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

Co-authored-by: Ibrahim <93064150+IbrahimCSAE@users.noreply.github.com>
Co-authored-by: Bill Wallace <wayfarer3130@gmail.com>
Co-authored-by: Chao Sui <chao.sui@curvebeamai.com>
Co-authored-by: Jaseel-trenser <108331536+Jaseel-trenser@users.noreply.github.com>

.circleci/config.yml

@@ -180,10 +180,6 @@ jobs:
       - run:
           name: Authenticate with NPM registry
           command: echo "//registry.npmjs.org/:_authToken=$NPM_TOKEN" > ~/repo/.npmrc
-      - run:
-          name: Increase the event emitter limit
-          command: |
-            node ./increaseEventEmitterLimit.mjs
       - run:
           name: build half of the packages (to avoid out of memory in circleci)
           command: |
@@ -230,10 +226,6 @@ jobs:
       - run:
           name: Authenticate with NPM registry
           command: echo "//registry.npmjs.org/:_authToken=$NPM_TOKEN" > ~/repo/.npmrc
-      - run:
-          name: Increase the event emitter limit
-          command: |
-            node ./increaseEventEmitterLimit.mjs
       - run:
           name: build half of the packages (to avoid out of memory in circleci)
           command: |
@@ -385,7 +377,7 @@ jobs:
           - yarn-berry
         type: enum
       parallelism:
-        default: 1
+        default: 4
         description: |
           Number of Circle machines to use for load balancing, min 1
           (requires `parallel` and `record` flags in your `cypress-command`)

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

@@ -5,8 +5,6 @@ server {
     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;

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

@@ -7,8 +7,6 @@ server {
     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;

.github/workflows/playwright.yml

@@ -8,6 +8,8 @@ jobs:
   playwright-tests:
     timeout-minutes: 60
     runs-on: ubuntu-latest
+    container:
+      image: mcr.microsoft.com/playwright:v1.49.0-noble
     strategy:
       fail-fast: false
       matrix:
@@ -23,7 +25,9 @@ jobs:
       - name: Install Playwright Browsers
         run: npx playwright install --with-deps
       - name: Run Playwright tests
-        run: export NODE_OPTIONS="--max_old_space_size=8192" && npx playwright test --shard=${{ matrix.shardIndex }}/${{ matrix.shardTotal }}
+        run:
+          export NODE_OPTIONS="--max_old_space_size=8192" && npx playwright test --shard=${{
+          matrix.shardIndex }}/${{ matrix.shardTotal }}
 
       - name: Upload blob report to GitHub Actions Artifacts
         if: ${{ !cancelled() }}

.scripts/dicom-json-generator.js

@@ -4,26 +4,34 @@
  * The JSON file can be used to load the study into the OHIF Viewer. You can get more detail
  * in the DICOM JSON Data source on docs.ohif.org
  *
- * Usage: node dicomStudyToJSONLaunch.js <studyFolder> <urlPrefix> <outputJSONPath>
+ * Usage: node dicom-json-generator.js <studyFolder> <urlPrefix> <outputJSONPath> <optional scheme>
  *
  * params:
- * - studyFolder: path to the study folder
+ * - studyFolder: path to the study folder which contains the DICOM files
  * - urlPrefix: prefix to the url that will be used to load the study into the viewer. For instance
  *   we use https://ohif-assets.s3.us-east-2.amazonaws.com/dicom-json/data as the urlPrefix for the
  *   example since the data is hosted on S3 and each study is in a folder. So the url in the generated
  *   json file for the first instance of the first series of the first study will be
  *   dicomweb:https://ohif-assets.s3.us-east-2.amazonaws.com/dicom-json/data/Series1/Instance1
+ *
+ *   as you see the dicomweb is a prefix that is used to load the data into the viewer, which is suited when
+ *   the .dcm file is hosted statically and can be accessed via a URL (like our example above)
+ *   However, you can specify a new scheme bellow.
+ *
  * - outputJSONPath: path to the output JSON file
+ * - scheme: default dicomweb if not provided
  */
 const dcmjs = require('dcmjs');
 const path = require('path');
 const fs = require('fs').promises;
 
 const args = process.argv.slice(2);
-const [studyDirectory, urlPrefix, outputPath] = args;
+const [studyDirectory, urlPrefix, outputPath, scheme = 'dicomweb'] = args;
 
-if (args.length !== 3) {
-  console.error('Usage: node dicomStudyToJSONLaunch.js <studyFolder> <urlPrefix> <outputJSONPath>');
+if (args.length < 3 || args.length > 4) {
+  console.error(
+    'Usage: node dicom-json-generator.js <studyFolder> <urlPrefix> <outputJSONPath> [scheme]'
+  );
   process.exit(1);
 }
 
@@ -31,7 +39,7 @@ const model = {
   studies: [],
 };
 
-async function convertDICOMToJSON(studyDirectory, urlPrefix, outputPath) {
+async function convertDICOMToJSON(studyDirectory, urlPrefix, outputPath, scheme) {
   try {
     const files = await recursiveReadDir(studyDirectory);
     console.debug('Processing...');
@@ -42,7 +50,7 @@ async function convertDICOMToJSON(studyDirectory, urlPrefix, outputPath) {
         const dicomDict = dcmjs.data.DicomMessage.readFile(arrayBuffer.buffer);
         const instance = dcmjs.data.DicomMetaDictionary.naturalizeDataset(dicomDict.dict);
 
-        instance.fileLocation = createImageId(file, urlPrefix, studyDirectory);
+        instance.fileLocation = createImageId(file, urlPrefix, studyDirectory, scheme);
         processInstance(instance);
       }
     }
@@ -77,10 +85,10 @@ async function recursiveReadDir(dir) {
   return results;
 }
 
-function createImageId(fileLocation, urlPrefix, studyDirectory) {
+function createImageId(fileLocation, urlPrefix, studyDirectory, scheme) {
   const relativePath = path.relative(studyDirectory, fileLocation);
   const normalizedPath = path.normalize(relativePath).replace(/\\/g, '/');
-  return `dicomweb:${urlPrefix}${normalizedPath}`;
+  return `${scheme}:${urlPrefix}${normalizedPath}`;
 }
 
 function processInstance(instance) {
@@ -262,4 +270,4 @@ function createInstanceMetaDataMultiFrame(instance) {
   return instances;
 }
 
-convertDICOMToJSON(studyDirectory, urlPrefix, outputPath);
+convertDICOMToJSON(studyDirectory, urlPrefix, outputPath, scheme);

.vscode/extensions.json

@@ -1,6 +1,7 @@
 {
   "recommendations": [
     "esbenp.prettier-vscode",
+    "streetsidesoftware.code-spell-checker",
     "dbaeumer.vscode-eslint",
     "mikestead.dotenv",
     "bungcip.better-toml",

.vscode/settings.json

@@ -1,4 +1,5 @@
 {
+  "editor.defaultFormatter": "esbenp.prettier-vscode",
   "editor.rulers": [80, 120],
   // ===
   // Spacing
@@ -14,23 +15,100 @@
   // Event Triggers
   // ===
   "editor.formatOnSave": true,
-  "eslint.autoFixOnSave": true,
   "eslint.run": "onSave",
-  "eslint.validate": [
-    {
-      "language": "javascript",
-      "autoFix": true
-    },
-    {
-      "language": "javascriptreact",
-      "autoFix": true
-    }
-  ],
   "jest.autoRun": "off",
   "prettier.disableLanguages": ["html"],
   "prettier.endOfLine": "lf",
   "workbench.colorCustomizations": {},
   "editor.codeActionsOnSave": {
     "source.fixAll.eslint": "explicit"
-  }
+  },
+  "cSpell.userWords": [
+    "aabb",
+    "architectured",
+    "attrname",
+    "Barksy",
+    "browserslist",
+    "bulkdata",
+    "Cacheable",
+    "cfun",
+    "clonedeep",
+    "Colormap",
+    "Colormaps",
+    "Comlink",
+    "cornerstonejs",
+    "Crosshairs",
+    "datasource",
+    "dcmjs",
+    "decache",
+    "decached",
+    "decaching",
+    "deepmerge",
+    "Dicom",
+    "dicomweb",
+    "DISPLAYSETS",
+    "glwindow",
+    "grababble",
+    "grabbable",
+    "Hounsfield",
+    "Interactable",
+    "Interactor",
+    "istyle",
+    "kitware",
+    "labelmap",
+    "labelmaps",
+    "livewire",
+    "Mergeable",
+    "multiframe",
+    "nifti",
+    "ofun",
+    "OHIF",
+    "polylines",
+    "POLYSEG",
+    "prapogation",
+    "precisionmetrics",
+    "prefetch",
+    "Prescaled",
+    "pydicom",
+    "Radiopharmaceutical",
+    "rasterizing",
+    "reconstructable",
+    "Rehydratable",
+    "renderable",
+    "resampler",
+    "resemblejs",
+    "reslice",
+    "resliced",
+    "Reslices",
+    "roadmap",
+    "ROADMAPS",
+    "Segmentations",
+    "semibold",
+    "sitk",
+    "SUBRESOLUTION",
+    "suvbsa",
+    "suvbw",
+    "suvlbm",
+    "textbox",
+    "thresholded",
+    "thresholding",
+    "timepoint",
+    "timepoints",
+    "TMTV",
+    "TOOLGROUP",
+    "tqdm",
+    "transferables",
+    "typedoc",
+    "unsubscriptions",
+    "uuidv",
+    "viewplane",
+    "viewports",
+    "Voxel",
+    "Voxels",
+    "Vtkjs",
+    "wado",
+    "wadors",
+    "wadouri",
+    "workerpool"
+  ]
 }

.webpack/webpack.base.js

@@ -14,14 +14,14 @@ const TerserJSPlugin = require('terser-webpack-plugin');
 // const vtkRules = require('vtk.js/Utilities/config/dependency.js').webpack.core
 //   .rules;
 // ~~ RULES
-const loadShadersRule = require('./rules/loadShaders.js');
+// const loadShadersRule = require('./rules/loadShaders.js');
 const loadWebWorkersRule = require('./rules/loadWebWorkers.js');
 const transpileJavaScriptRule = require('./rules/transpileJavaScript.js');
 const cssToJavaScript = require('./rules/cssToJavaScript.js');
-const stylusToJavaScript = require('./rules/stylusToJavaScript.js');
+// Only uncomment for old v2 stylus
+// const stylusToJavaScript = require('./rules/stylusToJavaScript.js');
 const ReactRefreshWebpackPlugin = require('@pmmmwh/react-refresh-webpack-plugin');
 
-
 // ~~ ENV VARS
 const NODE_ENV = process.env.NODE_ENV;
 const QUICK_BUILD = process.env.QUICK_BUILD;
@@ -57,10 +57,6 @@ if (!process.env.APP_CONFIG) {
 }
 
 module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
-  if (!process.env.NODE_ENV) {
-    throw new Error('process.env.NODE_ENV not set');
-  }
-
   const mode = NODE_ENV === 'production' ? 'production' : 'development';
   const isProdBuild = NODE_ENV === 'production';
   const isQuickBuild = QUICK_BUILD === 'true';
@@ -98,16 +94,20 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
       type: 'filesystem',
     },
     module: {
-      noParse: [/(codec)/, /(dicomicc)/],
+      noParse: [/(dicomicc)/],
       rules: [
-        ...(isProdBuild ? [] : [{
-          test: /\.[jt]sx?$/,
-          exclude: /node_modules/,
-          loader: 'babel-loader',
-          options: {
-            plugins: ['react-refresh/babel'],
-          },
-        }]),
+        ...(isProdBuild
+          ? []
+          : [
+              {
+                test: /\.[jt]sx?$/,
+                exclude: /node_modules/,
+                loader: 'babel-loader',
+                options: {
+                  plugins: isProdBuild ? [] : ['react-refresh/babel'],
+                },
+              },
+            ]),
         {
           test: /\.svg?$/,
           oneOf: [
@@ -122,11 +122,11 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
                           name: 'preset-default',
                           params: {
                             overrides: {
-                              removeViewBox: false
+                              removeViewBox: false,
                             },
                           },
                         },
-                      ]
+                      ],
                     },
                     prettier: false,
                     svgo: true,
@@ -140,11 +140,6 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
             },
           ],
         },
-        {
-          test: /\.js$/,
-          enforce: 'pre',
-          use: 'source-map-loader',
-        },
         transpileJavaScriptRule(mode),
         loadWebWorkersRule,
         // loadShadersRule,
@@ -184,8 +179,8 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
         '@hooks': path.resolve(__dirname, '../platform/app/src/hooks'),
         '@routes': path.resolve(__dirname, '../platform/app/src/routes'),
         '@state': path.resolve(__dirname, '../platform/app/src/state'),
-        '@cornerstonejs/dicom-image-loader':
-          '@cornerstonejs/dicom-image-loader/dist/dynamic-import/cornerstoneDICOMImageLoader.min.js',
+        'dicom-microscopy-viewer':
+          'dicom-microscopy-viewer/dist/dynamic-import/dicomMicroscopyViewer.min.js',
       },
       // Which directories to search when resolving modules
       modules: [
@@ -213,7 +208,7 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
       new webpack.ProvidePlugin({
         Buffer: ['buffer', 'Buffer'],
       }),
-      ...(isProdBuild ? [] : [new ReactRefreshWebpackPlugin()]),
+      ...(isProdBuild ? [] : [new ReactRefreshWebpackPlugin({ overlay: false })]),
       // Uncomment to generate bundle analyzer
       // new BundleAnalyzerPlugin(),
     ],

CHANGELOG.md

@@ -3,6 +3,560 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [3.9.3](https://github.com/OHIF/Viewers/compare/v3.9.2...v3.9.3) (2025-01-21)
+
+
+### Bug Fixes
+
+* **header tools in volume3D:** All header tools are enabled in volume3D viewport  ([#4681](https://github.com/OHIF/Viewers/issues/4681)) ([b19d7af](https://github.com/OHIF/Viewers/commit/b19d7af9ff81beedbcb8f6198ef21783f94782fa))
+* OHIF 3.9 Recovery 3 ([#4697](https://github.com/OHIF/Viewers/issues/4697)) ([5d4f2e2](https://github.com/OHIF/Viewers/commit/5d4f2e2a8e62f8de97d56a4e3f17be6018e9f2eb))
+
+
+
+
+
+## [3.9.2](https://github.com/OHIF/Viewers/compare/v3.9.1...v3.9.2) (2024-12-03)
+
+
+### Bug Fixes
+
+* **modes:** don't attempt to retrieve a stage index if HPs  ([#4552](https://github.com/OHIF/Viewers/issues/4552)) ([e5286d9](https://github.com/OHIF/Viewers/commit/e5286d9fc2449da50b738e7e6208d489cce1633e))
+* **multiframe:** metadata handling of NM studies and loading order ([#4540](https://github.com/OHIF/Viewers/issues/4540)) ([71f06dc](https://github.com/OHIF/Viewers/commit/71f06dcd3e6d24f1e3d931f7db756c26038927da))
+
+
+
+
+
+## [3.9.1](https://github.com/OHIF/Viewers/compare/v3.9.0...v3.9.1) (2024-11-13)
+
+
+### Bug Fixes
+
+* publish version 3.9 ([#4491](https://github.com/OHIF/Viewers/issues/4491)) ([2f7bb02](https://github.com/OHIF/Viewers/commit/2f7bb02387a19e953e5f09aad06b72d96cffcbd1))
+* **ui:** Scrolling and display fixes for study panel ([#4494](https://github.com/OHIF/Viewers/issues/4494)) ([4f8281b](https://github.com/OHIF/Viewers/commit/4f8281b04a1eae6890e7ecd94f8a61c281217d3f))
+* video playback ([#4497](https://github.com/OHIF/Viewers/issues/4497)) ([610faa5](https://github.com/OHIF/Viewers/commit/610faa5a2738da5eabc40e57e338c359f481e852))
+
+
+
+
+
+# [3.9.0](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.111...v3.9.0) (2024-11-12)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
+# [3.9.0-beta.111](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.110...v3.9.0-beta.111) (2024-11-12)
+
+
+### Bug Fixes
+
+* Have an addIcon that adds to both ui and ui-next ([#4490](https://github.com/OHIF/Viewers/issues/4490)) ([4a12523](https://github.com/OHIF/Viewers/commit/4a125236ddbf8a4a95fb9c5820f511d0224e663f))
+* Measurement Tracking: Various UI and functionality improvements ([#4481](https://github.com/OHIF/Viewers/issues/4481)) ([62b2748](https://github.com/OHIF/Viewers/commit/62b27488471c9d5979142e2d15872a85778b90ed))
+* **styles:** several fixes for different styles ([#4483](https://github.com/OHIF/Viewers/issues/4483)) ([a5f0376](https://github.com/OHIF/Viewers/commit/a5f03764d1fe07b55635c52c5dac38ab5e694ba1))
+
+
+
+
+
+# [3.9.0-beta.110](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.109...v3.9.0-beta.110) (2024-11-11)
+
+
+### Bug Fixes
+
+* **bugs:** Update dependencies and enhance UI components ([#4478](https://github.com/OHIF/Viewers/issues/4478)) ([05d41c5](https://github.com/OHIF/Viewers/commit/05d41c52068a3b7ba249f15ecdf71838c352fd30))
+
+
+
+
+
+# [3.9.0-beta.109](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.108...v3.9.0-beta.109) (2024-11-08)
+
+
+### Bug Fixes
+
+* **style:** worklist shifting ([#4477](https://github.com/OHIF/Viewers/issues/4477)) ([8fb8b3b](https://github.com/OHIF/Viewers/commit/8fb8b3bfd1c887cd67fc058629d7aba598c76f9e))
+
+
+
+
+
+# [3.9.0-beta.108](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.107...v3.9.0-beta.108) (2024-11-07)
+
+
+### Bug Fixes
+
+* **tmtv:** fix toggle one up weird behaviours ([#4473](https://github.com/OHIF/Viewers/issues/4473)) ([aa2b649](https://github.com/OHIF/Viewers/commit/aa2b649444eb4fe5422e72ea7830a709c4d24a90))
+
+
+
+
+
+# [3.9.0-beta.107](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.106...v3.9.0-beta.107) (2024-11-06)
+
+
+### Bug Fixes
+
+* build ([#4471](https://github.com/OHIF/Viewers/issues/4471)) ([3d11ef2](https://github.com/OHIF/Viewers/commit/3d11ef28f213361ec7586809317bd219fa70e742))
+
+
+
+
+
+# [3.9.0-beta.106](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.105...v3.9.0-beta.106) (2024-11-06)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
+# [3.9.0-beta.105](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.104...v3.9.0-beta.105) (2024-11-05)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
+# [3.9.0-beta.104](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.103...v3.9.0-beta.104) (2024-10-30)
+
+
+### Bug Fixes
+
+* **ui:** show ui notification on displaySet load error ([#4447](https://github.com/OHIF/Viewers/issues/4447)) ([4f20523](https://github.com/OHIF/Viewers/commit/4f20523109ecbb7ec5a6d5f2c97f7e73f81cda09))
+
+
+
+
+
+# [3.9.0-beta.103](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.102...v3.9.0-beta.103) (2024-10-29)
+
+
+### Bug Fixes
+
+* **ui:** display error in ui while loading seg ([#4433](https://github.com/OHIF/Viewers/issues/4433)) ([2e96371](https://github.com/OHIF/Viewers/commit/2e96371b0631a9e5d411b0142300708ab8ba7d27))
+
+
+
+
+
+# [3.9.0-beta.102](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.101...v3.9.0-beta.102) (2024-10-29)
+
+
+### Bug Fixes
+
+* **packages:** http-proxy-middleware vulnerability ([#4443](https://github.com/OHIF/Viewers/issues/4443)) ([0610425](https://github.com/OHIF/Viewers/commit/06104257402e872d447e59cb166184d9a3548f8b))
+
+
+
+
+
+# [3.9.0-beta.101](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.100...v3.9.0-beta.101) (2024-10-18)
+
+
+### Features
+
+* **new-study-panel:** default to list view for non thumbnail series, change default fitler to all, and add more menu to thumbnail items with a dicom tag browser ([#4417](https://github.com/OHIF/Viewers/issues/4417)) ([a7fd9fa](https://github.com/OHIF/Viewers/commit/a7fd9fa5bfff7a1b533d99cb96f7147a35fd528f))
+
+
+
+
+
+# [3.9.0-beta.100](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.99...v3.9.0-beta.100) (2024-10-17)
+
+
+### Bug Fixes
+
+* **tmtv:** prevent fusion row in tmtv from getting inverted unexpectedly ([#4420](https://github.com/OHIF/Viewers/issues/4420)) ([33af9bb](https://github.com/OHIF/Viewers/commit/33af9bb021ff3a6c3b683d4df2c730413400ff8a))
+
+
+
+
+
+# [3.9.0-beta.99](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.98...v3.9.0-beta.99) (2024-10-17)
+
+
+### Bug Fixes
+
+* **3d-viewport:** exception was being thrown and 3d viewpot not getting resized. ([#4366](https://github.com/OHIF/Viewers/issues/4366)) ([433cc80](https://github.com/OHIF/Viewers/commit/433cc8089db6aa218c9075bd0eeb7952a7e4f028))
+* **createReport:** early return on cancel in prompt ([#4243](https://github.com/OHIF/Viewers/issues/4243)) ([2ec4692](https://github.com/OHIF/Viewers/commit/2ec4692eaf2349e21b141a2c0b5b104ee10f7a28))
+* **dicomjson:** Update getUIDsFromImageID to work with json data source + update getDisplaySetImageUIDs to work with mixed sop class json ([#4322](https://github.com/OHIF/Viewers/issues/4322)) ([3dd0666](https://github.com/OHIF/Viewers/commit/3dd0666c0c090cbd66161f24bc9795f96abb3697))
+* **hp-presets:** select the active displaySet when toggling an HP preset, not a random one from the series panel ([#4365](https://github.com/OHIF/Viewers/issues/4365)) ([ace67b3](https://github.com/OHIF/Viewers/commit/ace67b3bbb6be4e8c78e613e20d3e10b93762bf7))
+* **sr:** load existing point, if there is 2nd point in renderableData (Fix rotation in arrow annotation) ([#4356](https://github.com/OHIF/Viewers/issues/4356)) ([7353f7f](https://github.com/OHIF/Viewers/commit/7353f7f069446f8484278c2cff5b09149cfa23eb))
+* **tools:** check if seriesNumber is an undefined properly ([#4338](https://github.com/OHIF/Viewers/issues/4338)) ([307b144](https://github.com/OHIF/Viewers/commit/307b14476be41b10b861d6a8474f7386b5107618))
+* **typo:** type in fourup preset ([#4426](https://github.com/OHIF/Viewers/issues/4426)) ([03aad4e](https://github.com/OHIF/Viewers/commit/03aad4eba24e33a266a6d91eaf74df52dc2a550e))
+* **updateIndex:** getNumberOfSlices is defined when used with a 3D viewport ([#4424](https://github.com/OHIF/Viewers/issues/4424)) ([d5bcf54](https://github.com/OHIF/Viewers/commit/d5bcf54e23ef68abd85c5f0ea671feca637c4f49))
+
+
+### Features
+
+* **hangingProtocols:** added selection of the HangingProtocol stage from the url ([#4310](https://github.com/OHIF/Viewers/issues/4310)) ([fa2435d](https://github.com/OHIF/Viewers/commit/fa2435d5e94e5f903404ca94687b086f90f8d1f8))
+* **SR:** SCOORD3D point annotations support for stack viewports ([#4315](https://github.com/OHIF/Viewers/issues/4315)) ([ac1cad2](https://github.com/OHIF/Viewers/commit/ac1cad25af12ee0f7d508647e3134ed724d9b4d3))
+
+
+
+
+
+# [3.9.0-beta.98](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.97...v3.9.0-beta.98) (2024-10-15)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
+# [3.9.0-beta.97](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.96...v3.9.0-beta.97) (2024-10-11)
+
+
+### Bug Fixes
+
+* **auth:** oidc-react-issue ([#4410](https://github.com/OHIF/Viewers/issues/4410)) ([e849199](https://github.com/OHIF/Viewers/commit/e849199eb0a9ecba4f9845aa1e07df775d5ded9b))
+
+
+
+
+
+# [3.9.0-beta.96](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.95...v3.9.0-beta.96) (2024-10-10)
+
+
+### Bug Fixes
+
+* **fossa:** update fossa to track licenses correctly ([#4411](https://github.com/OHIF/Viewers/issues/4411)) ([ec685ef](https://github.com/OHIF/Viewers/commit/ec685ef5b9c8bfa5bff3bbf869eb394548ae1cab))
+
+
+
+
+
+# [3.9.0-beta.95](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.94...v3.9.0-beta.95) (2024-10-08)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
+# [3.9.0-beta.94](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.93...v3.9.0-beta.94) (2024-10-04)
+
+
+### Features
+
+* **tours:** freeze versions and add licensings doc ([#4407](https://github.com/OHIF/Viewers/issues/4407)) ([60a8d51](https://github.com/OHIF/Viewers/commit/60a8d5154a5d6d2b121bd93aeacf12d97ef9f8cb))
+
+
+
+
+
+# [3.9.0-beta.93](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.92...v3.9.0-beta.93) (2024-10-04)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
+# [3.9.0-beta.92](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.91...v3.9.0-beta.92) (2024-10-01)
+
+
+### Bug Fixes
+
+* **Select:** select clear button ([#4398](https://github.com/OHIF/Viewers/issues/4398)) ([a11cd6d](https://github.com/OHIF/Viewers/commit/a11cd6d6cbe20d7d986430befb3398f910a03ada))
+
+
+
+
+
+# [3.9.0-beta.91](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.90...v3.9.0-beta.91) (2024-10-01)
+
+
+### Bug Fixes
+
+* **dependent:** high priority vulnerabilities ([#4396](https://github.com/OHIF/Viewers/issues/4396)) ([b4f08ad](https://github.com/OHIF/Viewers/commit/b4f08adfb638e5df11bb77d3c1b128b5efdf77a7))
+
+
+
+
+
+# [3.9.0-beta.90](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.89...v3.9.0-beta.90) (2024-09-30)
+
+
+### Bug Fixes
+
+* 🐛 Fix imports for ui-next ([#4394](https://github.com/OHIF/Viewers/issues/4394)) ([43efed2](https://github.com/OHIF/Viewers/commit/43efed207e0d8d13bcbf52fab14c1be034d22d0c))
+
+
+
+
+
+# [3.9.0-beta.89](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.88...v3.9.0-beta.89) (2024-09-27)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
+# [3.9.0-beta.88](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.87...v3.9.0-beta.88) (2024-09-24)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
+# [3.9.0-beta.87](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.86...v3.9.0-beta.87) (2024-09-19)
+
+
+### Bug Fixes
+
+* **ui:** Fixed study component open and closed feedback in Studies panel ([#4384](https://github.com/OHIF/Viewers/issues/4384)) ([365d824](https://github.com/OHIF/Viewers/commit/365d824b98e03b87db294878abde6823abdcf409))
+
+
+
+
+
+# [3.9.0-beta.86](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.85...v3.9.0-beta.86) (2024-09-19)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
+# [3.9.0-beta.85](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.84...v3.9.0-beta.85) (2024-09-17)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
+# [3.9.0-beta.84](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.83...v3.9.0-beta.84) (2024-09-12)
+
+
+### Features
+
+* **toolbar:** enable extensions to change toolbar button sections ([#4367](https://github.com/OHIF/Viewers/issues/4367)) ([1bfce0a](https://github.com/OHIF/Viewers/commit/1bfce0a03cbbb4cc1f69e8b5d1d72244b30d6b46))
+
+
+
+
+
+# [3.9.0-beta.83](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.82...v3.9.0-beta.83) (2024-09-11)
+
+
+### Features
+
+* **studies-panel:** New OHIF study panel - under experimental flag ([#4254](https://github.com/OHIF/Viewers/issues/4254)) ([7a96406](https://github.com/OHIF/Viewers/commit/7a96406a116e46e62c396855fa64f434e2984b58))
+
+
+
+
+
+# [3.9.0-beta.82](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.81...v3.9.0-beta.82) (2024-09-05)
+
+
+### Bug Fixes
+
+* Add kheops integration into OHIF v3 again ([#4345](https://github.com/OHIF/Viewers/issues/4345)) ([e1feffa](https://github.com/OHIF/Viewers/commit/e1feffa42553d6c8650a4aceb09f72c637126660))
+
+
+
+
+
+# [3.9.0-beta.81](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.80...v3.9.0-beta.81) (2024-08-27)
+
+
+### Bug Fixes
+
+* 🐛 SeriesInstanceUID fallback + update retrieve metadata filtered to check for lazy ([#4346](https://github.com/OHIF/Viewers/issues/4346)) ([14498d4](https://github.com/OHIF/Viewers/commit/14498d4e9a6a57324b8be9f0b314f2901459dc4a))
+
+
+
+
+
+# [3.9.0-beta.80](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.79...v3.9.0-beta.80) (2024-08-16)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
+# [3.9.0-beta.79](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.78...v3.9.0-beta.79) (2024-08-16)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
+# [3.9.0-beta.78](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.77...v3.9.0-beta.78) (2024-08-15)
+
+
+### Features
+
+* Add CS3D WSI and Video Viewports and add annotation navigation for MPR ([#4182](https://github.com/OHIF/Viewers/issues/4182)) ([7599ec9](https://github.com/OHIF/Viewers/commit/7599ec9421129dcade94e6fa6ec7908424ab3134))
+
+
+
+
+
+# [3.9.0-beta.77](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.76...v3.9.0-beta.77) (2024-08-15)
+
+
+### Bug Fixes
+
+* **roundNumber:** handle negative numbers properly ([#4336](https://github.com/OHIF/Viewers/issues/4336)) ([7377db8](https://github.com/OHIF/Viewers/commit/7377db8d280a90515fe099cb580607450cb146a5))
+
+
+
+
+
+# [3.9.0-beta.76](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.75...v3.9.0-beta.76) (2024-08-08)
+
+
+### Bug Fixes
+
+* unexpected mpr measurements ([#4332](https://github.com/OHIF/Viewers/issues/4332)) ([ab6e341](https://github.com/OHIF/Viewers/commit/ab6e341731652a4fa894fcb576eb23dc95aefa11))
+
+
+
+
+
+# [3.9.0-beta.75](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.74...v3.9.0-beta.75) (2024-08-07)
+
+
+### Bug Fixes
+
+* **ui:** Tailwind build errors ([#4329](https://github.com/OHIF/Viewers/issues/4329)) ([8e7cc11](https://github.com/OHIF/Viewers/commit/8e7cc1152917f562ea7e6a5f3f7e492b300dc564))
+
+
+
+
+
+# [3.9.0-beta.74](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.73...v3.9.0-beta.74) (2024-08-06)
+
+
+### Bug Fixes
+
+* **url:** series query param filtering ([#4328](https://github.com/OHIF/Viewers/issues/4328)) ([9b10303](https://github.com/OHIF/Viewers/commit/9b10303a2efa809096156d4a2322b2b46f160a91))
+
+
+
+
+
+# [3.9.0-beta.73](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.72...v3.9.0-beta.73) (2024-08-02)
+
+
+### Features
+
+* **ui:** Created design and added core components for ui-next ([#4324](https://github.com/OHIF/Viewers/issues/4324)) ([9036418](https://github.com/OHIF/Viewers/commit/90364189b865514cc471786d2f91c270517e98fc))
+
+
+
+
+
+# [3.9.0-beta.72](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.71...v3.9.0-beta.72) (2024-07-31)
+
+
+### Bug Fixes
+
+* customization types ([#4321](https://github.com/OHIF/Viewers/issues/4321)) ([72bef63](https://github.com/OHIF/Viewers/commit/72bef63ef6e63395ba18ff91a39294913966e9db))
+
+
+
+
+
+# [3.9.0-beta.71](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.70...v3.9.0-beta.71) (2024-07-30)
+
+
+### Bug Fixes
+
+* ip SSRF improper categorization ([#4319](https://github.com/OHIF/Viewers/issues/4319)) ([aa0e5a5](https://github.com/OHIF/Viewers/commit/aa0e5a59379453bb8e6a4f286447576744ea6bf5))
+
+
+
+
+
+# [3.9.0-beta.70](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.69...v3.9.0-beta.70) (2024-07-30)
+
+
+### Bug Fixes
+
+* **ui:** remove border-border class ([#4317](https://github.com/OHIF/Viewers/issues/4317)) ([d402ded](https://github.com/OHIF/Viewers/commit/d402ded8c36631f8009b7b15b2f1c7a02cd09f6c))
+
+
+
+
+
+# [3.9.0-beta.69](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.68...v3.9.0-beta.69) (2024-07-27)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
+# [3.9.0-beta.68](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.67...v3.9.0-beta.68) (2024-07-26)
+
+
+### Bug Fixes
+
+* **dicom:** Update multiframe DICOM JSON parsing for correct image ID generation ([#4307](https://github.com/OHIF/Viewers/issues/4307)) ([16b7aa4](https://github.com/OHIF/Viewers/commit/16b7aa4f6538b81e5915e47b9209d74575895dfe))
+
+
+
+
+
+# [3.9.0-beta.67](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.66...v3.9.0-beta.67) (2024-07-26)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
+# [3.9.0-beta.66](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.65...v3.9.0-beta.66) (2024-07-24)
+
+
+### Features
+
+* **pmap:** added support for parametric map ([#4284](https://github.com/OHIF/Viewers/issues/4284)) ([fc0064f](https://github.com/OHIF/Viewers/commit/fc0064fd9d8cdc8fde81b81f0e71fd5d077ca22b))
+
+
+
+
+
+# [3.9.0-beta.65](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.64...v3.9.0-beta.65) (2024-07-23)
+
+
+### Features
+
+* **SR:** text structured report (TEXT, CODE, NUM, PNAME, DATE, TIME and DATETIME) ([#4287](https://github.com/OHIF/Viewers/issues/4287)) ([246ebab](https://github.com/OHIF/Viewers/commit/246ebab6ebf5431a704a1861a5804045b9644ba4))
+
+
+
+
+
+# [3.9.0-beta.64](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.63...v3.9.0-beta.64) (2024-07-19)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
+# [3.9.0-beta.63](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.62...v3.9.0-beta.63) (2024-07-10)
+
+**Note:** Version bump only for package ohif-monorepo-root
+
+
+
+
+
 # [3.9.0-beta.62](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.61...v3.9.0-beta.62) (2024-07-09)
 
