PropTypes.object.isRequired,
   onElementEnabled: PropTypes.func,
+  isJumpToMeasurementDisabled: PropTypes.bool,
   // Note: you SHOULD NOT use the initialImageIdOrIndex for manipulation
   // of the imageData in the OHIFCornerstoneViewport. This prop is used
   // to set the initial state of the viewport's first image to render
-  initialImageIdOrIndex: PropTypes.oneOfType([
-    PropTypes.string,
-    PropTypes.number,
-  ]),
+  initialImageIdOrIndex: PropTypes.oneOfType([PropTypes.string, PropTypes.number]),
 };
 
 export default OHIFCornerstoneViewport;

extensions/cornerstone/src/Viewport/Overlays/CornerstoneOverlays.tsx

@@ -6,7 +6,7 @@ import ViewportOrientationMarkers from './ViewportOrientationMarkers';
 import ViewportImageSliceLoadingIndicator from './ViewportImageSliceLoadingIndicator';
 
 function CornerstoneOverlays(props) {
-  const { viewportIndex, element, scrollbarHeight, servicesManager } = props;
+  const { viewportId, element, scrollbarHeight, servicesManager } = props;
   const { cornerstoneViewportService } = servicesManager.services;
   const [imageSliceData, setImageSliceData] = useState({
     imageIndex: 0,
@@ -18,7 +18,7 @@ function CornerstoneOverlays(props) {
     const { unsubscribe } = cornerstoneViewportService.subscribe(
       cornerstoneViewportService.EVENTS.VIEWPORT_DATA_CHANGED,
       props => {
-        if (props.viewportIndex !== viewportIndex) {
+        if (props.viewportId !== viewportId) {
           return;
         }
 
@@ -29,15 +29,14 @@ function CornerstoneOverlays(props) {
     return () => {
       unsubscribe();
     };
-  }, [viewportIndex]);
+  }, [viewportId]);
 
   if (!element) {
     return null;
   }
 
   if (viewportData) {
-    const viewportInfo =
-      cornerstoneViewportService.getViewportInfoByIndex(viewportIndex);
+    const viewportInfo = cornerstoneViewportService.getViewportInfo(viewportId);
 
     if (viewportInfo?.viewportOptions?.customViewportProps?.hideOverlays) {
       return null;
@@ -47,7 +46,7 @@ function CornerstoneOverlays(props) {
   return (
     <div className="noselect">
       <ViewportImageScrollbar
-        viewportIndex={viewportIndex}
+        viewportId={viewportId}
         viewportData={viewportData}
         element={element}
         imageSliceData={imageSliceData}
@@ -59,7 +58,7 @@ function CornerstoneOverlays(props) {
       <CustomizableViewportOverlay
         imageSliceData={imageSliceData}
         viewportData={viewportData}
-        viewportIndex={viewportIndex}
+        viewportId={viewportId}
         servicesManager={servicesManager}
         element={element}
       />
@@ -74,7 +73,7 @@ function CornerstoneOverlays(props) {
         element={element}
         viewportData={viewportData}
         servicesManager={servicesManager}
-        viewportIndex={viewportIndex}
+        viewportId={viewportId}
       />
     </div>
   );

extensions/cornerstone/src/Viewport/Overlays/CustomizableViewportOverlay.tsx

@@ -3,12 +3,7 @@ import { vec3 } from 'gl-matrix';
 import PropTypes from 'prop-types';
 import { metaData, Enums, utilities } from '@cornerstonejs/core';
 import { ViewportOverlay } from '@ohif/ui';
-import {
-  formatPN,
-  formatDICOMDate,
-  formatDICOMTime,
-  formatNumberPrecision,
-} from './utils';
+import { formatPN, formatDICOMDate, formatDICOMTime, formatNumberPrecision } from './utils';
 import { InstanceMetadata } from 'platform/core/src/types';
 import { ServicesManager } from '@ohif/core';
 import { ImageSliceData } from '@cornerstonejs/core/dist/esm/types';
@@ -21,7 +16,6 @@ interface OverlayItemProps {
   element: any;
   viewportData: any;
   imageSliceData: ImageSliceData;
-  viewportIndex: number | null;
   servicesManager: ServicesManager;
   instance: InstanceMetadata;
   customization: any;
@@ -56,13 +50,9 @@ function VOIOverlayItem({ voi, customization }: OverlayItemProps) {
       style={{ color: (customization && customization.color) || undefined }}
     >
       <span className="mr-1 shrink-0">W:</span>
-      <span className="ml-1 mr-2 font-light shrink-0">
-        {windowWidth.toFixed(0)}
-      </span>
+      <span className="ml-1 mr-2 shrink-0 font-light">{windowWidth.toFixed(0)}</span>
       <span className="mr-1 shrink-0">L:</span>
-      <span className="ml-1 font-light shrink-0">
-        {windowCenter.toFixed(0)}
-      </span>
+      <span className="ml-1 shrink-0 font-light">{windowCenter.toFixed(0)}</span>
     </div>
   );
 }
@@ -114,14 +104,11 @@ function CustomizableViewportOverlay({
   element,
   viewportData,
   imageSliceData,
-  viewportIndex,
+  viewportId,
   servicesManager,
 }) {
-  const {
-    toolbarService,
-    cornerstoneViewportService,
-    customizationService,
-  } = servicesManager.services;
+  const { toolbarService, cornerstoneViewportService, customizationService } =
+    servicesManager.services;
   const [voi, setVOI] = useState({ windowCenter: null, windowWidth: null });
   const [scale, setScale] = useState(1);
   const [activeTools, setActiveTools] = useState([]);
@@ -150,15 +137,10 @@ function CustomizableViewportOverlay({
 
   const instanceNumber = useMemo(() => {
     if (viewportData != null) {
-      return _getInstanceNumber(
-        viewportData,
-        viewportIndex,
-        imageIndex,
-        cornerstoneViewportService
-      );
+      return _getInstanceNumber(viewportData, viewportId, imageIndex, cornerstoneViewportService);
     }
     return null;
-  }, [viewportData, viewportIndex, imageIndex, cornerstoneViewportService]);
+  }, [viewportData, viewportId, imageIndex, cornerstoneViewportService]);
 
   /**
    * Initial toolbar state
@@ -179,10 +161,7 @@ function CustomizableViewportOverlay({
       }
 
       const { lower, upper } = range;
-      const { windowWidth, windowCenter } = utilities.windowLevel.toWindowLevel(
-        lower,
-        upper
-      );
+      const { windowWidth, windowCenter } = utilities.windowLevel.toWindowLevel(lower, upper);
 
       setVOI({ windowCenter, windowWidth });
     };
@@ -192,7 +171,7 @@ function CustomizableViewportOverlay({
     return () => {
       element.removeEventListener(Enums.Events.VOI_MODIFIED, updateVOI);
     };
-  }, [viewportIndex, viewportData, voi, element]);
+  }, [viewportId, viewportData, voi, element]);
 
   /**
    * Updating the scale when the viewport changes its zoom
@@ -205,9 +184,7 @@ function CustomizableViewportOverlay({
         previousCamera.parallelScale !== camera.parallelScale ||
         previousCamera.scale !== camera.scale
       ) {
-        const viewport = cornerstoneViewportService.getCornerstoneViewportByIndex(
-          viewportIndex
-        );
+        const viewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
 
         if (!viewport) {
           return;
@@ -226,8 +203,7 @@ function CustomizableViewportOverlay({
 
         const { spacing } = imageData;
         // convert parallel scale to scale
-        const scale =
-          (element.clientHeight * spacing[0] * 0.5) / camera.parallelScale;
+        const scale = (element.clientHeight * spacing[0] * 0.5) / camera.parallelScale;
         setScale(scale);
       }
     };
@@ -237,7 +213,7 @@ function CustomizableViewportOverlay({
     return () => {
       element.removeEventListener(Enums.Events.CAMERA_MODIFIED, updateScale);
     };
-  }, [viewportIndex, viewportData, cornerstoneViewportService, element]);
+  }, [viewportId, viewportData, cornerstoneViewportService, element]);
 
   /**
    * Updating the active tools when the toolbar changes
@@ -262,7 +238,7 @@ function CustomizableViewportOverlay({
         element,
         viewportData,
         imageSliceData,
-        viewportIndex,
+        viewportId,
         servicesManager,
         customization: item,
         formatters: {
@@ -296,7 +272,7 @@ function CustomizableViewportOverlay({
       element,
       viewportData,
       imageSliceData,
-      viewportIndex,
+      viewportId,
       servicesManager,
       customizationService,
       instance,
@@ -343,9 +319,7 @@ function CustomizableViewportOverlay({
     return (
       <>
         {items.map((item, i) => (
-          <div key={`bottomLeftOverlayItem_${i}`}>
-            {_renderOverlayItem(item)}
-          </div>
+          <div key={`bottomLeftOverlayItem_${i}`}>{_renderOverlayItem(item)}</div>
         ))}
       </>
     );
@@ -356,9 +330,7 @@ function CustomizableViewportOverlay({
     return (
       <>
         {items.map((item, i) => (
-          <div key={`bottomRightOverlayItem_${i}`}>
-            {_renderOverlayItem(item)}
-          </div>
+          <div key={`bottomRightOverlayItem_${i}`}>{_renderOverlayItem(item)}</div>
         ))}
       </>
     );
@@ -379,7 +351,7 @@ function _getViewportInstance(viewportData, imageIndex) {
   if (viewportData.viewportType === Enums.ViewportType.STACK) {
     imageId = viewportData.data.imageIds[imageIndex];
   } else if (viewportData.viewportType === Enums.ViewportType.ORTHOGRAPHIC) {
-    const volumes = viewportData.volumes;
+    const volumes = viewportData.data;
     if (volumes && volumes.length == 1) {
       const volume = volumes[0];
       imageId = volume.imageIds[imageIndex];
@@ -388,12 +360,7 @@ function _getViewportInstance(viewportData, imageIndex) {
   return imageId ? metaData.get('instance', imageId) || {} : {};
 }
 
-function _getInstanceNumber(
-  viewportData,
-  viewportIndex,
-  imageIndex,
-  cornerstoneViewportService
-) {
+function _getInstanceNumber(viewportData, viewportId, imageIndex, cornerstoneViewportService) {
   let instanceNumber;
 
   if (viewportData.viewportType === Enums.ViewportType.STACK) {
@@ -406,7 +373,7 @@ function _getInstanceNumber(
     instanceNumber = _getInstanceNumberFromVolume(
       viewportData,
       imageIndex,
-      viewportIndex,
+      viewportId,
       cornerstoneViewportService
     );
   }
@@ -436,12 +403,7 @@ function _getInstanceNumberFromStack(viewportData, imageIndex) {
 // Since volume viewports can be in any view direction, they can render
 // a reconstructed image which don't have imageIds; therefore, no instance and instanceNumber
 // Here we check if viewport is in the acquisition direction and if so, we get the instanceNumber
-function _getInstanceNumberFromVolume(
-  viewportData,
-  imageIndex,
-  viewportIndex,
-  cornerstoneViewportService
-) {
+function _getInstanceNumberFromVolume(viewportData, viewportId, cornerstoneViewportService) {
   const volumes = viewportData.volumes;
 
   // Todo: support fusion of acquisition plane which has instanceNumber
@@ -452,9 +414,7 @@ function _getInstanceNumberFromVolume(
   const volume = volumes[0];
   const { direction, imageIds } = volume;
 
-  const cornerstoneViewport = cornerstoneViewportService.getCornerstoneViewportByIndex(
-    viewportIndex
-  );
+  const cornerstoneViewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
 
   if (!cornerstoneViewport) {
     return;
@@ -477,8 +437,7 @@ function _getInstanceNumberFromVolume(
       return {};
     }
 
-    const { instanceNumber } =
-      metaData.get('generalImageModule', imageId) || {};
+    const { instanceNumber } = metaData.get('generalImageModule', imageId) || {};
     return parseInt(instanceNumber);
   }
 }
@@ -486,7 +445,7 @@ function _getInstanceNumberFromVolume(
 CustomizableViewportOverlay.propTypes = {
   viewportData: PropTypes.object,
   imageIndex: PropTypes.number,
-  viewportIndex: PropTypes.number,
+  viewportId: PropTypes.string,
 };
 
 export default CustomizableViewportOverlay;

extensions/cornerstone/src/Viewport/Overlays/ViewportImageScrollbar.tsx

@@ -7,34 +7,24 @@ import { ServicesManger } from '@ohif/core';
 
 function CornerstoneImageScrollbar({
   viewportData,
-  viewportIndex,
+  viewportId,
   element,
   imageSliceData,
   setImageSliceData,
   scrollbarHeight,
   servicesManager,
 }) {
-  const {
-    cineService,
-    cornerstoneViewportService,
-  } = (servicesManager as ServicesManger).services;
+  const { cineService, cornerstoneViewportService } = (servicesManager as ServicesManger).services;
 
-  const onImageScrollbarChange = (imageIndex, viewportIndex) => {
-    const viewportInfo = cornerstoneViewportService.getViewportInfoByIndex(
-      viewportIndex
-    );
-
-    const viewportId = viewportInfo.getViewportId();
-    const viewport = cornerstoneViewportService.getCornerstoneViewport(
-      viewportId
-    );
+  const onImageScrollbarChange = (imageIndex, viewportId) => {
+    const viewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
 
     const { isCineEnabled } = cineService.getState();
 
     if (isCineEnabled) {
       // on image scrollbar change, stop the CINE if it is playing
       cineService.stopClip(element);
-      cineService.setCine({ id: viewportIndex, isPlaying: false });
+      cineService.setCine({ id: viewportId, isPlaying: false });
     }
 
     csToolsUtils.jumpToSlice(viewport.element, {
@@ -48,9 +38,7 @@ function CornerstoneImageScrollbar({
       return;
     }
 
-    const viewport = cornerstoneViewportService.getCornerstoneViewportByIndex(
-      viewportIndex
-    );
+    const viewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
 
     if (!viewport) {
       return;
@@ -79,7 +67,7 @@ function CornerstoneImageScrollbar({
       const { imageIndex, numberOfSlices } = sliceData;
       setImageSliceData({ imageIndex, numberOfSlices });
     }
-  }, [viewportIndex, viewportData]);
+  }, [viewportId, viewportData]);
 
   useEffect(() => {
     if (viewportData?.viewportType !== Enums.ViewportType.STACK) {
@@ -95,16 +83,10 @@ function CornerstoneImageScrollbar({
       });
     };
 
-    element.addEventListener(
-      Enums.Events.STACK_VIEWPORT_SCROLL,
-      updateStackIndex
-    );
+    element.addEventListener(Enums.Events.STACK_VIEWPORT_SCROLL, updateStackIndex);
 
     return () => {
-      element.removeEventListener(
-        Enums.Events.STACK_VIEWPORT_SCROLL,
-        updateStackIndex
-      );
+      element.removeEventListener(Enums.Events.STACK_VIEWPORT_SCROLL, updateStackIndex);
     };
   }, [viewportData, element]);
 
@@ -122,19 +104,14 @@ function CornerstoneImageScrollbar({
     element.addEventListener(Enums.Events.VOLUME_NEW_IMAGE, updateVolumeIndex);
 
     return () => {
-      element.removeEventListener(
-        Enums.Events.VOLUME_NEW_IMAGE,
-        updateVolumeIndex
-      );
+      element.removeEventListener(Enums.Events.VOLUME_NEW_IMAGE, updateVolumeIndex);
     };
   }, [viewportData, element]);
 
   return (
     <ImageScrollbar
-      onChange={evt => onImageScrollbarChange(evt, viewportIndex)}
-      max={
-        imageSliceData.numberOfSlices ? imageSliceData.numberOfSlices - 1 : 0
-      }
+      onChange={evt => onImageScrollbarChange(evt, viewportId)}
+      max={imageSliceData.numberOfSlices ? imageSliceData.numberOfSlices - 1 : 0}
       height={scrollbarHeight}
       value={imageSliceData.imageIndex}
     />
@@ -143,7 +120,7 @@ function CornerstoneImageScrollbar({
 
 CornerstoneImageScrollbar.propTypes = {
   viewportData: PropTypes.object,
-  viewportIndex: PropTypes.number.isRequired,
+  viewportId: PropTypes.string.isRequired,
   element: PropTypes.instanceOf(Element),
   scrollbarHeight: PropTypes.string,
   imageSliceData: PropTypes.object.isRequired,

extensions/cornerstone/src/Viewport/Overlays/ViewportImageSliceLoadingIndicator.tsx

@@ -33,26 +33,14 @@ function ViewportImageSliceLoadingIndicator({ viewportData, element }) {
   };
 
   useEffect(() => {
-    element.addEventListener(
-      Enums.Events.STACK_VIEWPORT_SCROLL,
-      setLoadingState
-    );
+    element.addEventListener(Enums.Events.STACK_VIEWPORT_SCROLL, setLoadingState);
     element.addEventListener(Enums.Events.IMAGE_LOAD_ERROR, setErrorState);
-    element.addEventListener(
-      Enums.Events.STACK_NEW_IMAGE,
-      setFinishLoadingState
-    );
+    element.addEventListener(Enums.Events.STACK_NEW_IMAGE, setFinishLoadingState);
 
     return () => {
-      element.removeEventListener(
-        Enums.Events.STACK_VIEWPORT_SCROLL,
-        setLoadingState
-      );
+      element.removeEventListener(Enums.Events.STACK_VIEWPORT_SCROLL, setLoadingState);
 
-      element.removeEventListener(
-        Enums.Events.STACK_NEW_IMAGE,
-        setFinishLoadingState
-      );
+      element.removeEventListener(Enums.Events.STACK_NEW_IMAGE, setFinishLoadingState);
 
       element.removeEventListener(Enums.Events.IMAGE_LOAD_ERROR, setErrorState);
     };
@@ -61,8 +49,8 @@ function ViewportImageSliceLoadingIndicator({ viewportData, element }) {
   if (error) {
     return (
       <>
-        <div className="bg-black opacity-50 absolute h-full w-full top-0 left-0">
-          <div className="flex transparent items-center justify-center w-full h-full">
+        <div className="absolute top-0 left-0 h-full w-full bg-black opacity-50">
+          <div className="transparent flex h-full w-full items-center justify-center">
             <p className="text-primary-light text-xl font-light">
               <h4>Error Loading Image</h4>
               <p>An error has occurred.</p>
@@ -78,8 +66,8 @@ function ViewportImageSliceLoadingIndicator({ viewportData, element }) {
     return (
       // IMPORTANT: we need to use the pointer-events-none class to prevent the loading indicator from
       // interacting with the mouse, since scrolling should propagate to the viewport underneath
-      <div className="pointer-events-none bg-black opacity-50 absolute h-full w-full top-0 left-0">
-        <div className="flex transparent items-center justify-center w-full h-full">
+      <div className="pointer-events-none absolute top-0 left-0 h-full w-full bg-black opacity-50">
+        <div className="transparent flex h-full w-full items-center justify-center">
           <p className="text-primary-light text-xl font-light">Loading...</p>
         </div>
       </div>

extensions/cornerstone/src/Viewport/Overlays/ViewportOrientationMarkers.tsx

@@ -13,16 +13,13 @@ import { vec3 } from 'gl-matrix';
 
 import './ViewportOrientationMarkers.css';
 
-const {
-  getOrientationStringLPS,
-  invertOrientationStringLPS,
-} = utilities.orientation;
+const { getOrientationStringLPS, invertOrientationStringLPS } = utilities.orientation;
 
 function ViewportOrientationMarkers({
   element,
   viewportData,
   imageSliceData,
-  viewportIndex,
+  viewportId,
   servicesManager,
   orientationMarkers = ['top', 'left'],
 }) {
@@ -33,9 +30,7 @@ function ViewportOrientationMarkers({
   const { cornerstoneViewportService } = servicesManager.services;
 
   useEffect(() => {
-    const cameraModifiedListener = (
-      evt: Types.EventTypes.CameraModifiedEvent
-    ) => {
+    const cameraModifiedListener = (evt: Types.EventTypes.CameraModifiedEvent) => {
       const { rotation, previousCamera, camera } = evt.detail;
 
       if (rotation !== undefined) {
@@ -57,16 +52,10 @@ function ViewportOrientationMarkers({
       }
     };
 
-    element.addEventListener(
-      Enums.Events.CAMERA_MODIFIED,
-      cameraModifiedListener
-    );
+    element.addEventListener(Enums.Events.CAMERA_MODIFIED, cameraModifiedListener);
 
     return () => {
-      element.removeEventListener(
-        Enums.Events.CAMERA_MODIFIED,
-        cameraModifiedListener
-      );
+      element.removeEventListener(Enums.Events.CAMERA_MODIFIED, cameraModifiedListener);
     };
   }, []);
 
@@ -85,8 +74,7 @@ function ViewportOrientationMarkers({
         return false;
       }
 
-      ({ rowCosines, columnCosines } =
-        metaData.get('imagePlaneModule', imageId) || {});
+      ({ rowCosines, columnCosines } = metaData.get('imagePlaneModule', imageId) || {});
     } else {
       if (!element || !getEnabledElement(element)) {
         return '';
@@ -114,9 +102,7 @@ function ViewportOrientationMarkers({
       flipHorizontal
     );
 
-    const ohifViewport = cornerstoneViewportService.getViewportInfoByIndex(
-      viewportIndex
-    );
+    const ohifViewport = cornerstoneViewportService.getViewportInfo(viewportId);
 
     if (!ohifViewport) {
       console.log('ViewportOrientationMarkers::No viewport');
@@ -126,9 +112,7 @@ function ViewportOrientationMarkers({
 
     // Todo: probably this can be done in a better way in which we identify bright
     // background
-    const isLight = backgroundColor
-      ? csUtils.isEqual(backgroundColor, [1, 1, 1])
-      : false;
+    const isLight = backgroundColor ? csUtils.isEqual(backgroundColor, [1, 1, 1]) : false;
 
     return orientationMarkers.map((m, index) => (
       <div
@@ -174,13 +158,7 @@ ViewportOrientationMarkers.defaultProps = {
  * @param {*} rotation in degrees
  * @returns
  */
-function _getOrientationMarkers(
-  rowCosines,
-  columnCosines,
-  rotation,
-  flipVertical,
-  flipHorizontal
-) {
+function _getOrientationMarkers(rowCosines, columnCosines, rotation, flipVertical, flipHorizontal) {
   const rowString = getOrientationStringLPS(rowCosines);
   const columnString = getOrientationStringLPS(columnCosines);
   const oppositeRowString = invertOrientationStringLPS(rowString);

extensions/cornerstone/src/Viewport/Overlays/ViewportOverlay.tsx

@@ -11,13 +11,10 @@ function CornerstoneViewportOverlay({
   element,
   viewportData,
   imageSliceData,
-  viewportIndex,
+  viewportId,
   servicesManager,
 }) {
-  const {
-    cornerstoneViewportService,
-    toolbarService,
-  } = servicesManager.services;
+  const { cornerstoneViewportService, toolbarService } = servicesManager.services;
   const [voi, setVOI] = useState({ windowCenter: null, windowWidth: null });
   const [scale, setScale] = useState(1);
   const [activeTools, setActiveTools] = useState([]);
@@ -60,10 +57,7 @@ function CornerstoneViewportOverlay({
       }
 
       const { lower, upper } = range;
-      const { windowWidth, windowCenter } = utilities.windowLevel.toWindowLevel(
-        lower,
-        upper
-      );
+      const { windowWidth, windowCenter } = utilities.windowLevel.toWindowLevel(lower, upper);
 
       setVOI({ windowCenter, windowWidth });
     };
@@ -73,7 +67,7 @@ function CornerstoneViewportOverlay({
     return () => {
       element.removeEventListener(Enums.Events.VOI_MODIFIED, updateVOI);
     };
-  }, [viewportIndex, viewportData, voi, element]);
+  }, [viewportId, viewportData, voi, element]);
 
   /**
    * Updating the scale when the viewport changes its zoom
@@ -86,9 +80,7 @@ function CornerstoneViewportOverlay({
         previousCamera.parallelScale !== camera.parallelScale ||
         previousCamera.scale !== camera.scale
       ) {
-        const viewport = cornerstoneViewportService.getCornerstoneViewportByIndex(
-          viewportIndex
-        );
+        const viewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
 
         if (!viewport) {
           return;
@@ -107,8 +99,7 @@ function CornerstoneViewportOverlay({
 
         const { spacing } = imageData;
         // convert parallel scale to scale
-        const scale =
-          (element.clientHeight * spacing[0] * 0.5) / camera.parallelScale;
+        const scale = (element.clientHeight * spacing[0] * 0.5) / camera.parallelScale;
         setScale(scale);
       }
     };
@@ -118,7 +109,7 @@ function CornerstoneViewportOverlay({
     return () => {
       element.removeEventListener(Enums.Events.CAMERA_MODIFIED, updateScale);
     };
-  }, [viewportIndex, viewportData]);
+  }, [viewportId, viewportData]);
 
   const getTopLeftContent = useCallback(() => {
     const { windowWidth, windowCenter } = voi;
@@ -168,7 +159,7 @@ function CornerstoneViewportOverlay({
       instanceNumber = _getInstanceNumberFromVolume(
         viewportData,
         imageIndex,
-        viewportIndex,
+        viewportId,
         cornerstoneViewportService
       );
     }
@@ -183,15 +174,13 @@ function CornerstoneViewportOverlay({
         </span>
       </div>
     );
-  }, [imageSliceData, viewportData, viewportIndex]);
+  }, [imageSliceData, viewportData, viewportId]);
 
   if (!viewportData) {
     return null;
   }
 
-  const ohifViewport = cornerstoneViewportService.getViewportInfoByIndex(
-    viewportIndex
-  );
+  const ohifViewport = cornerstoneViewportService.getViewportInfo(viewportId);
 
   if (!ohifViewport) {
     return null;
@@ -201,9 +190,7 @@ function CornerstoneViewportOverlay({
 