 

DATACITATION.md

@@ -10,6 +10,7 @@ Please find below the list of datasets used on the demo page, along with their r
 
 
 ## Platforms
+
 ### NIH NCI IDC
 
 - Fedorov, A., Longabaugh, W.J., Pot, D., Clunie, D.A., Pieper, S., Aerts, H.J., Homeyer, A., Lewis, R., Akbarzadeh, A., Bontempi, D. and Clifford, W., 2021. NCI imaging data commons. Cancer research, 81(16), p.4188.
@@ -147,3 +148,150 @@ Stony Brook University COVID-19 Positive Cases (COVID-19-NY-SBU)
 ### 2.16.840.1.114362.1.11972228.22789312658.616067305.306.2
 
 https://data.kitware.com/
+
+
+### 1.2.276.0.7230010.3.1.2.296485376.1.1665793212.499772
+### 2.25.269859997690759739055099378767846712697
+### 1.3.6.1.4.1.14519.5.2.1.5099.8010.217836670708542506360829799868
+### 1.3.6.1.4.1.14519.5.2.1.4792.2001.232252967813565730694525674696
+### 1.3.6.1.4.1.14519.5.2.1.4792.2001.105216574054253895819671475627
+### 1.3.6.1.4.1.5962.99.1.1117.5035.1620319789811.1.2.1
+### 1.3.6.1.4.1.5962.99.1.1123.9231.1620326176300.1.2.1
+### 1.3.6.1.4.1.5962.99.1.1126.3483.1620329455972.1.2.1
+
+https://github.com/ImagingInformatics/hackathon-images
+
+### 2.16.124.113543.6004.101.103.20021117.162333.1
+### 2.16.124.113543.6004.101.103.20021117.190619.1
+### 2.16.124.113543.6004.101.103.20021117.123455.1
+### 2.16.124.113543.6004.101.103.20021117.061159.1
+
+https://www.aapm.org/
+
+
+### 1.2.840.113619.2.30.1.1762295590.1623.978668949.886
+
+
+### 1.2.276.0.7230010.3.1.2.447481088.1.1669202398.851612
+
+Custom data SPECT, specifically I123-FP-CIT (DaTSCAN) SPECT, evaluates the dopaminergic system to diagnose Parkinson's disease, especially when tremor symptoms are unclear. It helps distinguish Parkinson's disease from treatment-related tremor.
+
+
+
+### 1.3.6.1.4.1.9328.50.1.54652
+
+https://www.cancerimagingarchive.net/collection/rider-pilot/
+
+Lung Image Database Consortium (LIDC). (2023) RIDER Pilot [Data set]. The Cancer Imaging Archive (TCIA). https://doi.org/10.7937/m87f-mz83
+
+### 1.3.6.1.4.1.14519.5.2.1.331759366792756327296606233801322964986
+
+Mayr, N., Yuh, W. T. C., Bowen, S., Harkenrider, M., Knopp, M. V., Lee, E. Y.-P., Leung, E., Lo, S. S., Small Jr., W., & Wolfson, A. H. (2023). Cervical Cancer – Tumor Heterogeneity: Serial Functional and Molecular Imaging Across the Radiation Therapy Course in Advanced Cervical Cancer (Version 1) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/ERZ5-QZ59
+
+https://www.cancerimagingarchive.net/collection/cc-tumor-heterogeneity/
+
+### 1.3.6.1.4.1.14519.5.2.1.297577087050970310787702792940607009472
+
+Eslick, E. M., Kipritidis, J., Gradinscak, D., Stevens, M. J., Bailey, D. L., Harris, B., Booth, J. T., & Keall, P. J. (2022). CT Ventilation as a functional imaging modality for lung cancer radiotherapy (CT-vs-PET-Ventilation-Imaging) (Version 1) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/3ppx-7s22
+
+https://www.cancerimagingarchive.net/collection/ct-vs-pet-ventilation-imaging/
+
+
+### 1.3.6.1.4.1.14519.5.2.1.2103.7010.634114621738943599785009586807
+### 1.3.6.1.4.1.14519.5.2.1.2103.7010.135953723682765205394176991681
+
+Huang, W., Tudorica, A., Chui, S., Kemmer, K., Naik, A., Troxell, M., Oh, K., Roy, N., Afzal, A., & Holtorf, M. (2014). Variations of dynamic contrast-enhanced magnetic resonance imaging in evaluation of breast cancer therapy response: a multicenter data analysis challenge (QIN Breast DCE-MRI) (Version 2) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/k9/tcia.2014.a2n1ixox
+
+https://www.cancerimagingarchive.net/collection/qin-breast-dce-mri/
+
+
+### 1.3.6.1.4.1.14519.5.2.1.1.24766180081901755714059656629507905556
+
+
+Cancer Moonshot Biobank. (2023). Cancer Moonshoot Biobank – Acute Myeloid Leukemia (CMB-AML) (Version 4) [Dataset]. The Cancer Imaging Archive. https://doi.org/10.7937/PCTE-6M66
+
+https://www.cancerimagingarchive.net/collection/cmb-aml/
+
+### 1.3.6.1.4.1.14519.5.2.1.3098.5025.285242291560760827564488897577
+
+https://www.cancerimagingarchive.net/collection/anti-pd-1_lung/
+
+Madhavi, P., Patel, S., & Tsao, A. S. (2019). Data from Anti-PD-1 Immunotherapy Lung [Data set]. The Cancer Imaging Archive. DOI:  10.7937/tcia.2019.zjjwb9ip
+
+### 1.3.6.1.4.1.14519.5.2.1.1.84416332615988066829602832830236187384
+
+https://www.cancerimagingarchive.net/collection/cmb-pca/
+
+Cancer Moonshot Biobank. (2022). Cancer Moonshot Biobank – Prostate Cancer Collection (CMB-PCA) (Version 7) [Dataset]. The Cancer Imaging Archive. https://doi.org/10.7937/25T7-6Y12
+
+### 1.3.6.1.4.1.32722.99.99.239341353911714368772597187099978969331
+
+Aerts, H. J. W. L., Wee, L., Rios Velazquez, E., Leijenaar, R. T. H., Parmar, C., Grossmann, P., Carvalho, S., Bussink, J., Monshouwer, R., Haibe-Kains, B., Rietveld, D., Hoebers, F., Rietbergen, M. M., Leemans, C. R., Dekker, A., Quackenbush, J., Gillies, R. J., Lambin, P. (2014). Data From NSCLC-Radiomics (version 4) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2015.PF0M9REI
+
+https://www.cancerimagingarchive.net/collection/nsclc-radiomics/
+
+### 1.3.6.1.4.1.14519.5.2.1.7085.2626.494695569589117268722281491772
+
+https://www.cancerimagingarchive.net/collection/cptac-ucec/
+
+
+National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2019). The Clinical Proteomic Tumor Analysis Consortium Uterine Corpus Endometrial Carcinoma Collection (CPTAC-UCEC) (Version 12) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2018.3R3JUISW
+
+### 1.3.6.1.4.1.14519.5.2.1.207544490797667703011829289839681390478
+
+https://www.cancerimagingarchive.net/collection/remind/
+
+Juvekar, P., Dorent, R., Kögl, F., Torio, E., Barr, C., Rigolo, L., Galvin, C., Jowkar, N., Kazi, A., Haouchine, N., Cheema, H., Navab, N., Pieper, S., Wells, W. M., Bi, W. L., Golby, A., Frisken, S., & Kapur, T. (2023). The Brain Resection Multimodal Imaging Database (ReMIND) (Version 1) [dataset]. The Cancer Imaging Archive. https://doi.org/10.7937/3RAG-D070
+
+### 1.3.12.2.1107.5.1.4.60175.30000008042114404745300000010
+
+Gavrielides, M. A., Kinnard, L. M., Myers, K. J., Peregoy, J., Pritchard, W. F., Zeng, R., Esparza, J., Karanian, J., & Petrick, N. (2015). Data From Phantom FDA [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/k9/TCIA.2015.orbjkmux
+
+https://www.cancerimagingarchive.net/collection/phantom-fda/
+
+
+### 1.3.6.1.4.1.14519.5.2.1.6834.5010.992793141464713669479982159310
+
+https://www.cancerimagingarchive.net/collection/4d-lung/
+
+
+Hugo, G. D., Weiss, E., Sleeman, W. C., Balik, S., Keall, P. J., Lu, J., & Williamson, J. F. (2016). Data from 4D Lung Imaging of NSCLC Patients (Version 2) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2016.ELN8YGLE
+
+
+### 1.3.6.1.4.1.9328.50.17.15423521354819720574322014551955370036
+
+https://www.cancerimagingarchive.net/collection/rider-lung-pet-ct/
+
+Muzi P, Wanner M, & Kinahan P. (2015). Data From RIDER Lung PET-CT. The Cancer Imaging Archive. https://doi.org/10.7937/k9/tcia.2015.ofip7tvm
+
+### 1.3.6.1.4.1.14519.5.2.1.9823.1001.134394060407147891170882809392
+
+https://www.cancerimagingarchive.net/collection/prostate-mri/
+
+Choyke P, Turkbey B, Pinto P, Merino M, Wood B. (2016). Data From PROSTATE-MRI. The Cancer Imaging Archive. http://doi.org/10.7937/K9/TCIA.2016.6046GUDv
+
+### 1.3.6.1.4.1.14519.5.2.1.191696062987463500085282581898315738844
+
+https://www.cancerimagingarchive.net/collection/upenn-gbm/
+
+Bakas, S., Sako, C., Akbari, H., Bilello, M., Sotiras, A., Shukla, G., Rudie, J. D., Flores Santamaria, N., Fathi Kazerooni, A., Pati, S., Rathore, S., Mamourian, E., Ha, S. M., Parker, W., Doshi, J., Baid, U., Bergman, M., Binder, Z. A., Verma, R., … Davatzikos, C. (2021). Multi-parametric magnetic resonance imaging (mpMRI) scans for de novo Glioblastoma (GBM) patients from the University of Pennsylvania Health System (UPENN-GBM) (Version 2) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.709X-DN49
+
+### 1.3.6.1.4.1.14519.5.2.1.4792.2001.921758700577562664959693695481
+
+https://www.cancerimagingarchive.net/collection/breast-diagnosis/
+
+Bloch, B. Nicolas, Jain, Ashali, & Jaffe, C. Carl. (2015). BREAST-DIAGNOSIS [Data set]. The Cancer Imaging Archive. http://doi.org/10.7937/K9/TCIA.2015.SDNRQXXR
+
+
+### 1.3.6.1.4.1.14519.5.2.1.1620.1225.189514895974227080410265976065
+
+Comstock, C. E., Gatsonis, C., Newstead, G. M., Snyder, B. S., Gareen, I. F., Bergin, J. T., Rahbar, H., Sung, J. S., Jacobs, C., Harvey, J. A., Nicholson, M. H., Ward, R. C., Holt, J., Prather, A., Miller, K. D., Schnall, M. D., & Kuhl, C. K. (2023). Abbreviated Breast MRI and Digital Tomosynthesis Mammography in Screening Women With Dense Breasts (EA1141) (Version 1) [dataset]. The Cancer Imaging Archive. https://doi.org/10.7937/2BAS-HR33
+
+https://www.cancerimagingarchive.net/collection/ea1141/
+
+### 1.2.276.0.7230010.3.1.2.2155604110.4180.1021041295.21
+
+From OFFIS DICOM-Team
+
+https://www.offis.de/
+OFFIS DICOM-Team

README.md

@@ -142,13 +142,11 @@ Here is a schematic representation of our development workflow:
 
 ### Getting Started
 
-1. [Fork this repository][how-to-fork]
-2. [Clone your forked repository][how-to-clone]
-   - `git clone https://github.com/YOUR-USERNAME/Viewers.git`
-3. Navigate to the cloned project's directory
-4. Add this repo as a `remote` named `upstream`
-   - `git remote add upstream https://github.com/OHIF/Viewers.git`
-5. `yarn install` to restore dependencies and link projects
+1. Clone the repository
+   - `git clone https://github.com/OHIF/Viewers.git`
+2. Navigate to the cloned project's directory
+3. `yarn install` to restore dependencies and link projects
+4. `yarn dev` to start the development server
 
 #### To Develop
 
@@ -168,7 +166,7 @@ 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 `package.json` files.
 
-| Yarn Commands                | Description                                                   |
+| Commands                | Description                                                   |
 | ---------------------------- | ------------------------------------------------------------- |
 | **Develop**                  |                                                               |
 | `dev` or `start`             | Default development experience for Viewer                     |
@@ -333,4 +331,4 @@ MIT © [OHIF](https://github.com/OHIF)
 [vtk-npm]: https://www.npmjs.com/package/@ohif/extension-vtk
 <!-- prettier-ignore-end -->
 
-[![FOSSA Status](https://app.fossa.io/api/projects/git%2Bgithub.com%2FOHIF%2FViewers.svg?type=large)](https://app.fossa.io/projects/git%2Bgithub.com%2FOHIF%2FViewers?ref=badge_large)
+[![FOSSA Status](https://app.fossa.com/api/projects/git%2Bgithub.com%2FOHIF%2FViewers.svg?type=large&issueType=license)](https://app.fossa.com/projects/git%2Bgithub.com%2FOHIF%2FViewers?ref=badge_large&issueType=license)

addOns/externals/devDependencies/CHANGELOG.md

@@ -3,6 +3,436 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [3.9.3](https://github.com/OHIF/Viewers/compare/v3.9.2...v3.9.3) (2025-01-21)
+
+
+### Bug Fixes
+
+* OHIF 3.9 Recovery 3 ([#4697](https://github.com/OHIF/Viewers/issues/4697)) ([5d4f2e2](https://github.com/OHIF/Viewers/commit/5d4f2e2a8e62f8de97d56a4e3f17be6018e9f2eb))
+
+
+
+
+
+## [3.9.2](https://github.com/OHIF/Viewers/compare/v3.9.1...v3.9.2) (2024-12-03)
+
+
+### Bug Fixes
+
+* **modes:** don't attempt to retrieve a stage index if HPs  ([#4552](https://github.com/OHIF/Viewers/issues/4552)) ([e5286d9](https://github.com/OHIF/Viewers/commit/e5286d9fc2449da50b738e7e6208d489cce1633e))
+
+
+
+
+
+## [3.9.1](https://github.com/OHIF/Viewers/compare/v3.9.0...v3.9.1) (2024-11-13)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.111...v3.9.0) (2024-11-12)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.111](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.110...v3.9.0-beta.111) (2024-11-12)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.110](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.109...v3.9.0-beta.110) (2024-11-11)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.109](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.108...v3.9.0-beta.109) (2024-11-08)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.108](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.107...v3.9.0-beta.108) (2024-11-07)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.107](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.106...v3.9.0-beta.107) (2024-11-06)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.106](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.105...v3.9.0-beta.106) (2024-11-06)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.105](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.104...v3.9.0-beta.105) (2024-11-05)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.104](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.103...v3.9.0-beta.104) (2024-10-30)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.103](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.102...v3.9.0-beta.103) (2024-10-29)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.102](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.101...v3.9.0-beta.102) (2024-10-29)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.101](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.100...v3.9.0-beta.101) (2024-10-18)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.100](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.99...v3.9.0-beta.100) (2024-10-17)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.99](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.98...v3.9.0-beta.99) (2024-10-17)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.98](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.97...v3.9.0-beta.98) (2024-10-15)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.97](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.96...v3.9.0-beta.97) (2024-10-11)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.96](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.95...v3.9.0-beta.96) (2024-10-10)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.95](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.94...v3.9.0-beta.95) (2024-10-08)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.94](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.93...v3.9.0-beta.94) (2024-10-04)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.93](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.92...v3.9.0-beta.93) (2024-10-04)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.92](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.91...v3.9.0-beta.92) (2024-10-01)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.91](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.90...v3.9.0-beta.91) (2024-10-01)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.90](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.89...v3.9.0-beta.90) (2024-09-30)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.89](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.88...v3.9.0-beta.89) (2024-09-27)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.88](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.87...v3.9.0-beta.88) (2024-09-24)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.87](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.86...v3.9.0-beta.87) (2024-09-19)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.86](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.85...v3.9.0-beta.86) (2024-09-19)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.85](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.84...v3.9.0-beta.85) (2024-09-17)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.84](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.83...v3.9.0-beta.84) (2024-09-12)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.83](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.82...v3.9.0-beta.83) (2024-09-11)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.82](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.81...v3.9.0-beta.82) (2024-09-05)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.81](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.80...v3.9.0-beta.81) (2024-08-27)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.80](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.79...v3.9.0-beta.80) (2024-08-16)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.79](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.78...v3.9.0-beta.79) (2024-08-16)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.78](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.77...v3.9.0-beta.78) (2024-08-15)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.77](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.76...v3.9.0-beta.77) (2024-08-15)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.76](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.75...v3.9.0-beta.76) (2024-08-08)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.75](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.74...v3.9.0-beta.75) (2024-08-07)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.74](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.73...v3.9.0-beta.74) (2024-08-06)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.73](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.72...v3.9.0-beta.73) (2024-08-02)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.72](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.71...v3.9.0-beta.72) (2024-07-31)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.71](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.70...v3.9.0-beta.71) (2024-07-30)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.70](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.69...v3.9.0-beta.70) (2024-07-30)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.69](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.68...v3.9.0-beta.69) (2024-07-27)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.68](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.67...v3.9.0-beta.68) (2024-07-26)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.67](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.66...v3.9.0-beta.67) (2024-07-26)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.66](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.65...v3.9.0-beta.66) (2024-07-24)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.65](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.64...v3.9.0-beta.65) (2024-07-23)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.64](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.63...v3.9.0-beta.64) (2024-07-19)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.63](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.62...v3.9.0-beta.63) (2024-07-10)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
 # [3.9.0-beta.62](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.61...v3.9.0-beta.62) (2024-07-09)
 
 **Note:** Version bump only for package @externals/devDependencies

addOns/externals/devDependencies/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@externals/devDependencies",
   "description": "External dev dependencies - put dev build dependencies here",
-  "version": "3.9.0-beta.62",
+  "version": "3.9.3",
   "license": "MIT",
   "private": true,
   "engines": {
@@ -10,7 +10,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@kitware/vtk.js": "30.4.1",
+    "@kitware/vtk.js": "32.1.1",
     "clsx": "^2.1.1",
     "core-js": "^3.2.1",
     "moment": "^2.9.4"
@@ -68,7 +68,7 @@
     "prettier-plugin-tailwindcss": "^0.5.4",
     "react-refresh": "^0.14.2",
     "semver": "^7.5.1",
-    "serve": "^14.2.0",
+    "serve": "^14.2.4",
     "shader-loader": "^1.3.1",
     "shx": "^0.3.3",
     "source-map-loader": "^4.0.1",
@@ -77,9 +77,9 @@
     "stylus": "^0.59.0",
     "stylus-loader": "^7.1.3",
     "terser-webpack-plugin": "^5.1.4",
-    "typescript": "4.6.4",
+    "typescript": "5.5.4",
     "unused-webpack-plugin": "2.4.0",
-    "webpack": "5.89.0",
+    "webpack": "5.94.0",
     "webpack-bundle-analyzer": "^4.8.0",
     "webpack-cli": "^4.7.2",
     "webpack-dev-server": "4.7.3",

addOns/externals/dicom-microscopy-viewer/CHANGELOG.md

@@ -3,6 +3,430 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [3.9.3](https://github.com/OHIF/Viewers/compare/v3.9.2...v3.9.3) (2025-01-21)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+## [3.9.2](https://github.com/OHIF/Viewers/compare/v3.9.1...v3.9.2) (2024-12-03)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+## [3.9.1](https://github.com/OHIF/Viewers/compare/v3.9.0...v3.9.1) (2024-11-13)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.111...v3.9.0) (2024-11-12)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.111](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.110...v3.9.0-beta.111) (2024-11-12)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.110](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.109...v3.9.0-beta.110) (2024-11-11)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.109](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.108...v3.9.0-beta.109) (2024-11-08)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.108](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.107...v3.9.0-beta.108) (2024-11-07)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.107](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.106...v3.9.0-beta.107) (2024-11-06)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.106](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.105...v3.9.0-beta.106) (2024-11-06)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.105](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.104...v3.9.0-beta.105) (2024-11-05)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.104](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.103...v3.9.0-beta.104) (2024-10-30)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.103](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.102...v3.9.0-beta.103) (2024-10-29)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.102](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.101...v3.9.0-beta.102) (2024-10-29)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.101](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.100...v3.9.0-beta.101) (2024-10-18)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.100](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.99...v3.9.0-beta.100) (2024-10-17)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.99](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.98...v3.9.0-beta.99) (2024-10-17)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.98](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.97...v3.9.0-beta.98) (2024-10-15)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.97](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.96...v3.9.0-beta.97) (2024-10-11)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.96](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.95...v3.9.0-beta.96) (2024-10-10)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.95](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.94...v3.9.0-beta.95) (2024-10-08)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.94](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.93...v3.9.0-beta.94) (2024-10-04)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.93](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.92...v3.9.0-beta.93) (2024-10-04)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.92](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.91...v3.9.0-beta.92) (2024-10-01)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.91](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.90...v3.9.0-beta.91) (2024-10-01)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.90](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.89...v3.9.0-beta.90) (2024-09-30)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.89](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.88...v3.9.0-beta.89) (2024-09-27)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.88](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.87...v3.9.0-beta.88) (2024-09-24)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.87](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.86...v3.9.0-beta.87) (2024-09-19)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.86](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.85...v3.9.0-beta.86) (2024-09-19)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.85](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.84...v3.9.0-beta.85) (2024-09-17)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.84](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.83...v3.9.0-beta.84) (2024-09-12)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.83](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.82...v3.9.0-beta.83) (2024-09-11)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.82](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.81...v3.9.0-beta.82) (2024-09-05)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.81](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.80...v3.9.0-beta.81) (2024-08-27)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.80](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.79...v3.9.0-beta.80) (2024-08-16)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.79](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.78...v3.9.0-beta.79) (2024-08-16)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.78](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.77...v3.9.0-beta.78) (2024-08-15)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.77](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.76...v3.9.0-beta.77) (2024-08-15)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.76](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.75...v3.9.0-beta.76) (2024-08-08)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.75](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.74...v3.9.0-beta.75) (2024-08-07)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.74](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.73...v3.9.0-beta.74) (2024-08-06)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.73](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.72...v3.9.0-beta.73) (2024-08-02)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.72](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.71...v3.9.0-beta.72) (2024-07-31)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.71](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.70...v3.9.0-beta.71) (2024-07-30)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.70](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.69...v3.9.0-beta.70) (2024-07-30)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.69](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.68...v3.9.0-beta.69) (2024-07-27)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.68](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.67...v3.9.0-beta.68) (2024-07-26)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.67](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.66...v3.9.0-beta.67) (2024-07-26)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.66](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.65...v3.9.0-beta.66) (2024-07-24)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.65](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.64...v3.9.0-beta.65) (2024-07-23)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.64](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.63...v3.9.0-beta.64) (2024-07-19)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.63](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.62...v3.9.0-beta.63) (2024-07-10)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
 # [3.9.0-beta.62](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.61...v3.9.0-beta.62) (2024-07-09)
 
 **Note:** Version bump only for package @externals/dicom-microscopy-viewer

addOns/externals/dicom-microscopy-viewer/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@externals/dicom-microscopy-viewer",
   "description": "External reference to dicom-microscopy-viewer",
-  "version": "3.9.0-beta.62",
+  "version": "3.9.3",
   "license": "MIT",
   "dependencies": {
     "dicom-microscopy-viewer": "^0.46.1"

addOns/package.json

@@ -45,7 +45,7 @@
     "glob-parent": "^6.0.2",
     "trim": "^1.0.0",
     "package-json": "^8.1.0",
-    "typescript": "4.6.4",
+    "typescript": "5.5.4",
     "sharp": "^0.32.6"
   }
 }

commit.txt

@@ -1 +1 @@
-38c19fab77cdb21d14bdae35813d73f43012cbd7
+5d4f2e2a8e62f8de97d56a4e3f17be6018e9f2eb

extensions/cornerstone-dicom-pmap/.webpack/webpack.dev.js

@@ -0,0 +1,12 @@
+const path = require('path');
+const webpackCommon = require('./../../../.webpack/webpack.base.js');
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+
+const ENTRY = {
+  app: `${SRC_DIR}/index.tsx`,
+};
+
+module.exports = (env, argv) => {
+  return webpackCommon(env, argv, { SRC_DIR, DIST_DIR, ENTRY });
+};

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

@@ -0,0 +1,54 @@
+const webpack = require('webpack');
+const { merge } = require('webpack-merge');
+const path = require('path');
+const webpackCommon = require('./../../../.webpack/webpack.base.js');
+const MiniCssExtractPlugin = require('mini-css-extract-plugin');
+
+const pkg = require('./../package.json');
+
+const ROOT_DIR = path.join(__dirname, '../');
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+const ENTRY = {
+  app: `${SRC_DIR}/index.tsx`,
+};
+
+const outputName = `ohif-${pkg.name.split('/').pop()}`;
+
+module.exports = (env, argv) => {
+  const commonConfig = webpackCommon(env, argv, { SRC_DIR, DIST_DIR, ENTRY });
+
+  return merge(commonConfig, {
+    stats: {
+      colors: true,
+      hash: true,
+      timings: true,
+      assets: true,
+      chunks: false,
+      chunkModules: false,
+      modules: false,
+      children: false,
+      warnings: true,
+    },
+    optimization: {
+      minimize: true,
+      sideEffects: true,
+    },
+    output: {
+      path: ROOT_DIR,
+      library: 'ohif-extension-cornerstone-dicom-pmap',
+      libraryTarget: 'umd',
+      filename: pkg.main,
+    },
+    externals: [/\b(vtk.js)/, /\b(dcmjs)/, /\b(gl-matrix)/, /^@ohif/, /^@cornerstonejs/],
+    plugins: [
+      new webpack.optimize.LimitChunkCountPlugin({
+        maxChunks: 1,
+      }),
+      new MiniCssExtractPlugin({
+        filename: `./dist/${outputName}.css`,
+        chunkFilename: `./dist/${outputName}.css`,
+      }),
+    ],
+  });
+};

extensions/cornerstone-dicom-pmap/CHANGELOG.md

@@ -0,0 +1,428 @@
+# Change Log
+
+All notable changes to this project will be documented in this file.
+See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+## [3.9.3](https://github.com/OHIF/Viewers/compare/v3.9.2...v3.9.3) (2025-01-21)
+
+
+### Bug Fixes
+
+* OHIF 3.9 Recovery 3 ([#4697](https://github.com/OHIF/Viewers/issues/4697)) ([5d4f2e2](https://github.com/OHIF/Viewers/commit/5d4f2e2a8e62f8de97d56a4e3f17be6018e9f2eb))
+
+
+
+
+
+## [3.9.2](https://github.com/OHIF/Viewers/compare/v3.9.1...v3.9.2) (2024-12-03)
+
+
+### Bug Fixes
+
+* **modes:** don't attempt to retrieve a stage index if HPs  ([#4552](https://github.com/OHIF/Viewers/issues/4552)) ([e5286d9](https://github.com/OHIF/Viewers/commit/e5286d9fc2449da50b738e7e6208d489cce1633e))
+* **multiframe:** metadata handling of NM studies and loading order ([#4540](https://github.com/OHIF/Viewers/issues/4540)) ([71f06dc](https://github.com/OHIF/Viewers/commit/71f06dcd3e6d24f1e3d931f7db756c26038927da))
+
+
+
+
+
+## [3.9.1](https://github.com/OHIF/Viewers/compare/v3.9.0...v3.9.1) (2024-11-13)
+
+
+### Bug Fixes
+
+* video playback ([#4497](https://github.com/OHIF/Viewers/issues/4497)) ([610faa5](https://github.com/OHIF/Viewers/commit/610faa5a2738da5eabc40e57e338c359f481e852))
+
+
+
+
+
+# [3.9.0](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.111...v3.9.0) (2024-11-12)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.111](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.110...v3.9.0-beta.111) (2024-11-12)
+
+
+### Bug Fixes
+
+* Measurement Tracking: Various UI and functionality improvements ([#4481](https://github.com/OHIF/Viewers/issues/4481)) ([62b2748](https://github.com/OHIF/Viewers/commit/62b27488471c9d5979142e2d15872a85778b90ed))
+
+
+
+
+
+# [3.9.0-beta.110](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.109...v3.9.0-beta.110) (2024-11-11)
+
+
+### Bug Fixes
+
+* **bugs:** Update dependencies and enhance UI components ([#4478](https://github.com/OHIF/Viewers/issues/4478)) ([05d41c5](https://github.com/OHIF/Viewers/commit/05d41c52068a3b7ba249f15ecdf71838c352fd30))
+
+
+
+
+
+# [3.9.0-beta.109](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.108...v3.9.0-beta.109) (2024-11-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.108](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.107...v3.9.0-beta.108) (2024-11-07)
+
+
+### Bug Fixes
+
+* **tmtv:** fix toggle one up weird behaviours ([#4473](https://github.com/OHIF/Viewers/issues/4473)) ([aa2b649](https://github.com/OHIF/Viewers/commit/aa2b649444eb4fe5422e72ea7830a709c4d24a90))
+
+
+
+
+
+# [3.9.0-beta.107](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.106...v3.9.0-beta.107) (2024-11-06)
+
+
+### Bug Fixes
+
+* build ([#4471](https://github.com/OHIF/Viewers/issues/4471)) ([3d11ef2](https://github.com/OHIF/Viewers/commit/3d11ef28f213361ec7586809317bd219fa70e742))
+
+
+
+
+
+# [3.9.0-beta.106](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.105...v3.9.0-beta.106) (2024-11-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.105](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.104...v3.9.0-beta.105) (2024-11-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.104](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.103...v3.9.0-beta.104) (2024-10-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.103](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.102...v3.9.0-beta.103) (2024-10-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.102](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.101...v3.9.0-beta.102) (2024-10-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.101](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.100...v3.9.0-beta.101) (2024-10-18)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.100](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.99...v3.9.0-beta.100) (2024-10-17)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.99](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.98...v3.9.0-beta.99) (2024-10-17)
+
+
+### Features
+
+* **SR:** SCOORD3D point annotations support for stack viewports ([#4315](https://github.com/OHIF/Viewers/issues/4315)) ([ac1cad2](https://github.com/OHIF/Viewers/commit/ac1cad25af12ee0f7d508647e3134ed724d9b4d3))
+
+
+
+
+
+# [3.9.0-beta.98](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.97...v3.9.0-beta.98) (2024-10-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.97](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.96...v3.9.0-beta.97) (2024-10-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.96](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.95...v3.9.0-beta.96) (2024-10-10)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.95](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.94...v3.9.0-beta.95) (2024-10-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.94](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.93...v3.9.0-beta.94) (2024-10-04)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.93](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.92...v3.9.0-beta.93) (2024-10-04)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.92](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.91...v3.9.0-beta.92) (2024-10-01)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.91](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.90...v3.9.0-beta.91) (2024-10-01)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.90](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.89...v3.9.0-beta.90) (2024-09-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.89](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.88...v3.9.0-beta.89) (2024-09-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.88](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.87...v3.9.0-beta.88) (2024-09-24)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.87](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.86...v3.9.0-beta.87) (2024-09-19)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.86](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.85...v3.9.0-beta.86) (2024-09-19)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.85](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.84...v3.9.0-beta.85) (2024-09-17)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.84](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.83...v3.9.0-beta.84) (2024-09-12)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.83](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.82...v3.9.0-beta.83) (2024-09-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.82](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.81...v3.9.0-beta.82) (2024-09-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.81](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.80...v3.9.0-beta.81) (2024-08-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.80](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.79...v3.9.0-beta.80) (2024-08-16)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.79](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.78...v3.9.0-beta.79) (2024-08-16)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.78](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.77...v3.9.0-beta.78) (2024-08-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.77](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.76...v3.9.0-beta.77) (2024-08-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.76](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.75...v3.9.0-beta.76) (2024-08-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.75](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.74...v3.9.0-beta.75) (2024-08-07)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.74](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.73...v3.9.0-beta.74) (2024-08-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.73](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.72...v3.9.0-beta.73) (2024-08-02)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.72](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.71...v3.9.0-beta.72) (2024-07-31)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.71](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.70...v3.9.0-beta.71) (2024-07-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.70](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.69...v3.9.0-beta.70) (2024-07-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.69](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.68...v3.9.0-beta.69) (2024-07-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.68](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.67...v3.9.0-beta.68) (2024-07-26)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.67](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.66...v3.9.0-beta.67) (2024-07-26)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.66](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.65...v3.9.0-beta.66) (2024-07-24)
+
+
+### Features
+
+* **pmap:** added support for parametric map ([#4284](https://github.com/OHIF/Viewers/issues/4284)) ([fc0064f](https://github.com/OHIF/Viewers/commit/fc0064fd9d8cdc8fde81b81f0e71fd5d077ca22b))

extensions/cornerstone-dicom-pmap/LICENSE

@@ -0,0 +1,20 @@
+MIT License
+
+Copyright (c) 2023 Open Health Imaging Foundation
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

extensions/cornerstone-dicom-pmap/README.md

@@ -0,0 +1,12 @@
+# dicom-pmap
+## Description
+
+DICOM PMAP read workflow. This extension will allow you to load a DICOM Parametric
+Map image and display it on OHIF.
+
+## Author
+
+OHIF
+
+## License
+MIT