   // Todo: probably this can be done in a better way in which we identify bright
   // background
-  const isLight = backgroundColor
-    ? utilities.isEqual(backgroundColor, [1, 1, 1])
-    : false;
+  const isLight = backgroundColor ? utilities.isEqual(backgroundColor, [1, 1, 1]) : false;
 
   return (
     <ViewportOverlay
@@ -240,7 +227,7 @@ function _getInstanceNumberFromStack(viewportData, imageIndex) {
 function _getInstanceNumberFromVolume(
   viewportData,
   imageIndex,
-  viewportIndex,
+  viewportId,
   cornerstoneViewportService
 ) {
   const volumes = viewportData.volumes;
@@ -253,9 +240,7 @@ function _getInstanceNumberFromVolume(
   const volume = volumes[0];
   const { direction, imageIds } = volume;
 
-  const cornerstoneViewport = cornerstoneViewportService.getCornerstoneViewportByIndex(
-    viewportIndex
-  );
+  const cornerstoneViewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
 
   if (!cornerstoneViewport) {
     return;
@@ -278,8 +263,7 @@ function _getInstanceNumberFromVolume(
       return {};
     }
 
-    const { instanceNumber } =
-      metaData.get('generalImageModule', imageId) || {};
+    const { instanceNumber } = metaData.get('generalImageModule', imageId) || {};
     return parseInt(instanceNumber);
   }
 }
@@ -287,7 +271,7 @@ function _getInstanceNumberFromVolume(
 CornerstoneViewportOverlay.propTypes = {
   viewportData: PropTypes.object,
   imageIndex: PropTypes.number,
-  viewportIndex: PropTypes.number,
+  viewportId: PropTypes.string,
   servicesManager: PropTypes.instanceOf(ServicesManager),
 };
 

extensions/cornerstone/src/Viewport/Overlays/utils.ts

@@ -79,18 +79,12 @@ export function formatPN(name) {
  */
 export function getCompression(imageId) {
   const generalImageModule = metaData.get('generalImageModule', imageId) || {};
-  const {
-    lossyImageCompression,
-    lossyImageCompressionRatio,
-    lossyImageCompressionMethod,
-  } = generalImageModule;
+  const { lossyImageCompression, lossyImageCompressionRatio, lossyImageCompressionMethod } =
+    generalImageModule;
 
   if (lossyImageCompression === '01' && lossyImageCompressionRatio !== '') {
     const compressionMethod = lossyImageCompressionMethod || 'Lossy: ';
-    const compressionRatio = formatNumberPrecision(
-      lossyImageCompressionRatio,
-      2
-    );
+    const compressionRatio = formatNumberPrecision(lossyImageCompressionRatio, 2);
     return compressionMethod + compressionRatio + ' : 1';
   }
 

extensions/cornerstone/src/commandsModule.ts

@@ -18,6 +18,7 @@ import toggleStackImageSync from './utils/stackSync/toggleStackImageSync';
 import { getFirstAnnotationSelected } from './utils/measurementServiceMappings/utils/selection';
 import getActiveViewportEnabledElement from './utils/getActiveViewportEnabledElement';
 import { CornerstoneServices } from './types';
+import ImageOverlayViewerTool from './tools/ImageOverlayViewerTool';
 
 function commandsModule({
   servicesManager,
@@ -28,6 +29,7 @@ function commandsModule({
     toolGroupService,
     cineService,
     toolbarService,
+    stateSyncService,
     uiDialogService,
     cornerstoneViewportService,
     uiNotificationService,
@@ -56,9 +58,7 @@ function commandsModule({
         // filter by allowed selected tools from config property (if there is any)
         const isToolAllowed =
           !optionsToUse.allowedSelectedTools ||
-          optionsToUse.allowedSelectedTools.includes(
-            firstAnnotationSelected?.metadata?.toolName
-          );
+          optionsToUse.allowedSelectedTools.includes(firstAnnotationSelected?.metadata?.toolName);
         if (isToolAllowed) {
           optionsToUse.nearbyToolData = firstAnnotationSelected;
         } else {
@@ -88,10 +88,7 @@ function commandsModule({
     },
 
     getNearbyToolData({ nearbyToolData, element, canvasCoordinates }) {
-      return (
-        nearbyToolData ??
-        cstUtils.getAnnotationNearPoint(element, canvasCoordinates)
-      );
+      return nearbyToolData ?? cstUtils.getAnnotationNearPoint(element, canvasCoordinates);
     },
     getNearbyAnnotation({ element, canvasCoordinates }) {
       const nearbyToolData = actions.getNearbyToolData({
@@ -108,18 +105,14 @@ function commandsModule({
         }
 
         const { renderingEngineId, viewportId } = enabledElement;
-        const toolGroup = ToolGroupManager.getToolGroupForViewport(
-          viewportId,
-          renderingEngineId
-        );
+        const toolGroup = ToolGroupManager.getToolGroupForViewport(viewportId, renderingEngineId);
 
         const toolInstance = toolGroup.getToolInstance(toolName);
 
         return toolInstance?.constructor?.isAnnotation ?? true;
       };
 
-      return nearbyToolData?.metadata?.toolName &&
-        isAnnotation(nearbyToolData.metadata.toolName)
+      return nearbyToolData?.metadata?.toolName && isAnnotation(nearbyToolData.metadata.toolName)
         ? nearbyToolData
         : null;
     },
@@ -152,11 +145,7 @@ function commandsModule({
             label,
           });
 
-          measurementService.update(
-            updatedMeasurement.uid,
-            updatedMeasurement,
-            true
-          );
+          measurementService.update(updatedMeasurement.uid, updatedMeasurement, true);
         },
         false
       );
@@ -219,27 +208,20 @@ function commandsModule({
           }
         }
       }
-      measurementService.update(
-        updatedMeasurement.uid,
-        updatedMeasurement,
-        true
-      );
+      measurementService.update(updatedMeasurement.uid, updatedMeasurement, true);
     },
 
     // Retrieve value commands
     getActiveViewportEnabledElement: _getActiveViewportEnabledElement,
 
     setViewportActive: ({ viewportId }) => {
-      const viewportInfo = cornerstoneViewportService.getViewportInfo(
-        viewportId
-      );
+      const viewportInfo = cornerstoneViewportService.getViewportInfo(viewportId);
       if (!viewportInfo) {
         console.warn('No viewport found for viewportId:', viewportId);
         return;
       }
 
-      const viewportIndex = viewportInfo.getViewportIndex();
-      viewportGridService.setActiveViewportIndex(viewportIndex);
+      viewportGridService.setActiveViewportId(viewportId);
     },
     arrowTextCallback: ({ callback, data }) => {
       callInputDialog(uiDialogService, data, callback);
@@ -249,9 +231,7 @@ function commandsModule({
       const { isCineEnabled } = cineService.getState();
       cineService.setIsCineEnabled(!isCineEnabled);
       toolbarService.setButton('Cine', { props: { isActive: !isCineEnabled } });
-      viewports.forEach((_, index) =>
-        cineService.setCine({ id: index, isPlaying: false })
-      );
+      viewports.forEach((_, index) => cineService.setCine({ id: index, isPlaying: false }));
     },
     setWindowLevel({ window, level, toolGroupId }) {
       // convert to numbers
@@ -259,9 +239,7 @@ function commandsModule({
       const windowCenterNum = Number(level);
 
       const { viewportId } = _getActiveViewportEnabledElement();
-      const viewportToolGroupId = toolGroupService.getToolGroupForViewport(
-        viewportId
-      );
+      const viewportToolGroupId = toolGroupService.getToolGroupForViewport(viewportId);
 
       if (toolGroupId && toolGroupId !== viewportToolGroupId) {
         return;
@@ -271,10 +249,7 @@ function commandsModule({
       const renderingEngine = cornerstoneViewportService.getRenderingEngine();
       const viewport = renderingEngine.getViewport(viewportId);
 
-      const { lower, upper } = csUtils.windowLevel.toLowHighRange(
-        windowWidthNum,
-        windowCenterNum
-      );
+      const { lower, upper } = csUtils.windowLevel.toLowHighRange(windowWidthNum, windowCenterNum);
 
       viewport.setProperties({
         voiRange: {
@@ -292,7 +267,7 @@ function commandsModule({
       toolbarService.recordInteraction(props);
     },
 
-    setToolActive: ({ toolName, toolGroupId = null }) => {
+    setToolActive: ({ toolName, toolGroupId = null, toggledState }) => {
       if (toolName === 'Crosshairs') {
         const activeViewportToolGroup = toolGroupService.getToolGroup(null);
 
@@ -309,9 +284,11 @@ function commandsModule({
         }
       }
 
-      const { viewports } = viewportGridService.getState() || {
-        viewports: [],
-      };
+      const { viewports } = viewportGridService.getState();
+
+      if (!viewports.size) {
+        return;
+      }
 
       const toolGroup = toolGroupService.getToolGroup(toolGroupId);
       const toolGroupViewportIds = toolGroup?.getViewportIds?.();
@@ -321,14 +298,8 @@ function commandsModule({
         return;
       }
 
-      const filteredViewports = viewports.filter(viewport => {
-        if (!viewport.viewportOptions) {
-          return false;
-        }
-
-        return toolGroupViewportIds.includes(
-          viewport.viewportOptions.viewportId
-        );
+      const filteredViewports = Array.from(viewports.values()).filter(viewport => {
+        return toolGroupViewportIds.includes(viewport.viewportId);
       });
 
       if (!filteredViewports.length) {
@@ -357,6 +328,14 @@ function commandsModule({
           toolGroup.setToolPassive(activeToolName);
         }
       }
+
+      // If there is a toggle state, then simply set the enabled/disabled state without
+      // setting the tool active.
+      if (toggledState != null) {
+        toggledState ? toolGroup.setToolEnabled(toolName) : toolGroup.setToolDisabled(toolName);
+        return;
+      }
+
       // Set the new toolName to be active
       toolGroup.setToolActive(toolName, {
         bindings: [
@@ -367,13 +346,9 @@ function commandsModule({
       });
     },
     showDownloadViewportModal: () => {
-      const { activeViewportIndex } = viewportGridService.getState();
+      const { activeViewportId } = viewportGridService.getState();
 
-      if (
-        !cornerstoneViewportService.getCornerstoneViewportByIndex(
-          activeViewportIndex
-        )
-      ) {
+      if (!cornerstoneViewportService.getCornerstoneViewport(activeViewportId)) {
         // Cannot download a non-cornerstone viewport (image).
         uiNotificationService.show({
           title: 'Download Image',
@@ -390,7 +365,7 @@ function commandsModule({
           content: CornerstoneViewportDownloadForm,
           title: 'Download High Quality Image',
           contentProps: {
-            activeViewportIndex,
+            activeViewportId,
             onClose: uiModalService.hide,
             cornerstoneViewportService,
           },
@@ -457,11 +432,9 @@ function commandsModule({
 
       const { viewport } = enabledElement;
 
-      if (viewport instanceof StackViewport) {
-        const { invert } = viewport.getProperties();
-        viewport.setProperties({ invert: !invert });
-        viewport.render();
-      }
+      const { invert } = viewport.getProperties();
+      viewport.setProperties({ invert: !invert });
+      viewport.render();
     },
     resetViewport: () => {
       const enabledElement = _getActiveViewportEnabledElement();
@@ -514,9 +487,7 @@ function commandsModule({
         }
         viewport = enabledElement.viewport;
       } else {
-        viewport = cornerstoneViewportService.getCornerstoneViewport(
-          gridViewport.id
-        );
+        viewport = cornerstoneViewportService.getCornerstoneViewport(gridViewport.id);
       }
 
       // Get number of slices
@@ -526,14 +497,12 @@ function commandsModule({
       if (viewport instanceof StackViewport) {
         numberOfSlices = viewport.getImageIds().length;
       } else if (viewport instanceof VolumeViewport) {
-        numberOfSlices = csUtils.getImageSliceDataForVolumeViewport(viewport)
-          .numberOfSlices;
+        numberOfSlices = csUtils.getImageSliceDataForVolumeViewport(viewport).numberOfSlices;
       } else {
         throw new Error('Unsupported viewport type');
       }
 
-      const jumpIndex =
-        imageIndex < 0 ? numberOfSlices + imageIndex : imageIndex;
+      const jumpIndex = imageIndex < 0 ? numberOfSlices + imageIndex : imageIndex;
       if (jumpIndex >= numberOfSlices || jumpIndex < 0) {
         throw new Error(`Can't jump to ${imageIndex}`);
       }
@@ -554,15 +523,8 @@ function commandsModule({
 
       cstUtils.scroll(viewport, options);
     },
-    setViewportColormap: ({
-      viewportIndex,
-      displaySetInstanceUID,
-      colormap,
-      immediate = false,
-    }) => {
-      const viewport = cornerstoneViewportService.getCornerstoneViewportByIndex(
-        viewportIndex
-      );
+    setViewportColormap: ({ viewportId, displaySetInstanceUID, colormap, immediate = false }) => {
+      const viewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
 
       const actorEntries = viewport.getActors();
 