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

@@ -0,0 +1,44 @@
+module.exports = {
+  plugins: ['@babel/plugin-proposal-class-properties'],
+  env: {
+    test: {
+      presets: [
+        [
+          // TODO: https://babeljs.io/blog/2019/03/19/7.4.0#migration-from-core-js-2
+          '@babel/preset-env',
+          {
+            modules: 'commonjs',
+            debug: false,
+          },
+          '@babel/preset-typescript',
+        ],
+        '@babel/preset-react',
+      ],
+      plugins: [
+        '@babel/plugin-proposal-object-rest-spread',
+        '@babel/plugin-syntax-dynamic-import',
+        '@babel/plugin-transform-regenerator',
+        '@babel/plugin-transform-runtime',
+      ],
+    },
+    production: {
+      presets: [
+        // WebPack handles ES6 --> Target Syntax
+        ['@babel/preset-env', { modules: false }],
+        '@babel/preset-react',
+        '@babel/preset-typescript',
+      ],
+      ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
+    },
+    development: {
+      presets: [
+        // WebPack handles ES6 --> Target Syntax
+        ['@babel/preset-env', { modules: false }],
+        '@babel/preset-react',
+        '@babel/preset-typescript',
+      ],
+      plugins: ['react-hot-loader/babel'],
+      ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
+    },
+  },
+};

extensions/cornerstone-dicom-pmap/package.json

@@ -0,0 +1,54 @@
+{
+  "name": "@ohif/extension-cornerstone-dicom-pmap",
+  "version": "3.9.3",
+  "description": "DICOM Parametric Map read workflow",
+  "author": "OHIF",
+  "license": "MIT",
+  "main": "dist/ohif-extension-cornerstone-dicom-pmap.umd.js",
+  "module": "src/index.tsx",
+  "files": [
+    "dist/**",
+    "public/**",
+    "README.md"
+  ],
+  "repository": "OHIF/Viewers",
+  "keywords": [
+    "ohif-extension"
+  ],
+  "publishConfig": {
+    "access": "public"
+  },
+  "engines": {
+    "node": ">=14",
+    "npm": ">=6",
+    "yarn": ">=1.18.0"
+  },
+  "scripts": {
+    "clean": "shx rm -rf dist",
+    "clean:deep": "yarn run clean && shx rm -rf node_modules",
+    "dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --output-pathinfo",
+    "dev:dicom-pmap": "yarn run dev",
+    "build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
+    "build:package-1": "yarn run build",
+    "start": "yarn run dev"
+  },
+  "peerDependencies": {
+    "@ohif/core": "3.9.3",
+    "@ohif/extension-cornerstone": "3.9.3",
+    "@ohif/extension-default": "3.9.3",
+    "@ohif/i18n": "3.9.3",
+    "prop-types": "^15.6.2",
+    "react": "^18.3.1",
+    "react-dom": "^18.3.1",
+    "react-i18next": "^12.2.2",
+    "react-router": "^6.8.1",
+    "react-router-dom": "^6.8.1"
+  },
+  "dependencies": {
+    "@babel/runtime": "^7.20.13",
+    "@cornerstonejs/adapters": "^2.2.20",
+    "@cornerstonejs/core": "^2.2.20",
+    "@kitware/vtk.js": "32.1.1",
+    "react-color": "^2.19.3"
+  }
+}

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

@@ -0,0 +1,244 @@
+import { utils } from '@ohif/core';
+import { metaData, cache, utilities as csUtils, volumeLoader } from '@cornerstonejs/core';
+import { adaptersPMAP } from '@cornerstonejs/adapters';
+import { SOPClassHandlerId } from './id';
+import { dicomLoaderService } from '@ohif/extension-cornerstone';
+
+const VOLUME_LOADER_SCHEME = 'cornerstoneStreamingImageVolume';
+const sopClassUids = ['1.2.840.10008.5.1.4.1.1.30'];
+
+function _getDisplaySetsFromSeries(
+  instances,
+  servicesManager: AppTypes.ServicesManager,
+  extensionManager
+) {
+  const instance = instances[0];
+
+  const {
+    StudyInstanceUID,
+    SeriesInstanceUID,
+    SOPInstanceUID,
+    SeriesDescription,
+    SeriesNumber,
+    SeriesDate,
+    SOPClassUID,
+    wadoRoot,
+    wadoUri,
+    wadoUriRoot,
+  } = instance;
+
+  const displaySet = {
+    // Parametric map use to have the same modality as its referenced volume but
+    // "PMAP" is used in the viewer even though this is not a valid DICOM modality
+    Modality: 'PMAP',
+    isReconstructable: true, // by default for now
+    displaySetInstanceUID: `pmap.${utils.guid()}`,
+    SeriesDescription,
+    SeriesNumber,
+    SeriesDate,
+    SOPInstanceUID,
+    SeriesInstanceUID,
+    StudyInstanceUID,
+    SOPClassHandlerId,
+    SOPClassUID,
+    referencedImages: null,
+    referencedSeriesInstanceUID: null,
+    referencedDisplaySetInstanceUID: null,
+    referencedVolumeURI: null,
+    referencedVolumeId: null,
+    isDerivedDisplaySet: true,
+    loadStatus: {
+      loading: false,
+      loaded: false,
+    },
+    sopClassUids,
+    instance,
+    instances: [instance],
+    wadoRoot,
+    wadoUriRoot,
+    wadoUri,
+    isOverlayDisplaySet: true,
+  };
+
+  const referencedSeriesSequence = instance.ReferencedSeriesSequence;
+
+  if (!referencedSeriesSequence) {
+    console.error('ReferencedSeriesSequence is missing for the parametric map');
+    return;
+  }
+
+  const referencedSeries = referencedSeriesSequence[0] || referencedSeriesSequence;
+
+  displaySet.referencedImages = instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
+  displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID;
+
+  // Does not get the referenced displaySet during parametric displaySet creation
+  // because it is still not available (getDisplaySetByUID returns `undefined`).
+  displaySet.getReferenceDisplaySet = () => {
+    const { displaySetService } = servicesManager.services;
+
+    if (displaySet.referencedDisplaySetInstanceUID) {
+      return displaySetService.getDisplaySetByUID(displaySet.referencedDisplaySetInstanceUID);
+    }
+
+    const referencedDisplaySets = displaySetService.getDisplaySetsForSeries(
+      displaySet.referencedSeriesInstanceUID
+    );
+
+    if (!referencedDisplaySets || referencedDisplaySets.length === 0) {
+      throw new Error('Referenced displaySet is missing for the parametric map');
+    }
+
+    const referencedDisplaySet = referencedDisplaySets[0];
+
+    displaySet.referencedDisplaySetInstanceUID = referencedDisplaySet.displaySetInstanceUID;
+
+    return referencedDisplaySet;
+  };
+
+  // Does not get the referenced volumeId during parametric displaySet creation because the
+  // referenced displaySet is still not available  (getDisplaySetByUID returns `undefined`).
+  displaySet.getReferencedVolumeId = () => {
+    if (displaySet.referencedVolumeId) {
+      return displaySet.referencedVolumeId;
+    }
+
+    const referencedDisplaySet = displaySet.getReferenceDisplaySet();
+    const referencedVolumeURI = referencedDisplaySet.displaySetInstanceUID;
+    const referencedVolumeId = `${VOLUME_LOADER_SCHEME}:${referencedVolumeURI}`;
+
+    displaySet.referencedVolumeURI = referencedVolumeURI;
+    displaySet.referencedVolumeId = referencedVolumeId;
+
+    return referencedVolumeId;
+  };
+
+  displaySet.load = async ({ headers }) =>
+    await _load(displaySet, servicesManager, extensionManager, headers);
+
+  return [displaySet];
+}
+
+const getRangeFromPixelData = (pixelData: Float32Array) => {
+  let lowest = pixelData[0];
+  let highest = pixelData[0];
+
+  for (let i = 1; i < pixelData.length; i++) {
+    if (pixelData[i] < lowest) {
+      lowest = pixelData[i];
+    }
+    if (pixelData[i] > highest) {
+      highest = pixelData[i];
+    }
+  }
+
+  return [lowest, highest];
+};
+
+async function _load(
+  displaySet,
+  servicesManager: AppTypes.ServicesManager,
+  extensionManager,
+  headers
+) {
+  const volumeId = `${VOLUME_LOADER_SCHEME}:${displaySet.displaySetInstanceUID}`;
+  const volumeLoadObject = cache.getVolumeLoadObject(volumeId);
+
+  if (volumeLoadObject) {
+    return volumeLoadObject.promise;
+  }
+
+  displaySet.loading = true;
+  displaySet.isLoaded = false;
+
+  // 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.
+  const promise = _loadParametricMap({
+    extensionManager,
+    displaySet,
+    headers,
+  });
+
+  cache.putVolumeLoadObject(volumeId, { promise }).catch(err => {
+    throw err;
+  });
+
+  promise
+    .then(() => {
+      displaySet.loading = false;
+      displaySet.isLoaded = true;
+      // Broadcast that loading is complete
+      servicesManager.services.segmentationService._broadcastEvent(
+        servicesManager.services.segmentationService.EVENTS.SEGMENTATION_LOADING_COMPLETE,
+        {
+          pmapDisplaySet: displaySet,
+        }
+      );
+    })
+    .catch(err => {
+      displaySet.loading = false;
+      displaySet.isLoaded = false;
+      throw err;
+    });
+
+  return promise;
+}
+
+async function _loadParametricMap({ displaySet, headers }: withAppTypes) {
+  const arrayBuffer = await dicomLoaderService.findDicomDataPromise(displaySet, null, headers);
+  const referencedVolumeId = displaySet.getReferencedVolumeId();
+  const cachedReferencedVolume = cache.getVolume(referencedVolumeId);
+
+  // Parametric map can be loaded only if its referenced volume exists otherwise it will fail
+  if (!cachedReferencedVolume) {
+    throw new Error(
+      'Referenced Volume is missing for the PMAP, and stack viewport PMAP is not supported yet'
+    );
+  }
+
+  const { imageIds } = cachedReferencedVolume;
+  const results = await adaptersPMAP.Cornerstone3D.ParametricMap.generateToolState(
+    imageIds,
+    arrayBuffer,
+    metaData
+  );
+  const { pixelData } = results;
+  const TypedArrayConstructor = pixelData.constructor;
+  const paramMapId = displaySet.displaySetInstanceUID;
+
+  const derivedVolume = await volumeLoader.createAndCacheDerivedVolume(referencedVolumeId, {
+    volumeId: paramMapId,
+    targetBuffer: {
+      type: TypedArrayConstructor.name,
+    },
+  });
+
+  const newPixelData = new TypedArrayConstructor(pixelData.length);
+  for (let i = 0; i < pixelData.length; i++) {
+    newPixelData[i] = pixelData[i] * 100;
+  }
+  derivedVolume.voxelManager.setCompleteScalarDataArray(newPixelData);
+  const range = getRangeFromPixelData(newPixelData);
+  const windowLevel = csUtils.windowLevel.toWindowLevel(range[0], range[1]);
+
+  derivedVolume.metadata.voiLut = [windowLevel];
+  derivedVolume.loadStatus = { loaded: true };
+
+  return derivedVolume;
+}
+
+function getSopClassHandlerModule({ servicesManager, extensionManager }) {
+  const getDisplaySetsFromSeries = instances => {
+    return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
+  };
+
+  return [
+    {
+      name: 'dicom-pmap',
+      sopClassUids,
+      getDisplaySetsFromSeries,
+    },
+  ];
+}
+
+export default getSopClassHandlerModule;

extensions/cornerstone-dicom-pmap/src/id.js

@@ -0,0 +1,7 @@
+import packageJson from '../package.json';
+
+const id = packageJson.name;
+const SOPClassHandlerName = 'dicom-pmap';
+const SOPClassHandlerId = `${id}.sopClassHandlerModule.${SOPClassHandlerName}`;
+
+export { id, SOPClassHandlerId, SOPClassHandlerName };

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

@@ -0,0 +1,39 @@
+import { id } from './id';
+import React from 'react';
+import getSopClassHandlerModule from './getSopClassHandlerModule';
+
+const Component = React.lazy(() => {
+  return import(/* webpackPrefetch: true */ './viewports/OHIFCornerstonePMAPViewport');
+});
+
+const OHIFCornerstonePMAPViewport = props => {
+  return (
+    <React.Suspense fallback={<div>Loading...</div>}>
+      <Component {...props} />
+    </React.Suspense>
+  );
+};
+
+/**
+ * You can remove any of the following modules if you don't need them.
+ */
+const extension = {
+  id,
+  getViewportModule({ servicesManager, extensionManager, commandsManager }) {
+    const ExtendedOHIFCornerstonePMAPViewport = props => {
+      return (
+        <OHIFCornerstonePMAPViewport
+          servicesManager={servicesManager}
+          extensionManager={extensionManager}
+          commandsManager={commandsManager}
+          {...props}
+        />
+      );
+    };
+
+    return [{ name: 'dicom-pmap', component: ExtendedOHIFCornerstonePMAPViewport }];
+  },
+  getSopClassHandlerModule,
+};
+
+export default extension;

extensions/cornerstone-dicom-pmap/src/viewports/OHIFCornerstonePMAPViewport.tsx

@@ -0,0 +1,206 @@
+import PropTypes from 'prop-types';
+import React, { useCallback, useEffect, useRef, useState } from 'react';
+import { useViewportGrid, LoadingIndicatorTotalPercent } from '@ohif/ui';
+
+function OHIFCornerstonePMAPViewport(props: withAppTypes) {
+  const {
+    displaySets,
+    children,
+    viewportOptions,
+    displaySetOptions,
+    servicesManager,
+    extensionManager,
+  } = props;
+  const viewportId = viewportOptions.viewportId;
+  const { displaySetService, segmentationService, uiNotificationService } =
+    servicesManager.services;
+
+  // PMAP viewport will always have a single display set
+  if (displaySets.length !== 1) {
+    throw new Error('PMAP viewport must have a single display set');
+  }
+
+  const pmapDisplaySet = displaySets[0];
+  const [viewportGrid, viewportGridService] = useViewportGrid();
+  const referencedDisplaySetRef = useRef(null);
+  const { viewports, activeViewportId } = viewportGrid;
+  const referencedDisplaySet = pmapDisplaySet.getReferenceDisplaySet();
+  const referencedDisplaySetMetadata = _getReferencedDisplaySetMetadata(
+    referencedDisplaySet,
+    pmapDisplaySet
+  );
+
+  referencedDisplaySetRef.current = {
+    displaySet: referencedDisplaySet,
+    metadata: referencedDisplaySetMetadata,
+  };
+
+  const [pmapIsLoading, setPmapIsLoading] = useState(!pmapDisplaySet.isLoaded);
+
+  // Add effect to listen for loading complete
+  useEffect(() => {
+    const { unsubscribe } = segmentationService.subscribe(
+      segmentationService.EVENTS.SEGMENTATION_LOADING_COMPLETE,
+      evt => {
+        if (evt.pmapDisplaySet?.displaySetInstanceUID === pmapDisplaySet.displaySetInstanceUID) {
+          setPmapIsLoading(false);
+        }
+      }
+    );
+
+    return () => {
+      unsubscribe();
+    };
+  }, [pmapDisplaySet]);
+
+  const getCornerstoneViewport = useCallback(() => {
+    const { displaySet: referencedDisplaySet } = referencedDisplaySetRef.current;
+    const { component: Component } = extensionManager.getModuleEntry(
+      '@ohif/extension-cornerstone.viewportModule.cornerstone'
+    );
+
+    displaySetOptions.unshift({});
+    const [pmapDisplaySetOptions] = displaySetOptions;
+
+    // Make sure `options` exists
+    pmapDisplaySetOptions.options = pmapDisplaySetOptions.options ?? {};
+
+    Object.assign(pmapDisplaySetOptions.options, {
+      colormap: {
+        name: 'rainbow_2',
+        opacity: [
+          { value: 0, opacity: 0 },
+          { value: 0.25, opacity: 0.25 },
+          { value: 0.5, opacity: 0.5 },
+          { value: 0.75, opacity: 0.75 },
+          { value: 0.9, opacity: 0.99 },
+        ],
+      },
+      voi: {
+        windowCenter: 50,
+        windowWidth: 100,
+      },
+    });
+
+    uiNotificationService.show({
+      title: 'Parametric Map',
+      type: 'warning',
+      message: 'The values are multiplied by 100 in the viewport for better visibility',
+    });
+
+    return (
+      <Component
+        {...props}
+        // Referenced + PMAP displaySets must be passed as parameter in this order
+        displaySets={[referencedDisplaySet, pmapDisplaySet]}
+        viewportOptions={{
+          viewportType: 'volume',
+          orientation: viewportOptions.orientation,
+          viewportId: viewportOptions.viewportId,
+          presentationIds: viewportOptions.presentationIds,
+        }}
+        displaySetOptions={[{}, pmapDisplaySetOptions]}
+      ></Component>
+    );
+  }, [
+    extensionManager,
+    displaySetOptions,
+    props,
+    pmapDisplaySet,
+    viewportOptions.orientation,
+    viewportOptions.viewportId,
+  ]);
+
+  // Cleanup the PMAP viewport when the viewport is destroyed
+  useEffect(() => {
+    const onDisplaySetsRemovedSubscription = displaySetService.subscribe(
+      displaySetService.EVENTS.DISPLAY_SETS_REMOVED,
+      ({ displaySetInstanceUIDs }) => {
+        const activeViewport = viewports.get(activeViewportId);
+        if (displaySetInstanceUIDs.includes(activeViewport.displaySetInstanceUID)) {
+          viewportGridService.setDisplaySetsForViewport({
+            viewportId: activeViewportId,
+            displaySetInstanceUIDs: [],
+          });
+        }
+      }
+    );
+
+    return () => {
+      onDisplaySetsRemovedSubscription.unsubscribe();
+    };
+  }, [activeViewportId, displaySetService, viewportGridService, viewports]);
+
+  let childrenWithProps = null;
+
+  if (children && children.length) {
+    childrenWithProps = children.map((child, index) => {
+      return (
+        child &&
+        React.cloneElement(child, {
+          viewportId,
+          key: index,
+        })
+      );
+    });
+  }
+
+  return (
+    <>
+      <div className="relative flex h-full w-full flex-row overflow-hidden">
+        {pmapIsLoading && (
+          <LoadingIndicatorTotalPercent
+            className="h-full w-full"
+            totalNumbers={null}
+            percentComplete={null}
+            loadingText="Loading Parametric Map..."
+          />
+        )}
+        {getCornerstoneViewport()}
+        {childrenWithProps}
+      </div>
+    </>
+  );
+}
+
+OHIFCornerstonePMAPViewport.propTypes = {
+  displaySets: PropTypes.arrayOf(PropTypes.object),
+  viewportId: PropTypes.string.isRequired,
+  dataSource: PropTypes.object,
+  children: PropTypes.node,
+};
+
+function _getReferencedDisplaySetMetadata(referencedDisplaySet, pmapDisplaySet) {
+  const { SharedFunctionalGroupsSequence } = pmapDisplaySet.instance;
+
+  const SharedFunctionalGroup = Array.isArray(SharedFunctionalGroupsSequence)
+    ? SharedFunctionalGroupsSequence[0]
+    : SharedFunctionalGroupsSequence;
+
+  const { PixelMeasuresSequence } = SharedFunctionalGroup;
+
+  const PixelMeasures = Array.isArray(PixelMeasuresSequence)
+    ? PixelMeasuresSequence[0]
+    : PixelMeasuresSequence;
+
+  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,
+    StudyDate: image0.StudyDate,
+    SeriesDescription: image0.SeriesDescription,
+    SeriesInstanceUID: image0.SeriesInstanceUID,
+    SeriesNumber: image0.SeriesNumber,
+    ManufacturerModelName: image0.ManufacturerModelName,
+    SpacingBetweenSlices: image0.SpacingBetweenSlices || SpacingBetweenSlices,
+  };
+
+  return referencedDisplaySetMetadata;
+}
+
+export default OHIFCornerstonePMAPViewport;

extensions/cornerstone-dicom-rt/CHANGELOG.md

@@ -3,6 +3,433 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [3.9.3](https://github.com/OHIF/Viewers/compare/v3.9.2...v3.9.3) (2025-01-21)
+
+
+### Bug Fixes
+
+* OHIF 3.9 Recovery 3 ([#4697](https://github.com/OHIF/Viewers/issues/4697)) ([5d4f2e2](https://github.com/OHIF/Viewers/commit/5d4f2e2a8e62f8de97d56a4e3f17be6018e9f2eb))
+
+
+
+
+
+## [3.9.2](https://github.com/OHIF/Viewers/compare/v3.9.1...v3.9.2) (2024-12-03)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+## [3.9.1](https://github.com/OHIF/Viewers/compare/v3.9.0...v3.9.1) (2024-11-13)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.111...v3.9.0) (2024-11-12)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.111](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.110...v3.9.0-beta.111) (2024-11-12)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.110](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.109...v3.9.0-beta.110) (2024-11-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.109](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.108...v3.9.0-beta.109) (2024-11-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.108](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.107...v3.9.0-beta.108) (2024-11-07)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.107](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.106...v3.9.0-beta.107) (2024-11-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.106](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.105...v3.9.0-beta.106) (2024-11-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.105](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.104...v3.9.0-beta.105) (2024-11-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.104](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.103...v3.9.0-beta.104) (2024-10-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.103](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.102...v3.9.0-beta.103) (2024-10-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.102](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.101...v3.9.0-beta.102) (2024-10-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.101](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.100...v3.9.0-beta.101) (2024-10-18)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.100](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.99...v3.9.0-beta.100) (2024-10-17)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.99](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.98...v3.9.0-beta.99) (2024-10-17)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.98](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.97...v3.9.0-beta.98) (2024-10-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.97](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.96...v3.9.0-beta.97) (2024-10-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.96](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.95...v3.9.0-beta.96) (2024-10-10)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.95](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.94...v3.9.0-beta.95) (2024-10-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.94](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.93...v3.9.0-beta.94) (2024-10-04)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.93](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.92...v3.9.0-beta.93) (2024-10-04)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.92](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.91...v3.9.0-beta.92) (2024-10-01)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.91](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.90...v3.9.0-beta.91) (2024-10-01)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.90](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.89...v3.9.0-beta.90) (2024-09-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.89](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.88...v3.9.0-beta.89) (2024-09-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.88](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.87...v3.9.0-beta.88) (2024-09-24)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.87](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.86...v3.9.0-beta.87) (2024-09-19)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.86](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.85...v3.9.0-beta.86) (2024-09-19)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.85](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.84...v3.9.0-beta.85) (2024-09-17)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.84](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.83...v3.9.0-beta.84) (2024-09-12)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.83](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.82...v3.9.0-beta.83) (2024-09-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.82](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.81...v3.9.0-beta.82) (2024-09-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.81](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.80...v3.9.0-beta.81) (2024-08-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.80](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.79...v3.9.0-beta.80) (2024-08-16)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.79](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.78...v3.9.0-beta.79) (2024-08-16)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.78](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.77...v3.9.0-beta.78) (2024-08-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.77](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.76...v3.9.0-beta.77) (2024-08-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.76](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.75...v3.9.0-beta.76) (2024-08-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.75](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.74...v3.9.0-beta.75) (2024-08-07)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.74](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.73...v3.9.0-beta.74) (2024-08-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.73](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.72...v3.9.0-beta.73) (2024-08-02)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.72](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.71...v3.9.0-beta.72) (2024-07-31)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.71](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.70...v3.9.0-beta.71) (2024-07-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.70](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.69...v3.9.0-beta.70) (2024-07-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.69](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.68...v3.9.0-beta.69) (2024-07-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.68](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.67...v3.9.0-beta.68) (2024-07-26)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.67](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.66...v3.9.0-beta.67) (2024-07-26)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.66](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.65...v3.9.0-beta.66) (2024-07-24)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.65](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.64...v3.9.0-beta.65) (2024-07-23)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.64](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.63...v3.9.0-beta.64) (2024-07-19)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
+# [3.9.0-beta.63](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.62...v3.9.0-beta.63) (2024-07-10)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt
+
+
+
+
+
 # [3.9.0-beta.62](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.61...v3.9.0-beta.62) (2024-07-09)
 
 **Note:** Version bump only for package @ohif/extension-cornerstone-dicom-rt

extensions/cornerstone-dicom-rt/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone-dicom-rt",
-  "version": "3.9.0-beta.62",
+  "version": "3.9.3",
   "description": "DICOM RT read workflow",
   "author": "OHIF",
   "license": "MIT",
@@ -33,10 +33,10 @@
     "start": "yarn run dev"
   },
   "peerDependencies": {
-    "@ohif/core": "3.9.0-beta.62",
-    "@ohif/extension-cornerstone": "3.9.0-beta.62",
-    "@ohif/extension-default": "3.9.0-beta.62",
-    "@ohif/i18n": "3.9.0-beta.62",
+    "@ohif/core": "3.9.3",
+    "@ohif/extension-cornerstone": "3.9.3",
+    "@ohif/extension-default": "3.9.3",
+    "@ohif/i18n": "3.9.3",
     "prop-types": "^15.6.2",
     "react": "^18.3.1",
     "react-dom": "^18.3.1",

extensions/cornerstone-dicom-rt/src/getCommandsModule.ts

@@ -0,0 +1,55 @@
+import { SegmentationRepresentations } from '@cornerstonejs/tools/enums';
+
+const commandsModule = ({ commandsManager, servicesManager }: withAppTypes) => {
+  const services = servicesManager.services;
+  const { displaySetService, viewportGridService } = services;
+
+  const actions = {
+    hydrateRTSDisplaySet: ({ displaySet, viewportId }) => {
+      if (displaySet.Modality !== 'RTSTRUCT') {
+        throw new Error('Display set is not an RTSTRUCT');
+      }
+
+      const referencedDisplaySet = displaySetService.getDisplaySetByUID(
+        displaySet.referencedDisplaySetInstanceUID
+      );
+
+      // update the previously stored segmentationPresentation with the new viewportId
+      // presentation so that when we put the referencedDisplaySet back in the viewport
+      // it will have the correct segmentation representation hydrated
+      commandsManager.runCommand('updateStoredSegmentationPresentation', {
+        displaySet: displaySet,
+        type: SegmentationRepresentations.Contour,
+      });
+
+      // update the previously stored positionPresentation with the new viewportId
+      // presentation so that when we put the referencedDisplaySet back in the viewport
+      // it will be in the correct position zoom and pan
+      commandsManager.runCommand('updateStoredPositionPresentation', {
+        viewportId,
+        displaySetInstanceUID: referencedDisplaySet.displaySetInstanceUID,
+      });
+
+      viewportGridService.setDisplaySetsForViewport({
+        viewportId,
+        displaySetInstanceUIDs: [referencedDisplaySet.displaySetInstanceUID],
+      });
+    },
+  };
+
+  const definitions = {
+    hydrateRTSDisplaySet: {
+      commandFn: actions.hydrateRTSDisplaySet,
+      storeContexts: [],
+      options: {},
+    },
+  };
+
+  return {
+    actions,
+    definitions,
+    defaultContext: 'cornerstone-dicom-rt',
+  };
+};
+
+export default commandsModule;

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

@@ -72,22 +72,27 @@ function _getDisplaySetsFromSeries(
   displaySet.referencedImages = instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
   displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID;
 
-  displaySet.getReferenceDisplaySet = () => {
-    const { displaySetService } = servicesManager.services;
-    const referencedDisplaySets = displaySetService.getDisplaySetsForSeries(
-      displaySet.referencedSeriesInstanceUID
+  const { displaySetService } = servicesManager.services;
+  const referencedDisplaySets = displaySetService.getDisplaySetsForSeries(
+    displaySet.referencedSeriesInstanceUID
+  );
+
+  if (!referencedDisplaySets || referencedDisplaySets.length === 0) {
+    // Instead of throwing error, subscribe to display sets added
+    const { unsubscribe } = displaySetService.subscribe(
+      displaySetService.EVENTS.DISPLAY_SETS_ADDED,
+      ({ displaySetsAdded }) => {
+        const addedDisplaySet = displaySetsAdded[0];
+        if (addedDisplaySet.SeriesInstanceUID === displaySet.referencedSeriesInstanceUID) {
+          displaySet.referencedDisplaySetInstanceUID = addedDisplaySet.displaySetInstanceUID;
+          unsubscribe();
+        }
+      }
     );
-
-    if (!referencedDisplaySets || referencedDisplaySets.length === 0) {
-      throw new Error('Referenced DisplaySet is missing for the RT');
-    }
-
+  } else {
     const referencedDisplaySet = referencedDisplaySets[0];
-
     displaySet.referencedDisplaySetInstanceUID = referencedDisplaySet.displaySetInstanceUID;
-
-    return referencedDisplaySet;
-  };
+  }
 
   displaySet.load = ({ headers }) => _load(displaySet, servicesManager, extensionManager, headers);
 
@@ -111,19 +116,13 @@ function _load(rtDisplaySet, servicesManager: AppTypes.ServicesManager, extensio
   // and also return the same promise to any other callers.
   loadPromises[SOPInstanceUID] = new Promise(async (resolve, reject) => {
     if (!rtDisplaySet.structureSet) {
-      const structureSet = await loadRTStruct(
-        extensionManager,
-        rtDisplaySet,
-        rtDisplaySet.getReferenceDisplaySet(),
-        headers
-      );
+      const structureSet = await loadRTStruct(extensionManager, rtDisplaySet, headers);
 
       rtDisplaySet.structureSet = structureSet;
     }
 
-    const suppressEvents = true;
     segmentationService
-      .createSegmentationForRTDisplaySet(rtDisplaySet, null, suppressEvents)
+      .createSegmentationForRTDisplaySet(rtDisplaySet)
       .then(() => {
         rtDisplaySet.loading = false;
         resolve();

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

@@ -2,6 +2,7 @@ import { id } from './id';
 import React from 'react';
 import { Types } from '@ohif/core';
 import getSopClassHandlerModule from './getSopClassHandlerModule';
+import getCommandsModule from './getCommandsModule';
 
 const Component = React.lazy(() => {
   return import(/* webpackPrefetch: true */ './viewports/OHIFCornerstoneRTViewport');
@@ -24,6 +25,7 @@ const extension: Types.Extensions.Extension = {
    * You ID can be anything you want, but it should be unique.
    */
   id,
+  getCommandsModule,
 
   /**
    * PanelModule should provide a list of panels that will be available in OHIF

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

@@ -89,12 +89,7 @@ async function checkAndLoadContourData(instance, datasource) {
   });
 }
 