@@ -578,17 +540,15 @@ function commandsModule({
         viewport.render();
       }
     },
-    incrementActiveViewport: () => {
-      const { activeViewportIndex, viewports } = viewportGridService.getState();
-      const nextViewportIndex = (activeViewportIndex + 1) % viewports.length;
-      viewportGridService.setActiveViewportIndex(nextViewportIndex);
-    },
-    decrementActiveViewport: () => {
-      const { activeViewportIndex, viewports } = viewportGridService.getState();
+    changeActiveViewport: ({ direction = 1 }) => {
+      const { activeViewportId, viewports } = viewportGridService.getState();
+      const viewportIds = Array.from(viewports.keys());
+      const currentIndex = viewportIds.indexOf(activeViewportId);
       const nextViewportIndex =
-        (activeViewportIndex - 1 + viewports.length) % viewports.length;
-      viewportGridService.setActiveViewportIndex(nextViewportIndex);
+        (currentIndex + direction + viewportIds.length) % viewportIds.length;
+      viewportGridService.setActiveViewportId(viewportIds[nextViewportIndex] as string);
     },
+
     toggleStackImageSync: ({ toggledState }) => {
       toggleStackImageSync({
         getEnabledElement,
@@ -596,19 +556,13 @@ function commandsModule({
         toggledState,
       });
     },
-    toggleReferenceLines: ({ toggledState }) => {
-      const { activeViewportIndex } = viewportGridService.getState();
-      const viewportInfo = cornerstoneViewportService.getViewportInfoByIndex(
-        activeViewportIndex
-      );
+    setSourceViewportForReferenceLinesTool: ({ toggledState }) => {
+      const { activeViewportId } = viewportGridService.getState();
+      const viewportInfo = cornerstoneViewportService.getViewportInfo(activeViewportId);
 
       const viewportId = viewportInfo.getViewportId();
       const toolGroup = toolGroupService.getToolGroupForViewport(viewportId);
 
-      if (!toggledState) {
-        toolGroup.setToolDisabled(ReferenceLinesTool.toolName);
-      }
-
       toolGroup.setToolConfiguration(
         ReferenceLinesTool.toolName,
         {
@@ -616,7 +570,9 @@ function commandsModule({
         },
         true // overwrite
       );
-      toolGroup.setToolEnabled(ReferenceLinesTool.toolName);
+    },
+    storePresentation: ({ viewportId }) => {
+      cornerstoneViewportService.storePresentation({ viewportId });
     },
   };
 
@@ -673,10 +629,11 @@ function commandsModule({
       options: { rotation: -90 },
     },
     incrementActiveViewport: {
-      commandFn: actions.incrementActiveViewport,
+      commandFn: actions.changeActiveViewport,
     },
     decrementActiveViewport: {
-      commandFn: actions.decrementActiveViewport,
+      commandFn: actions.changeActiveViewport,
+      options: { direction: -1 },
     },
     flipViewportHorizontal: {
       commandFn: actions.flipViewportHorizontal,
@@ -739,8 +696,13 @@ function commandsModule({
     toggleStackImageSync: {
       commandFn: actions.toggleStackImageSync,
     },
-    toggleReferenceLines: {
-      commandFn: actions.toggleReferenceLines,
+    setSourceViewportForReferenceLinesTool: {
+      commandFn: actions.setSourceViewportForReferenceLinesTool,
+    },
+    storePresentation: {
+      commandFn: actions.storePresentation,
+      storeContexts: [],
+      options: {},
     },
   };
 

extensions/cornerstone/src/components/CinePlayer/CinePlayer.tsx

@@ -0,0 +1,97 @@
+import React, { useEffect } from 'react';
+import { CinePlayer, useCine, useViewportGrid } from '@ohif/ui';
+import { Enums, eventTarget } from '@cornerstonejs/core';
+
+function WrappedCinePlayer({ enabledVPElement, viewportId, servicesManager }) {
+  const { toolbarService, customizationService } = servicesManager.services;
+  const [{ isCineEnabled, cines }, cineService] = useCine();
+  const [{ activeViewportId }] = useViewportGrid();
+
+  const { component: CinePlayerComponent = CinePlayer } =
+    customizationService.get('cinePlayer') ?? {};
+
+  const handleCineClose = () => {
+    toolbarService.recordInteraction({
+      groupId: 'MoreTools',
+      itemId: 'cine',
+      interactionType: 'toggle',
+      commands: [
+        {
+          commandName: 'toggleCine',
+          commandOptions: {},
+          context: 'CORNERSTONE',
+        },
+      ],
+    });
+  };
+
+  const cineHandler = () => {
+    if (!cines || !cines[viewportId] || !enabledVPElement) {
+      return;
+    }
+
+    const cine = cines[viewportId];
+    const isPlaying = cine.isPlaying || false;
+    const frameRate = cine.frameRate || 24;
+
+    const validFrameRate = Math.max(frameRate, 1);
+
+    if (isPlaying) {
+      cineService.playClip(enabledVPElement, {
+        framesPerSecond: validFrameRate,
+      });
+    } else {
+      cineService.stopClip(enabledVPElement);
+    }
+  };
+
+  useEffect(() => {
+    eventTarget.addEventListener(Enums.Events.STACK_VIEWPORT_NEW_STACK, cineHandler);
+
+    return () => {
+      cineService.setCine({ id: viewportId, isPlaying: false });
+      eventTarget.removeEventListener(Enums.Events.STACK_VIEWPORT_NEW_STACK, cineHandler);
+    };
+  }, [enabledVPElement]);
+
+  useEffect(() => {
+    if (!cines || !cines[viewportId] || !enabledVPElement) {
+      return;
+    }
+
+    cineHandler();
+
+    return () => {
+      if (enabledVPElement && cines?.[viewportId]?.isPlaying) {
+        cineService.stopClip(enabledVPElement);
+      }
+    };
+  }, [cines, viewportId, cineService, enabledVPElement, cineHandler]);
+
+  const cine = cines[viewportId];
+  const isPlaying = (cine && cine.isPlaying) || false;
+
+  return (
+    isCineEnabled && (
+      <CinePlayerComponent
+        className="absolute left-1/2 bottom-3 -translate-x-1/2"
+        isPlaying={isPlaying}
+        onClose={handleCineClose}
+        onPlayPauseChange={isPlaying =>
+          cineService.setCine({
+            id: activeViewportId,
+            isPlaying,
+          })
+        }
+        onFrameRateChange={frameRate =>
+          cineService.setCine({
+            id: activeViewportId,
+            frameRate,
+          })
+        }
+      />
+    )
+  );
+}
+
+export default WrappedCinePlayer;

extensions/cornerstone/src/components/CinePlayer/index.ts

@@ -0,0 +1,3 @@
+import CinePlayer from './CinePlayer';
+
+export default CinePlayer;

extensions/cornerstone/src/components/DicomUpload/DicomUpload.css

@@ -1,6 +1,23 @@
 .dicom-upload-drop-area-border-dash {
-  background-image: repeating-linear-gradient(to right, #7BB2CE 0%, #7BB2CE 50%, transparent 50%, transparent 100%), repeating-linear-gradient(to right, #7BB2CE 0%, #7BB2CE 50%, transparent 50%, transparent 100%), repeating-linear-gradient(to bottom, #7BB2CE 0%, #7BB2CE 50%, transparent 50%, transparent 100%), repeating-linear-gradient(to bottom, #7BB2CE 0%, #7BB2CE 50%, transparent 50%, transparent 100%);
-  background-position: left top, left bottom, left top, right top;
+  background-image: repeating-linear-gradient(
+      to right,
+      #7bb2ce 0%,
+      #7bb2ce 50%,
+      transparent 50%,
+      transparent 100%
+    ),
+    repeating-linear-gradient(to right, #7bb2ce 0%, #7bb2ce 50%, transparent 50%, transparent 100%),
+    repeating-linear-gradient(to bottom, #7bb2ce 0%, #7bb2ce 50%, transparent 50%, transparent 100%),
+    repeating-linear-gradient(to bottom, #7bb2ce 0%, #7bb2ce 50%, transparent 50%, transparent 100%);
+  background-position:
+    left top,
+    left bottom,
+    left top,
+    right top;
   background-repeat: repeat-x, repeat-x, repeat-y, repeat-y;
-  background-size: 20px 3px, 20px 3px, 3px 20px, 3px 20px;
+  background-size:
+    20px 3px,
+    20px 3px,
+    3px 20px,
+    3px 20px;
 }

extensions/cornerstone/src/components/DicomUpload/DicomUpload.tsx

@@ -5,7 +5,7 @@ import PropTypes from 'prop-types';
 import classNames from 'classnames';
 import DicomFileUploader from '../../utils/DicomFileUploader';
 import DicomUploadProgress from './DicomUploadProgress';
-import { Button } from '@ohif/ui';
+import { Button, ButtonEnums } from '@ohif/ui';
 import './DicomUpload.css';
 
 type DicomUploadProps = {
@@ -14,19 +14,13 @@ type DicomUploadProps = {
   onStarted: () => void;
 };
 
-function DicomUpload({
-  dataSource,
-  onComplete,
-  onStarted,
-}: DicomUploadProps): ReactElement {
+function DicomUpload({ dataSource, onComplete, onStarted }: DicomUploadProps): ReactElement {
   const baseClassNames = 'min-h-[480px] flex flex-col bg-black select-none';
   const [dicomFileUploaderArr, setDicomFileUploaderArr] = useState([]);
 
   const onDrop = useCallback(async acceptedFiles => {
     onStarted();
-    setDicomFileUploaderArr(
-      acceptedFiles.map(file => new DicomFileUploader(file, dataSource))
-    );
+    setDicomFileUploaderArr(acceptedFiles.map(file => new DicomFileUploader(file, dataSource)));
   }, []);
 
   const getDropZoneComponent = (): ReactElement => {
@@ -40,15 +34,16 @@ function DicomUpload({
         {({ getRootProps }) => (
           <div
             {...getRootProps()}
-            className="m-5 dicom-upload-drop-area-border-dash flex flex-col items-center justify-center h-full"
+            className="dicom-upload-drop-area-border-dash m-5 flex h-full flex-col items-center justify-center"
           >
             <div className="flex gap-3">
-              <Dropzone onDrop={onDrop} noDrag>
+              <Dropzone
+                onDrop={onDrop}
+                noDrag
+              >
                 {({ getRootProps, getInputProps }) => (
                   <div {...getRootProps()}>
                     <Button
-                      variant="contained"
-                      color="primary"
                       disabled={false}
                       onClick={() => {}}
                     >
@@ -58,13 +53,14 @@ function DicomUpload({
                   </div>
                 )}
               </Dropzone>
-              <Dropzone onDrop={onDrop} noDrag>
+              <Dropzone
+                onDrop={onDrop}
+                noDrag
+              >
                 {({ getRootProps, getInputProps }) => (
                   <div {...getRootProps()}>
                     <Button
-                      variant="contained"
-                      color="primaryDark"
-                      border="primaryActive"
+                      type={ButtonEnums.type.secondary}
                       disabled={false}
                       onClick={() => {}}
                     >
@@ -80,9 +76,7 @@ function DicomUpload({
               </Dropzone>
             </div>
             <div className="pt-5">or drag images or folders here</div>
-            <div className="pt-3 text-aqua-pale text-lg">
-              (DICOM files supported)
-            </div>
+            <div className="text-aqua-pale pt-3 text-lg">(DICOM files supported)</div>
           </div>
         )}
       </Dropzone>
@@ -99,9 +93,7 @@ function DicomUpload({
           />
         </div>
       ) : (
-        <div className={classNames('h-[480px]', baseClassNames)}>
-          {getDropZoneComponent()}
-        </div>
+        <div className={classNames('h-[480px]', baseClassNames)}>{getDropZoneComponent()}</div>
       )}
     </>
   );

extensions/cornerstone/src/components/DicomUpload/DicomUploadProgress.tsx

@@ -1,10 +1,4 @@
-import React, {
-  useCallback,
-  useEffect,
-  useRef,
-  useState,
-  ReactElement,
-} from 'react';
+import React, { useCallback, useEffect, useRef, useState, ReactElement } from 'react';
 import PropTypes from 'prop-types';
 import { Button, Icon, ProgressLoadingBar } from '@ohif/ui';
 import DicomFileUploader, {
@@ -39,18 +33,14 @@ const BASE_INTERVAL_TIME = 15000;
 // calculate the upload rate.
 const UPLOAD_RATE_THRESHOLD = 75;
 
-const NO_WRAP_ELLIPSIS_CLASS_NAMES =
-  'text-ellipsis whitespace-nowrap overflow-hidden';
+const NO_WRAP_ELLIPSIS_CLASS_NAMES = 'text-ellipsis whitespace-nowrap overflow-hidden';
 
 function DicomUploadProgress({
   dicomFileUploaderArr,
   onComplete,
 }: DicomUploadProgressProps): ReactElement {
   const [totalUploadSize] = useState(
-    dicomFileUploaderArr.reduce(
-      (acc, fileUploader) => acc + fileUploader.getFileSize(),
-      0
-    )
+    dicomFileUploaderArr.reduce((acc, fileUploader) => acc + fileUploader.getFileSize(), 0)
   );
 
   const currentUploadSizeRef = useRef<number>(0);
@@ -83,15 +73,13 @@ function DicomUploadProgress({
     let intervalStartTime = Date.now();
 
     const setUploadRateRef = () => {
-      const uploadSizeFromStartOfInterval =
-        currentUploadSizeRef.current - intervalStartUploadSize;
+      const uploadSizeFromStartOfInterval = currentUploadSizeRef.current - intervalStartUploadSize;
 
       const now = Date.now();
       const timeSinceStartOfInterval = now - intervalStartTime;
 
       // Calculate and set the upload rate (ref)
-      uploadRateRef.current =
-        uploadSizeFromStartOfInterval / timeSinceStartOfInterval;
+      uploadRateRef.current = uploadSizeFromStartOfInterval / timeSinceStartOfInterval;
 
       // Reset the interval starting values.
       intervalStartUploadSize = currentUploadSizeRef.current;
@@ -134,28 +122,19 @@ function DicomUploadProgress({
       const updateProgress = (percentComplete: number) => {
         const previousFileUploadSize = currentFileUploadSize;
 
-        currentFileUploadSize = Math.round(
-          (percentComplete / 100) * fileUploader.getFileSize()
-        );
+        currentFileUploadSize = Math.round((percentComplete / 100) * fileUploader.getFileSize());
 
         currentUploadSizeRef.current = Math.min(
           totalUploadSize,
-          currentUploadSizeRef.current -
-            previousFileUploadSize +
-            currentFileUploadSize
+          currentUploadSizeRef.current - previousFileUploadSize + currentFileUploadSize
         );
 
-        setPercentComplete(
-          (currentUploadSizeRef.current / totalUploadSize) * 100
-        );
+        setPercentComplete((currentUploadSizeRef.current / totalUploadSize) * 100);
 
         if (uploadRateRef.current !== 0) {
-          const uploadSizeRemaining =
-            totalUploadSize - currentUploadSizeRef.current;
+          const uploadSizeRemaining = totalUploadSize - currentUploadSizeRef.current;
 
-          const timeRemaining = Math.round(
-            uploadSizeRemaining / uploadRateRef.current
-          );
+          const timeRemaining = Math.round(uploadSizeRemaining / uploadRateRef.current);
 
           if (currentTimeRemaining === null) {
             currentTimeRemaining = timeRemaining;
@@ -168,9 +147,7 @@ function DicomUploadProgress({
           // due to rounding, inaccuracies in the estimate and slight variations
           // in upload rates over time.
           if (timeRemaining < ONE_MINUTE) {
-            const currentSecondsRemaining = Math.ceil(
-              currentTimeRemaining / ONE_SECOND
-            );
+            const currentSecondsRemaining = Math.ceil(currentTimeRemaining / ONE_SECOND);
             const secondsRemaining = Math.ceil(timeRemaining / ONE_SECOND);
             const delta = secondsRemaining - currentSecondsRemaining;
             if (delta < 0 || delta > 2) {
@@ -181,9 +158,7 @@ function DicomUploadProgress({
           }
 
           if (timeRemaining < ONE_HOUR) {
-            const currentMinutesRemaining = Math.ceil(
-              currentTimeRemaining / ONE_MINUTE
-            );
+            const currentMinutesRemaining = Math.ceil(currentTimeRemaining / ONE_MINUTE);
             const minutesRemaining = Math.ceil(timeRemaining / ONE_MINUTE);
             const delta = minutesRemaining - currentMinutesRemaining;
             if (delta < 0 || delta > 2) {
@@ -199,9 +174,7 @@ function DicomUploadProgress({
         }
       };
 
-      const progressCallback = (
-        progressEvent: DicomFileUploaderProgressEvent
-      ) => {
+      const progressCallback = (progressEvent: DicomFileUploaderProgressEvent) => {
         updateProgress(progressEvent.percentComplete);
       };
 
@@ -249,16 +222,12 @@ function DicomUploadProgress({
 
     if (timeRemaining < ONE_MINUTE) {
       const secondsRemaining = Math.ceil(timeRemaining / ONE_SECOND);
-      return `${secondsRemaining} ${
-        secondsRemaining === 1 ? 'second' : 'seconds'
-      }`;
+      return `${secondsRemaining} ${secondsRemaining === 1 ? 'second' : 'seconds'}`;
     }
 
     if (timeRemaining < ONE_HOUR) {
       const minutesRemaining = Math.ceil(timeRemaining / ONE_MINUTE);
-      return `${minutesRemaining} ${
-        minutesRemaining === 1 ? 'minute' : 'minutes'
-      }`;
+      return `${minutesRemaining} ${minutesRemaining === 1 ? 'minute' : 'minutes'}`;
     }
 
     const hoursRemaining = Math.ceil(timeRemaining / ONE_HOUR);
@@ -278,9 +247,7 @@ function DicomUploadProgress({
   const showInfiniteProgressBar = useCallback((): boolean => {
     return (
       getPercentCompleteRounded() < 1 &&
-      (progressBarContainerRef?.current?.offsetWidth ?? 0) *
-        (percentComplete / 100) <
-        1
+      (progressBarContainerRef?.current?.offsetWidth ?? 0) * (percentComplete / 100) < 1
     );
   }, [getPercentCompleteRounded, percentComplete]);
 
@@ -300,17 +267,13 @@ function DicomUploadProgress({
 
   const getNumCompletedAndTimeRemainingComponent = (): ReactElement => {
     return (
-      <div className="text-lg px-1 pb-4 h-14 flex bg-primary-dark items-center">
+      <div className="bg-primary-dark flex h-14 items-center px-1 pb-4 text-lg">
         {numFilesCompleted === dicomFileUploaderArr.length ? (
           <>
-            <span className={NO_WRAP_ELLIPSIS_CLASS_NAMES}>{`${
-              dicomFileUploaderArr.length
-            } ${
+            <span className={NO_WRAP_ELLIPSIS_CLASS_NAMES}>{`${dicomFileUploaderArr.length} ${
               dicomFileUploaderArr.length > 1 ? 'files' : 'file'
             } completed.`}</span>
             <Button
-              variant="contained"
-              color="primary"
               disabled={false}
               className="ml-auto"
               onClick={onComplete}
@@ -326,18 +289,14 @@ function DicomUploadProgress({
             >
               {`${numFilesCompleted} of ${dicomFileUploaderArr.length}`}&nbsp;
             </span>
+            <span className={NO_WRAP_ELLIPSIS_CLASS_NAMES}>{' files completed.'}&nbsp;</span>
             <span className={NO_WRAP_ELLIPSIS_CLASS_NAMES}>
-              {' files completed.'}&nbsp;
-            </span>
-            <span className={NO_WRAP_ELLIPSIS_CLASS_NAMES}>
-              {timeRemaining
-                ? `Less than ${getFormattedTimeRemaining()} remaining. `
-                : ''}
+              {timeRemaining ? `Less than ${getFormattedTimeRemaining()} remaining. ` : ''}
             </span>
             <span
               className={classNames(
                 NO_WRAP_ELLIPSIS_CLASS_NAMES,
-                'cursor-pointer text-primary-active hover:text-primary-light active:text-aqua-pale ml-auto'
+                'text-primary-active hover:text-primary-light active:text-aqua-pale ml-auto cursor-pointer'
               )}
               onClick={cancelAllUploads}
             >
@@ -351,14 +310,13 @@ function DicomUploadProgress({
 
   const getShowFailedOnlyIconComponent = (): ReactElement => {
     return (
-      <div className="ml-auto flex justify-center w-6">
+      <div className="ml-auto flex w-6 justify-center">
         {numFails > 0 && (
-          <div
-            onClick={() =>
-              setShowFailedOnly(currentShowFailedOnly => !currentShowFailedOnly)
-            }
-          >
-            <Icon className="cursor-pointer" name="icon-status-alert"></Icon>
+          <div onClick={() => setShowFailedOnly(currentShowFailedOnly => !currentShowFailedOnly)}>
+            <Icon
+              className="cursor-pointer"
+              name="icon-status-alert"
+            ></Icon>
           </div>
         )}
       </div>
@@ -367,31 +325,28 @@ function DicomUploadProgress({
 
   const getPercentCompleteComponent = (): ReactElement => {
     return (
-      <div className="overflow-y-scroll ohif-scrollbar px-2 border-b border-secondary-light">
-        <div className="flex w-full p-2.5 items-center min-h-14">
+      <div className="ohif-scrollbar border-secondary-light overflow-y-scroll border-b px-2">
+        <div className="min-h-14 flex w-full items-center p-2.5">
           {numFilesCompleted === dicomFileUploaderArr.length ? (
             <>
-              <div className="text-xl text-primary-light">
+              <div className="text-primary-light text-xl">
                 {numFails > 0
-                  ? `Completed with ${numFails} ${
-                      numFails > 1 ? 'errors' : 'error'
-                    }!`
+                  ? `Completed with ${numFails} ${numFails > 1 ? 'errors' : 'error'}!`
                   : 'Completed!'}
               </div>
               {getShowFailedOnlyIconComponent()}
             </>
           ) : (
             <>
-              <div ref={progressBarContainerRef} className="flex-grow">
+              <div
+                ref={progressBarContainerRef}
+                className="flex-grow"
+              >
                 <ProgressLoadingBar
-                  progress={
-                    showInfiniteProgressBar()
-                      ? undefined
-                      : Math.min(100, percentComplete)
-                  }
+                  progress={showInfiniteProgressBar() ? undefined : Math.min(100, percentComplete)}
                 ></ProgressLoadingBar>
               </div>
-              <div className="w-24 ml-1 flex items-center">
+              <div className="ml-1 flex w-24 items-center">
                 <div className="w-10 text-right">{`${getPercentCompleteRounded()}%`}</div>
                 {getShowFailedOnlyIconComponent()}
               </div>
@@ -403,16 +358,15 @@ function DicomUploadProgress({
   };
 
   return (
-    <div className="flex flex-col grow">
+    <div className="flex grow flex-col">
       {getNumCompletedAndTimeRemainingComponent()}
-      <div className="flex flex-col bg-black text-lg overflow-hidden grow">
+      <div className="flex grow flex-col overflow-hidden bg-black text-lg">
         {getPercentCompleteComponent()}
-        <div className="overflow-y-scroll ohif-scrollbar px-2 grow h-1">
+        <div className="ohif-scrollbar h-1 grow overflow-y-scroll px-2">
           {dicomFileUploaderArr
             .filter(
               dicomFileUploader =>
-                !showFailedOnly ||
-                dicomFileUploader.getStatus() === UploadStatus.Failed
+                !showFailedOnly || dicomFileUploader.getStatus() === UploadStatus.Failed
             )
             .map(dicomFileUploader => (
               <DicomUploadProgressItem
@@ -427,9 +381,7 @@ function DicomUploadProgress({
 }
 
 DicomUploadProgress.propTypes = {
-  dicomFileUploaderArr: PropTypes.arrayOf(
-    PropTypes.instanceOf(DicomFileUploader)
-  ).isRequired,
+  dicomFileUploaderArr: PropTypes.arrayOf(PropTypes.instanceOf(DicomFileUploader)).isRequired,
   onComplete: PropTypes.func.isRequired,
 };
 

extensions/cornerstone/src/components/DicomUpload/DicomUploadProgressItem.tsx

@@ -1,10 +1,4 @@
-import React, {
-  ReactElement,
-  memo,
-  useCallback,
-  useEffect,
-  useState,
-} from 'react';
+import React, { ReactElement, memo, useCallback, useEffect, useState } from 'react';
 import PropTypes from 'prop-types';
 import DicomFileUploader, {
   DicomFileUploaderProgressEvent,
@@ -21,13 +15,10 @@ type DicomUploadProgressItemProps = {
 // eslint-disable-next-line react/display-name
 const DicomUploadProgressItem = memo(
   ({ dicomFileUploader }: DicomUploadProgressItemProps): ReactElement => {
-    const [percentComplete, setPercentComplete] = useState(
-      dicomFileUploader.getPercentComplete()
-    );
+    const [percentComplete, setPercentComplete] = useState(dicomFileUploader.getPercentComplete());
     const [failedReason, setFailedReason] = useState('');
     const [status, setStatus] = useState(dicomFileUploader.getStatus());
 