-export default async function loadRTStruct(
-  extensionManager,
-  rtStructDisplaySet,
-  referencedDisplaySet,
-  headers
-) {
+export default async function loadRTStruct(extensionManager, rtStructDisplaySet, headers) {
   const utilityModule = extensionManager.getModuleEntry(
     '@ohif/extension-cornerstone.utilityModule.common'
   );
@@ -102,8 +97,6 @@ export default async function loadRTStruct(
   const { bulkDataURI } = dataSource.getConfig?.() || {};
 
   const { dicomLoaderService } = utilityModule.exports;
-  const imageIdSopInstanceUidPairs =
-    _getImageIdSopInstanceUidPairsForDisplaySet(referencedDisplaySet);
 
   // Set here is loading is asynchronous.
   // If this function throws its set back to false.
@@ -133,6 +126,7 @@ export default async function loadRTStruct(
     SeriesInstanceUID: instance.SeriesInstanceUID,
     ROIContours: [],
     visible: true,
+    ReferencedSOPInstanceUIDsSet: new Set(),
   };
 
   for (let i = 0; i < ROIContourSequence.length; i++) {
@@ -149,7 +143,7 @@ export default async function loadRTStruct(
 
     const contourPoints = [];
     for (let c = 0; c < ContourSequenceArray.length; c++) {
-      const { ContourImageSequence, ContourData, NumberOfContourPoints, ContourGeometricType } =
+      const { ContourData, NumberOfContourPoints, ContourGeometricType, ContourImageSequence } =
         ContourSequenceArray[c];
 
       let isSupported = false;
@@ -180,6 +174,12 @@ export default async function loadRTStruct(
         type: ContourGeometricType,
         isSupported,
       });
+
+      if (ContourImageSequence?.ReferencedSOPInstanceUID) {
+        structureSet.ReferencedSOPInstanceUIDsSet.add(
+          ContourImageSequence?.ReferencedSOPInstanceUID
+        );
+      }
     }
 
     _setROIContourMetadata(
@@ -194,24 +194,6 @@ export default async function loadRTStruct(
   return structureSet;
 }
 
-const _getImageId = (imageIdSopInstanceUidPairs, sopInstanceUID) => {
-  const imageIdSopInstanceUidPairsEntry = imageIdSopInstanceUidPairs.find(
-    imageIdSopInstanceUidPairsEntry =>
-      imageIdSopInstanceUidPairsEntry.sopInstanceUID === sopInstanceUID
-  );
-
-  return imageIdSopInstanceUidPairsEntry ? imageIdSopInstanceUidPairsEntry.imageId : null;
-};
-
-function _getImageIdSopInstanceUidPairsForDisplaySet(referencedDisplaySet) {
-  return referencedDisplaySet.images.map(image => {
-    return {
-      imageId: image.imageId,
-      sopInstanceUID: image.SOPInstanceUID,
-    };
-  });
-}
-
 function _setROIContourMetadata(
   structureSet,
   StructureSetROISequence,

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

@@ -10,7 +10,6 @@ function promptHydrateRT({
   servicesManager,
   rtDisplaySet,
   viewportId,
-  toolGroupId = 'default',
   preHydrateCallbacks,
   hydrateRTDisplaySet,
 }: withAppTypes) {
@@ -27,16 +26,13 @@ function promptHydrateRT({
         callback();
       });
 
-      window.setTimeout(async () => {
-        const isHydrated = await hydrateRTDisplaySet({
-          rtDisplaySet,
-          viewportId,
-          toolGroupId,
-          servicesManager,
-        });
+      const isHydrated = await hydrateRTDisplaySet({
+        rtDisplaySet,
+        viewportId,
+        servicesManager,
+      });
 
-        resolve(isHydrated);
-      }, 0);
+      resolve(isHydrated);
     }
   });
 }

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

@@ -4,7 +4,9 @@ import { useViewportGrid, LoadingIndicatorTotalPercent, ViewportActionArrows } f
 
 import promptHydrateRT from '../utils/promptHydrateRT';
 import _getStatusComponent from './_getStatusComponent';
+
 import createRTToolGroupAndAddTools from '../utils/initRTToolGroup';
+import { usePositionPresentationStore } from '@ohif/extension-cornerstone';
 
 const RT_TOOLGROUP_BASE_NAME = 'RTToolGroup';
 
@@ -41,8 +43,8 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
   const [viewportGrid, viewportGridService] = useViewportGrid();
 
   // States
-  const [isToolGroupCreated, setToolGroupCreated] = useState(false);
   const [selectedSegment, setSelectedSegment] = useState(1);
+  const { setPositionPresentation } = usePositionPresentationStore();
 
   // Hydration means that the RT is opened and segments are loaded into the
   // segmentation panel, and RT is also rendered on any viewport that is in the
@@ -62,7 +64,10 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
 
   const { viewports, activeViewportId } = viewportGrid;
 
-  const referencedDisplaySet = rtDisplaySet.getReferenceDisplaySet();
+  const referencedDisplaySetInstanceUID = rtDisplaySet.referencedDisplaySetInstanceUID;
+  const referencedDisplaySet = displaySetService.getDisplaySetByUID(
+    referencedDisplaySetInstanceUID
+  );
   const referencedDisplaySetMetadata = _getReferencedDisplaySetMetadata(referencedDisplaySet);
 
   referencedDisplaySetRef.current = {
@@ -91,12 +96,15 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
     });
   }, [viewportGrid]);
 
-  const hydrateRTDisplaySet = ({ rtDisplaySet, viewportId }) => {
-    commandsManager.runCommand('loadSegmentationDisplaySetsForViewport', {
-      displaySets: [rtDisplaySet],
-      viewportId,
-    });
-  };
+  const hydrateRTDisplaySet = useCallback(
+    ({ rtDisplaySet, viewportId }) => {
+      commandsManager.runCommand('hydrateRTSDisplaySet', {
+        displaySet: rtDisplaySet,
+        viewportId,
+      });
+    },
+    [commandsManager]
+  );
 
   const getCornerstoneViewport = useCallback(() => {
     const { component: Component } = extensionManager.getModuleEntry(
@@ -115,6 +123,7 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
           toolGroupId: toolGroupId,
           orientation: viewportOptions.orientation,
           viewportId: viewportOptions.viewportId,
+          presentationIds: viewportOptions.presentationIds,
         }}
         onElementEnabled={evt => {
           props.onElementEnabled?.(evt);
@@ -143,10 +152,10 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
         newSelectedSegmentIndex = numberOfSegments - 1;
       }
 
-      segmentationService.jumpToSegmentCenter(segmentationId, newSelectedSegmentIndex, toolGroupId);
+      segmentationService.jumpToSegmentCenter(segmentationId, newSelectedSegmentIndex, viewportId);
       setSelectedSegment(newSelectedSegmentIndex);
     },
-    [selectedSegment]
+    [selectedSegment, segmentationService]
   );
 
   useEffect(() => {
@@ -177,6 +186,19 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
           setRtIsLoading(false);
         }
 
+        if (rtDisplaySet?.firstSegmentedSliceImageId && viewportOptions?.presentationIds) {
+          const { firstSegmentedSliceImageId } = rtDisplaySet;
+          const { presentationIds } = viewportOptions;
+
+          setPositionPresentation(presentationIds.positionPresentationId, {
+            viewportType: 'stack',
+            viewReference: {
+              referencedImageId: firstSegmentedSliceImageId,
+            },
+            viewPresentation: {},
+          });
+        }
+
         if (evt.overlappingSegments) {
           uiNotificationService.show({
             title: 'Overlapping Segments',
@@ -239,11 +261,9 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
 
     toolGroup = createRTToolGroupAndAddTools(toolGroupService, customizationService, toolGroupId);
 
-    setToolGroupCreated(true);
-
     return () => {
       // remove the segmentation representations if seg displayset changed
-      segmentationService.removeSegmentationRepresentationFromToolGroup(toolGroupId);
+      segmentationService.removeSegmentationRepresentations(viewportId);
 
       toolGroupService.destroyToolGroup(toolGroupId);
     };
@@ -254,11 +274,27 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
 
     return () => {
       // remove the segmentation representations if seg displayset changed
-      segmentationService.removeSegmentationRepresentationFromToolGroup(toolGroupId);
+      segmentationService.removeSegmentationRepresentations(viewportId);
       referencedDisplaySetRef.current = null;
     };
   }, [rtDisplaySet]);
 
+  const onStatusClick = useCallback(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,
+      viewportId,
+    });
+
+    setIsHydrated(isHydrated);
+  }, [hydrateRTDisplaySet, rtDisplaySet, storePresentationState, viewportId]);
+
   // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   let childrenWithProps = null;
 
@@ -282,24 +318,8 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
     });
   }
 
-  const onStatusClick = useCallback(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,
-      viewportId,
-    });
-
-    setIsHydrated(isHydrated);
-  }, [hydrateRTDisplaySet, rtDisplaySet, storePresentationState, viewportId]);
-
   useEffect(() => {
-    viewportActionCornersService.setComponents([
+    viewportActionCornersService.addComponents([
       {
         viewportId,
         id: 'viewportStatusComponent',
@@ -318,7 +338,7 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
             key="actionArrows"
             onArrowsClick={onSegmentChange}
             className={
-              viewportId === activeViewportId ? 'visible' : 'invisible group-hover:visible'
+              viewportId === activeViewportId ? 'visible' : 'invisible group-hover/pane:visible'
             }
           ></ViewportActionArrows>
         ),

extensions/cornerstone-dicom-seg/CHANGELOG.md

@@ -3,6 +3,469 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [3.9.3](https://github.com/OHIF/Viewers/compare/v3.9.2...v3.9.3) (2025-01-21)
+
+
+### Bug Fixes
+
+* OHIF 3.9 Recovery 3 ([#4697](https://github.com/OHIF/Viewers/issues/4697)) ([5d4f2e2](https://github.com/OHIF/Viewers/commit/5d4f2e2a8e62f8de97d56a4e3f17be6018e9f2eb))
+
+
+
+
+
+## [3.9.2](https://github.com/OHIF/Viewers/compare/v3.9.1...v3.9.2) (2024-12-03)
+
+
+### Bug Fixes
+
+* **modes:** don't attempt to retrieve a stage index if HPs  ([#4552](https://github.com/OHIF/Viewers/issues/4552)) ([e5286d9](https://github.com/OHIF/Viewers/commit/e5286d9fc2449da50b738e7e6208d489cce1633e))
+* **multiframe:** metadata handling of NM studies and loading order ([#4540](https://github.com/OHIF/Viewers/issues/4540)) ([71f06dc](https://github.com/OHIF/Viewers/commit/71f06dcd3e6d24f1e3d931f7db756c26038927da))
+
+
+
+
+
+## [3.9.1](https://github.com/OHIF/Viewers/compare/v3.9.0...v3.9.1) (2024-11-13)
+
+
+### Bug Fixes
+
+* video playback ([#4497](https://github.com/OHIF/Viewers/issues/4497)) ([610faa5](https://github.com/OHIF/Viewers/commit/610faa5a2738da5eabc40e57e338c359f481e852))
+
+
+
+
+
+# [3.9.0](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.111...v3.9.0) (2024-11-12)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.111](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.110...v3.9.0-beta.111) (2024-11-12)
+
+
+### Bug Fixes
+
+* Measurement Tracking: Various UI and functionality improvements ([#4481](https://github.com/OHIF/Viewers/issues/4481)) ([62b2748](https://github.com/OHIF/Viewers/commit/62b27488471c9d5979142e2d15872a85778b90ed))
+
+
+
+
+
+# [3.9.0-beta.110](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.109...v3.9.0-beta.110) (2024-11-11)
+
+
+### Bug Fixes
+
+* **bugs:** Update dependencies and enhance UI components ([#4478](https://github.com/OHIF/Viewers/issues/4478)) ([05d41c5](https://github.com/OHIF/Viewers/commit/05d41c52068a3b7ba249f15ecdf71838c352fd30))
+
+
+
+
+
+# [3.9.0-beta.109](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.108...v3.9.0-beta.109) (2024-11-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.108](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.107...v3.9.0-beta.108) (2024-11-07)
+
+
+### Bug Fixes
+
+* **tmtv:** fix toggle one up weird behaviours ([#4473](https://github.com/OHIF/Viewers/issues/4473)) ([aa2b649](https://github.com/OHIF/Viewers/commit/aa2b649444eb4fe5422e72ea7830a709c4d24a90))
+
+
+
+
+
+# [3.9.0-beta.107](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.106...v3.9.0-beta.107) (2024-11-06)
+
+
+### Bug Fixes
+
+* build ([#4471](https://github.com/OHIF/Viewers/issues/4471)) ([3d11ef2](https://github.com/OHIF/Viewers/commit/3d11ef28f213361ec7586809317bd219fa70e742))
+
+
+
+
+
+# [3.9.0-beta.106](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.105...v3.9.0-beta.106) (2024-11-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.105](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.104...v3.9.0-beta.105) (2024-11-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.104](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.103...v3.9.0-beta.104) (2024-10-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.103](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.102...v3.9.0-beta.103) (2024-10-29)
+
+
+### Bug Fixes
+
+* **ui:** display error in ui while loading seg ([#4433](https://github.com/OHIF/Viewers/issues/4433)) ([2e96371](https://github.com/OHIF/Viewers/commit/2e96371b0631a9e5d411b0142300708ab8ba7d27))
+
+
+
+
+
+# [3.9.0-beta.102](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.101...v3.9.0-beta.102) (2024-10-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.101](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.100...v3.9.0-beta.101) (2024-10-18)
+
+
+### Features
+
+* **new-study-panel:** default to list view for non thumbnail series, change default fitler to all, and add more menu to thumbnail items with a dicom tag browser ([#4417](https://github.com/OHIF/Viewers/issues/4417)) ([a7fd9fa](https://github.com/OHIF/Viewers/commit/a7fd9fa5bfff7a1b533d99cb96f7147a35fd528f))
+
+
+
+
+
+# [3.9.0-beta.100](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.99...v3.9.0-beta.100) (2024-10-17)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.99](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.98...v3.9.0-beta.99) (2024-10-17)
+
+
+### Bug Fixes
+
+* **createReport:** early return on cancel in prompt ([#4243](https://github.com/OHIF/Viewers/issues/4243)) ([2ec4692](https://github.com/OHIF/Viewers/commit/2ec4692eaf2349e21b141a2c0b5b104ee10f7a28))
+
+
+### Features
+
+* **SR:** SCOORD3D point annotations support for stack viewports ([#4315](https://github.com/OHIF/Viewers/issues/4315)) ([ac1cad2](https://github.com/OHIF/Viewers/commit/ac1cad25af12ee0f7d508647e3134ed724d9b4d3))
+
+
+
+
+
+# [3.9.0-beta.98](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.97...v3.9.0-beta.98) (2024-10-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.97](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.96...v3.9.0-beta.97) (2024-10-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.96](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.95...v3.9.0-beta.96) (2024-10-10)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.95](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.94...v3.9.0-beta.95) (2024-10-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.94](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.93...v3.9.0-beta.94) (2024-10-04)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.93](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.92...v3.9.0-beta.93) (2024-10-04)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.92](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.91...v3.9.0-beta.92) (2024-10-01)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.91](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.90...v3.9.0-beta.91) (2024-10-01)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.90](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.89...v3.9.0-beta.90) (2024-09-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.89](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.88...v3.9.0-beta.89) (2024-09-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.88](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.87...v3.9.0-beta.88) (2024-09-24)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.87](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.86...v3.9.0-beta.87) (2024-09-19)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.86](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.85...v3.9.0-beta.86) (2024-09-19)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.85](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.84...v3.9.0-beta.85) (2024-09-17)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.84](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.83...v3.9.0-beta.84) (2024-09-12)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.83](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.82...v3.9.0-beta.83) (2024-09-11)
+
+
+### Features
+
+* **studies-panel:** New OHIF study panel - under experimental flag ([#4254](https://github.com/OHIF/Viewers/issues/4254)) ([7a96406](https://github.com/OHIF/Viewers/commit/7a96406a116e46e62c396855fa64f434e2984b58))
+
+
+
+
+
+# [3.9.0-beta.82](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.81...v3.9.0-beta.82) (2024-09-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.81](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.80...v3.9.0-beta.81) (2024-08-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.80](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.79...v3.9.0-beta.80) (2024-08-16)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.79](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.78...v3.9.0-beta.79) (2024-08-16)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.78](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.77...v3.9.0-beta.78) (2024-08-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.77](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.76...v3.9.0-beta.77) (2024-08-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.76](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.75...v3.9.0-beta.76) (2024-08-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.75](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.74...v3.9.0-beta.75) (2024-08-07)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.74](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.73...v3.9.0-beta.74) (2024-08-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.73](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.72...v3.9.0-beta.73) (2024-08-02)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.72](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.71...v3.9.0-beta.72) (2024-07-31)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.71](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.70...v3.9.0-beta.71) (2024-07-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.70](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.69...v3.9.0-beta.70) (2024-07-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.69](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.68...v3.9.0-beta.69) (2024-07-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.68](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.67...v3.9.0-beta.68) (2024-07-26)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.67](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.66...v3.9.0-beta.67) (2024-07-26)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.66](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.65...v3.9.0-beta.66) (2024-07-24)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.65](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.64...v3.9.0-beta.65) (2024-07-23)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.64](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.63...v3.9.0-beta.64) (2024-07-19)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
+# [3.9.0-beta.63](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.62...v3.9.0-beta.63) (2024-07-10)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg
+
+
+
+
+
 # [3.9.0-beta.62](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.61...v3.9.0-beta.62) (2024-07-09)
 
 **Note:** Version bump only for package @ohif/extension-cornerstone-dicom-seg

extensions/cornerstone-dicom-seg/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone-dicom-seg",
-  "version": "3.9.0-beta.62",
+  "version": "3.9.3",
   "description": "DICOM SEG read workflow",
   "author": "OHIF",
   "license": "MIT",
@@ -33,10 +33,10 @@
     "start": "yarn run dev"
   },
   "peerDependencies": {
-    "@ohif/core": "3.9.0-beta.62",
-    "@ohif/extension-cornerstone": "3.9.0-beta.62",
-    "@ohif/extension-default": "3.9.0-beta.62",
-    "@ohif/i18n": "3.9.0-beta.62",
+    "@ohif/core": "3.9.3",
+    "@ohif/extension-cornerstone": "3.9.3",
+    "@ohif/extension-default": "3.9.3",
+    "@ohif/i18n": "3.9.3",
     "prop-types": "^15.6.2",
     "react": "^18.3.1",
     "react-dom": "^18.3.1",
@@ -46,9 +46,9 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/adapters": "^1.81.6",
-    "@cornerstonejs/core": "^1.81.6",
-    "@kitware/vtk.js": "30.4.1",
+    "@cornerstonejs/adapters": "^2.2.20",
+    "@cornerstonejs/core": "^2.2.20",
+    "@kitware/vtk.js": "32.1.1",
     "react-color": "^2.19.3"
   }
 }

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

@@ -14,18 +14,22 @@ import vtkImageMarchingSquares from '@kitware/vtk.js/Filters/General/ImageMarchi
 import vtkDataArray from '@kitware/vtk.js/Common/Core/DataArray';
 import vtkImageData from '@kitware/vtk.js/Common/DataModel/ImageData';
 
-import {
-  updateViewportsForSegmentationRendering,
-  getUpdatedViewportsForSegmentation,
-  getTargetViewport,
-} from './utils/hydrationUtils';
 const { segmentation: segmentationUtils } = utilities;
 
 const { datasetToBlob } = dcmjs.data;
 
+const getTargetViewport = ({ viewportId, viewportGridService }) => {
+  const { viewports, activeViewportId } = viewportGridService.getState();
+  const targetViewportId = viewportId || activeViewportId;
+
+  const viewport = viewports.get(targetViewportId);
+
+  return viewport;
+};
+
 const {
   Cornerstone3D: {
-    Segmentation: { generateLabelMaps2DFrom3D, generateSegmentation },
+    Segmentation: { generateSegmentation },
   },
 } = adaptersSEG;
 
@@ -42,87 +46,14 @@ const commandsModule = ({
   extensionManager,
 }: Types.Extensions.ExtensionParams): Types.Extensions.CommandsModule => {
   const {
-    uiNotificationService,
     segmentationService,
     uiDialogService,
     displaySetService,
     viewportGridService,
     toolGroupService,
-    cornerstoneViewportService,
-  } = servicesManager.services;
+  } = servicesManager.services as AppTypes.Services;
 
   const actions = {
-    /**
-     * Retrieves a list of viewports that require updates in preparation for segmentation rendering.
-     * This function evaluates viewports based on their compatibility with the provided segmentation's
-     * frame of reference UID and appends them to the updated list if they should render the segmentation.
-     *
-     * @param {Object} params - Parameters for the function.
-     * @param params.viewportId - the ID of the viewport to be updated.
-     * @param params.servicesManager - The services manager
-     * @param params.referencedDisplaySetInstanceUID - Optional UID for the referenced display set instance.
-     *
-     * @returns {Array} Returns an array of viewports that require updates for segmentation rendering.
-     */
-    getUpdatedViewportsForSegmentation,
-    /**
-     * Creates an empty segmentation for a specified viewport.
-     * It first checks if the display set associated with the viewport is reconstructable.
-     * If not, it raises a notification error. Otherwise, it creates a new segmentation
-     * for the display set after handling the necessary steps for making the viewport
-     * a volume viewport first
-     *
-     * @param {Object} params - Parameters for the function.
-     * @param params.viewportId - the target viewport ID.
-     *
-     */
-    createEmptySegmentationForViewport: async ({ viewportId }) => {
-      const viewport = getTargetViewport({ viewportId, viewportGridService });
-      // Todo: add support for multiple display sets
-      const displaySetInstanceUID = viewport.displaySetInstanceUIDs[0];
-
-      const displaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
-
-      if (!displaySet.isReconstructable) {
-        uiNotificationService.show({
-          title: 'Segmentation',
-          message: 'Segmentation is not supported for non-reconstructible displaysets yet',
-          type: 'error',
-        });
-        return;
-      }
-
-      updateViewportsForSegmentationRendering({
-        viewportId,
-        servicesManager,
-        displaySet,
-        loadFn: async () => {
-          const currentSegmentations = segmentationService.getSegmentations();
-          const segmentationId = await segmentationService.createSegmentationForDisplaySet(
-            displaySetInstanceUID,
-            { label: `Segmentation ${currentSegmentations.length + 1}` }
-          );
-
-          const toolGroupId = viewport.viewportOptions.toolGroupId;
-
-          await segmentationService.addSegmentationRepresentationToToolGroup(
-            toolGroupId,
-            segmentationId
-          );
-
-          // Add only one segment for now
-          segmentationService.addSegment(segmentationId, {
-            toolGroupId,
-            segmentIndex: 1,
-            properties: {
-              label: 'Segment 1',
-            },
-          });
-
-          return segmentationId;
-        },
-      });
-    },
     /**
      * Loads segmentations for a specified viewport.
      * The function prepares the viewport for rendering, then loads the segmentation details.
@@ -134,106 +65,30 @@ const commandsModule = ({
      *
      */
     loadSegmentationsForViewport: async ({ segmentations, viewportId }) => {
-      updateViewportsForSegmentationRendering({
-        viewportId,
-        servicesManager,
-        loadFn: async () => {
-          // Todo: handle adding more than one segmentation
-          const viewport = getTargetViewport({ viewportId, viewportGridService });
-          const displaySetInstanceUID = viewport.displaySetInstanceUIDs[0];
-
-          const segmentation = segmentations[0];
-          const segmentationId = segmentation.id;
-          const label = segmentation.label;
-          const segments = segmentation.segments;
-
-          delete segmentation.segments;
-
-          await segmentationService.createSegmentationForDisplaySet(displaySetInstanceUID, {
-            segmentationId,
-            label,
-          });
-
-          if (segmentation.scalarData) {
-            const labelmapVolume = segmentationService.getLabelmapVolume(segmentationId);
-            labelmapVolume.scalarData.set(segmentation.scalarData);
-          }
-
-          segmentationService.addOrUpdateSegmentation(segmentation);
-
-          const toolGroupId = viewport.viewportOptions.toolGroupId;
-          await segmentationService.addSegmentationRepresentationToToolGroup(
-            toolGroupId,
-            segmentationId
-          );
-
-          segments.forEach(segment => {
-            if (segment === null) {
-              return;
-            }
-            segmentationService.addSegment(segmentationId, {
-              segmentIndex: segment.segmentIndex,
-              toolGroupId,
-              properties: {
-                color: segment.color,
-                label: segment.label,
-                opacity: segment.opacity,
-                isLocked: segment.isLocked,
-                visibility: segment.isVisible,
-                active: segmentation.activeSegmentIndex === segment.segmentIndex,
-              },
-            });
-          });
-
-          if (segmentation.centroidsIJK) {
-            segmentationService.setCentroids(segmentation.id, segmentation.centroidsIJK);
-          }
-
-          return segmentationId;
-        },
-      });
-    },
-    /**
-     * Loads segmentation display sets for a specified viewport.
-     * Depending on the modality of the display set (SEG or RTSTRUCT),
-     * it chooses the appropriate service function to create
-     * the segmentation for the display set.
-     * The function then prepares the viewport for rendering segmentation.
-     *
-     * @param {Object} params - Parameters for the function.
-     * @param params.viewportId - ID of the viewport where the segmentation display sets should be loaded.
-     * @param params.displaySets - Array of display sets to be loaded for segmentation.
-     *
-     */
-    loadSegmentationDisplaySetsForViewport: async ({ viewportId, displaySets }) => {
       // Todo: handle adding more than one segmentation
-      const displaySet = displaySets[0];
-      const referencedDisplaySet = displaySetService.getDisplaySetByUID(
-        displaySet.referencedDisplaySetInstanceUID
-      );
-      const viewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
-      const initialSliceIndex = viewport.getSliceIndex();
+      const viewport = getTargetViewport({ viewportId, viewportGridService });
+      const displaySetInstanceUID = viewport.displaySetInstanceUIDs[0];
 
-      updateViewportsForSegmentationRendering({
-        viewportId,
-        servicesManager,
-        displaySet,
-        loadFn: async () => {
-          const segDisplaySet = displaySet;
-          const suppressEvents = false;
-          const serviceFunction =
-            segDisplaySet.Modality === 'SEG'
-              ? 'createSegmentationForSEGDisplaySet'
-              : 'createSegmentationForRTDisplaySet';
+      const segmentation = segmentations[0];
+      const segmentationId = segmentation.segmentationId;
+      const label = segmentation.config.label;
+      const segments = segmentation.config.segments;
 
-          const boundFn = segmentationService[serviceFunction].bind(segmentationService);
-          const segmentationId = await boundFn(segDisplaySet, null, suppressEvents);
-          const segmentation = segmentationService.getSegmentation(segmentationId);
-          segmentation.description = `S${referencedDisplaySet.SeriesNumber}: ${referencedDisplaySet.SeriesDescription}`;
-          return segmentationId;
-        },
-        initialSliceIndex,
+      const displaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
+
+      await segmentationService.createLabelmapForDisplaySet(displaySet, {
+        segmentationId,
+        segments,
+        label,
       });
+
+      segmentationService.addOrUpdateSegmentation(segmentation);
+
+      await segmentationService.addSegmentationRepresentation(viewport.viewportId, {
+        segmentationId,
+      });
+
+      return segmentationId;
     },
     /**
      * Generates a segmentation from a given segmentation ID.
@@ -251,25 +106,61 @@ const commandsModule = ({
     generateSegmentation: ({ segmentationId, options = {} }) => {
       const segmentation = cornerstoneToolsSegmentation.state.getSegmentation(segmentationId);
 
-      const { referencedVolumeId } = segmentation.representationData.LABELMAP;
+      const { imageIds } = segmentation.representationData.Labelmap;
 
-      const segmentationVolume = cache.getVolume(segmentationId);
-      const referencedVolume = cache.getVolume(referencedVolumeId);
-      const referencedImages = referencedVolume.getCornerstoneImages();
+      const segImages = imageIds.map(imageId => cache.getImage(imageId));
+      const referencedImages = segImages.map(image => cache.getImage(image.referencedImageId));
 
-      const labelmapObj = generateLabelMaps2DFrom3D(segmentationVolume);
+      const labelmaps2D = [];
 
-      // Generate fake metadata as an example
-      labelmapObj.metadata = [];
+      let z = 0;
+
+      for (const segImage of segImages) {
+        const segmentsOnLabelmap = new Set();
+        const pixelData = segImage.getPixelData();
+        const { rows, columns } = segImage;
+
+        // Use a single pass through the pixel data
+        for (let i = 0; i < pixelData.length; i++) {
+          const segment = pixelData[i];
+          if (segment !== 0) {
+            segmentsOnLabelmap.add(segment);
+          }
+        }
+
+        labelmaps2D[z++] = {
+          segmentsOnLabelmap: Array.from(segmentsOnLabelmap),
+          pixelData,
+          rows,
+          columns,
+        };
+      }
+
+      const allSegmentsOnLabelmap = labelmaps2D.map(labelmap => labelmap.segmentsOnLabelmap);
+
+      const labelmap3D = {
+        segmentsOnLabelmap: Array.from(new Set(allSegmentsOnLabelmap.flat())),
+        metadata: [],
+        labelmaps2D,
+      };
 
       const segmentationInOHIF = segmentationService.getSegmentation(segmentationId);
-      segmentationInOHIF.segments.forEach(segment => {
+      const representations = segmentationService.getRepresentationsForSegmentation(segmentationId);
+
+      Object.entries(segmentationInOHIF.segments).forEach(([segmentIndex, segment]) => {
         // segmentation service already has a color for each segment
         if (!segment) {
           return;
         }
-        const segmentIndex = segment.segmentIndex;
-        const { label, color } = segment;
+
+        const { label } = segment;
+
+        const firstRepresentation = representations[0];
+        const color = segmentationService.getSegmentColor(
+          firstRepresentation.viewportId,
+          segmentationId,
+          segment.segmentIndex
+        );
 
         const RecommendedDisplayCIELabValue = dcmjs.data.Colors.rgb2DICOMLAB(
           color.slice(0, 3).map(value => value / 255)
@@ -292,12 +183,12 @@ const commandsModule = ({
             CodeMeaning: 'Tissue',
           },
         };
-        labelmapObj.metadata[segmentIndex] = segmentMetadata;
+        labelmap3D.metadata[segmentIndex] = segmentMetadata;
       });
 
       const generatedSegmentation = generateSegmentation(
         referencedImages,
-        labelmapObj,
+        labelmap3D,
         metaData,
         options
       );
@@ -339,7 +230,7 @@ const commandsModule = ({
         extensionManager,
       });
 
-      if (promptResult.action !== 1 && promptResult.value) {
+      if (promptResult.action !== 1 && !promptResult.value) {
         return;
       }
 
@@ -445,18 +336,19 @@ const commandsModule = ({
   };
 
   const definitions = {
-    getUpdatedViewportsForSegmentation: {
-      commandFn: actions.getUpdatedViewportsForSegmentation,
-    },
+    /**
+     * Obsolete?
+     */
     loadSegmentationDisplaySetsForViewport: {
       commandFn: actions.loadSegmentationDisplaySetsForViewport,
     },
+    /**
+     * Obsolete?
+     */
     loadSegmentationsForViewport: {
       commandFn: actions.loadSegmentationsForViewport,
     },
-    createEmptySegmentationForViewport: {
-      commandFn: actions.createEmptySegmentationForViewport,
-    },
+
     generateSegmentation: {
       commandFn: actions.generateSegmentation,
     },

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

@@ -20,6 +20,17 @@ const segProtocol: Types.HangingProtocol.Protocol = {
       viewportType: 'stack',
       toolGroupId: 'default',
       allowUnmatchedView: true,
+      syncGroups: [
+        {
+          type: 'hydrateseg',
+          id: 'sameFORId',
+          source: true,
+          target: true,
+          // options: {
+          //   matchingRules: ['sameFOR'],
+          // },
+        },
+      ],
     },
     displaySets: [
       {
@@ -52,7 +63,20 @@ const segProtocol: Types.HangingProtocol.Protocol = {
       },
       viewports: [
         {
-          viewportOptions: { allowUnmatchedView: true },
+          viewportOptions: {
+            allowUnmatchedView: true,
+            syncGroups: [
+              {
+                type: 'hydrateseg',
+                id: 'sameFORId',
+                source: true,
+                target: true,
+                // options: {
+                //   matchingRules: ['sameFOR'],
+                // },
+              },
+            ],
+          },
           displaySets: [
             {
               id: 'segDisplaySetId',