-    console.info(`${dicomFileUploader.getFileId()}`);
     const isComplete = useCallback(() => {
       return (
         status === UploadStatus.Failed ||
@@ -63,7 +54,10 @@ const DicomUploadProgressItem = memo(
       switch (dicomFileUploader.getStatus()) {
         case UploadStatus.Success:
           return (
-            <Icon name="status-tracked" className="text-primary-light"></Icon>
+            <Icon
+              name="status-tracked"
+              className="text-primary-light"
+            ></Icon>
           );
         case UploadStatus.InProgress:
           return <Icon name="icon-transferring"></Icon>;
@@ -77,27 +71,25 @@ const DicomUploadProgressItem = memo(
     };
 
     return (
-      <div className="flex w-full p-2.5 text-lg min-h-14 items-center border-b border-secondary-light overflow-hidden">
-        <div className="flex flex-col gap-1 self-top w-0 grow shrink">
+      <div className="min-h-14 border-secondary-light flex w-full items-center overflow-hidden border-b p-2.5 text-lg">
+        <div className="self-top flex w-0 shrink grow flex-col gap-1">
           <div className="flex gap-4">
-            <div className="flex w-6 justify-center items-center shrink-0">
-              {getStatusIcon()}
-            </div>
-            <div className="text-ellipsis whitespace-nowrap overflow-hidden">
+            <div className="flex w-6 shrink-0 items-center justify-center">{getStatusIcon()}</div>
+            <div className="overflow-hidden text-ellipsis whitespace-nowrap">
               {dicomFileUploader.getFileName()}
             </div>
           </div>
           {failedReason && <div className="pl-10">{failedReason}</div>}
         </div>
-        <div className="w-24 flex items-center">
+        <div className="flex w-24 items-center">
           {!isComplete() && (
             <>
               {dicomFileUploader.getStatus() === UploadStatus.InProgress && (
                 <div className="w-10 text-right">{percentComplete}%</div>
               )}
-              <div className="flex cursor-pointer ml-auto">
+              <div className="ml-auto flex cursor-pointer">
                 <Icon
-                  className="self-center text-primary-active"
+                  className="text-primary-active self-center"
                   name="close"
                   onClick={cancelUpload}
                 />

extensions/cornerstone/src/getHangingProtocolModule.ts

@@ -4,9 +4,8 @@ const mpr: Types.HangingProtocol.Protocol = {
   id: 'mpr',
   name: 'Multi-Planar Reconstruction',
   locked: true,
-  hasUpdatedPriorsInformation: false,
   createdDate: '2021-02-23',
-  modifiedDate: '2023-04-03',
+  modifiedDate: '2023-08-15',
   availableTo: {},
   editableBy: {},
   // Unknown number of priors referenced - so just match any study
@@ -89,6 +88,7 @@ const mpr: Types.HangingProtocol.Protocol = {
       viewports: [
         {
           viewportOptions: {
+            viewportId: 'mpr-axial',
             toolGroupId: 'mpr',
             viewportType: 'volume',
             orientation: 'axial',
@@ -112,6 +112,7 @@ const mpr: Types.HangingProtocol.Protocol = {
         },
         {
           viewportOptions: {
+            viewportId: 'mpr-sagittal',
             toolGroupId: 'mpr',
             viewportType: 'volume',
             orientation: 'sagittal',
@@ -135,6 +136,7 @@ const mpr: Types.HangingProtocol.Protocol = {
         },
         {
           viewportOptions: {
+            viewportId: 'mpr-coronal',
             toolGroupId: 'mpr',
             viewportType: 'volume',
             orientation: 'coronal',
@@ -164,7 +166,6 @@ const mpr: Types.HangingProtocol.Protocol = {
 const mprAnd3DVolumeViewport = {
   id: 'mprAnd3DVolumeViewport',
   locked: true,
-  hasUpdatedPriorsInformation: false,
   name: 'mpr',
   createdDate: '2023-03-15T10:29:44.894Z',
   modifiedDate: '2023-03-15T10:29:44.894Z',

extensions/cornerstone/src/index.tsx

@@ -24,7 +24,6 @@ import { toolNames } from './initCornerstoneTools';
 import { getEnabledElement, reset as enabledElementReset } from './state';
 import dicomLoaderService from './utils/dicomLoaderService';
 import getActiveViewportEnabledElement from './utils/getActiveViewportEnabledElement';
-import { registerColormap } from './utils/colormap/transferFunctionHelpers';
 
 import { id } from './id';
 import * as csWADOImageLoader from './initWADOImageLoader.js';
@@ -32,9 +31,7 @@ import { measurementMappingUtils } from './utils/measurementServiceMappings';
 import type { PublicViewportOptions } from './services/ViewportService/Viewport';
 
 const Component = React.lazy(() => {
-  return import(
-    /* webpackPrefetch: true */ './Viewport/OHIFCornerstoneViewport'
-  );
+  return import(/* webpackPrefetch: true */ './Viewport/OHIFCornerstoneViewport');
 });
 
 const OHIFCornerstoneViewport = props => {
@@ -62,7 +59,6 @@ const cornerstoneExtension: Types.Extensions.Extension = {
       imageRetrievalPoolManager.clearRequestStack(type);
     });
 
-    csWADOImageLoader.destroy();
     enabledElementReset();
   },
 
@@ -71,9 +67,7 @@ const cornerstoneExtension: Types.Extensions.Extension = {
    *
    * @param configuration.csToolsConfig - Passed directly to `initCornerstoneTools`
    */
-  preRegistration: function (
-    props: Types.Extensions.ExtensionParams
-  ): Promise<void> {
+  preRegistration: function (props: Types.Extensions.ExtensionParams): Promise<void> {
     const { servicesManager } = props;
     servicesManager.registerService(CornerstoneViewportService.REGISTRATION);
     servicesManager.registerService(ToolGroupService.REGISTRATION);
@@ -141,5 +135,10 @@ const cornerstoneExtension: Types.Extensions.Extension = {
 };
 
 export type { PublicViewportOptions };
-export { measurementMappingUtils, CornerstoneExtensionTypes, toolNames , getActiveViewportEnabledElement};
+export {
+  measurementMappingUtils,
+  CornerstoneExtensionTypes,
+  toolNames,
+  getActiveViewportEnabledElement,
+};
 export default cornerstoneExtension;

extensions/cornerstone/src/init.tsx

@@ -26,6 +26,7 @@ import nthLoader from './utils/nthLoader';
 import interleaveTopToBottom from './utils/interleaveTopToBottom';
 import initContextMenu from './initContextMenu';
 import initDoubleClick from './initDoubleClick';
+import { CornerstoneServices } from './types';
 
 // TODO: Cypress tests are currently grabbing this from the window?
 window.cornerstone = cornerstone;
@@ -48,31 +49,23 @@ export default async function init({
     ...cornerstone.getConfiguration(),
     rendering: {
       ...cornerstone.getConfiguration().rendering,
-      strictZSpacingForVolumeViewport:
-        appConfig.strictZSpacingForVolumeViewport,
+      strictZSpacingForVolumeViewport: appConfig.strictZSpacingForVolumeViewport,
     },
   });
 
-  // For debugging large datasets
-  const MAX_CACHE_SIZE_1GB = 1073741824;
-  const maxCacheSize = appConfig.maxCacheSize;
-  cornerstone.cache.setMaxCacheSize(
-    maxCacheSize ? maxCacheSize : MAX_CACHE_SIZE_1GB
-  );
+  // For debugging large datasets, otherwise prefer the defaults
+  const { maxCacheSize } = appConfig;
+  if (maxCacheSize) {
+    cornerstone.cache.setMaxCacheSize(maxCacheSize);
+  }
 
   initCornerstoneTools();
 
-  Settings.getRuntimeSettings().set(
-    'useCursors',
-    Boolean(appConfig.useCursors)
-  );
+  Settings.getRuntimeSettings().set('useCursors', Boolean(appConfig.useCursors));
 
   const {
     userAuthenticationService,
-    measurementService,
     customizationService,
-    displaySetService,
-    uiDialogService,
     uiModalService,
     uiNotificationService,
     cineService,
@@ -81,28 +74,21 @@ export default async function init({
     toolGroupService,
     viewportGridService,
     stateSyncService,
-  } = servicesManager.services;
+  } = servicesManager.services as CornerstoneServices;
 
   window.services = servicesManager.services;
   window.extensionManager = extensionManager;
   window.commandsManager = commandsManager;
 
-  if (
-    appConfig.showWarningMessageForCrossOrigin &&
-    !window.crossOriginIsolated
-  ) {
+  if (appConfig.showWarningMessageForCrossOrigin && !window.crossOriginIsolated) {
     uiNotificationService.show({
       title: 'Cross Origin Isolation',
-      message:
-        'Cross Origin Isolation is not enabled, volume rendering will not work (e.g., MPR)',
+      message: 'Cross Origin Isolation is not enabled, volume rendering will not work (e.g., MPR)',
       type: 'warning',
     });
   }
 
-  if (
-    appConfig.showCPUFallbackMessage &&
-    cornerstone.getShouldUseCPURendering()
-  ) {
+  if (appConfig.showCPUFallbackMessage && cornerstone.getShouldUseCPURendering()) {
     _showCPURenderingModal(uiModalService, hangingProtocolService);
   }
 
@@ -122,18 +108,14 @@ export default async function init({
     clearOnModeExit: true,
   });
 
-  const labelmapRepresentation =
-    cornerstoneTools.Enums.SegmentationRepresentations.Labelmap;
+  const labelmapRepresentation = cornerstoneTools.Enums.SegmentationRepresentations.Labelmap;
 
-  cornerstoneTools.segmentation.config.setGlobalRepresentationConfig(
-    labelmapRepresentation,
-    {
-      fillAlpha: 0.3,
-      fillAlphaInactive: 0.2,
-      outlineOpacity: 1,
-      outlineOpacityInactive: 0.65,
-    }
-  );
+  cornerstoneTools.segmentation.config.setGlobalRepresentationConfig(labelmapRepresentation, {
+    fillAlpha: 0.3,
+    fillAlphaInactive: 0.2,
+    outlineOpacity: 1,
+    outlineOpacityInactive: 0.65,
+  });
 
   const metadataProvider = OHIF.classes.MetadataProvider;
 
@@ -142,14 +124,8 @@ export default async function init({
     cornerstoneStreamingImageVolumeLoader
   );
 
-  hangingProtocolService.registerImageLoadStrategy(
-    'interleaveCenter',
-    interleaveCenterLoader
-  );
-  hangingProtocolService.registerImageLoadStrategy(
-    'interleaveTopToBottom',
-    interleaveTopToBottom
-  );
+  hangingProtocolService.registerImageLoadStrategy('interleaveCenter', interleaveCenterLoader);
+  hangingProtocolService.registerImageLoadStrategy('interleaveTopToBottom', interleaveTopToBottom);
   hangingProtocolService.registerImageLoadStrategy('nth', nthLoader);
 
   // add metadata providers
@@ -166,12 +142,10 @@ export default async function init({
     prefetch: appConfig?.maxNumRequests?.prefetch || 10,
   };
 
-  initWADOImageLoader(userAuthenticationService, appConfig);
+  initWADOImageLoader(userAuthenticationService, appConfig, extensionManager);
 
   /* Measurement Service */
-  this.measurementServiceSource = connectToolsToMeasurementService(
-    servicesManager
-  );
+  this.measurementServiceSource = connectToolsToMeasurementService(servicesManager);
 
   initCineService(cineService);
 
@@ -181,31 +155,18 @@ export default async function init({
     volumeInputArrayMap => {
       for (const entry of volumeInputArrayMap.entries()) {
         const [viewportId, volumeInputArray] = entry;
-        const viewport = cornerstoneViewportService.getCornerstoneViewport(
-          viewportId
-        );
+        const viewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
 
-        const ohifViewport = cornerstoneViewportService.getViewportInfo(
-          viewportId
-        );
+        const ohifViewport = cornerstoneViewportService.getViewportInfo(viewportId);
 
-        const {
-          lutPresentationStore,
-          positionPresentationStore,
-        } = stateSyncService.getState();
+        const { lutPresentationStore, positionPresentationStore } = stateSyncService.getState();
         const { presentationIds } = ohifViewport.getViewportOptions();
         const presentations = {
-          positionPresentation:
-            positionPresentationStore[presentationIds?.positionPresentationId],
-          lutPresentation:
-            lutPresentationStore[presentationIds?.lutPresentationId],
+          positionPresentation: positionPresentationStore[presentationIds?.positionPresentationId],
+          lutPresentation: lutPresentationStore[presentationIds?.lutPresentationId],
         };
 
-        cornerstoneViewportService.setVolumesForViewport(
-          viewport,
-          volumeInputArray,
-          presentations
-        );
+        cornerstoneViewportService.setVolumesForViewport(viewport, volumeInputArray, presentations);
       }
     }
   );
@@ -228,9 +189,7 @@ export default async function init({
 
   const resetCrosshairs = evt => {
     const { element } = evt.detail;
-    const { viewportId, renderingEngineId } = cornerstone.getEnabledElement(
-      element
-    );
+    const { viewportId, renderingEngineId } = cornerstone.getEnabledElement(element);
 
     const toolGroup = cornerstoneTools.ToolGroupManager.getToolGroupForViewport(
       viewportId,
@@ -256,10 +215,7 @@ export default async function init({
     const { element } = evt.detail;
     element.addEventListener(EVENTS.CAMERA_RESET, resetCrosshairs);
 
-    eventTarget.addEventListener(
-      EVENTS.STACK_VIEWPORT_NEW_STACK,
-      newStackCallback
-    );
+    eventTarget.addEventListener(EVENTS.STACK_VIEWPORT_NEW_STACK, newStackCallback);
   }
 
   function elementDisabledHandler(evt) {
@@ -274,20 +230,13 @@ export default async function init({
     // );
   }
 
-  eventTarget.addEventListener(
-    EVENTS.ELEMENT_ENABLED,
-    elementEnabledHandler.bind(null)
-  );
+  eventTarget.addEventListener(EVENTS.ELEMENT_ENABLED, elementEnabledHandler.bind(null));
 
-  eventTarget.addEventListener(
-    EVENTS.ELEMENT_DISABLED,
-    elementDisabledHandler.bind(null)
-  );
+  eventTarget.addEventListener(EVENTS.ELEMENT_DISABLED, elementDisabledHandler.bind(null));
 
   viewportGridService.subscribe(
-    viewportGridService.EVENTS.ACTIVE_VIEWPORT_INDEX_CHANGED,
-    ({ viewportIndex, viewportId }) => {
-      viewportId = viewportId || `viewport-${viewportIndex}`;
+    viewportGridService.EVENTS.ACTIVE_VIEWPORT_ID_CHANGED,
+    ({ viewportId }) => {
       const toolGroup = toolGroupService.getToolGroupForViewport(viewportId);
 
       if (!toolGroup || !toolGroup._toolInstances?.['ReferenceLines']) {
@@ -296,8 +245,7 @@ export default async function init({
 
       // check if reference lines are active
       const referenceLinesEnabled =
-        toolGroup._toolInstances['ReferenceLines'].mode ===
-        Enums.ToolModes.Enabled;
+        toolGroup._toolInstances['ReferenceLines'].mode === Enums.ToolModes.Enabled;
 
       if (!referenceLinesEnabled) {
         return;
@@ -322,10 +270,9 @@ function CPUModal() {
   return (
     <div>
       <p>
-        Your computer does not have enough GPU power to support the default GPU
-        rendering mode. OHIF has switched to CPU rendering mode. Please note
-        that CPU rendering does not support all features such as Volume
-        Rendering, Multiplanar Reconstruction, and Segmentation Overlays.
+        Your computer does not have enough GPU power to support the default GPU rendering mode. OHIF
+        has switched to CPU rendering mode. Please note that CPU rendering does not support all
+        features such as Volume Rendering, Multiplanar Reconstruction, and Segmentation Overlays.
       </p>
     </div>
   );

extensions/cornerstone/src/initContextMenu.ts

@@ -35,9 +35,15 @@ const DEFAULT_CONTEXT_MENU_CLICKS = {
 function getEventName(evt) {
   const button = evt.detail.event.which;
   const nameArr = [];
-  if (evt.detail.event.altKey) nameArr.push('alt');
-  if (evt.detail.event.ctrlKey) nameArr.push('ctrl');
-  if (evt.detail.event.shiftKey) nameArr.push('shift');
+  if (evt.detail.event.altKey) {
+    nameArr.push('alt');
+  }
+  if (evt.detail.event.ctrlKey) {
+    nameArr.push('ctrl');
+  }
+  if (evt.detail.event.shiftKey) {
+    nameArr.push('shift');
+  }
   nameArr.push('button');
   nameArr.push(button);
   return nameArr.join('');
@@ -54,10 +60,8 @@ function initContextMenu({
    */
   const cornerstoneViewportHandleEvent = (name, evt) => {
     const customizations =
-      customizationService.get('cornerstoneViewportClickCommands') ||
-      DEFAULT_CONTEXT_MENU_CLICKS;
+      customizationService.get('cornerstoneViewportClickCommands') || DEFAULT_CONTEXT_MENU_CLICKS;
     const toRun = customizations[name];
-    console.log('initContextMenu::cornerstoneViewportHandleEvent', name, toRun);
     const options = {
       nearbyToolData: findNearbyToolData(commandsManager, evt),
       event: evt,
@@ -73,35 +77,24 @@ function initContextMenu({
   function elementEnabledHandler(evt) {
     const { viewportId, element } = evt.detail;
     const viewportInfo = cornerstoneViewportService.getViewportInfo(viewportId);
-    if (!viewportInfo) return;
-    const viewportIndex = viewportInfo.getViewportIndex();
+    if (!viewportInfo) {
+      return;
+    }
     // TODO check update upstream
-    setEnabledElement(viewportIndex, element);
+    setEnabledElement(viewportId, element);
 
-    element.addEventListener(
-      cs3DToolsEvents.MOUSE_CLICK,
-      cornerstoneViewportHandleClick
-    );
+    element.addEventListener(cs3DToolsEvents.MOUSE_CLICK, cornerstoneViewportHandleClick);
   }
 
   function elementDisabledHandler(evt) {
     const { element } = evt.detail;
 
-    element.removeEventListener(
-      cs3DToolsEvents.MOUSE_CLICK,
-      cornerstoneViewportHandleClick
-    );
+    element.removeEventListener(cs3DToolsEvents.MOUSE_CLICK, cornerstoneViewportHandleClick);
   }
 
-  eventTarget.addEventListener(
-    EVENTS.ELEMENT_ENABLED,
-    elementEnabledHandler.bind(null)
-  );
+  eventTarget.addEventListener(EVENTS.ELEMENT_ENABLED, elementEnabledHandler.bind(null));
 
-  eventTarget.addEventListener(
-    EVENTS.ELEMENT_DISABLED,
-    elementDisabledHandler.bind(null)
-  );
+  eventTarget.addEventListener(EVENTS.ELEMENT_DISABLED, elementDisabledHandler.bind(null));
 }
 
 export default initContextMenu;

extensions/cornerstone/src/initCornerstoneTools.js

@@ -28,6 +28,7 @@ import {
 } from '@cornerstonejs/tools';
 
 import CalibrationLineTool from './tools/CalibrationLineTool';
+import ImageOverlayViewerTool from './tools/ImageOverlayViewerTool';
 
 export default function initCornerstoneTools(configuration = {}) {
   CrosshairsTool.isAnnotation = false;
@@ -58,6 +59,7 @@ export default function initCornerstoneTools(configuration = {}) {
   addTool(ReferenceLinesTool);
   addTool(CalibrationLineTool);
   addTool(TrackballRotateTool);
+  addTool(ImageOverlayViewerTool);
 
   // Modify annotation tools to use dashed lines on SR
   const annotationStyle = {
@@ -99,6 +101,7 @@ const toolNames = {
   ReferenceLines: ReferenceLinesTool.toolName,
   CalibrationLine: CalibrationLineTool.toolName,
   TrackballRotateTool: TrackballRotateTool.toolName,
+  ImageOverlayViewer: ImageOverlayViewerTool.toolName,
 };
 
 export { toolNames };

extensions/cornerstone/src/initDoubleClick.ts

@@ -21,9 +21,15 @@ const DEFAULT_DOUBLE_CLICK = {
  */
 function getDoubleClickEventName(evt: CustomEvent) {
   const nameArr = [];
-  if (evt.detail.event.altKey) nameArr.push('alt');
-  if (evt.detail.event.ctrlKey) nameArr.push('ctrl');
-  if (evt.detail.event.shiftKey) nameArr.push('shift');
+  if (evt.detail.event.altKey) {
+    nameArr.push('alt');
+  }
+  if (evt.detail.event.ctrlKey) {
+    nameArr.push('ctrl');
+  }
+  if (evt.detail.event.shiftKey) {
+    nameArr.push('shift');
+  }
   nameArr.push('doubleClick');
   return nameArr.join('');
 }
@@ -33,10 +39,7 @@ export type initDoubleClickArgs = {
   commandsManager: CommandsManager;
 };
 
-function initDoubleClick({
-  customizationService,
-  commandsManager,
-}: initDoubleClickArgs): void {
+function initDoubleClick({ customizationService, commandsManager }: initDoubleClickArgs): void {
   const cornerstoneViewportHandleDoubleClick = (evt: CustomEvent) => {
     // Do not allow double click on a tool.
     const nearbyToolData = findNearbyToolData(commandsManager, evt);
@@ -48,8 +51,7 @@ function initDoubleClick({
 
     // Allows for the customization of the double click on a viewport.
     const customizations =
-      customizationService.get('cornerstoneViewportClickCommands') ||
-      DEFAULT_DOUBLE_CLICK;
+      customizationService.get('cornerstoneViewportClickCommands') || DEFAULT_DOUBLE_CLICK;
 
     const toRun = customizations[eventName];
 
@@ -78,15 +80,9 @@ function initDoubleClick({
     );
   }
 
-  eventTarget.addEventListener(
-    EVENTS.ELEMENT_ENABLED,
-    elementEnabledHandler.bind(null)
-  );
+  eventTarget.addEventListener(EVENTS.ELEMENT_ENABLED, elementEnabledHandler.bind(null));
 
-  eventTarget.addEventListener(
-    EVENTS.ELEMENT_DISABLED,
-    elementDisabledHandler.bind(null)
-  );
+  eventTarget.addEventListener(EVENTS.ELEMENT_DISABLED, elementDisabledHandler.bind(null));
 }
 
 export default initDoubleClick;

extensions/cornerstone/src/initMeasurementService.js

@@ -127,11 +127,8 @@ const initMeasurementService = (
 };
 
 const connectToolsToMeasurementService = servicesManager => {
-  const {
-    measurementService,
-    displaySetService,
-    cornerstoneViewportService,
-  } = servicesManager.services;
+  const { measurementService, displaySetService, cornerstoneViewportService } =
+    servicesManager.services;
   const csTools3DVer1MeasurementSource = initMeasurementService(
     measurementService,
     displaySetService,
@@ -153,10 +150,7 @@ const connectToolsToMeasurementService = servicesManager => {
       } = annotationAddedEventDetail;
       const { toolName } = metadata;
 
-      if (
-        csToolsEvent.type === completedEvt &&
-        toolName === toolNames.CalibrationLine
-      ) {
+      if (csToolsEvent.type === completedEvt && toolName === toolNames.CalibrationLine) {
         // show modal to input the measurement (mm)
         onCompletedCalibrationLine(servicesManager, csToolsEvent)
           .then(
@@ -212,10 +206,8 @@ const connectToolsToMeasurementService = servicesManager => {
     try {
       const annotationSelectionEventDetail = csToolsEvent.detail;
 
-      const {
-        added: addedSelectedAnnotationUIDs,
-        removed: removedSelectedAnnotationUIDs,
-      } = annotationSelectionEventDetail;
+      const { added: addedSelectedAnnotationUIDs, removed: removedSelectedAnnotationUIDs } =
+        annotationSelectionEventDetail;
 
       if (removedSelectedAnnotationUIDs) {
         removedSelectedAnnotationUIDs.forEach(annotationUID =>
@@ -283,12 +275,8 @@ const connectMeasurementServiceToTools = (
   cornerstoneViewportService,
   measurementSource
 ) => {
-  const {
-    MEASUREMENT_REMOVED,
-    MEASUREMENTS_CLEARED,
-    MEASUREMENT_UPDATED,
-    RAW_MEASUREMENT_ADDED,
-  } = measurementService.EVENTS;
+  const { MEASUREMENT_REMOVED, MEASUREMENTS_CLEARED, MEASUREMENT_UPDATED, RAW_MEASUREMENT_ADDED } =
+    measurementService.EVENTS;
 
   const csTools3DVer1MeasurementSource = measurementService.getSource(
     CORNERSTONE_3D_TOOLS_SOURCE_NAME,
@@ -351,11 +339,7 @@ const connectMeasurementServiceToTools = (
         return;
       }
 
-      const {
-        referenceSeriesUID,
-        referenceStudyUID,
-        SOPInstanceUID,
-      } = measurement;
+      const { referenceSeriesUID, referenceStudyUID, SOPInstanceUID } = measurement;
 
       const instance = DicomMetadataStore.getInstance(
         referenceStudyUID,
@@ -368,9 +352,7 @@ const connectMeasurementServiceToTools = (
 
       if (measurement?.metadata?.referencedImageId) {
         imageId = measurement.metadata.referencedImageId;
-        frameNumber = getSOPInstanceAttributes(
-          measurement.metadata.referencedImageId
-        ).frameNumber;
+        frameNumber = getSOPInstanceAttributes(measurement.metadata.referencedImageId).frameNumber;
       } else {
         imageId = dataSource.getImageIdsForInstance({ instance });
       }

extensions/cornerstone/src/initWADOImageLoader.js

@@ -1,11 +1,9 @@
 import * as cornerstone from '@cornerstonejs/core';
 import { volumeLoader } from '@cornerstonejs/core';
 import { cornerstoneStreamingImageVolumeLoader } from '@cornerstonejs/streaming-image-volume-loader';
-import dicomImageLoader, {
-  webWorkerManager,
-} from '@cornerstonejs/dicom-image-loader';
+import dicomImageLoader, { webWorkerManager } from '@cornerstonejs/dicom-image-loader';
 import dicomParser from 'dicom-parser';
-import { errorHandler } from '@ohif/core';
+import { errorHandler, utils } from '@ohif/core';
 
 const { registerVolumeLoader } = volumeLoader;
 
@@ -35,15 +33,13 @@ function initWebWorkers(appConfig) {
 
 export default function initWADOImageLoader(
   userAuthenticationService,
-  appConfig
+  appConfig,
+  extensionManager
 ) {
   dicomImageLoader.external.cornerstone = cornerstone;
   dicomImageLoader.external.dicomParser = dicomParser;
 
-  registerVolumeLoader(
-    'cornerstoneStreamingImageVolume',
-    cornerstoneStreamingImageVolumeLoader
-  );
+  registerVolumeLoader('cornerstoneStreamingImageVolume', cornerstoneStreamingImageVolumeLoader);
 
   dicomImageLoader.configure({
     decodeConfig: {
@@ -54,19 +50,18 @@ export default function initWADOImageLoader(
       // we should set this flag to false.
       convertFloatPixelDataToInt: false,
     },
-    beforeSend: function(xhr) {
+    beforeSend: function (xhr) {
+      //TODO should be removed in the future and request emitted by DicomWebDataSource
+      const sourceConfig = extensionManager.getActiveDataSource()?.[0].getConfig() ?? {};
       const headers = userAuthenticationService.getAuthorizationHeader();
+      const acceptHeader = utils.generateAcceptHeader(
+        sourceConfig.acceptHeader,
+        sourceConfig.requestTransferSyntaxUID,
+        sourceConfig.omitQuotationForMultipartRequest
+      );
 