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

@@ -1,80 +0,0 @@
-import React from 'react';
-
-import { useAppConfig } from '@state';
-import { Toolbox } from '@ohif/ui';
-import PanelSegmentation from './panels/PanelSegmentation';
-
-const getPanelModule = ({
-  commandsManager,
-  servicesManager,
-  extensionManager,
-  configuration,
-  title,
-}: withAppTypes) => {
-  const { customizationService } = servicesManager.services;
-
-  const wrappedPanelSegmentation = configuration => {
-    const [appConfig] = useAppConfig();
-
-    return (
-      <PanelSegmentation
-        commandsManager={commandsManager}
-        servicesManager={servicesManager}
-        extensionManager={extensionManager}
-        configuration={{
-          ...configuration,
-          disableEditing: appConfig.disableEditing,
-          ...customizationService.get('segmentation.panel'),
-        }}
-      />
-    );
-  };
-
-  const wrappedPanelSegmentationWithTools = configuration => {
-    const [appConfig] = useAppConfig();
-
-    return (
-      <>
-        <Toolbox
-          commandsManager={commandsManager}
-          servicesManager={servicesManager}
-          extensionManager={extensionManager}
-          buttonSectionId="segmentationToolbox"
-          title="Segmentation Tools"
-          configuration={{
-            ...configuration,
-          }}
-        />
-        <PanelSegmentation
-          commandsManager={commandsManager}
-          servicesManager={servicesManager}
-          extensionManager={extensionManager}
-          configuration={{
-            ...configuration,
-            disableEditing: appConfig.disableEditing,
-            ...customizationService.get('segmentation.panel'),
-          }}
-        />
-      </>
-    );
-  };
-
-  return [
-    {
-      name: 'panelSegmentation',
-      iconName: 'tab-segmentation',
-      iconLabel: 'Segmentation',
-      label: 'Segmentation',
-      component: wrappedPanelSegmentation,
-    },
-    {
-      name: 'panelSegmentationWithTools',
-      iconName: 'tab-segmentation',
-      iconLabel: 'Segmentation',
-      label: 'Segmentation',
-      component: wrappedPanelSegmentationWithTools,
-    },
-  ];
-};
-
-export default getPanelModule;

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

@@ -1,6 +1,6 @@
 import { utils } from '@ohif/core';
-import { metaData, cache, triggerEvent, eventTarget } from '@cornerstonejs/core';
-import { CONSTANTS } from '@cornerstonejs/tools';
+import { metaData, triggerEvent, eventTarget } from '@cornerstonejs/core';
+import { CONSTANTS, segmentation as cstSegmentation } from '@cornerstonejs/tools';
 import { adaptersSEG, Enums } from '@cornerstonejs/adapters';
 
 import { SOPClassHandlerId } from './id';
@@ -70,28 +70,32 @@ function _getDisplaySetsFromSeries(
 
   displaySet.referencedImages = instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
   displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID;
+  const { displaySetService } = servicesManager.services;
+  const referencedDisplaySets = displaySetService.getDisplaySetsForSeries(
+    displaySet.referencedSeriesInstanceUID
+  );
 
-  displaySet.getReferenceDisplaySet = () => {
-    const { displaySetService } = servicesManager.services;
-    const referencedDisplaySets = displaySetService.getDisplaySetsForSeries(
-      displaySet.referencedSeriesInstanceUID
+  const referencedDisplaySet = referencedDisplaySets[0];
+
+  if (!referencedDisplaySet) {
+    // subscribe to display sets added which means at some point it will be available
+    const { unsubscribe } = displaySetService.subscribe(
+      displaySetService.EVENTS.DISPLAY_SETS_ADDED,
+      ({ displaySetsAdded }) => {
+        // here we can also do a little bit of search, since sometimes DICOM SEG
+        // does not contain the referenced display set uid , and we can just
+        // see which of the display sets added is more similar and assign it
+        // to the referencedDisplaySet
+        const addedDisplaySet = displaySetsAdded[0];
+        if (addedDisplaySet.SeriesInstanceUID === displaySet.referencedSeriesInstanceUID) {
+          displaySet.referencedDisplaySetInstanceUID = addedDisplaySet.displaySetInstanceUID;
+          unsubscribe();
+        }
+      }
     );
-
-    if (!referencedDisplaySets || referencedDisplaySets.length === 0) {
-      throw new Error('Referenced DisplaySet is missing for the SEG');
-    }
-
-    const referencedDisplaySet = referencedDisplaySets[0];
-
+  } else {
     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;
-    const referencedVolumeId = `cornerstoneStreamingImageVolume:${displaySet.referencedVolumeURI}`;
-    displaySet.referencedVolumeId = referencedVolumeId;
-
-    return referencedDisplaySet;
-  };
+  }
 
   displaySet.load = async ({ headers }) =>
     await _load(displaySet, servicesManager, extensionManager, headers);
@@ -111,7 +115,7 @@ function _load(
   if (
     (segDisplaySet.loading || segDisplaySet.isLoaded) &&
     loadPromises[SOPInstanceUID] &&
-    _segmentationExists(segDisplaySet, segmentationService)
+    _segmentationExists(segDisplaySet)
   ) {
     return loadPromises[SOPInstanceUID];
   }
@@ -122,17 +126,21 @@ function _load(
   // 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) {
-      await _loadSegments({
-        extensionManager,
-        servicesManager,
-        segDisplaySet,
-        headers,
-      });
+      try {
+        await _loadSegments({
+          extensionManager,
+          servicesManager,
+          segDisplaySet,
+          headers,
+        });
+      } catch (e) {
+        segDisplaySet.loading = false;
+        return reject(e);
+      }
     }
 
-    const suppressEvents = true;
     segmentationService
-      .createSegmentationForSEGDisplaySet(segDisplaySet, null, suppressEvents)
+      .createSegmentationForSEGDisplaySet(segDisplaySet)
       .then(() => {
         segDisplaySet.loading = false;
         resolve();
@@ -161,20 +169,20 @@ async function _loadSegments({
   const { dicomLoaderService } = utilityModule.exports;
   const arrayBuffer = await dicomLoaderService.findDicomDataPromise(segDisplaySet, null, headers);
 
-  const cachedReferencedVolume = cache.getVolume(segDisplaySet.referencedVolumeId);
+  const referencedDisplaySet = servicesManager.services.displaySetService.getDisplaySetByUID(
+    segDisplaySet.referencedDisplaySetInstanceUID
+  );
 
-  if (!cachedReferencedVolume) {
-    throw new Error(
-      'Referenced Volume is missing for the SEG, and stack viewport SEG is not supported yet'
-    );
+  if (!referencedDisplaySet) {
+    throw new Error('referencedDisplaySet is missing for SEG');
   }
 
-  const { imageIds } = cachedReferencedVolume;
+  const { instances: images } = referencedDisplaySet;
+  const imageIds = images.map(({ imageId }) => imageId);
 
   // 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, {
@@ -226,9 +234,8 @@ async function _loadSegments({
   Object.assign(segDisplaySet, results);
 }
 
-function _segmentationExists(segDisplaySet, segmentationService: AppTypes.SegmentationService) {
-  // This should be abstracted with the CornerstoneCacheService
-  return segmentationService.getSegmentation(segDisplaySet.displaySetInstanceUID);
+function _segmentationExists(segDisplaySet) {
+  return cstSegmentation.state.getSegmentation(segDisplaySet.displaySetInstanceUID);
 }
 
 function getSopClassHandlerModule({ servicesManager, extensionManager }) {

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

@@ -8,7 +8,7 @@ export function getToolbarModule({ servicesManager }: withAppTypes) {
         // forcing the button to have black background since initially
         // it is designed for the toolbox not the toolbar on top
         // we should then branch the buttonSectionId to have different styles
-        const segmentations = segmentationService.getSegmentations();
+        const segmentations = segmentationService.getSegmentationRepresentations(viewportId);
         if (!segmentations?.length) {
           return {
             disabled: true,

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

@@ -3,7 +3,6 @@ import React from 'react';
 
 import getSopClassHandlerModule from './getSopClassHandlerModule';
 import getHangingProtocolModule from './getHangingProtocolModule';
-import getPanelModule from './getPanelModule';
 import getCommandsModule from './commandsModule';
 import { getToolbarModule } from './getToolbarModule';
 
@@ -28,13 +27,6 @@ const extension = {
    * You ID can be anything you want, but it should be unique.
    */
   id,
-  /**
-   * PanelModule should provide a list of panels that will be available in OHIF
-   * for Modes to consume and render. Each panel is defined by a {name,
-   * iconName, iconLabel, label, component} object. Example of a panel module
-   * is the StudyBrowserPanel that is provided by the default extension in OHIF.
-   */
-  getPanelModule,
   getCommandsModule,
   getToolbarModule,
   getViewportModule({ servicesManager, extensionManager, commandsManager }) {

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

@@ -1,386 +0,0 @@
-import { createReportAsync } from '@ohif/extension-default';
-import React, { useEffect, useState, useCallback } from 'react';
-import PropTypes from 'prop-types';
-import { SegmentationGroupTable, SegmentationGroupTableExpanded } from '@ohif/ui';
-import { SegmentationPanelMode } from '../types/segmentation';
-import callInputDialog from './callInputDialog';
-import callColorPickerDialog from './colorPickerDialog';
-import { useTranslation } from 'react-i18next';
-
-const components = {
-  [SegmentationPanelMode.Expanded]: SegmentationGroupTableExpanded,
-  [SegmentationPanelMode.Dropdown]: SegmentationGroupTable,
-};
-
-export default function PanelSegmentation({
-  servicesManager,
-  commandsManager,
-  extensionManager,
-  configuration,
-}: withAppTypes) {
-  const {
-    segmentationService,
-    viewportGridService,
-    uiDialogService,
-    displaySetService,
-    cornerstoneViewportService,
-  } = servicesManager.services;
-
-  const { t } = useTranslation('PanelSegmentation');
-
-  const [selectedSegmentationId, setSelectedSegmentationId] = useState(null);
-  const [addSegmentationClassName, setAddSegmentationClassName] = useState('');
-  const [segmentationConfiguration, setSegmentationConfiguration] = useState(
-    segmentationService.getConfiguration()
-  );
-
-  const [segmentations, setSegmentations] = useState(() => segmentationService.getSegmentations());
-
-  useEffect(() => {
-    // ~~ Subscription
-    const added = segmentationService.EVENTS.SEGMENTATION_ADDED;
-    const updated = segmentationService.EVENTS.SEGMENTATION_UPDATED;
-    const removed = segmentationService.EVENTS.SEGMENTATION_REMOVED;
-    const subscriptions = [];
-
-    [added, updated, removed].forEach(evt => {
-      const { unsubscribe } = segmentationService.subscribe(evt, () => {
-        const segmentations = segmentationService.getSegmentations();
-        setSegmentations(segmentations);
-        setSegmentationConfiguration(segmentationService.getConfiguration());
-      });
-      subscriptions.push(unsubscribe);
-    });
-
-    return () => {
-      subscriptions.forEach(unsub => {
-        unsub();
-      });
-    };
-  }, []);
-
-  // temporary measure to not allow add segmentation when the selected viewport
-  // is stack viewport
-  useEffect(() => {
-    const handleActiveViewportChange = viewportId => {
-      const displaySetUIDs = viewportGridService.getDisplaySetsUIDsForViewport(
-        viewportId || viewportGridService.getActiveViewportId()
-      );
-
-      if (!displaySetUIDs) {
-        return;
-      }
-
-      const isReconstructable =
-        displaySetUIDs?.some(displaySetUID => {
-          const displaySet = displaySetService.getDisplaySetByUID(displaySetUID);
-          return displaySet?.isReconstructable;
-        }) || false;
-
-      if (isReconstructable) {
-        setAddSegmentationClassName('');
-      } else {
-        setAddSegmentationClassName('ohif-disabled');
-      }
-    };
-
-    // Handle initial state
-    handleActiveViewportChange();
-
-    const changedGrid = viewportGridService.EVENTS.ACTIVE_VIEWPORT_ID_CHANGED;
-    const ready = viewportGridService.EVENTS.VIEWPORTS_READY;
-
-    const subsGrid = [];
-    [ready, changedGrid].forEach(evt => {
-      const { unsubscribe } = viewportGridService.subscribe(evt, ({ viewportId }) => {
-        handleActiveViewportChange(viewportId);
-      });
-
-      subsGrid.push(unsubscribe);
-    });
-
-    const changedData = cornerstoneViewportService.EVENTS.VIEWPORT_DATA_CHANGED;
-
-    const subsData = [];
-    [changedData].forEach(evt => {
-      const { unsubscribe } = cornerstoneViewportService.subscribe(evt, () => {
-        handleActiveViewportChange();
-      });
-
-      subsData.push(unsubscribe);
-    });
-
-    // Clean up
-    return () => {
-      subsGrid.forEach(unsub => unsub());
-      subsData.forEach(unsub => unsub());
-    };
-  }, []);
-
-  const getToolGroupIds = segmentationId => {
-    const toolGroupIds = segmentationService.getToolGroupIdsWithSegmentation(segmentationId);
-
-    return toolGroupIds;
-  };
-
-  const onSegmentationAdd = async () => {
-    commandsManager.runCommand('createEmptySegmentationForViewport', {
-      viewportId: viewportGridService.getActiveViewportId(),
-    });
-  };
-
-  const onSegmentationClick = (segmentationId: string) => {
-    segmentationService.setActiveSegmentationForToolGroup(segmentationId);
-  };
-
-  const onSegmentationDelete = (segmentationId: string) => {
-    segmentationService.remove(segmentationId);
-  };
-
-  const onSegmentAdd = segmentationId => {
-    segmentationService.addSegment(segmentationId);
-  };
-
-  const onSegmentClick = (segmentationId, segmentIndex) => {
-    segmentationService.setActiveSegment(segmentationId, segmentIndex);
-
-    const toolGroupIds = getToolGroupIds(segmentationId);
-
-    toolGroupIds.forEach(toolGroupId => {
-      // const toolGroupId =
-      segmentationService.setActiveSegmentationForToolGroup(segmentationId, toolGroupId);
-      segmentationService.jumpToSegmentCenter(segmentationId, segmentIndex, toolGroupId);
-    });
-  };
-
-  const onSegmentEdit = (segmentationId, segmentIndex) => {
-    const segmentation = segmentationService.getSegmentation(segmentationId);
-
-    const segment = segmentation.segments[segmentIndex];
-    const { label } = segment;
-
-    callInputDialog(uiDialogService, label, (label, actionId) => {
-      if (label === '') {
-        return;
-      }
-
-      segmentationService.setSegmentLabel(segmentationId, segmentIndex, label);
-    });
-  };
-
-  const onSegmentationEdit = segmentationId => {
-    const segmentation = segmentationService.getSegmentation(segmentationId);
-    const { label } = segmentation;
-
-    callInputDialog(uiDialogService, label, (label, actionId) => {
-      if (label === '') {
-        return;
-      }
-
-      segmentationService.addOrUpdateSegmentation(
-        {
-          id: segmentationId,
-          label,
-        },
-        false, // suppress event
-        true // notYetUpdatedAtSource
-      );
-    });
-  };
-
-  const onSegmentColorClick = (segmentationId, segmentIndex) => {
-    const segmentation = segmentationService.getSegmentation(segmentationId);
-
-    const segment = segmentation.segments[segmentIndex];
-    const { color, opacity } = segment;
-
-    const rgbaColor = {
-      r: color[0],
-      g: color[1],
-      b: color[2],
-      a: opacity / 255.0,
-    };
-
-    callColorPickerDialog(uiDialogService, rgbaColor, (newRgbaColor, actionId) => {
-      if (actionId === 'cancel') {
-        return;
-      }
-
-      segmentationService.setSegmentRGBAColor(segmentationId, segmentIndex, [
-        newRgbaColor.r,
-        newRgbaColor.g,
-        newRgbaColor.b,
-        newRgbaColor.a * 255.0,
-      ]);
-    });
-  };
-
-  const onSegmentDelete = (segmentationId, segmentIndex) => {
-    segmentationService.removeSegment(segmentationId, segmentIndex);
-  };
-
-  // segment hide
-  const onToggleSegmentVisibility = (segmentationId, segmentIndex) => {
-    const segmentation = segmentationService.getSegmentation(segmentationId);
-    const segmentInfo = segmentation.segments[segmentIndex];
-    const isVisible = !segmentInfo.isVisible;
-    const toolGroupIds = getToolGroupIds(segmentationId);
-
-    // Todo: right now we apply the visibility to all tool groups
-    toolGroupIds.forEach(toolGroupId => {
-      segmentationService.setSegmentVisibility(
-        segmentationId,
-        segmentIndex,
-        isVisible,
-        toolGroupId
-      );
-    });
-  };
-
-  const onToggleSegmentLock = (segmentationId, segmentIndex) => {
-    segmentationService.toggleSegmentLocked(segmentationId, segmentIndex);
-  };
-
-  const onToggleSegmentationVisibility = segmentationId => {
-    segmentationService.toggleSegmentationVisibility(segmentationId);
-    const segmentation = segmentationService.getSegmentation(segmentationId);
-    const isVisible = segmentation.isVisible;
-    const segments = segmentation.segments;
-
-    const toolGroupIds = getToolGroupIds(segmentationId);
-
-    toolGroupIds.forEach(toolGroupId => {
-      segments.forEach((segment, segmentIndex) => {
-        segmentationService.setSegmentVisibility(
-          segmentationId,
-          segmentIndex,
-          isVisible,
-          toolGroupId
-        );
-      });
-    });
-  };
-
-  const _setSegmentationConfiguration = useCallback(
-    (segmentationId, key, value) => {
-      segmentationService.setConfiguration({
-        segmentationId,
-        [key]: value,
-      });
-    },
-    [segmentationService]
-  );
-
-  const onSegmentationDownload = segmentationId => {
-    commandsManager.runCommand('downloadSegmentation', {
-      segmentationId,
-    });
-  };
-
-  const storeSegmentation = async segmentationId => {
-    const datasources = extensionManager.getActiveDataSource();
-
-    const displaySetInstanceUIDs = await createReportAsync({
-      servicesManager,
-      getReport: () =>
-        commandsManager.runCommand('storeSegmentation', {
-          segmentationId,
-          dataSource: datasources[0],
-        }),
-      reportType: 'Segmentation',
-    });
-
-    // Show the exported report in the active viewport as read only (similar to SR)
-    if (displaySetInstanceUIDs) {
-      // clear the segmentation that we exported, similar to the storeMeasurement
-      // where we remove the measurements and prompt again the user if they would like
-      // to re-read the measurements in a SR read only viewport
-      segmentationService.remove(segmentationId);
-
-      viewportGridService.setDisplaySetsForViewport({
-        viewportId: viewportGridService.getActiveViewportId(),
-        displaySetInstanceUIDs,
-      });
-    }
-  };
-
-  const onSegmentationDownloadRTSS = segmentationId => {
-    commandsManager.runCommand('downloadRTSS', {
-      segmentationId,
-    });
-  };
-
-  const SegmentationGroupTableComponent =
-    components[configuration?.segmentationPanelMode] || SegmentationGroupTable;
-  const allowAddSegment = configuration?.addSegment;
-  const onSegmentationAddWrapper =
-    configuration?.onSegmentationAdd && typeof configuration?.onSegmentationAdd === 'function'
-      ? configuration?.onSegmentationAdd
-      : onSegmentationAdd;
-
-  return (
-    <SegmentationGroupTableComponent
-      title={t('Segmentations')}
-      segmentations={segmentations}
-      disableEditing={configuration.disableEditing}
-      activeSegmentationId={selectedSegmentationId || ''}
-      onSegmentationAdd={onSegmentationAddWrapper}
-      addSegmentationClassName={addSegmentationClassName}
-      showAddSegment={allowAddSegment}
-      onSegmentationClick={onSegmentationClick}
-      onSegmentationDelete={onSegmentationDelete}
-      onSegmentationDownload={onSegmentationDownload}
-      onSegmentationDownloadRTSS={onSegmentationDownloadRTSS}
-      storeSegmentation={storeSegmentation}
-      onSegmentationEdit={onSegmentationEdit}
-      onSegmentClick={onSegmentClick}
-      onSegmentEdit={onSegmentEdit}
-      onSegmentAdd={onSegmentAdd}
-      onSegmentColorClick={onSegmentColorClick}
-      onSegmentDelete={onSegmentDelete}
-      onToggleSegmentVisibility={onToggleSegmentVisibility}
-      onToggleSegmentLock={onToggleSegmentLock}
-      onToggleSegmentationVisibility={onToggleSegmentationVisibility}
-      showDeleteSegment={true}
-      segmentationConfig={{ initialConfig: segmentationConfiguration }}
-      setRenderOutline={value =>
-        _setSegmentationConfiguration(selectedSegmentationId, 'renderOutline', value)
-      }
-      setOutlineOpacityActive={value =>
-        _setSegmentationConfiguration(selectedSegmentationId, 'outlineOpacity', value)
-      }
-      setRenderFill={value =>
-        _setSegmentationConfiguration(selectedSegmentationId, 'renderFill', value)
-      }
-      setRenderInactiveSegmentations={value =>
-        _setSegmentationConfiguration(selectedSegmentationId, 'renderInactiveSegmentations', value)
-      }
-      setOutlineWidthActive={value =>
-        _setSegmentationConfiguration(selectedSegmentationId, 'outlineWidthActive', value)
-      }
-      setFillAlpha={value =>
-        _setSegmentationConfiguration(selectedSegmentationId, 'fillAlpha', value)
-      }
-      setFillAlphaInactive={value =>
-        _setSegmentationConfiguration(selectedSegmentationId, 'fillAlphaInactive', value)
-      }
-    />
-  );
-}
-
-PanelSegmentation.propTypes = {
-  commandsManager: PropTypes.shape({
-    runCommand: PropTypes.func.isRequired,
-  }),
-  servicesManager: PropTypes.shape({
-    services: PropTypes.shape({
-      segmentationService: PropTypes.shape({
-        getSegmentation: PropTypes.func.isRequired,
-        getSegmentations: PropTypes.func.isRequired,
-        toggleSegmentationVisibility: PropTypes.func.isRequired,
-        subscribe: PropTypes.func.isRequired,
-        EVENTS: PropTypes.object.isRequired,
-      }).isRequired,
-    }).isRequired,
-  }).isRequired,
-};

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

@@ -1,62 +0,0 @@
-import React from 'react';
-import { Input, Dialog, ButtonEnums } from '@ohif/ui';
-
-function callInputDialog(uiDialogService, label, callback) {
-  const dialogId = 'enter-segment-label';
-
-  const onSubmitHandler = ({ action, value }) => {
-    switch (action.id) {
-      case 'save':
-        callback(value.label, action.id);
-        break;
-      case 'cancel':
-        callback('', action.id);
-        break;
-    }
-    uiDialogService.dismiss({ id: dialogId });
-  };
-
-  if (uiDialogService) {
-    uiDialogService.create({
-      id: dialogId,
-      centralize: true,
-      isDraggable: false,
-      showOverlay: true,
-      content: Dialog,
-      contentProps: {
-        title: 'Segment',
-        value: { label },
-        noCloseButton: true,
-        onClose: () => uiDialogService.dismiss({ id: dialogId }),
-        actions: [
-          { id: 'cancel', text: 'Cancel', type: ButtonEnums.type.secondary },
-          { id: 'save', text: 'Confirm', type: ButtonEnums.type.primary },
-        ],
-        onSubmit: onSubmitHandler,
-        body: ({ value, setValue }) => {
-          return (
-            <Input
-              label="Enter the segment label"
-              labelClassName="text-white text-[14px] leading-[1.2]"
-              autoFocus
-              className="border-primary-main bg-black"
-              type="text"
-              value={value.label}
-              onChange={event => {
-                event.persist();
-                setValue(value => ({ ...value, label: event.target.value }));
-              }}
-              onKeyPress={event => {
-                if (event.key === 'Enter') {
-                  onSubmitHandler({ value, action: { id: 'save' } });
-                }
-              }}
-            />
-          );
-        },
-      },
-    });
-  }
-}
-
-export default callInputDialog;

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

@@ -1,33 +0,0 @@
-// Todo: use defaults in cs3d
-const initialState = {
-  renderOutline: true,
-  renderFill: true,
-  outlineOpacity: 0.9,
-  outlineWidth: 3,
-  fillOpacity: 0.9,
-  fillOpacityInactive: 0.8,
-  renderInactiveSegmentations: true,
-};
-
-const reducer = (state, action) => {
-  switch (action.type) {
-    case 'RENDER_OUTLINE':
-      return { ...state, renderOutline: action.payload.value };
-    case 'RENDER_FILL':
-      return { ...state, renderFill: action.payload.value };
-    case 'SET_OUTLINE_OPACITY':
-      return { ...state, outlineOpacity: action.payload.value };
-    case 'SET_OUTLINE_WIDTH':
-      return { ...state, outlineWidth: action.payload.value };
-    case 'SET_FILL_OPACITY':
-      return { ...state, fillOpacity: action.payload.value };
-    case 'SET_FILL_OPACITY_INACTIVE':
-      return { ...state, fillOpacityInactive: action.payload.value };
-    case 'RENDER_INACTIVE_SEGMENTATIONS':
-      return { ...state, renderInactiveSegmentations: action.payload.value };
-    default:
-      return state;
-  }
-};
-
-export { initialState, reducer };

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

@@ -1,203 +0,0 @@
-import { Enums, cache } from '@cornerstonejs/core';
-
-/**
- * Updates the viewports in preparation for rendering segmentations.
- * Evaluates each viewport to determine which need modifications,
- * then for those viewports, changes them to a volume type and ensures
- * they are ready for segmentation rendering.
- *
- * @param {Object} params - Parameters for the function.
- * @param params.viewportId - ID of the viewport to be updated.
- * @param params.loadFn - Function to load the segmentation data.
- * @param params.servicesManager - The services manager.
- * @param params.displaySet -  the display set.
- * @param params.initialSliceIndex - The initial slice index.
- *
- * @returns Returns true upon successful update of viewports for segmentation rendering.
- */
-async function updateViewportsForSegmentationRendering({
-  viewportId,
-  loadFn,
-  servicesManager,
-  displaySet,
-  initialSliceIndex = null,
-}: {
-  viewportId: string;
-  loadFn: () => Promise<string>;
-  servicesManager: AppTypes.ServicesManager;
-  displaySet?: any;
-  initialSliceIndex?: number;
-}) {
-  const { cornerstoneViewportService, segmentationService, viewportGridService } =
-    servicesManager.services;
-
-  const viewport = getTargetViewport({ viewportId, viewportGridService });
-  const targetViewportId = viewport.viewportOptions.viewportId;
-
-  const referencedDisplaySetInstanceUID =
-    displaySet?.referencedDisplaySetInstanceUID || viewport?.displaySetInstanceUIDs[0];
-
-  const updatedViewports = getUpdatedViewportsForSegmentation({
-    viewportId,
-    servicesManager,
-    displaySet,
-  });
-
-  // create Segmentation callback which needs to be waited until
-  // the volume is created (if coming from stack)
-  const createSegmentationForVolume = async () => {
-    const segmentationId = await loadFn();
-    segmentationService.hydrateSegmentation(segmentationId);
-  };
-
-  // the reference volume that is used to draw the segmentation. so check if the
-  // volume exists in the cache (the target Viewport is already a volume viewport)
-  const volumeExists = Array.from(cache._volumeCache.keys()).some(volumeId =>
-    volumeId.includes(referencedDisplaySetInstanceUID)
-  );
-
-  updatedViewports.forEach(async viewport => {
-    viewport.viewportOptions = {
-      ...viewport.viewportOptions,
-      viewportType: displaySet?.Modality === 'RTSTRUCT' ? 'stack' : 'volume',
-      needsRerendering: true,
-    };
-    const viewportId = viewport.viewportId;
-
-    // maintain the prehydration slice on the target viewport only
-    if (viewportId === targetViewportId) {
-      viewport.viewportOptions.initialImageOptions = {
-        index: initialSliceIndex,
-        useOnce: true,
-      };
-    }
-
-    const csViewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
-    const prevCamera = csViewport.getCamera();
-
-    // only run the createSegmentationForVolume for the targetViewportId
-    // since the rest will get handled by cornerstoneViewportService
-    if ((volumeExists || displaySet.Modality === 'RTSTRUCT') && viewportId === targetViewportId) {
-      await createSegmentationForVolume();
-      return;
-    }
-
-    const createNewSegmentationWhenVolumeMounts = async evt => {
-      const isTheActiveViewportVolumeMounted = evt.detail.volumeActors?.find(ac =>
-        ac.uid.includes(referencedDisplaySetInstanceUID)
-      );
-
-      // Note: make sure to re-grab the viewport since it might have changed
-      // during the time it took for the volume to be mounted, for instance
-      // the stack viewport has been changed to a volume viewport
-      const volumeViewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
-      volumeViewport.setCamera(prevCamera);
-
-      volumeViewport.element.removeEventListener(
-        Enums.Events.VOLUME_VIEWPORT_NEW_VOLUME,
-        createNewSegmentationWhenVolumeMounts
-      );
-
-      if (!isTheActiveViewportVolumeMounted) {
-        // it means it is one of those other updated viewports so just update the camera
-        return;
-      }
-
-      if (viewportId === targetViewportId) {
-        await createSegmentationForVolume();
-      }
-    };
-
-    csViewport.element.addEventListener(
-      Enums.Events.VOLUME_VIEWPORT_NEW_VOLUME,
-      createNewSegmentationWhenVolumeMounts
-    );
-  });
-
-  // Set the displaySets for the viewports that require to be updated
-  viewportGridService.setDisplaySetsForViewports(updatedViewports);
-
-  return true;
-}
-
-const getTargetViewport = ({ viewportId, viewportGridService }) => {
-  const { viewports, activeViewportId } = viewportGridService.getState();
-  const targetViewportId = viewportId || activeViewportId;
-
-  const viewport = viewports.get(targetViewportId);
-
-  return viewport;
-};
-
-/**
- * Retrieves a list of viewports that require updates in preparation for segmentation rendering.
- * This function evaluates viewports based on their compatibility with the provided segmentation's
- * frame of reference UID and appends them to the updated list if they should render the segmentation.
- *
- * @param {Object} params - Parameters for the function.
- * @param params.viewportId - the ID of the viewport to be updated.
- * @param params.servicesManager - The services manager
- * @param params.displaySet -  the display set.
- *
- * @returns {Array} Returns an array of viewports that require updates for segmentation rendering.
- */
-function getUpdatedViewportsForSegmentation({
-  viewportId,
-  servicesManager,
-  displaySet,
-}: withAppTypes) {
-  const { hangingProtocolService, displaySetService, segmentationService, viewportGridService } =
-    servicesManager.services;
-
-  const { viewports, isHangingProtocolLayout } = viewportGridService.getState();
-
-  const viewport = getTargetViewport({ viewportId, viewportGridService });
-  const targetViewportId = viewport.viewportOptions.viewportId;
-
-  const displaySetInstanceUIDs = viewports.get(targetViewportId).displaySetInstanceUIDs;
-
-  const referenceDisplaySetInstanceUID =
-    displaySet?.referencedDisplaySetInstanceUID || displaySetInstanceUIDs[0];
-
-  const referencedDisplaySet = displaySetService.getDisplaySetByUID(referenceDisplaySetInstanceUID);
-  const segmentationFrameOfReferenceUID = referencedDisplaySet.instances[0].FrameOfReferenceUID;
-
-  const updatedViewports = hangingProtocolService.getViewportsRequireUpdate(
-    targetViewportId,
-    referenceDisplaySetInstanceUID,
-    isHangingProtocolLayout
-  );
-
-  viewports.forEach((viewport, viewportId) => {
-    if (
-      targetViewportId === viewportId ||
-      updatedViewports.find(v => v.viewportId === viewportId)
-    ) {
-      return;
-    }
-
-    const shouldDisplaySeg = segmentationService.shouldRenderSegmentation(
-      viewport.displaySetInstanceUIDs,
-      segmentationFrameOfReferenceUID
-    );
-
-    if (shouldDisplaySeg) {
-      updatedViewports.push({
-        viewportId,
-        displaySetInstanceUIDs: viewport.displaySetInstanceUIDs,
-        viewportOptions: {
-          viewportType: displaySet?.Modality === 'RTSTRUCT' ? 'stack' : 'volume',
-          needsRerendering: true,
-        },
-      });
-    }
-  });
-
-  return updatedViewports.filter(v => v.viewportOptions?.viewportType !== 'volume3d');
-}
-
-export {
-  updateViewportsForSegmentationRendering,
-  getUpdatedViewportsForSegmentation,
-  getTargetViewport,
-};

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

@@ -11,7 +11,7 @@ function promptHydrateSEG({
   segDisplaySet,
   viewportId,
   preHydrateCallbacks,
-  hydrateSEGDisplaySet,
+  hydrateCallback,
 }: withAppTypes) {
   const { uiViewportDialogService } = servicesManager.services;
   const extensionManager = servicesManager._extensionManager;
@@ -28,7 +28,7 @@ function promptHydrateSEG({
       });
 
       window.setTimeout(async () => {
-        const isHydrated = await hydrateSEGDisplaySet({
+        const isHydrated = await hydrateCallback({
           segDisplaySet,
           viewportId,
         });