-      // Request:
-      // JPEG-LS Lossless (1.2.840.10008.1.2.4.80) if available, otherwise accept
-      // whatever transfer-syntax the origin server provides.
-      // For now we use image/jls and image/x-jls because some servers still use the old type
-      // http://dicom.nema.org/medical/dicom/current/output/html/part18.html
       const xhrRequestHeaders = {
-        Accept: appConfig.omitQuotationForMultipartRequest
-          ? 'multipart/related; type=application/octet-stream'
-          : 'multipart/related; type="application/octet-stream"',
-        // 'multipart/related; type="image/x-jls", multipart/related; type="image/jls"; transfer-syntax="1.2.840.10008.1.2.4.80", multipart/related; type="image/x-jls", multipart/related; type="application/octet-stream"; transfer-syntax=*',
+        Accept: acceptHeader,
       };
 
       if (headers) {

extensions/cornerstone/src/services/CornerstoneCacheService/CornerstoneCacheService.ts

@@ -1,16 +1,8 @@
 import { ServicesManager, Types } from '@ohif/core';
-import {
-  cache as cs3DCache,
-  Enums,
-  volumeLoader,
-  utilities as utils,
-} from '@cornerstonejs/core';
+import { cache as cs3DCache, Enums, volumeLoader, utilities as utils } from '@cornerstonejs/core';
 
 import getCornerstoneViewportType from '../../utils/getCornerstoneViewportType';
-import {
-  StackViewportData,
-  VolumeViewportData,
-} from '../../types/CornerstoneCacheService';
+import { StackViewportData, VolumeViewportData } from '../../types/CornerstoneCacheService';
 
 const VOLUME_LOADER_SCHEME = 'cornerstoneStreamingImageVolume';
 
@@ -18,9 +10,7 @@ class CornerstoneCacheService {
   static REGISTRATION = {
     name: 'cornerstoneCacheService',
     altName: 'CornerstoneCacheService',
-    create: ({
-      servicesManager,
-    }: Types.Extensions.ExtensionParams): CornerstoneCacheService => {
+    create: ({ servicesManager }: Types.Extensions.ExtensionParams): CornerstoneCacheService => {
       return new CornerstoneCacheService(servicesManager);
     },
   };
@@ -77,11 +67,7 @@ class CornerstoneCacheService {
       cs3DViewportType === Enums.ViewportType.ORTHOGRAPHIC ||
       cs3DViewportType === Enums.ViewportType.VOLUME_3D
     ) {
-      viewportData = await this._getVolumeViewportData(
-        dataSource,
-        displaySets,
-        cs3DViewportType
-      );
+      viewportData = await this._getVolumeViewportData(dataSource, displaySets, cs3DViewportType);
     }
 
     viewportData.viewportType = cs3DViewportType;
@@ -134,20 +120,14 @@ class CornerstoneCacheService {
     // For Stack Viewport we don't have fusion currently
     const displaySet = displaySets[0];
 
-    let stackImageIds = this.stackImageIds.get(
-      displaySet.displaySetInstanceUID
-    );
+    let stackImageIds = this.stackImageIds.get(displaySet.displaySetInstanceUID);
 
     if (!stackImageIds) {
       stackImageIds = this._getCornerstoneStackImageIds(displaySet, dataSource);
       this.stackImageIds.set(displaySet.displaySetInstanceUID, stackImageIds);
     }
 
-    const {
-      displaySetInstanceUID,
-      StudyInstanceUID,
-      isCompositeStack,
-    } = displaySet;
+    const { displaySetInstanceUID, StudyInstanceUID, isCompositeStack } = displaySet;
 
     const StackViewportData: StackViewportData = {
       viewportType,
@@ -196,31 +176,22 @@ class CornerstoneCacheService {
         continue;
       }
 
-      const volumeLoaderSchema =
-        displaySet.volumeLoaderSchema ?? VOLUME_LOADER_SCHEME;
+      const volumeLoaderSchema = displaySet.volumeLoaderSchema ?? VOLUME_LOADER_SCHEME;
 
       const volumeId = `${volumeLoaderSchema}:${displaySet.displaySetInstanceUID}`;
 
-      let volumeImageIds = this.volumeImageIds.get(
-        displaySet.displaySetInstanceUID
-      );
+      let volumeImageIds = this.volumeImageIds.get(displaySet.displaySetInstanceUID);
 
       let volume = cs3DCache.getVolume(volumeId);
 
       if (!volumeImageIds || !volume) {
-        volumeImageIds = this._getCornerstoneVolumeImageIds(
-          displaySet,
-          dataSource
-        );
+        volumeImageIds = this._getCornerstoneVolumeImageIds(displaySet, dataSource);
 
         volume = await volumeLoader.createAndCacheVolume(volumeId, {
           imageIds: volumeImageIds,
         });
 
-        this.volumeImageIds.set(
-          displaySet.displaySetInstanceUID,
-          volumeImageIds
-        );
+        this.volumeImageIds.set(displaySet.displaySetInstanceUID, volumeImageIds);
       }
 
       volumeData.push({
@@ -268,10 +239,7 @@ class CornerstoneCacheService {
   }
 
   private _getCornerstoneVolumeImageIds(displaySet, dataSource): string[] {
-    const stackImageIds = this._getCornerstoneStackImageIds(
-      displaySet,
-      dataSource
-    );
+    const stackImageIds = this._getCornerstoneStackImageIds(displaySet, dataSource);
 
     return stackImageIds;
   }

extensions/cornerstone/src/services/SegmentationService/RTSTRUCT/mapROIContoursToRTStructData.ts

@@ -7,32 +7,27 @@
  * @returns An array of object that includes data, id, segmentIndex, color
  * and geometry Id
  */
-export function mapROIContoursToRTStructData(
-  structureSet: unknown,
-  rtDisplaySetUID: unknown
-) {
-  return structureSet.ROIContours.map(
-    ({ contourPoints, ROINumber, ROIName, colorArray }) => {
-      const data = contourPoints.map(({ points, ...rest }) => {
-        const newPoints = points.map(({ x, y, z }) => {
-          return [x, y, z];
-        });
-
-        return {
-          ...rest,
-          points: newPoints,
-        };
+export function mapROIContoursToRTStructData(structureSet: unknown, rtDisplaySetUID: unknown) {
+  return structureSet.ROIContours.map(({ contourPoints, ROINumber, ROIName, colorArray }) => {
+    const data = contourPoints.map(({ points, ...rest }) => {
+      const newPoints = points.map(({ x, y, z }) => {
+        return [x, y, z];
       });
 
-      const id = ROIName || ROINumber;
-
       return {
-        data,
-        id,
-        segmentIndex: ROINumber,
-        color: colorArray,
-        geometryId: `${rtDisplaySetUID}:${id}:segmentIndex-${ROINumber}`,
+        ...rest,
+        points: newPoints,
       };
-    }
-  );
+    });
+
+    const id = ROIName || ROINumber;
+
+    return {
+      data,
+      id,
+      segmentIndex: ROINumber,
+      color: colorArray,
+      geometryId: `${rtDisplaySetUID}:${id}:segmentIndex-${ROINumber}`,
+    };
+  });
 }

extensions/cornerstone/src/services/SyncGroupService/SyncGroupService.ts

@@ -1,8 +1,4 @@
-import {
-  synchronizers,
-  SynchronizerManager,
-  Synchronizer,
-} from '@cornerstonejs/tools';
+import { synchronizers, SynchronizerManager, Synchronizer } from '@cornerstonejs/tools';
 
 import { pubSubServiceInterface, Types, ServicesManager } from '@ohif/core';
 
@@ -14,10 +10,7 @@ const EVENTS = {
  * @params options - are an optional set of options associated with the first
  * sync group declared.
  */
-export type SyncCreator = (
-  type: string,
-  options?: Record<string, unknown>
-) => Synchronizer;
+export type SyncCreator = (id: string, options?: Record<string, unknown>) => Synchronizer;
 
 export type SyncGroup = {
   type: string;
@@ -40,9 +33,7 @@ export default class SyncGroupService {
   static REGISTRATION = {
     name: 'syncGroupService',
     altName: 'SyncGroupService',
-    create: ({
-      servicesManager,
-    }: Types.Extensions.ExtensionParams): SyncGroupService => {
+    create: ({ servicesManager }: Types.Extensions.ExtensionParams): SyncGroupService => {
       return new SyncGroupService(servicesManager);
     },
   };
@@ -65,11 +56,7 @@ export default class SyncGroupService {
     Object.assign(this, pubSubServiceInterface);
   }
 
-  private _createSynchronizer(
-    type: string,
-    id: string,
-    options
-  ): Synchronizer | undefined {
+  private _createSynchronizer(type: string, id: string, options): Synchronizer | undefined {
     const syncCreator = this.synchronizerCreators[type.toLowerCase()];
     if (syncCreator) {
       return syncCreator(id, options);
@@ -83,7 +70,7 @@ export default class SyncGroupService {
    * @param type is the type of the synchronizer to create
    * @param creator
    */
-  public setSynchronizer(type: string, creator: SyncCreator): void {
+  public addSynchronizerType(type: string, creator: SyncCreator): void {
     this.synchronizerCreators[type.toLowerCase()] = creator;
   }
 
@@ -109,19 +96,11 @@ export default class SyncGroupService {
       return;
     }
 
-    const syncGroupsArray = Array.isArray(syncGroups)
-      ? syncGroups
-      : [syncGroups];
+    const syncGroupsArray = Array.isArray(syncGroups) ? syncGroups : [syncGroups];
 
     syncGroupsArray.forEach(syncGroup => {
       const syncGroupObj = asSyncGroup(syncGroup);
-      const {
-        type,
-        target = true,
-        source = true,
-        options = {},
-        id = type,
-      } = syncGroupObj;
+      const { type, target = true, source = true, options = {}, id = type } = syncGroupObj;
 
       const synchronizer = this._getOrCreateSynchronizer(type, id, options);
       synchronizer.setOptions(viewportId, options);

extensions/cornerstone/src/services/ToolGroupService/ToolGroupService.ts

@@ -24,9 +24,7 @@ export default class ToolGroupService {
   public static REGISTRATION = {
     name: 'toolGroupService',
     altName: 'ToolGroupService',
-    create: ({
-      servicesManager,
-    }: OhifTypes.Extensions.ExtensionParams): ToolGroupService => {
+    create: ({ servicesManager }: OhifTypes.Extensions.ExtensionParams): ToolGroupService => {
       return new ToolGroupService(servicesManager);
     },
   };
@@ -40,10 +38,7 @@ export default class ToolGroupService {
   EVENTS: { [key: string]: string };
 
   constructor(serviceManager) {
-    const {
-      cornerstoneViewportService,
-      viewportGridService,
-    } = serviceManager.services;
+    const { cornerstoneViewportService, viewportGridService } = serviceManager.services;
     this.cornerstoneViewportService = cornerstoneViewportService;
     this.viewportGridService = viewportGridService;
     this.listeners = {};
@@ -66,19 +61,14 @@ export default class ToolGroupService {
 
     if (!toolGroupIdToUse) {
       // Use the active viewport's tool group if no tool group id is provided
-      const enabledElement = getActiveViewportEnabledElement(
-        this.viewportGridService
-      );
+      const enabledElement = getActiveViewportEnabledElement(this.viewportGridService);
 
       if (!enabledElement) {
         return;
       }
 
       const { renderingEngineId, viewportId } = enabledElement;
-      const toolGroup = ToolGroupManager.getToolGroupForViewport(
-        viewportId,
-        renderingEngineId
-      );
+      const toolGroup = ToolGroupManager.getToolGroupForViewport(viewportId, renderingEngineId);
 
       if (!toolGroup) {
         console.warn(
@@ -103,10 +93,7 @@ export default class ToolGroupService {
 
   public getToolGroupForViewport(viewportId: string): Types.IToolGroup | void {
     const renderingEngine = this.cornerstoneViewportService.getRenderingEngine();
-    return ToolGroupManager.getToolGroupForViewport(
-      viewportId,
-      renderingEngine.id
-    );
+    return ToolGroupManager.getToolGroupForViewport(viewportId, renderingEngine.id);
   }
 
   public getActiveToolForViewport(viewportId: string): string {
@@ -133,10 +120,7 @@ export default class ToolGroupService {
     renderingEngineId: string,
     deleteToolGroupIfEmpty?: boolean
   ): void {
-    const toolGroup = ToolGroupManager.getToolGroupForViewport(
-      viewportId,
-      renderingEngineId
-    );
+    const toolGroup = ToolGroupManager.getToolGroupForViewport(viewportId, renderingEngineId);
 
     if (!toolGroup) {
       return;
@@ -193,11 +177,7 @@ export default class ToolGroupService {
     return toolGroup;
   }
 
-  public addToolsToToolGroup(
-    toolGroupId: string,
-    tools: Array<Tool>,
-    configs: any = {}
-  ): void {
+  public addToolsToToolGroup(toolGroupId: string, tools: Array<Tool>, configs: any = {}): void {
     const toolGroup = ToolGroupManager.getToolGroup(toolGroupId);
     // this.changeConfigurationIfNecessary(toolGroup, volumeId);
     this._addTools(toolGroup, tools, configs);