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

@@ -1,10 +1,11 @@
-import PropTypes from 'prop-types';
 import React, { useCallback, useEffect, useRef, useState } from 'react';
 import { useTranslation } from 'react-i18next';
 import { LoadingIndicatorTotalPercent, useViewportGrid, ViewportActionArrows } from '@ohif/ui';
 import createSEGToolGroupAndAddTools from '../utils/initSEGToolGroup';
 import promptHydrateSEG from '../utils/promptHydrateSEG';
 import _getStatusComponent from './_getStatusComponent';
+import { usePositionPresentationStore } from '@ohif/extension-cornerstone';
+import { SegmentationRepresentations } from '@cornerstonejs/tools/enums';
 
 const SEG_TOOLGROUP_BASE_NAME = 'SEGToolGroup';
 
@@ -37,11 +38,11 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
   }
 
   const segDisplaySet = displaySets[0];
-
   const [viewportGrid, viewportGridService] = useViewportGrid();
 
   // States
   const [selectedSegment, setSelectedSegment] = useState(1);
+  const { setPositionPresentation } = usePositionPresentationStore();
 
   // Hydration means that the SEG is opened and segments are loaded into the
   // segmentation panel, and SEG is also rendered on any viewport that is in the
@@ -61,7 +62,11 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
 
   const { viewports, activeViewportId } = viewportGrid;
 
-  const referencedDisplaySet = segDisplaySet.getReferenceDisplaySet();
+  const referencedDisplaySetInstanceUID = segDisplaySet.referencedDisplaySetInstanceUID;
+  const referencedDisplaySet = displaySetService.getDisplaySetByUID(
+    referencedDisplaySetInstanceUID
+  );
+
   const referencedDisplaySetMetadata = _getReferencedDisplaySetMetadata(
     referencedDisplaySet,
     segDisplaySet
@@ -98,18 +103,17 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
       '@ohif/extension-cornerstone.viewportModule.cornerstone'
     );
 
-    const { displaySet: referencedDisplaySet } = referencedDisplaySetRef.current;
-
     // Todo: jump to the center of the first segment
     return (
       <Component
         {...props}
-        displaySets={[referencedDisplaySet, segDisplaySet]}
+        displaySets={[segDisplaySet]}
         viewportOptions={{
-          viewportType: 'volume',
+          viewportType: viewportOptions.viewportType,
           toolGroupId: toolGroupId,
           orientation: viewportOptions.orientation,
           viewportId: viewportOptions.viewportId,
+          presentationIds: viewportOptions.presentationIds,
         }}
         onElementEnabled={evt => {
           props.onElementEnabled?.(evt);
@@ -139,12 +143,35 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
         newSelectedSegmentIndex = numberOfSegments - 1;
       }
 
-      segmentationService.jumpToSegmentCenter(segmentationId, newSelectedSegmentIndex, toolGroupId);
+      segmentationService.jumpToSegmentCenter(segmentationId, newSelectedSegmentIndex, viewportId);
       setSelectedSegment(newSelectedSegmentIndex);
     },
     [selectedSegment]
   );
 
+  const hydrateSEG = useCallback(() => {
+    // update the previously stored segmentationPresentation with the new viewportId
+    // presentation so that when we put the referencedDisplaySet back in the viewport
+    // it will have the correct segmentation representation hydrated
+    commandsManager.runCommand('updateStoredSegmentationPresentation', {
+      displaySet: segDisplaySet,
+      type: SegmentationRepresentations.Labelmap,
+    });
+
+    // update the previously stored positionPresentation with the new viewportId
+    // presentation so that when we put the referencedDisplaySet back in the viewport
+    // it will be in the correct position zoom and pan
+    commandsManager.runCommand('updateStoredPositionPresentation', {
+      viewportId,
+      displaySetInstanceUID: referencedDisplaySet.displaySetInstanceUID,
+    });
+
+    viewportGridService.setDisplaySetsForViewport({
+      viewportId,
+      displaySetInstanceUIDs: [referencedDisplaySet.displaySetInstanceUID],
+    });
+  }, [commandsManager, viewportId, referencedDisplaySet, segDisplaySet]);
+
   useEffect(() => {
     if (segIsLoading) {
       return;
@@ -155,21 +182,35 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
       viewportId,
       segDisplaySet,
       preHydrateCallbacks: [storePresentationState],
-      hydrateSEGDisplaySet,
+      hydrateCallback: hydrateSEG,
     }).then(isHydrated => {
       if (isHydrated) {
         setIsHydrated(true);
       }
     });
-  }, [servicesManager, viewportId, segDisplaySet, segIsLoading]);
+  }, [servicesManager, viewportId, segDisplaySet, segIsLoading, hydrateSEG]);
 
   useEffect(() => {
+    // on new seg display set, remove all segmentations from all viewports
+    segmentationService.clearSegmentationRepresentations(viewportId);
+
     const { unsubscribe } = segmentationService.subscribe(
       segmentationService.EVENTS.SEGMENTATION_LOADING_COMPLETE,
       evt => {
         if (evt.segDisplaySet.displaySetInstanceUID === segDisplaySet.displaySetInstanceUID) {
           setSegIsLoading(false);
         }
+
+        if (segDisplaySet?.firstSegmentedSliceImageId && viewportOptions?.presentationIds) {
+          const { firstSegmentedSliceImageId } = segDisplaySet;
+          const { presentationIds } = viewportOptions;
+
+          setPositionPresentation(presentationIds.positionPresentationId, {
+            viewReference: {
+              referencedImageId: firstSegmentedSliceImageId,
+            },
+          });
+        }
       }
     );
 
@@ -223,39 +264,31 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
       return;
     }
 
+    // keep the already stored segmentationPresentation for this viewport in memory
+    // so that we can restore it after hydrating the SEG
+    commandsManager.runCommand('updateStoredSegmentationPresentation', {
+      displaySet: segDisplaySet,
+      type: SegmentationRepresentations.Labelmap,
+    });
+
+    // always start fresh for this viewport since it is special type of viewport
+    // that should only show one segmentation at a time.
+    segmentationService.clearSegmentationRepresentations(viewportId);
+
     // 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);
 
     return () => {
       // remove the segmentation representations if seg displayset changed
-      segmentationService.removeSegmentationRepresentationFromToolGroup(toolGroupId);
+      // e.g., another seg displayset is dragged into the viewport
+      segmentationService.clearSegmentationRepresentations(viewportId);
 
       // Only destroy the viewport specific implementation
       toolGroupService.destroyToolGroup(toolGroupId);
     };
   }, []);
 
-  useEffect(() => {
-    setIsHydrated(segDisplaySet.isHydrated);
-
-    return () => {
-      // remove the segmentation representations if seg displayset changed
-      segmentationService.removeSegmentationRepresentationFromToolGroup(toolGroupId);
-      referencedDisplaySetRef.current = null;
-    };
-  }, [segDisplaySet]);
-
-  const hydrateSEGDisplaySet = useCallback(
-    ({ segDisplaySet, viewportId }) => {
-      commandsManager.runCommand('loadSegmentationDisplaySetsForViewport', {
-        displaySets: [segDisplaySet],
-        viewportId,
-      });
-    },
-    [commandsManager]
-  );
-
   const onStatusClick = useCallback(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
@@ -264,16 +297,11 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
     // 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,
-      viewportId,
-    });
-
-    setIsHydrated(isHydrated);
-  }, [hydrateSEGDisplaySet, segDisplaySet, storePresentationState, viewportId]);
+    hydrateSEG();
+  }, [storePresentationState, hydrateSEG]);
 
   useEffect(() => {
-    viewportActionCornersService.setComponents([
+    viewportActionCornersService.addComponents([
       {
         viewportId,
         id: 'viewportStatusComponent',
@@ -292,7 +320,7 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
             key="actionArrows"
             onArrowsClick={onSegmentChange}
             className={
-              viewportId === activeViewportId ? 'visible' : 'invisible group-hover:visible'
+              viewportId === activeViewportId ? 'visible' : 'invisible group-hover/pane:visible'
             }
           ></ViewportActionArrows>
         ),
@@ -332,18 +360,6 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
     });
   }
 
-  const {
-    PatientID,
-    PatientName,
-    PatientSex,
-    PatientAge,
-    SliceThickness,
-    ManufacturerModelName,
-    StudyDate,
-    SeriesDescription,
-    SpacingBetweenSlices,
-  } = referencedDisplaySetRef.current.metadata;
-
   return (
     <>
       <div className="relative flex h-full w-full flex-row overflow-hidden">
@@ -362,13 +378,6 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
   );
 }
 
-OHIFCornerstoneSEGViewport.propTypes = {
-  displaySets: PropTypes.arrayOf(PropTypes.object),
-  viewportId: PropTypes.string.isRequired,
-  dataSource: PropTypes.object,
-  children: PropTypes.node,
-};
-
 function _getReferencedDisplaySetMetadata(referencedDisplaySet, segDisplaySet) {
   const { SharedFunctionalGroupsSequence } = segDisplaySet.instance;
 

extensions/cornerstone-dicom-sr/CHANGELOG.md

@@ -3,6 +3,468 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [3.9.3](https://github.com/OHIF/Viewers/compare/v3.9.2...v3.9.3) (2025-01-21)
+
+
+### Bug Fixes
+
+* OHIF 3.9 Recovery 3 ([#4697](https://github.com/OHIF/Viewers/issues/4697)) ([5d4f2e2](https://github.com/OHIF/Viewers/commit/5d4f2e2a8e62f8de97d56a4e3f17be6018e9f2eb))
+
+
+
+
+
+## [3.9.2](https://github.com/OHIF/Viewers/compare/v3.9.1...v3.9.2) (2024-12-03)
+
+
+### Bug Fixes
+
+* **multiframe:** metadata handling of NM studies and loading order ([#4540](https://github.com/OHIF/Viewers/issues/4540)) ([71f06dc](https://github.com/OHIF/Viewers/commit/71f06dcd3e6d24f1e3d931f7db756c26038927da))
+
+
+
+
+
+## [3.9.1](https://github.com/OHIF/Viewers/compare/v3.9.0...v3.9.1) (2024-11-13)
+
+
+### Bug Fixes
+
+* video playback ([#4497](https://github.com/OHIF/Viewers/issues/4497)) ([610faa5](https://github.com/OHIF/Viewers/commit/610faa5a2738da5eabc40e57e338c359f481e852))
+
+
+
+
+
+# [3.9.0](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.111...v3.9.0) (2024-11-12)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.111](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.110...v3.9.0-beta.111) (2024-11-12)
+
+
+### Bug Fixes
+
+* Measurement Tracking: Various UI and functionality improvements ([#4481](https://github.com/OHIF/Viewers/issues/4481)) ([62b2748](https://github.com/OHIF/Viewers/commit/62b27488471c9d5979142e2d15872a85778b90ed))
+
+
+
+
+
+# [3.9.0-beta.110](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.109...v3.9.0-beta.110) (2024-11-11)
+
+
+### Bug Fixes
+
+* **bugs:** Update dependencies and enhance UI components ([#4478](https://github.com/OHIF/Viewers/issues/4478)) ([05d41c5](https://github.com/OHIF/Viewers/commit/05d41c52068a3b7ba249f15ecdf71838c352fd30))
+
+
+
+
+
+# [3.9.0-beta.109](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.108...v3.9.0-beta.109) (2024-11-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.108](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.107...v3.9.0-beta.108) (2024-11-07)
+
+
+### Bug Fixes
+
+* **tmtv:** fix toggle one up weird behaviours ([#4473](https://github.com/OHIF/Viewers/issues/4473)) ([aa2b649](https://github.com/OHIF/Viewers/commit/aa2b649444eb4fe5422e72ea7830a709c4d24a90))
+
+
+
+
+
+# [3.9.0-beta.107](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.106...v3.9.0-beta.107) (2024-11-06)
+
+
+### Bug Fixes
+
+* build ([#4471](https://github.com/OHIF/Viewers/issues/4471)) ([3d11ef2](https://github.com/OHIF/Viewers/commit/3d11ef28f213361ec7586809317bd219fa70e742))
+
+
+
+
+
+# [3.9.0-beta.106](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.105...v3.9.0-beta.106) (2024-11-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.105](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.104...v3.9.0-beta.105) (2024-11-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.104](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.103...v3.9.0-beta.104) (2024-10-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.103](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.102...v3.9.0-beta.103) (2024-10-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.102](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.101...v3.9.0-beta.102) (2024-10-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.101](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.100...v3.9.0-beta.101) (2024-10-18)
+
+
+### Features
+
+* **new-study-panel:** default to list view for non thumbnail series, change default fitler to all, and add more menu to thumbnail items with a dicom tag browser ([#4417](https://github.com/OHIF/Viewers/issues/4417)) ([a7fd9fa](https://github.com/OHIF/Viewers/commit/a7fd9fa5bfff7a1b533d99cb96f7147a35fd528f))
+
+
+
+
+
+# [3.9.0-beta.100](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.99...v3.9.0-beta.100) (2024-10-17)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.99](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.98...v3.9.0-beta.99) (2024-10-17)
+
+
+### Bug Fixes
+
+* **sr:** load existing point, if there is 2nd point in renderableData (Fix rotation in arrow annotation) ([#4356](https://github.com/OHIF/Viewers/issues/4356)) ([7353f7f](https://github.com/OHIF/Viewers/commit/7353f7f069446f8484278c2cff5b09149cfa23eb))
+
+
+### Features
+
+* **SR:** SCOORD3D point annotations support for stack viewports ([#4315](https://github.com/OHIF/Viewers/issues/4315)) ([ac1cad2](https://github.com/OHIF/Viewers/commit/ac1cad25af12ee0f7d508647e3134ed724d9b4d3))
+
+
+
+
+
+# [3.9.0-beta.98](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.97...v3.9.0-beta.98) (2024-10-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.97](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.96...v3.9.0-beta.97) (2024-10-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.96](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.95...v3.9.0-beta.96) (2024-10-10)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.95](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.94...v3.9.0-beta.95) (2024-10-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.94](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.93...v3.9.0-beta.94) (2024-10-04)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.93](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.92...v3.9.0-beta.93) (2024-10-04)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.92](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.91...v3.9.0-beta.92) (2024-10-01)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.91](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.90...v3.9.0-beta.91) (2024-10-01)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.90](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.89...v3.9.0-beta.90) (2024-09-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.89](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.88...v3.9.0-beta.89) (2024-09-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.88](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.87...v3.9.0-beta.88) (2024-09-24)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.87](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.86...v3.9.0-beta.87) (2024-09-19)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.86](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.85...v3.9.0-beta.86) (2024-09-19)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.85](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.84...v3.9.0-beta.85) (2024-09-17)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.84](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.83...v3.9.0-beta.84) (2024-09-12)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.83](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.82...v3.9.0-beta.83) (2024-09-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.82](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.81...v3.9.0-beta.82) (2024-09-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.81](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.80...v3.9.0-beta.81) (2024-08-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.80](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.79...v3.9.0-beta.80) (2024-08-16)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.79](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.78...v3.9.0-beta.79) (2024-08-16)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.78](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.77...v3.9.0-beta.78) (2024-08-15)
+
+
+### Features
+
+* Add CS3D WSI and Video Viewports and add annotation navigation for MPR ([#4182](https://github.com/OHIF/Viewers/issues/4182)) ([7599ec9](https://github.com/OHIF/Viewers/commit/7599ec9421129dcade94e6fa6ec7908424ab3134))
+
+
+
+
+
+# [3.9.0-beta.77](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.76...v3.9.0-beta.77) (2024-08-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.76](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.75...v3.9.0-beta.76) (2024-08-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.75](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.74...v3.9.0-beta.75) (2024-08-07)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.74](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.73...v3.9.0-beta.74) (2024-08-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.73](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.72...v3.9.0-beta.73) (2024-08-02)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.72](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.71...v3.9.0-beta.72) (2024-07-31)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.71](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.70...v3.9.0-beta.71) (2024-07-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.70](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.69...v3.9.0-beta.70) (2024-07-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.69](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.68...v3.9.0-beta.69) (2024-07-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.68](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.67...v3.9.0-beta.68) (2024-07-26)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.67](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.66...v3.9.0-beta.67) (2024-07-26)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.66](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.65...v3.9.0-beta.66) (2024-07-24)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.65](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.64...v3.9.0-beta.65) (2024-07-23)
+
+
+### Features
+
+* **SR:** text structured report (TEXT, CODE, NUM, PNAME, DATE, TIME and DATETIME) ([#4287](https://github.com/OHIF/Viewers/issues/4287)) ([246ebab](https://github.com/OHIF/Viewers/commit/246ebab6ebf5431a704a1861a5804045b9644ba4))
+
+
+
+
+
+# [3.9.0-beta.64](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.63...v3.9.0-beta.64) (2024-07-19)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
+# [3.9.0-beta.63](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.62...v3.9.0-beta.63) (2024-07-10)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr
+
+
+
+
+
 # [3.9.0-beta.62](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.61...v3.9.0-beta.62) (2024-07-09)
 
 **Note:** Version bump only for package @ohif/extension-cornerstone-dicom-sr

extensions/cornerstone-dicom-sr/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone-dicom-sr",
-  "version": "3.9.0-beta.62",
+  "version": "3.9.3",
   "description": "OHIF extension for an SR Cornerstone Viewport",
   "author": "OHIF",
   "license": "MIT",
@@ -34,10 +34,10 @@
     "test:unit:ci": "jest --ci --runInBand --collectCoverage --passWithNoTests"
   },
   "peerDependencies": {
-    "@ohif/core": "3.9.0-beta.62",
-    "@ohif/extension-cornerstone": "3.9.0-beta.62",
-    "@ohif/extension-measurement-tracking": "3.9.0-beta.62",
-    "@ohif/ui": "3.9.0-beta.62",
+    "@ohif/core": "3.9.3",
+    "@ohif/extension-cornerstone": "3.9.3",
+    "@ohif/extension-measurement-tracking": "3.9.3",
+    "@ohif/ui": "3.9.3",
     "dcmjs": "*",
     "dicom-parser": "^1.8.9",
     "hammerjs": "^2.0.8",
@@ -46,9 +46,9 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/adapters": "^1.82.0",
-    "@cornerstonejs/core": "^1.82.0",
-    "@cornerstonejs/tools": "^1.82.0",
+    "@cornerstonejs/adapters": "^2.2.20",
+    "@cornerstonejs/core": "^2.2.20",
+    "@cornerstonejs/tools": "^2.2.20",
     "classnames": "^2.3.2"
   }
 }

extensions/cornerstone-dicom-sr/src/components/OHIFCornerstoneSRContainer.tsx

@@ -0,0 +1,78 @@
+import PropTypes from 'prop-types';
+import React from 'react';
+import { OHIFCornerstoneSRContentItem } from './OHIFCornerstoneSRContentItem';
+
+export function OHIFCornerstoneSRContainer(props) {
+  const { container, nodeIndexesTree = [0], containerNumberedTree = [1] } = props;
+  const { ContinuityOfContent, ConceptNameCodeSequence } = container;
+  const { CodeMeaning } = ConceptNameCodeSequence ?? {};
+  let childContainerIndex = 1;
+  const contentItems = container.ContentSequence?.map((contentItem, i) => {
+    const { ValueType } = contentItem;
+    const childNodeLevel = [...nodeIndexesTree, i];
+    const key = childNodeLevel.join('.');
+
+    let Component;
+    let componentProps;
+
+    if (ValueType === 'CONTAINER') {
+      const childContainerNumberedTree = [...containerNumberedTree, childContainerIndex++];
+
+      Component = OHIFCornerstoneSRContainer;
+      componentProps = {
+        container: contentItem,
+        nodeIndexesTree: childNodeLevel,
+        containerNumberedTree: childContainerNumberedTree,
+      };
+    } else {
+      Component = OHIFCornerstoneSRContentItem;
+      componentProps = {
+        contentItem,
+        nodeIndexesTree: childNodeLevel,
+        continuityOfContent: ContinuityOfContent,
+      };
+    }
+
+    return (
+      <Component
+        key={key}
+        {...componentProps}
+      />
+    );
+  });
+
+  return (
+    <div>
+      <div className="font-bold">
+        {containerNumberedTree.join('.')}.&nbsp;
+        {CodeMeaning}
+      </div>
+      <div className="ml-4 mb-2">{contentItems}</div>
+    </div>
+  );
+}
+
+OHIFCornerstoneSRContainer.propTypes = {
+  /**
+   * A tree node that may contain another container or one or more content items
+   * (text, code, uidref, pname, etc.)
+   */
+  container: PropTypes.object,
+  /**
+   * A 0-based index list
+   */
+  nodeIndexesTree: PropTypes.arrayOf(PropTypes.number),
+  /**
+   * A 1-based index list that represents a container in a multi-level numbered
+   * list (tree).
+   *
+   * Example:
+   *  1. History
+   *    1.1. Chief Complaint
+   *    1.2. Present Illness
+   *    1.3. Past History
+   *    1.4. Family History
+   *  2. Findings
+   * */
+  containerNumberedTree: PropTypes.arrayOf(PropTypes.number),
+};

extensions/cornerstone-dicom-sr/src/components/OHIFCornerstoneSRContentItem.tsx

@@ -0,0 +1,63 @@
+import PropTypes from 'prop-types';
+import React from 'react';
+import { CodeNameCodeSequenceValues } from '../enums';
+import formatContentItemValue from '../utils/formatContentItem';
+
+const EMPTY_TAG_VALUE = '[empty]';
+
+function OHIFCornerstoneSRContentItem(props) {
+  const { contentItem, nodeIndexesTree, continuityOfContent } = props;
+  const { ConceptNameCodeSequence } = contentItem;
+  const { CodeValue, CodeMeaning } = ConceptNameCodeSequence;
+  const isChildFirstNode = nodeIndexesTree[nodeIndexesTree.length - 1] === 0;
+  const formattedValue = formatContentItemValue(contentItem) ?? EMPTY_TAG_VALUE;
+  const startWithAlphaNumCharRegEx = /^[a-zA-Z0-9]/;
+  const isContinuous = continuityOfContent === 'CONTINUOUS';
+  const isFinding = CodeValue === CodeNameCodeSequenceValues.Finding;
+  const addExtraSpace =
+    isContinuous && !isChildFirstNode && startWithAlphaNumCharRegEx.test(formattedValue?.[0]);
+
+  // Collapse sequences of white space preserving newline characters
+  let className = 'whitespace-pre-line';
+
+  if (CodeValue === CodeNameCodeSequenceValues.Finding) {
+    // Preserve spaces because it is common to see tabular text in a
+    // "Findings" ConceptNameCodeSequence
+    className = 'whitespace-pre-wrap';
+  }
+
+  if (isContinuous) {
+    return (
+      <>
+        <span
+          className={className}
+          title={CodeMeaning}
+        >
+          {addExtraSpace ? ' ' : ''}
+          {formattedValue}
+        </span>
+      </>
+    );
+  }
+
+  return (
+    <>
+      <div className="mb-2">
+        <span className="font-bold">{CodeMeaning}: </span>
+        {isFinding ? (
+          <pre>{formattedValue}</pre>
+        ) : (
+          <span className={className}>{formattedValue}</span>
+        )}
+      </div>
+    </>
+  );
+}
+
+OHIFCornerstoneSRContentItem.propTypes = {
+  contentItem: PropTypes.object,
+  nodeIndexesTree: PropTypes.arrayOf(PropTypes.number),
+  continuityOfContent: PropTypes.string,
+};
+
+export { OHIFCornerstoneSRContentItem };

extensions/cornerstone-dicom-sr/src/components/OHIFCornerstoneSRMeasurementViewport.tsx

@@ -9,17 +9,20 @@ import { Icon, Tooltip, useViewportGrid, ViewportActionArrows } from '@ohif/ui';
 import hydrateStructuredReport from '../utils/hydrateStructuredReport';
 import { useAppConfig } from '@state';
 import createReferencedImageDisplaySet from '../utils/createReferencedImageDisplaySet';
+import { usePositionPresentationStore } from '@ohif/extension-cornerstone';
 
 const MEASUREMENT_TRACKING_EXTENSION_ID = '@ohif/extension-measurement-tracking';
 
 const SR_TOOLGROUP_BASE_NAME = 'SRToolGroup';
 
-function OHIFCornerstoneSRViewport(props: withAppTypes) {
+function OHIFCornerstoneSRMeasurementViewport(props: withAppTypes) {
   const { children, dataSource, displaySets, viewportOptions, servicesManager, extensionManager } =
     props;
 
   const [appConfig] = useAppConfig();
 
+  const { setPositionPresentation } = usePositionPresentationStore();
+
   const {
     displaySetService,
     cornerstoneViewportService,
@@ -63,6 +66,7 @@ function OHIFCornerstoneSRViewport(props: withAppTypes) {
     trackedMeasurements = tracked?.[0];
     sendTrackedMeasurementsEvent = tracked?.[1];
   }
+
   if (!sendTrackedMeasurementsEvent) {
     // if no panels from measurement-tracking extension is used, this code will run
     trackedMeasurements = null;
@@ -72,6 +76,7 @@ function OHIFCornerstoneSRViewport(props: withAppTypes) {
         { servicesManager, extensionManager, appConfig },
         displaySetInstanceUID
       );
+
       const displaySets = displaySetService.getDisplaySetsForSeries(SeriesInstanceUIDs[0]);
       if (displaySets.length) {
         viewportGridService.setDisplaySetsForViewports([
@@ -84,6 +89,11 @@ function OHIFCornerstoneSRViewport(props: withAppTypes) {
     };
   }
 
+  /**
+   * Todo: what is this, not sure what it does regarding the react aspect,
+   * it is updating a local variable? which is not state.
+   */
+  const [isLocked, setIsLocked] = useState(trackedMeasurements?.context?.trackedSeries?.length > 0);
   /**
    * Store the tracking identifiers per viewport in order to be able to
    * show the SR measurements on the referenced image on the correct viewport,
@@ -135,30 +145,21 @@ function OHIFCornerstoneSRViewport(props: withAppTypes) {
         newMeasurementSelected,
         displaySetService
       ).then(({ referencedDisplaySet, referencedDisplaySetMetadata }) => {
+        if (!referencedDisplaySet || !referencedDisplaySetMetadata) {
+          return;
+        }
+
         setMeasurementSelected(newMeasurementSelected);
         setActiveImageDisplaySetData(referencedDisplaySet);
         setReferencedDisplaySetMetadata(referencedDisplaySetMetadata);
 
-        if (
-          referencedDisplaySet.displaySetInstanceUID ===
-          activeImageDisplaySetData?.displaySetInstanceUID
-        ) {
-          const { measurements } = srDisplaySet;
-
-          // it means that we have a new referenced display set, and the
-          // 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 csViewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
-
-          const imageIds = csViewport.getImageIds();
-
-          const imageIdIndex = imageIds.indexOf(measurements[newMeasurementSelected].imageId);
-
-          if (imageIdIndex !== -1) {
-            csViewport.setImageIdIndex(imageIdIndex);
-          }
-        }
+        const { presentationIds } = viewportOptions;
+        const measurement = srDisplaySet.measurements[newMeasurementSelected];
+        setPositionPresentation(presentationIds.positionPresentationId, {
+          viewReference: {
+            referencedImageId: measurement.imageId,
+          },
+        });
       });
     },
     [dataSource, srDisplaySet, activeImageDisplaySetData, viewportId]
@@ -180,10 +181,6 @@ function OHIFCornerstoneSRViewport(props: withAppTypes) {
       return null;
     }
 
-    const initialImageIndex = activeImageDisplaySetData.images.findIndex(
-      image => image.imageId === measurement.imageId
-    );
-
     return (
       <Component
         {...props}
@@ -208,7 +205,6 @@ function OHIFCornerstoneSRViewport(props: withAppTypes) {
           props.onElementEnabled?.(evt);
           onElementEnabled(evt);
         }}
-        initialImageIndex={initialImageIndex}
         isJumpToMeasurementDisabled={true}
       ></Component>
     );
@@ -278,28 +274,23 @@ function OHIFCornerstoneSRViewport(props: withAppTypes) {
    */
   useEffect(() => {
     const updateSR = async () => {
-    if (!srDisplaySet.isLoaded) {
-      await srDisplaySet.load();
-    }
-    if (!element || !srDisplaySet.isLoaded) {
-      return;
-    }
-    setTrackingIdentifiers(measurementSelected);
-    }
+      if (!srDisplaySet.isLoaded) {
+        await srDisplaySet.load();
+      }
+      if (!element || !srDisplaySet.isLoaded) {
+        return;
+      }
+      setTrackingIdentifiers(measurementSelected);
+    };
     updateSR();
   }, [measurementSelected, element, setTrackingIdentifiers, srDisplaySet]);
 
-  /**
-   * Todo: what is this, not sure what it does regarding the react aspect,
-   * it is updating a local variable? which is not state.
-   */
-  const [isLocked, setIsLocked] = useState(trackedMeasurements?.context?.trackedSeries?.length > 0);
   useEffect(() => {
     setIsLocked(trackedMeasurements?.context?.trackedSeries?.length > 0);
   }, [trackedMeasurements]);
 
   useEffect(() => {
-    viewportActionCornersService.setComponents([
+    viewportActionCornersService.addComponents([
       {
         viewportId,
         id: 'viewportStatusComponent',
@@ -367,7 +358,7 @@ function OHIFCornerstoneSRViewport(props: withAppTypes) {
   );
 }
 
-OHIFCornerstoneSRViewport.propTypes = {
+OHIFCornerstoneSRMeasurementViewport.propTypes = {
   displaySets: PropTypes.arrayOf(PropTypes.object),
   viewportId: PropTypes.string.isRequired,
   dataSource: PropTypes.object,
@@ -395,6 +386,10 @@ async function _getViewportReferencedDisplaySetData(
     displaySet.keyImageDisplaySet = createReferencedImageDisplaySet(displaySetService, displaySet);
   }
 
+  if (!displaySetInstanceUID) {
+    return { referencedDisplaySetMetadata: null, referencedDisplaySet: null };
+  }
+
   const referencedDisplaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
 
   const image0 = referencedDisplaySet.images[0];
@@ -508,4 +503,4 @@ function _getStatusComponent({
   );
 }
 
-export default OHIFCornerstoneSRViewport;
+export default OHIFCornerstoneSRMeasurementViewport;

extensions/cornerstone-dicom-sr/src/components/OHIFCornerstoneSRTextViewport.tsx

@@ -0,0 +1,32 @@
+import PropTypes from 'prop-types';
+import React from 'react';
+import { ExtensionManager } from '@ohif/core';
+import { OHIFCornerstoneSRContainer } from './OHIFCornerstoneSRContainer';
+
+function OHIFCornerstoneSRTextViewport(props: withAppTypes) {
+  const { displaySets } = props;
+  const displaySet = displaySets[0];
+  const instance = displaySet.instances[0];
+
+  return (
+    <div className="relative flex h-full w-full flex-col overflow-auto p-4 text-white">
+      <div>
+        {/* The root level is always a container */}
+        <OHIFCornerstoneSRContainer container={instance} />
+      </div>
+    </div>
+  );
+}
+
+OHIFCornerstoneSRTextViewport.propTypes = {
+  displaySets: PropTypes.arrayOf(PropTypes.object),
+  viewportId: PropTypes.string.isRequired,
+  dataSource: PropTypes.object,
+  children: PropTypes.node,
+  viewportLabel: PropTypes.string,
+  viewportOptions: PropTypes.object,
+  servicesManager: PropTypes.object.isRequired,
+  extensionManager: PropTypes.instanceOf(ExtensionManager).isRequired,
+};
+
+export default OHIFCornerstoneSRTextViewport;

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

@@ -0,0 +1,30 @@
+import PropTypes from 'prop-types';
+import React from 'react';
+import { ExtensionManager } from '@ohif/core';
+
+import OHIFCornerstoneSRMeasurementViewport from './OHIFCornerstoneSRMeasurementViewport';
+import OHIFCornerstoneSRTextViewport from './OHIFCornerstoneSRTextViewport';
+
+function OHIFCornerstoneSRViewport(props: withAppTypes) {
+  const { displaySets } = props;
+  const { isImagingMeasurementReport } = displaySets[0];
+
+  if (isImagingMeasurementReport) {
+    return <OHIFCornerstoneSRMeasurementViewport {...props}></OHIFCornerstoneSRMeasurementViewport>;
+  }
+
+  return <OHIFCornerstoneSRTextViewport {...props}></OHIFCornerstoneSRTextViewport>;
+}
+
+OHIFCornerstoneSRViewport.propTypes = {
+  displaySets: PropTypes.arrayOf(PropTypes.object),
+  viewportId: PropTypes.string.isRequired,
+  dataSource: PropTypes.object,
+  children: PropTypes.node,
+  viewportLabel: PropTypes.string,
+  viewportOptions: PropTypes.object,
+  servicesManager: PropTypes.object.isRequired,
+  extensionManager: PropTypes.instanceOf(ExtensionManager).isRequired,
+};
+
+export default OHIFCornerstoneSRViewport;

extensions/cornerstone-dicom-sr/src/constants/scoordTypes.js

@@ -1,7 +0,0 @@
-export default {
-  POINT: 'POINT',
-  MULTIPOINT: 'MULTIPOINT',
-  POLYLINE: 'POLYLINE',
-  CIRCLE: 'CIRCLE',
-  ELLIPSE: 'ELLIPSE',
-};

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

@@ -0,0 +1,44 @@
+import { adaptersSR } from '@cornerstonejs/adapters';
+
+const { CodeScheme: Cornerstone3DCodeScheme } = adaptersSR.Cornerstone3D;
+
+export const SCOORDTypes = {
+  POINT: 'POINT',
+  MULTIPOINT: 'MULTIPOINT',
+  POLYLINE: 'POLYLINE',
+  CIRCLE: 'CIRCLE',
+  ELLIPSE: 'ELLIPSE',
+};
+
+export const CodeNameCodeSequenceValues = {
+  ImagingMeasurementReport: '126000',
+  ImageLibrary: '111028',
+  ImagingMeasurements: '126010',
+  MeasurementGroup: '125007',
+  ImageLibraryGroup: '126200',
+  TrackingUniqueIdentifier: '112040',
+  TrackingIdentifier: '112039',
+  Finding: '121071',
+  FindingSite: 'G-C0E3', // SRT
+  FindingSiteSCT: '363698007', // SCT
+};
+
+export const CodingSchemeDesignators = {
+  SRT: 'SRT',
+  SCT: 'SCT',
+  CornerstoneCodeSchemes: [Cornerstone3DCodeScheme.CodingSchemeDesignator, 'CST4'],
+};
+
+export const RelationshipType = {
+  INFERRED_FROM: 'INFERRED FROM',
+  CONTAINS: 'CONTAINS',
+};
+
+const enums = {
+  CodeNameCodeSequenceValues,
+  CodingSchemeDesignators,
+  RelationshipType,
+  SCOORDTypes,
+};
+
+export default enums;

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

@@ -1,30 +1,37 @@
-import { SOPClassHandlerName, SOPClassHandlerId } from './id';
 import { utils, classes, DisplaySetService, Types } from '@ohif/core';
-import addDICOMSRDisplayAnnotation from './utils/addDICOMSRDisplayAnnotation';
-import isRehydratable from './utils/isRehydratable';
+import { Enums as CSExtensionEnums } from '@ohif/extension-cornerstone';
 import { adaptersSR } from '@cornerstonejs/adapters';
 
+import addSRAnnotation from './utils/addSRAnnotation';
+import isRehydratable from './utils/isRehydratable';
+import {
+  SOPClassHandlerName,
+  SOPClassHandlerId,
+  SOPClassHandlerId3D,
+  SOPClassHandlerName3D,
+} from './id';
+import { CodeNameCodeSequenceValues, CodingSchemeDesignators } from './enums';
+
+const { sopClassDictionary } = utils;
+const { CORNERSTONE_3D_TOOLS_SOURCE_NAME, CORNERSTONE_3D_TOOLS_SOURCE_VERSION } = CSExtensionEnums;
+const { ImageSet, MetadataProvider: metadataProvider } = classes;
+const { CodeScheme: Cornerstone3DCodeScheme } = adaptersSR.Cornerstone3D;
+
 type InstanceMetadata = Types.InstanceMetadata;
 
-const { CodeScheme: Cornerstone3DCodeScheme } = adaptersSR.Cornerstone3D;
-
-const { ImageSet, MetadataProvider: metadataProvider } = classes;
-
-// TODO ->
-// Add SR thumbnail
-// Make viewport
-// Get stacks from referenced displayInstanceUID and load into wrapped CornerStone viewport.
+/**
+ * TODO
+ * - [ ] Add SR thumbnail
+ * - [ ] Make viewport
+ * - [ ] Get stacks from referenced displayInstanceUID and load into wrapped CornerStone viewport
+ */
 
 const sopClassUids = [
-  '1.2.840.10008.5.1.4.1.1.88.11', //BASIC_TEXT_SR:
-  '1.2.840.10008.5.1.4.1.1.88.22', //ENHANCED_SR:
-  '1.2.840.10008.5.1.4.1.1.88.33', //COMPREHENSIVE_SR:
-  '1.2.840.10008.5.1.4.1.1.88.34', //COMPREHENSIVE_3D_SR:
+  sopClassDictionary.BasicTextSR,
+  sopClassDictionary.EnhancedSR,
+  sopClassDictionary.ComprehensiveSR,
 ];
 
-const CORNERSTONE_3D_TOOLS_SOURCE_NAME = 'Cornerstone3DTools';
-const CORNERSTONE_3D_TOOLS_SOURCE_VERSION = '0.1';
-
 const validateSameStudyUID = (uid: string, instances): void => {
   instances.forEach(it => {
     if (it.StudyInstanceUID !== uid) {
@@ -34,31 +41,6 @@ const validateSameStudyUID = (uid: string, instances): void => {
   });
 };
 
-const CodeNameCodeSequenceValues = {
-  ImagingMeasurementReport: '126000',
-  ImageLibrary: '111028',
-  ImagingMeasurements: '126010',
-  MeasurementGroup: '125007',
-  ImageLibraryGroup: '126200',
-  TrackingUniqueIdentifier: '112040',
-  TrackingIdentifier: '112039',
-  Finding: '121071',
-  FindingSite: 'G-C0E3', // SRT
-  CornerstoneFreeText: Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT, //
-};
-
-const CodingSchemeDesignators = {
-  SRT: 'SRT',
-  CornerstoneCodeSchemes: [Cornerstone3DCodeScheme.CodingSchemeDesignator, 'CST4'],
-};
-
-const RELATIONSHIP_TYPE = {
-  INFERRED_FROM: 'INFERRED FROM',
-  CONTAINS: 'CONTAINS',
-};
-
-const CORNERSTONE_FREETEXT_CODE_VALUE = 'CORNERSTONEFREETEXT';
-
 /**
  * Adds instances to the DICOM SR series, rather than creating a new
  * series, so that as SR's are saved, they append to the series, and the
@@ -113,22 +95,12 @@ function _getDisplaySetsFromSeries(
   } = instance;
   validateSameStudyUID(instance.StudyInstanceUID, instances);
 
-  if (
-    !ConceptNameCodeSequence ||
-    ConceptNameCodeSequence.CodeValue !== CodeNameCodeSequenceValues.ImagingMeasurementReport
-  ) {
-    servicesManager.services.uiNotificationService.show({
-      title: 'DICOM SR',
-      message:
-        'OHIF only supports TID1500 Imaging Measurement Report Structured Reports. The SR you’re trying to view is not supported.',
-      type: 'warning',
-      duration: 6000,
-    });
-    return [];
-  }
+  const is3DSR = SOPClassUID === sopClassDictionary.Comprehensive3DSR;
+
+  const isImagingMeasurementReport =
+    ConceptNameCodeSequence?.CodeValue === CodeNameCodeSequenceValues.ImagingMeasurementReport;
 
   const displaySet = {
-    //plugin: id,
     Modality: 'SR',
     displaySetInstanceUID: utils.guid(),
     SeriesDescription,
@@ -137,13 +109,14 @@ function _getDisplaySetsFromSeries(
     SOPInstanceUID,
     SeriesInstanceUID,
     StudyInstanceUID,
-    SOPClassHandlerId,
+    SOPClassHandlerId: is3DSR ? SOPClassHandlerId3D : SOPClassHandlerId,
     SOPClassUID,
     instances,
     referencedImages: null,
     measurements: null,
     isDerivedDisplaySet: true,
     isLoaded: false,
+    isImagingMeasurementReport,
     sopClassUids,
     instance,
     addInstances,
@@ -154,12 +127,21 @@ function _getDisplaySetsFromSeries(
   return [displaySet];
 }
 
-async function _load(displaySet, servicesManager: AppTypes.ServicesManager, extensionManager) {
+/**
+ * Loads the display set with the given services and extension manager.
+ * @param srDisplaySet - The display set to load.
+ * @param servicesManager - The services manager containing displaySetService and measurementService.
+ * @param extensionManager - The extension manager containing data sources.
+ */
+async function _load(
+  srDisplaySet: Types.DisplaySet,
+  servicesManager: AppTypes.ServicesManager,
+  extensionManager: AppTypes.ExtensionManager
+) {
   const { displaySetService, measurementService } = servicesManager.services;
   const dataSources = extensionManager.getDataSources();
   const dataSource = dataSources[0];
-
-  const { ContentSequence } = displaySet.instance;
+  const { ContentSequence } = srDisplaySet.instance;
 
   async function retrieveBulkData(obj, parentObj = null, key = null) {
     for (const prop in obj) {
@@ -170,9 +152,9 @@ async function _load(displaySet, servicesManager: AppTypes.ServicesManager, exte
       } else if (prop === 'BulkDataURI') {
         const value = await dataSource.retrieve.bulkDataURI({
           BulkDataURI: obj[prop],
-          StudyInstanceUID: displaySet.instance.StudyInstanceUID,
-          SeriesInstanceUID: displaySet.instance.SeriesInstanceUID,
-          SOPInstanceUID: displaySet.instance.SOPInstanceUID,
+          StudyInstanceUID: srDisplaySet.instance.StudyInstanceUID,
+          SeriesInstanceUID: srDisplaySet.instance.SeriesInstanceUID,
+          SOPInstanceUID: srDisplaySet.instance.SOPInstanceUID,
         });
         if (parentObj && key) {
           parentObj[key] = new Float32Array(value);
@@ -181,40 +163,47 @@ async function _load(displaySet, servicesManager: AppTypes.ServicesManager, exte
     }
   }
 
-  if (displaySet.isLoaded !== true) {
+  if (srDisplaySet.isLoaded !== true) {
     await retrieveBulkData(ContentSequence);
   }
 
-  displaySet.referencedImages = _getReferencedImagesList(ContentSequence);
-  displaySet.measurements = _getMeasurements(ContentSequence);
+  if (srDisplaySet.isImagingMeasurementReport) {
+    srDisplaySet.referencedImages = _getReferencedImagesList(ContentSequence);
+    srDisplaySet.measurements = _getMeasurements(ContentSequence);
+  } else {
+    srDisplaySet.referencedImages = [];
+    srDisplaySet.measurements = [];
+  }
 
   const mappings = measurementService.getSourceMappings(
     CORNERSTONE_3D_TOOLS_SOURCE_NAME,
     CORNERSTONE_3D_TOOLS_SOURCE_VERSION
   );
 
-  displaySet.isHydrated = false;
-  displaySet.isRehydratable = isRehydratable(displaySet, mappings);
-  displaySet.isLoaded = true;
+  srDisplaySet.isHydrated = false;
+  srDisplaySet.isRehydratable = isRehydratable(srDisplaySet, mappings);
+  srDisplaySet.isLoaded = true;
 
-  // Check currently added displaySets and add measurements if the sources exist.
+  /** Check currently added displaySets and add measurements if the sources exist */
   displaySetService.activeDisplaySets.forEach(activeDisplaySet => {
     _checkIfCanAddMeasurementsToDisplaySet(
-      displaySet,
+      srDisplaySet,
       activeDisplaySet,
       dataSource,
       servicesManager
     );
   });
 
-  // Subscribe to new displaySets as the source may come in after.
+  /** 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.
+    /**
+     * 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,
+        srDisplaySet,
         newDisplaySet,
         dataSource,
         servicesManager
@@ -223,6 +212,14 @@ async function _load(displaySet, servicesManager: AppTypes.ServicesManager, exte
   });
 }
 
+/**
+ * Checks if measurements can be added to a display set.
+ *
+ * @param srDisplaySet - The source display set containing measurements.
+ * @param newDisplaySet - The new display set to check if measurements can be added.
+ * @param dataSource - The data source used to retrieve image IDs.
+ * @param servicesManager - The services manager.
+ */
 function _checkIfCanAddMeasurementsToDisplaySet(
   srDisplaySet,
   newDisplaySet,
@@ -230,108 +227,103 @@ function _checkIfCanAddMeasurementsToDisplaySet(
   servicesManager: AppTypes.ServicesManager
 ) {
   const { customizationService } = servicesManager.services;
-  let unloadedMeasurements = srDisplaySet.measurements.filter(
+
+  const unloadedMeasurements = srDisplaySet.measurements.filter(
     measurement => measurement.loaded === false
   );
 
-  if (unloadedMeasurements.length === 0) {
-    // All already loaded!
+  if (
+    unloadedMeasurements.length === 0 ||
+    !(newDisplaySet instanceof ImageSet) ||
+    newDisplaySet.unsupported
+  ) {
     return;
   }
 
-  if ((!newDisplaySet) instanceof ImageSet) {
-    // This also filters out _this_ displaySet, as it is not an ImageSet.
+  // const { sopClassUids } = newDisplaySet;
+  // Create a Set for faster lookups
+  // const sopClassUidSet = new Set(sopClassUids);
+
+  // Create a Map to efficiently look up ImageIds by SOPInstanceUID and frame number
+  const imageIdMap = new Map<string, string>();
+  const imageIds = dataSource.getImageIdsForDisplaySet(newDisplaySet);
+
+  for (const imageId of imageIds) {
+    const { SOPInstanceUID, frameNumber } = metadataProvider.getUIDsFromImageID(imageId);
+    const key = `${SOPInstanceUID}:${frameNumber || 1}`;
+    imageIdMap.set(key, imageId);
+  }
+
+  if (!unloadedMeasurements?.length) {
     return;
   }
 
-  if (newDisplaySet.unsupported) {
-    return;
-  }
+  const is3DSR = srDisplaySet.SOPClassUID === sopClassDictionary.Comprehensive3DSR;
 
-  const { sopClassUids } = newDisplaySet;
+  for (let j = unloadedMeasurements.length - 1; j >= 0; j--) {
+    let measurement = unloadedMeasurements[j];
 
-  // Check if any have the newDisplaySet is the correct SOPClass.
-  unloadedMeasurements = unloadedMeasurements.filter(measurement =>
-    measurement.coords.some(coord =>
-      sopClassUids.includes(coord.ReferencedSOPSequence.ReferencedSOPClassUID)
-    )
-  );
+    const onBeforeSRAddMeasurement = customizationService.getModeCustomization(
+      'onBeforeSRAddMeasurement'
+    )?.value;
 
-  if (unloadedMeasurements.length === 0) {
-    // New displaySet isn't the correct SOPClass, so can't contain the referenced images.
-    return;
-  }
-
-  const SOPInstanceUIDs = [];
-
-  unloadedMeasurements.forEach(measurement => {
-    const { coords } = measurement;
-
-    coords.forEach(coord => {
-      const SOPInstanceUID = coord.ReferencedSOPSequence.ReferencedSOPInstanceUID;
-
-      if (!SOPInstanceUIDs.includes(SOPInstanceUID)) {
-        SOPInstanceUIDs.push(SOPInstanceUID);
-      }
-    });
-  });
-
-  const imageIdsForDisplaySet = dataSource.getImageIdsForDisplaySet(newDisplaySet);
-
-  for (const imageId of imageIdsForDisplaySet) {
-    if (!unloadedMeasurements.length) {
-      // All measurements loaded.
-      return;
+    if (typeof onBeforeSRAddMeasurement === 'function') {
+      measurement = onBeforeSRAddMeasurement({
+        measurement,
+        StudyInstanceUID: srDisplaySet.StudyInstanceUID,
+        SeriesInstanceUID: srDisplaySet.SeriesInstanceUID,
+      });
     }
 
-    const { SOPInstanceUID, frameNumber } = metadataProvider.getUIDsFromImageID(imageId);
+    // if it is 3d SR we can just add the SR annotation
+    if (is3DSR) {
+      addSRAnnotation(measurement, null, null);
+      measurement.loaded = true;
+      continue;
+    }
 
-    if (SOPInstanceUIDs.includes(SOPInstanceUID)) {
-      for (let j = unloadedMeasurements.length - 1; j >= 0; j--) {
-        let measurement = unloadedMeasurements[j];
+    const referencedSOPSequence = measurement.coords[0].ReferencedSOPSequence;
+    if (!referencedSOPSequence) {
+      continue;
+    }
 
-        const onBeforeSRAddMeasurement = customizationService.getModeCustomization(
-          'onBeforeSRAddMeasurement'
-        )?.value;
+    const { ReferencedSOPInstanceUID } = referencedSOPSequence;
+    const frame = referencedSOPSequence.ReferencedFrameNumber || 1;
+    const key = `${ReferencedSOPInstanceUID}:${frame}`;
+    const imageId = imageIdMap.get(key);
 
-        if (typeof onBeforeSRAddMeasurement === 'function') {
-          measurement = onBeforeSRAddMeasurement({
-            measurement,
-            StudyInstanceUID: srDisplaySet.StudyInstanceUID,
-            SeriesInstanceUID: srDisplaySet.SeriesInstanceUID,
-          });
-        }
+    if (
+      imageId &&
+      _measurementReferencesSOPInstanceUID(measurement, ReferencedSOPInstanceUID, frame)
+    ) {
+      addSRAnnotation(measurement, imageId, frame);
 
-        if (_measurementReferencesSOPInstanceUID(measurement, SOPInstanceUID, frameNumber)) {
-          const frame =
-            (measurement.coords[0].ReferencedSOPSequence &&
-              measurement.coords[0].ReferencedSOPSequence?.ReferencedFrameNumber) ||
-            1;
+      // Update measurement properties
+      measurement.loaded = true;
+      measurement.imageId = imageId;
+      measurement.displaySetInstanceUID = newDisplaySet.displaySetInstanceUID;
+      measurement.ReferencedSOPInstanceUID = ReferencedSOPInstanceUID;
+      measurement.frameNumber = frame;
 
-          /** Add DICOMSRDisplay annotation for the SR viewport (only) */
-          addDICOMSRDisplayAnnotation(measurement, imageId, frame);
-
-          /** Update measurement properties */
-          measurement.loaded = true;
-          measurement.imageId = imageId;
-          measurement.displaySetInstanceUID = newDisplaySet.displaySetInstanceUID;
-          measurement.ReferencedSOPInstanceUID =
-            measurement.coords[0].ReferencedSOPSequence.ReferencedSOPInstanceUID;
-          measurement.frameNumber = frame;
-          delete measurement.coords;
-
-          unloadedMeasurements.splice(j, 1);
-        }
-      }
+      unloadedMeasurements.splice(j, 1);
     }
   }
 }
 
+/**
+ * Checks if a measurement references a specific SOP Instance UID.
+ * @param measurement - The measurement object.
+ * @param SOPInstanceUID - The SOP Instance UID to check against.
+ * @param frameNumber - The frame number to check against (optional).
+ * @returns True if the measurement references the specified SOP Instance UID, false otherwise.
+ */
 function _measurementReferencesSOPInstanceUID(measurement, SOPInstanceUID, frameNumber) {
   const { coords } = measurement;
 
-  // NOTE: The ReferencedFrameNumber can be multiple values according to the DICOM
-  //  Standard. But for now, we will support only one ReferenceFrameNumber.
+  /**
+   * NOTE: The ReferencedFrameNumber can be multiple values according to the DICOM
+   * Standard. But for now, we will support only one ReferenceFrameNumber.
+   */
   const ReferencedFrameNumber =
     (measurement.coords[0].ReferencedSOPSequence &&
       measurement.coords[0].ReferencedSOPSequence?.ReferencedFrameNumber) ||
@@ -344,40 +336,62 @@ function _measurementReferencesSOPInstanceUID(measurement, SOPInstanceUID, frame
   for (let j = 0; j < coords.length; j++) {
     const coord = coords[j];
     const { ReferencedSOPInstanceUID } = coord.ReferencedSOPSequence;
-
     if (ReferencedSOPInstanceUID === SOPInstanceUID) {
       return true;
     }
   }
+
+  return false;
 }
 
+/**
+ * Retrieves the SOP class handler module.
+ *
+ * @param {Object} options - The options for retrieving the SOP class handler module.
+ * @param {Object} options.servicesManager - The services manager.
+ * @param {Object} options.extensionManager - The extension manager.
+ * @returns {Array} An array containing the SOP class handler module.
+ */
 function getSopClassHandlerModule({ servicesManager, extensionManager }) {
   const getDisplaySetsFromSeries = instances => {
     return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
   };
-
   return [
     {
       name: SOPClassHandlerName,
       sopClassUids,
       getDisplaySetsFromSeries,
     },
+    {
+      name: SOPClassHandlerName3D,
+      sopClassUids: [sopClassDictionary.Comprehensive3DSR],
+      getDisplaySetsFromSeries,
+    },
   ];
 }
 
+/**
+ * Retrieves the measurements from the ImagingMeasurementReportContentSequence.
+ *
+ * @param {Array} ImagingMeasurementReportContentSequence - The ImagingMeasurementReportContentSequence array.
+ * @returns {Array} - The array of measurements.
+ */
 function _getMeasurements(ImagingMeasurementReportContentSequence) {
   const ImagingMeasurements = ImagingMeasurementReportContentSequence.find(
     item =>
       item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.ImagingMeasurements
   );
 
+  if (!ImagingMeasurements) {
+    return [];
+  }
+
   const MeasurementGroups = _getSequenceAsArray(ImagingMeasurements.ContentSequence).filter(
     item => item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.MeasurementGroup
   );
 
   const mergedContentSequencesByTrackingUniqueIdentifiers =
     _getMergedContentSequencesByTrackingUniqueIdentifiers(MeasurementGroups);
-
   const measurements = [];
 
   Object.keys(mergedContentSequencesByTrackingUniqueIdentifiers).forEach(
@@ -386,7 +400,6 @@ function _getMeasurements(ImagingMeasurementReportContentSequence) {
         mergedContentSequencesByTrackingUniqueIdentifiers[trackingUniqueIdentifier];
 
       const measurement = _processMeasurement(mergedContentSequence);
-
       if (measurement) {
         measurements.push(measurement);
       }
@@ -396,6 +409,12 @@ function _getMeasurements(ImagingMeasurementReportContentSequence) {
   return measurements;
 }
 
+/**
+ * Retrieves merged content sequences by tracking unique identifiers.
+ *
+ * @param {Array} MeasurementGroups - The measurement groups.
+ * @returns {Object} - The merged content sequences by tracking unique identifiers.
+ */
 function _getMergedContentSequencesByTrackingUniqueIdentifiers(MeasurementGroups) {
   const mergedContentSequencesByTrackingUniqueIdentifiers = {};
 
@@ -407,7 +426,6 @@ function _getMergedContentSequencesByTrackingUniqueIdentifiers(MeasurementGroups
         item.ConceptNameCodeSequence.CodeValue ===
         CodeNameCodeSequenceValues.TrackingUniqueIdentifier
     );
-
     if (!TrackingUniqueIdentifierItem) {
       console.warn('No Tracking Unique Identifier, skipping ambiguous measurement.');
     }
@@ -436,6 +454,15 @@ function _getMergedContentSequencesByTrackingUniqueIdentifiers(MeasurementGroups
   return mergedContentSequencesByTrackingUniqueIdentifiers;
 }
 
+/**
+ * Processes the measurement based on the merged content sequence.
+ * If the merged content sequence contains SCOORD or SCOORD3D value types,
+ * it calls the _processTID1410Measurement function.
+ * Otherwise, it calls the _processNonGeometricallyDefinedMeasurement function.
+ *
+ * @param {Array<Object>} mergedContentSequence - The merged content sequence to process.
+ * @returns {any} - The processed measurement result.
+ */
 function _processMeasurement(mergedContentSequence) {
   if (
     mergedContentSequence.some(
@@ -448,11 +475,21 @@ function _processMeasurement(mergedContentSequence) {
   return _processNonGeometricallyDefinedMeasurement(mergedContentSequence);
 }
 
+/**
+ * Processes TID 1410 style measurements from the mergedContentSequence.
+ * TID 1410 style measurements have a SCOORD or SCOORD3D at the top level,
+ * and non-geometric representations where each NUM has "INFERRED FROM" SCOORD/SCOORD3D.
+ *
+ * @param mergedContentSequence - The merged content sequence containing the measurements.
+ * @returns The measurement object containing the loaded status, labels, coordinates, tracking unique identifier, and tracking identifier.
+ */
 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' || group.ValueType === 'SCOORD3D'
+  );
 
   const UIDREFContentItem = mergedContentSequence.find(group => group.ValueType === 'UIDREF');
 
@@ -479,7 +516,6 @@ function _processTID1410Measurement(mergedContentSequence) {
 
   NUMContentItems.forEach(item => {
     const { ConceptNameCodeSequence, MeasuredValueSequence } = item;
-
     if (MeasuredValueSequence) {
       measurement.labels.push(
         _getLabelFromMeasuredValueSequence(ConceptNameCodeSequence, MeasuredValueSequence)
@@ -487,12 +523,29 @@ function _processTID1410Measurement(mergedContentSequence) {
     }
   });
 
+  const findingSites = mergedContentSequence.filter(
+    item =>
+      item.ConceptNameCodeSequence.CodingSchemeDesignator === CodingSchemeDesignators.SCT &&
+      item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.FindingSiteSCT
+  );
+  if (findingSites.length) {
+    measurement.labels.push({
+      label: CodeNameCodeSequenceValues.FindingSiteSCT,
+      value: findingSites[0].ConceptCodeSequence.CodeMeaning,
+    });
+  }
+
   return measurement;
 }
 
+/**
+ * Processes the non-geometrically defined measurement from the merged content sequence.
+ *
+ * @param mergedContentSequence The merged content sequence containing the measurement data.
+ * @returns The processed measurement object.
+ */
 function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
   const NUMContentItems = mergedContentSequence.filter(group => group.ValueType === 'NUM');
-
   const UIDREFContentItem = mergedContentSequence.find(group => group.ValueType === 'UIDREF');
 
   const TrackingIdentifierContentItem = mergedContentSequence.find(
@@ -522,10 +575,10 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
     CodingSchemeDesignators.CornerstoneCodeSchemes.includes(
       finding.ConceptCodeSequence.CodingSchemeDesignator
     ) &&
-    finding.ConceptCodeSequence.CodeValue === CodeNameCodeSequenceValues.CornerstoneFreeText
+    finding.ConceptCodeSequence.CodeValue === Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT
   ) {
     measurement.labels.push({
-      label: CORNERSTONE_FREETEXT_CODE_VALUE,
+      label: Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT,
       value: finding.ConceptCodeSequence.CodeMeaning,
     });
   }
@@ -537,12 +590,13 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
         CodingSchemeDesignators.CornerstoneCodeSchemes.includes(
           FindingSite.ConceptCodeSequence.CodingSchemeDesignator
         ) &&
-        FindingSite.ConceptCodeSequence.CodeValue === CodeNameCodeSequenceValues.CornerstoneFreeText
+        FindingSite.ConceptCodeSequence.CodeValue ===
+          Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT
     );
 
     if (cornerstoneFreeTextFindingSite) {
       measurement.labels.push({
-        label: CORNERSTONE_FREETEXT_CODE_VALUE,
+        label: Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT,
         value: cornerstoneFreeTextFindingSite.ConceptCodeSequence.CodeMeaning,
       });
     }
@@ -552,15 +606,12 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
     const { ConceptNameCodeSequence, ContentSequence, MeasuredValueSequence } = item;
 
     const { ValueType } = ContentSequence;
-
     if (!ValueType === 'SCOORD') {
       console.warn(`Graphic ${ValueType} not currently supported, skipping annotation.`);
-
       return;
     }
 
     const coords = _getCoordsFromSCOORDOrSCOORD3D(ContentSequence);
-
     if (coords) {
       measurement.coords.push(coords);
     }
@@ -575,59 +626,62 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
   return measurement;
 }
 
-function _getCoordsFromSCOORDOrSCOORD3D(item) {
-  const { ValueType, RelationshipType, GraphicType, GraphicData } = item;
-
-  if (
-    !(
-      RelationshipType == RELATIONSHIP_TYPE.INFERRED_FROM ||
-      RelationshipType == RELATIONSHIP_TYPE.CONTAINS
-    )
-  ) {
-    console.warn(
-      `Relationshiptype === ${RelationshipType}. Cannot deal with NON TID-1400 SCOORD group with RelationshipType !== "INFERRED FROM" or "CONTAINS"`
-    );
-
-    return;
-  }
-
+/**
+ * Extracts coordinates from a graphic item of type SCOORD or SCOORD3D.
+ * @param {object} graphicItem - The graphic item containing the coordinates.
+ * @returns {object} - The extracted coordinates.
+ */
+const _getCoordsFromSCOORDOrSCOORD3D = graphicItem => {
+  const { ValueType, GraphicType, GraphicData } = graphicItem;
   const coords = { ValueType, GraphicType, GraphicData };
-
-  // ContentSequence has length of 1 as RelationshipType === 'INFERRED FROM'
-  if (ValueType === 'SCOORD') {
-    const { ReferencedSOPSequence } = item.ContentSequence;
-
-    coords.ReferencedSOPSequence = ReferencedSOPSequence;
-  } else if (ValueType === 'SCOORD3D') {
-    const { ReferencedFrameOfReferenceSequence } = item.ContentSequence;
-
-    coords.ReferencedFrameOfReferenceSequence = ReferencedFrameOfReferenceSequence;
-  }
-
+  coords.ReferencedSOPSequence = graphicItem.ContentSequence?.ReferencedSOPSequence;
+  coords.ReferencedFrameOfReferenceSequence =
+    graphicItem.ReferencedFrameOfReferenceUID ||
+    graphicItem.ContentSequence?.ReferencedFrameOfReferenceSequence;
   return coords;
-}
+};
 
+/**
+ * Retrieves the label and value from the provided ConceptNameCodeSequence and MeasuredValueSequence.
+ * @param {Object} ConceptNameCodeSequence - The ConceptNameCodeSequence object.
+ * @param {Object} MeasuredValueSequence - The MeasuredValueSequence object.
+ * @returns {Object} - An object containing the label and value.
+ *                    The label represents the CodeMeaning from the ConceptNameCodeSequence.
+ *                    The value represents the formatted NumericValue and CodeValue from the MeasuredValueSequence.
+ *                    Example: { label: 'Long Axis', value: '31.00 mm' }
+ */
 function _getLabelFromMeasuredValueSequence(ConceptNameCodeSequence, MeasuredValueSequence) {
   const { CodeMeaning } = ConceptNameCodeSequence;
   const { NumericValue, MeasurementUnitsCodeSequence } = MeasuredValueSequence;
   const { CodeValue } = MeasurementUnitsCodeSequence;
-
   const formatedNumericValue = NumericValue ? Number(NumericValue).toFixed(2) : '';
-
   return {
     label: CodeMeaning,
     value: `${formatedNumericValue} ${CodeValue}`,
   }; // E.g. Long Axis: 31.0 mm
 }
 
+/**
+ * Retrieves a list of referenced images from the Imaging Measurement Report Content Sequence.
+ *
+ * @param {Array} ImagingMeasurementReportContentSequence - The Imaging Measurement Report Content Sequence.
+ * @returns {Array} - The list of referenced images.
+ */
 function _getReferencedImagesList(ImagingMeasurementReportContentSequence) {
   const ImageLibrary = ImagingMeasurementReportContentSequence.find(
     item => item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.ImageLibrary
   );
 
+  if (!ImageLibrary) {
+    return [];
+  }
+
   const ImageLibraryGroup = _getSequenceAsArray(ImageLibrary.ContentSequence).find(
     item => item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.ImageLibraryGroup
   );
+  if (!ImageLibraryGroup) {
+    return [];
+  }
 
   const referencedImages = [];
 
@@ -651,6 +705,15 @@ function _getReferencedImagesList(ImagingMeasurementReportContentSequence) {
   return referencedImages;
 }
 
+/**
+ * Converts a DICOM sequence to an array.
+ * If the sequence is null or undefined, an empty array is returned.
+ * If the sequence is already an array, it is returned as is.
+ * Otherwise, the sequence is wrapped in an array and returned.
+ *
+ * @param {any} sequence - The DICOM sequence to convert.
+ * @returns {any[]} - The converted array.
+ */
 function _getSequenceAsArray(sequence) {
   if (!sequence) {
     return [];

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

@@ -5,4 +5,7 @@ const id = packageJson.name;
 const SOPClassHandlerName = 'dicom-sr';
 const SOPClassHandlerId = `${id}.sopClassHandlerModule.${SOPClassHandlerName}`;
 
-export { SOPClassHandlerName, SOPClassHandlerId, id };
+const SOPClassHandlerName3D = 'dicom-sr-3d';
+const SOPClassHandlerId3D = `${id}.sopClassHandlerModule.${SOPClassHandlerName3D}`;
+
+export { SOPClassHandlerName, SOPClassHandlerId, SOPClassHandlerName3D, SOPClassHandlerId3D, id };

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

@@ -8,9 +8,10 @@ import { id } from './id.js';
 import toolNames from './tools/toolNames';
 import hydrateStructuredReport from './utils/hydrateStructuredReport';
 import createReferencedImageDisplaySet from './utils/createReferencedImageDisplaySet';
+import Enums from './enums';
 
 const Component = React.lazy(() => {
-  return import(/* webpackPrefetch: true */ './viewports/OHIFCornerstoneSRViewport');
+  return import(/* webpackPrefetch: true */ './components/OHIFCornerstoneSRViewport');
 });
 
 const OHIFCornerstoneSRViewport = props => {
@@ -70,4 +71,4 @@ const dicomSRExtension = {
 export default dicomSRExtension;
 
 // Put static exports here so they can be type checked
-export { hydrateStructuredReport, createReferencedImageDisplaySet, srProtocol };
+export { hydrateStructuredReport, createReferencedImageDisplaySet, srProtocol, Enums, toolNames };

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

@@ -9,16 +9,28 @@ import {
   LengthTool,
   PlanarFreehandROITool,
   RectangleROITool,
+  utilities as csToolsUtils,
 } from '@cornerstonejs/tools';
+import { Types, MeasurementService } from '@ohif/core';
+import { StackViewport, utilities as csUtils } from '@cornerstonejs/core';
+import { Enums as CSExtensionEnums } from '@ohif/extension-cornerstone';
 import DICOMSRDisplayTool from './tools/DICOMSRDisplayTool';
+import SCOORD3DPointTool from './tools/SCOORD3DPointTool';
+import SRSCOOR3DProbeMapper from './utils/SRSCOOR3DProbeMapper';
 import addToolInstance from './utils/addToolInstance';
-import { Types } from '@ohif/core';
 import toolNames from './tools/toolNames';
 
+const { CORNERSTONE_3D_TOOLS_SOURCE_NAME, CORNERSTONE_3D_TOOLS_SOURCE_VERSION } = CSExtensionEnums;
+
 /**
  * @param {object} configuration
  */
-export default function init({ configuration = {} }: Types.Extensions.ExtensionParams): void {
+export default function init({
+  configuration = {},
+  servicesManager,
+}: Types.Extensions.ExtensionParams): void {
+  const { measurementService, cornerstoneViewportService } = servicesManager.services;
+
   addToolInstance(toolNames.DICOMSRDisplay, DICOMSRDisplayTool);
   addToolInstance(toolNames.SRLength, LengthTool);
   addToolInstance(toolNames.SRBidirectional, BidirectionalTool);
@@ -28,10 +40,26 @@ export default function init({ configuration = {} }: Types.Extensions.ExtensionP
   addToolInstance(toolNames.SRAngle, AngleTool);
   addToolInstance(toolNames.SRPlanarFreehandROI, PlanarFreehandROITool);
   addToolInstance(toolNames.SRRectangleROI, RectangleROITool);
+  addToolInstance(toolNames.SRSCOORD3DPoint, SCOORD3DPointTool);
 
   // TODO - fix the SR display of Cobb Angle, as it joins the two lines
   addToolInstance(toolNames.SRCobbAngle, CobbAngleTool);
 
+  const csTools3DVer1MeasurementSource = measurementService.getSource(
+    CORNERSTONE_3D_TOOLS_SOURCE_NAME,
+    CORNERSTONE_3D_TOOLS_SOURCE_VERSION
+  );
+
+  const { POINT } = measurementService.VALUE_TYPES;
+
+  measurementService.addMapping(
+    csTools3DVer1MeasurementSource,
+    'SRSCOORD3DPoint',
+    POINT,
+    SRSCOOR3DProbeMapper.toAnnotation,
+    SRSCOOR3DProbeMapper.toMeasurement
+  );
+
   // Modify annotation tools to use dashed lines on SR
   const dashedLine = {
     lineDash: '4,4',
@@ -49,4 +77,28 @@ export default function init({ configuration = {} }: Types.Extensions.ExtensionP
     SRRectangleROI: dashedLine,
     global: {},
   });
+
+  measurementService.subscribe(
+    MeasurementService.EVENTS.JUMP_TO_MEASUREMENT_LAYOUT,
+    ({ viewportId, measurement, isConsumed }) => {
+      if (isConsumed) {
+        return;
+      }
+      try {
+        const currentViewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
+        const { viewPlaneNormal } = currentViewport.getCamera();
+        const referencedImageId = csToolsUtils.getClosestImageIdForStackViewport(
+          currentViewport as StackViewport,
+          measurement.points[0],
+          viewPlaneNormal
+        );
+        const imageIndex = (currentViewport as StackViewport)
+          .getImageIds()
+          .indexOf(referencedImageId);
+        csUtils.jumpToSlice(currentViewport.element, { imageIndex });
+      } catch (error) {
+        console.warn('Unable to jump to image based on measurement coordinate', error);
+      }
+    }
+  );
 }

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

@@ -1,11 +1,11 @@
-import { SOPClassHandlerId } from './id';
+import { SOPClassHandlerId, SOPClassHandlerId3D } from './id';
 
 export default function onModeEnter({ servicesManager }) {
   const { displaySetService } = servicesManager.services;
   const displaySetCache = displaySetService.getDisplaySetCache();
 
   const srDisplaySets = [...displaySetCache.values()].filter(
-    ds => ds.SOPClassHandlerId === SOPClassHandlerId
+    ds => ds.SOPClassHandlerId === SOPClassHandlerId || ds.SOPClassHandlerId === SOPClassHandlerId3D
   );
 
   srDisplaySets.forEach(ds => {

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

@@ -7,10 +7,11 @@ import {
   Types as cs3DToolsTypes,
 } from '@cornerstonejs/tools';
 import { getTrackingUniqueIdentifiersForElement } from './modules/dicomSRModule';
-import SCOORD_TYPES from '../constants/scoordTypes';
+import { SCOORDTypes } from '../enums';
+import toolNames from './toolNames';
 
 export default class DICOMSRDisplayTool extends AnnotationTool {
-  static toolName = 'DICOMSRDisplay';
+  static toolName = toolNames.DICOMSRDisplay;
 
   constructor(
     toolProps = {},
@@ -112,19 +113,19 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
         let canvasCoordinatesAdapter;
 
         switch (GraphicType) {
-          case SCOORD_TYPES.POINT:
+          case SCOORDTypes.POINT:
             renderMethod = this.renderPoint;
             break;
-          case SCOORD_TYPES.MULTIPOINT:
+          case SCOORDTypes.MULTIPOINT:
             renderMethod = this.renderMultipoint;
             break;
-          case SCOORD_TYPES.POLYLINE:
+          case SCOORDTypes.POLYLINE:
             renderMethod = this.renderPolyLine;
             break;
-          case SCOORD_TYPES.CIRCLE:
+          case SCOORDTypes.CIRCLE:
             renderMethod = this.renderEllipse;
             break;
-          case SCOORD_TYPES.ELLIPSE:
+          case SCOORDTypes.ELLIPSE:
             renderMethod = this.renderEllipse;
             canvasCoordinatesAdapter = utilities.math.ellipse.getCanvasEllipseCorners;
             break;
@@ -229,7 +230,11 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
       // This gives us one point for arrow
       canvasCoordinates.push(viewport.worldToCanvas(point));
 
-      // We get the other point for the arrow by using the image size
+      if (data[1] !== undefined) {
+        canvasCoordinates.push(viewport.worldToCanvas(data[1]));
+      }
+      else{
+         // We get the other point for the arrow by using the image size
       const imagePixelModule = metaData.get('imagePixelModule', referencedImageId);
 
       let xOffset = 10;
@@ -248,6 +253,9 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
       ]);
 
       canvasCoordinates.push(viewport.worldToCanvas(arrowEnd));
+        
+      }
+     
 
       const arrowUID = `${index}`;
 
@@ -335,7 +343,7 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
     }
 
     const { annotationUID, data = {} } = annotation;
-    const { label } = data;
+    const { labels } = data;
     const { color } = options;
 
     let adaptedCanvasCoordinates = canvasCoordinates;
@@ -343,7 +351,7 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
     if (typeof canvasCoordinatesAdapter === 'function') {
       adaptedCanvasCoordinates = canvasCoordinatesAdapter(canvasCoordinates);
     }
-    const textLines = this._getTextBoxLinesFromLabels(label);
+    const textLines = this._getTextBoxLinesFromLabels(labels);
     const canvasTextBoxCoords = utilities.drawing.getTextBoxCoordsCanvas(adaptedCanvasCoordinates);
 
     if (!annotation.data?.handles?.textBox?.worldPosition) {

extensions/cornerstone-dicom-sr/src/tools/SCOORD3DPointTool.ts

@@ -0,0 +1,203 @@
+import { Types, metaData, utilities as csUtils } from '@cornerstonejs/core';
+import {
+  annotation,
+  drawing,
+  utilities,
+  Types as cs3DToolsTypes,
+  AnnotationDisplayTool,
+} from '@cornerstonejs/tools';
+import toolNames from './toolNames';
+import { Annotation } from '@cornerstonejs/tools/dist/types/types';
+
+export default class SCOORD3DPointTool extends AnnotationDisplayTool {
+  static toolName = toolNames.SRSCOORD3DPoint;
+
+  constructor(
+    toolProps = {},
+    defaultToolProps = {
+      configuration: {},
+    }
+  ) {
+    super(toolProps, defaultToolProps);
+  }
+
+  _getTextBoxLinesFromLabels(labels) {
+    // TODO -> max 5 for now (label + shortAxis + longAxis), need a generic solution for this!
+
+    const labelLength = Math.min(labels.length, 5);
+    const lines = [];
+
+    return lines;
+  }
+
+  // This tool should not inherit from AnnotationTool and we should not need
+  // to add the following lines.
+  isPointNearTool = () => null;
+  getHandleNearImagePoint = () => null;
+
+  renderAnnotation = (enabledElement: Types.IEnabledElement, svgDrawingHelper: any): void => {
+    const { viewport } = enabledElement;
+    const { element } = viewport;
+
+    const annotations = annotation.state.getAnnotations(this.getToolName(), element);
+
+    // Todo: We don't need this anymore, filtering happens in triggerAnnotationRender
+    if (!annotations?.length) {
+      return;
+    }
+
+    // Filter toolData to only render the data for the active SR.
+    const filteredAnnotations = annotations;
+    if (!viewport._actors?.size) {
+      return;
+    }
+
+    const styleSpecifier: cs3DToolsTypes.AnnotationStyle.StyleSpecifier = {
+      toolGroupId: this.toolGroupId,
+      toolName: this.getToolName(),
+      viewportId: enabledElement.viewport.id,
+    };
+
+    for (let i = 0; i < filteredAnnotations.length; i++) {
+      const annotation = filteredAnnotations[i];
+
+      const annotationUID = annotation.annotationUID;
+      const { renderableData } = annotation.data;
+      const { POINT: points } = renderableData;
+
+      styleSpecifier.annotationUID = annotationUID;
+
+      const lineWidth = this.getStyle('lineWidth', styleSpecifier, annotation);
+      const lineDash = this.getStyle('lineDash', styleSpecifier, annotation);
+      const color = this.getStyle('color', styleSpecifier, annotation);
+
+      const options = {
+        color,
+        lineDash,
+        lineWidth,
+      };
+
+      const point = points[0][0];
+
+      // check if viewport can render it
+      const viewable = viewport.isReferenceViewable(
+        { FrameOfReferenceUID: annotation.metadata.FrameOfReferenceUID, cameraFocalPoint: point },
+        { asNearbyProjection: true }
+      );
+
+      if (!viewable) {
+        continue;
+      }
+
+      // render the point
+      const arrowPointCanvas = viewport.worldToCanvas(point);
+      // Todo: configure this
+      const arrowEndCanvas = [arrowPointCanvas[0] + 20, arrowPointCanvas[1] + 20];
+      const canvasCoordinates = [arrowPointCanvas, arrowEndCanvas];
+
+      drawing.drawArrow(
+        svgDrawingHelper,
+        annotationUID,
+        '1',
+        canvasCoordinates[1],
+        canvasCoordinates[0],
+        {
+          color: options.color,
+          width: options.lineWidth,
+        }
+      );
+
+      this.renderTextBox(
+        svgDrawingHelper,
+        viewport,
+        canvasCoordinates,
+        annotation,
+        styleSpecifier,
+        options
+      );
+    }
+  };
+
+  renderTextBox(
+    svgDrawingHelper,
+    viewport,
+    canvasCoordinates,
+    annotation,
+    styleSpecifier,
+    options = {}
+  ) {
+    if (!canvasCoordinates || !annotation) {
+      return;
+    }
+
+    const { annotationUID, data = {} } = annotation;
+    const { labels } = data;
+
+    const textLines = [];
+
+    for (const label of labels) {
+      // make this generic
+      // fix this
+      if (label.label === '363698007') {
+        textLines.push(`Finding Site: ${label.value}`);
+      }
+    }
+
+    const { color } = options;
+
+    const adaptedCanvasCoordinates = canvasCoordinates;
+    // adapt coordinates if there is an adapter
+    const canvasTextBoxCoords = utilities.drawing.getTextBoxCoordsCanvas(adaptedCanvasCoordinates);
+
+    if (!annotation.data?.handles?.textBox?.worldPosition) {
+      annotation.data.handles.textBox.worldPosition = viewport.canvasToWorld(canvasTextBoxCoords);
+    }
+
+    const textBoxPosition = viewport.worldToCanvas(annotation.data.handles.textBox.worldPosition);
+
+    const textBoxUID = '1';
+    const textBoxOptions = this.getLinkedTextBoxStyle(styleSpecifier, annotation);
+
+    const boundingBox = drawing.drawLinkedTextBox(
+      svgDrawingHelper,
+      annotationUID,
+      textBoxUID,
+      textLines,
+      textBoxPosition,
+      canvasCoordinates,
+      {},
+      {
+        ...textBoxOptions,
+        color,
+      }
+    );
+
+    const { x: left, y: top, width, height } = boundingBox;
+
+    annotation.data.handles.textBox.worldBoundingBox = {
+      topLeft: viewport.canvasToWorld([left, top]),
+      topRight: viewport.canvasToWorld([left + width, top]),
+      bottomLeft: viewport.canvasToWorld([left, top + height]),
+      bottomRight: viewport.canvasToWorld([left + width, top + height]),
+    };
+  }
+
+  public getLinkedTextBoxStyle(
+    specifications: cs3DToolsTypes.AnnotationStyle.StyleSpecifier,
+    annotation?: Annotation
+  ): Record<string, unknown> {
+    // Todo: this function can be used to set different styles for different toolMode
+    // for the textBox.
+
+    return {
+      visibility: this.getStyle('textBoxVisibility', specifications, annotation),
+      fontFamily: this.getStyle('textBoxFontFamily', specifications, annotation),
+      fontSize: this.getStyle('textBoxFontSize', specifications, annotation),
+      color: this.getStyle('textBoxColor', specifications, annotation),
+      shadow: this.getStyle('textBoxShadow', specifications, annotation),
+      background: this.getStyle('textBoxBackground', specifications, annotation),
+      lineWidth: this.getStyle('textBoxLinkLineWidth', specifications, annotation),
+      lineDash: this.getStyle('textBoxLinkLineDash', specifications, annotation),
+    };
+  }
+}

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

@@ -1,7 +1,5 @@
-import DICOMSRDisplayTool from './DICOMSRDisplayTool';
-
 const toolNames = {
-  DICOMSRDisplay: DICOMSRDisplayTool.toolName,
+  DICOMSRDisplay: 'DICOMSRDisplay',
   SRLength: 'SRLength',
   SRBidirectional: 'SRBidirectional',
   SREllipticalROI: 'SREllipticalROI',
@@ -11,6 +9,7 @@ const toolNames = {
   SRCobbAngle: 'SRCobbAngle',
   SRRectangleROI: 'SRRectangleROI',
   SRPlanarFreehandROI: 'SRPlanarFreehandROI',
+  SRSCOORD3DPoint: 'SRSCOORD3DPoint',
 };
 
 export default toolNames;

extensions/cornerstone-dicom-sr/src/utils/SRSCOOR3DProbeMapper.ts

@@ -0,0 +1,62 @@
+const SRSCOOR3DProbe = {
+  toAnnotation: measurement => {},
+
+  /**
+   * Maps cornerstone annotation event data to measurement service format.
+   *
+   * @param {Object} cornerstone Cornerstone event data
+   * @return {Measurement} Measurement instance
+   */
+  toMeasurement: (
+    csToolsEventDetail,
+    displaySetService,
+    CornerstoneViewportService,
+    getValueTypeFromToolType,
+    customizationService
+  ) => {
+    const { annotation } = csToolsEventDetail;
+    const { metadata, data, annotationUID } = annotation;
+
+    if (!metadata || !data) {
+      console.warn('Probe tool: Missing metadata or data');
+      return null;
+    }
+
+    const { toolName } = metadata;
+    const { points } = data.handles;
+
+    const displayText = getDisplayText(annotation);
+    return {
+      uid: annotationUID,
+      points,
+      metadata,
+      toolName: metadata.toolName,
+      label: data.label,
+      displayText: displayText,
+      data: data.cachedStats,
+      type: getValueTypeFromToolType?.(toolName) ?? null,
+    };
+  },
+};
+
+function getDisplayText(annotation) {
+  const { data } = annotation;
+
+  if (!data) {
+    return [''];
+  }
+  const { labels } = data;
+
+  const displayText = [];
+
+  for (const label of labels) {
+    // make this generic
+    if (label.label === '33636980076') {
+      displayText.push(`Finding Site: ${label.value}`);
+    }
+  }
+
+  return displayText;
+}
+
+export default SRSCOOR3DProbe;

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

@@ -0,0 +1,67 @@
+import { Types, annotation } from '@cornerstonejs/tools';
+import { metaData } from '@cornerstonejs/core';
+
+import getRenderableData from './getRenderableData';
+import toolNames from '../tools/toolNames';
+
+export default function addSRAnnotation(measurement, imageId, frameNumber) {
+  let toolName = toolNames.DICOMSRDisplay;
+  const renderableData = measurement.coords.reduce((acc, coordProps) => {
+    acc[coordProps.GraphicType] = acc[coordProps.GraphicType] || [];
+    acc[coordProps.GraphicType].push(getRenderableData({ ...coordProps, imageId }));
+    return acc;
+  }, {});
+
+  const { TrackingUniqueIdentifier } = measurement;
+  const { ValueType: valueType, GraphicType: graphicType } = measurement.coords[0];
+  const graphicTypePoints = renderableData[graphicType];
+
+  /** TODO: Read the tool name from the DICOM SR identification type in the future. */
+  let frameOfReferenceUID = null;
+
+  if (imageId) {
+    const imagePlaneModule = metaData.get('imagePlaneModule', imageId);
+    frameOfReferenceUID = imagePlaneModule?.frameOfReferenceUID;
+  }
+
+  if (valueType === 'SCOORD3D') {
+    toolName = toolNames.SRSCOORD3DPoint;
+
+    // get the ReferencedFrameOfReferenceUID from the measurement
+    frameOfReferenceUID = measurement.coords[0].ReferencedFrameOfReferenceSequence;
+  }
+
+  const SRAnnotation: Types.Annotation = {
+    annotationUID: TrackingUniqueIdentifier,
+    highlighted: false,
+    isLocked: false,
+    invalidated: false,
+    metadata: {
+      toolName,
+      valueType,
+      graphicType,
+      FrameOfReferenceUID: frameOfReferenceUID,
+      referencedImageId: imageId,
+    },
+    data: {
+      label: measurement.labels?.[0]?.value || undefined,
+      displayText: measurement.displayText || undefined,
+      handles: {
+        textBox: measurement.textBox ?? {},
+        points: graphicTypePoints[0],
+      },
+      cachedStats: {},
+      frameNumber,
+      renderableData,
+      TrackingUniqueIdentifier,
+      labels: measurement.labels,
+    },
+  };
+
+  /**
+   * const annotationManager = annotation.annotationState.getAnnotationManager();
+   * was not triggering annotation_added events.
+   */
+  annotation.state.addAnnotation(SRAnnotation);
+  console.debug('Adding SR annotation:', SRAnnotation);
+}

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

@@ -1,8 +1,14 @@
 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;
+    constructor(toolProps, defaultToolProps) {
+      toolProps.configuration = toolProps.configuration
+        ? { ...toolProps.configuration, ...configuration }
+        : configuration;
+      super(toolProps, defaultToolProps);
+    }
   }
   addTool(InstanceClass);
 }

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

@@ -61,6 +61,11 @@ const createReferencedImageDisplaySet = (displaySetService, displaySet) => {
 
   const imageSet = new ImageSet(instances);
   const instance = instances[0];
+
+  if (!instance) {
+    return;
+  }
+
   imageSet.setAttributes({
     displaySetInstanceUID: imageSet.uid, // create a local alias for the imageSet UID
     SeriesDate: instance.SeriesDate,

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

@@ -0,0 +1,67 @@
+import { utils } from '@ohif/core';
+
+/**
+ * Formatters used to format each of the content items (SR "nodes") which can be
+ * text, code, UID ref, number, person name, date, time and date time. Each
+ * formatter must be a function with the following signature:
+ *
+ *    [VALUE_TYPE]: (contentItem) => string
+ *
+ */
+const contentItemFormatters = {
+  TEXT: contentItem => contentItem.TextValue,
+  CODE: contentItem => contentItem.ConceptCodeSequence?.[0]?.CodeMeaning,
+  UIDREF: contentItem => contentItem.UID,
+  NUM: contentItem => {
+    const measuredValue = contentItem.MeasuredValueSequence?.[0];
+
+    if (!measuredValue) {
+      return;
+    }
+
+    const { NumericValue, MeasurementUnitsCodeSequence } = measuredValue;
+    const { CodeValue } = MeasurementUnitsCodeSequence;
+
+    return `${NumericValue} ${CodeValue}`;
+  },
+  PNAME: contentItem => {
+    const personName = contentItem.PersonName?.[0];
+    return personName ? utils.formatPN(personName) : undefined;
+  },
+  DATE: contentItem => {
+    const { Date } = contentItem;
+    return Date ? utils.formatDate(Date) : undefined;
+  },
+  TIME: contentItem => {
+    const { Time } = contentItem;
+    return Time ? utils.formatTime(Time) : undefined;
+  },
+  DATETIME: contentItem => {
+    const { DateTime } = contentItem;
+
+    if (typeof DateTime !== 'string') {
+      return;
+    }
+
+    // 14 characters because it should be something like 20180614113714
+    if (DateTime.length < 14) {
+      return DateTime;
+    }
+
+    const dicomDate = DateTime.substring(0, 8);
+    const dicomTime = DateTime.substring(8, 14);
+    const formattedDate = utils.formatDate(dicomDate);
+    const formattedTime = utils.formatTime(dicomTime);
+
+    return `${formattedDate} ${formattedTime}`;
+  },
+};
+
+function formatContentItemValue(contentItem) {
+  const { ValueType } = contentItem;
+  const fnFormat = contentItemFormatters[ValueType];
+
+  return fnFormat ? fnFormat(contentItem) : `[${ValueType} is not supported]`;
+}
+
+export { formatContentItemValue as default, formatContentItemValue };

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

@@ -1,3 +1,7 @@
+import { adaptersSR } from '@cornerstonejs/adapters';
+
+const { CodeScheme: Cornerstone3DCodeScheme } = adaptersSR.Cornerstone3D;
+
 /**
  * Extracts the label from the toolData imported from dcmjs. We need to do this
  * as dcmjs does not depeend on OHIF/the measurementService, it just produces data for cornestoneTools.
@@ -9,13 +13,15 @@
 export default function getLabelFromDCMJSImportedToolData(toolData) {
   const { findingSites = [], finding } = toolData;
 
-  let freeTextLabel = findingSites.find(fs => fs.CodeValue === 'CORNERSTONEFREETEXT');
+  let freeTextLabel = findingSites.find(
+    fs => fs.CodeValue === Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT
+  );
 
   if (freeTextLabel) {
     return freeTextLabel.CodeMeaning;
   }
 
-  if (finding && finding.CodeValue === 'CORNERSTONEFREETEXT') {
+  if (finding && finding.CodeValue === Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT) {
     return finding.CodeMeaning;
   }
 }

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

@@ -1,106 +1,49 @@
 import { vec3 } from 'gl-matrix';
-import { Types, annotation } from '@cornerstonejs/tools';
 import { metaData, utilities, Types as csTypes } from '@cornerstonejs/core';
 
-import toolNames from '../tools/toolNames';
-import SCOORD_TYPES from '../constants/scoordTypes';
+import { SCOORDTypes } from '../enums';
 
 const EPSILON = 1e-4;
 
-export default function addDICOMSRDisplayAnnotation(measurement, imageId, frameNumber) {
-  const toolName = toolNames.DICOMSRDisplay;
-
-  const measurementData = {
-    TrackingUniqueIdentifier: measurement.TrackingUniqueIdentifier,
-    renderableData: {},
-    labels: measurement.labels,
-    imageId,
-  };
-
-  measurement.coords.forEach(coord => {
-    const { GraphicType, GraphicData } = coord;
-
-    if (measurementData.renderableData[GraphicType] === undefined) {
-      measurementData.renderableData[GraphicType] = [];
+const getRenderableCoords = ({ GraphicData, ValueType, imageId }) => {
+  const renderableData = [];
+  if (ValueType === 'SCOORD3D') {
+    for (let i = 0; i < GraphicData.length; i += 3) {
+      renderableData.push([GraphicData[i], GraphicData[i + 1], GraphicData[i + 2]]);
     }
+  } else {
+    for (let i = 0; i < GraphicData.length; i += 2) {
+      const worldPos = utilities.imageToWorldCoords(imageId, [GraphicData[i], GraphicData[i + 1]]);
+      renderableData.push(worldPos);
+    }
+  }
+  return renderableData;
+};
 
-    measurementData.renderableData[GraphicType].push(
-      _getRenderableData(GraphicType, GraphicData, imageId)
-    );
-  });
-
-  const imagePlaneModule = metaData.get('imagePlaneModule', imageId);
-
-  /**
-   * This annotation (DICOMSRDisplay) is only used by the SR viewport.
-   * This is used before the annotation is hydrated. If hydrated the measurement will be added
-   * to the measurement service and will be available for the other viewports.
-   */
-  const SRAnnotation: Types.Annotation = {
-    annotationUID: measurement.TrackingUniqueIdentifier,
-    highlighted: false,
-    isLocked: false,
-    invalidated: false,
-    metadata: {
-      toolName: toolName,
-      FrameOfReferenceUID: imagePlaneModule.frameOfReferenceUID,
-      referencedImageId: imageId,
-    },
-    data: {
-      label: measurement.labels,
-      handles: {
-        textBox: measurement.textBox ?? {},
-      },
-      cachedStats: {},
-      TrackingUniqueIdentifier: measurementData.TrackingUniqueIdentifier,
-      renderableData: measurementData.renderableData,
-      frameNumber,
-    },
-  };
-  const annotationManager = annotation.state.getAnnotationManager();
-  annotationManager.addAnnotation(SRAnnotation);
-}
-
-function _getRenderableData(GraphicType, GraphicData, imageId) {
-  let renderableData: csTypes.Point3[];
+function getRenderableData({ GraphicType, GraphicData, ValueType, imageId }) {
+  let renderableData = [];
 
   switch (GraphicType) {
-    case SCOORD_TYPES.POINT:
-    case SCOORD_TYPES.MULTIPOINT:
-    case SCOORD_TYPES.POLYLINE:
-      renderableData = [];
-
-      for (let i = 0; i < GraphicData.length; i += 2) {
-        const worldPos = utilities.imageToWorldCoords(imageId, [
-          GraphicData[i],
-          GraphicData[i + 1],
-        ]);
-
-        renderableData.push(worldPos);
-      }
-
+    case SCOORDTypes.POINT:
+    case SCOORDTypes.MULTIPOINT:
+    case SCOORDTypes.POLYLINE: {
+      renderableData = getRenderableCoords({ GraphicData, ValueType, imageId });
       break;
-    case SCOORD_TYPES.CIRCLE: {
-      const pointsWorld = [];
-      for (let i = 0; i < GraphicData.length; i += 2) {
-        const worldPos = utilities.imageToWorldCoords(imageId, [
-          GraphicData[i],
-          GraphicData[i + 1],
-        ]);
-
-        pointsWorld.push(worldPos);
-      }
-
+    }
+    case SCOORDTypes.CIRCLE: {
+      const pointsWorld: csTypes.Point3[] = getRenderableCoords({
+        GraphicData,
+        ValueType,
+        imageId,
+      });
       // We do not have an explicit draw circle svg helper in Cornerstone3D at
       // this time, but we can use the ellipse svg helper to draw a circle, so
       // here we reshape the data for that purpose.
       const center = pointsWorld[0];
       const onPerimeter = pointsWorld[1];
-
       const radius = vec3.distance(center, onPerimeter);
 
       const imagePlaneModule = metaData.get('imagePlaneModule', imageId);
-
       if (!imagePlaneModule) {
         throw new Error('No imagePlaneModule found');
       }
@@ -115,14 +58,12 @@ function _getRenderableData(GraphicType, GraphicData, imageId) {
 
       // we need to get major/minor axis (which are both the same size major = minor)
 
-      // first axisStart
       const firstAxisStart = vec3.create();
       vec3.scaleAndAdd(firstAxisStart, center, columnCosines, radius);
 
       const firstAxisEnd = vec3.create();
       vec3.scaleAndAdd(firstAxisEnd, center, columnCosines, -radius);
 
-      // second axisStart
       const secondAxisStart = vec3.create();
       vec3.scaleAndAdd(secondAxisStart, center, rowCosines, radius);
 
@@ -138,21 +79,16 @@ function _getRenderableData(GraphicType, GraphicData, imageId) {
 
       break;
     }
-    case SCOORD_TYPES.ELLIPSE: {
+    case SCOORDTypes.ELLIPSE: {
       // GraphicData is ordered as [majorAxisStartX, majorAxisStartY, majorAxisEndX, majorAxisEndY, minorAxisStartX, minorAxisStartY, minorAxisEndX, minorAxisEndY]
       // But Cornerstone3D points are ordered as top, bottom, left, right for the
       // ellipse so we need to identify if the majorAxis is horizontal or vertical
       // and then choose the correct points to use for the ellipse.
-
-      const pointsWorld: csTypes.Point3[] = [];
-      for (let i = 0; i < GraphicData.length; i += 2) {
-        const worldPos = utilities.imageToWorldCoords(imageId, [
-          GraphicData[i],
-          GraphicData[i + 1],
-        ]);
-
-        pointsWorld.push(worldPos);
-      }
+      const pointsWorld: csTypes.Point3[] = getRenderableCoords({
+        GraphicData,
+        ValueType,
+        imageId,
+      });
 
       const majorAxisStart = vec3.fromValues(...pointsWorld[0]);
       const majorAxisEnd = vec3.fromValues(...pointsWorld[1]);
@@ -202,3 +138,5 @@ function _getRenderableData(GraphicType, GraphicData, imageId) {
 
   return renderableData;
 }
+
+export default getRenderableData;

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

@@ -3,14 +3,12 @@ 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;
+import { Enums as CSExtensionEnums } from '@ohif/extension-cornerstone';
 
+const { locking } = CsAnnotation;
 const { guid } = OHIF.utils;
 const { MeasurementReport, CORNERSTONE_3D_TAG } = adaptersSR.Cornerstone3D;
-
-const CORNERSTONE_3D_TOOLS_SOURCE_NAME = 'Cornerstone3DTools';
-const CORNERSTONE_3D_TOOLS_SOURCE_VERSION = '0.1';
-
+const { CORNERSTONE_3D_TOOLS_SOURCE_NAME, CORNERSTONE_3D_TOOLS_SOURCE_VERSION } = CSExtensionEnums;
 const supportedLegacyCornerstoneTags = ['cornerstoneTools@^4.0.0'];
 
 const convertCode = (codingValues, code) => {
@@ -47,11 +45,19 @@ export default function hydrateStructuredReport(
   displaySetInstanceUID
 ) {
   const annotationManager = CsAnnotation.state.getAnnotationManager();
-  const disableEditing = appConfig?.disableEditing;
   const dataSource = extensionManager.getActiveDataSource()[0];
   const { measurementService, displaySetService, customizationService } = servicesManager.services;
 
   const codingValues = customizationService.getCustomization('codingValues', {});
+
+  const { disableEditing } = customizationService.getCustomization(
+    'PanelMeasurement.disableEditing',
+    {
+      id: 'default.disableEditing',
+      disableEditing: false,
+    }
+  );
+
   const displaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
 
   // TODO -> We should define a strict versioning somewhere.

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

@@ -4,7 +4,7 @@ const cornerstoneAdapters =
   adaptersSR.Cornerstone3D.MeasurementReport.CORNERSTONE_TOOL_CLASSES_BY_UTILITY_TYPE;
 
 const supportedLegacyCornerstoneTags = ['cornerstoneTools@^4.0.0'];
-const CORNERSTONE_3D_TAG = cornerstoneAdapters.CORNERSTONE_3D_TAG;
+const CORNERSTONE_3D_TAG = adaptersSR.Cornerstone3D.CORNERSTONE_3D_TAG;
 
 /**
  * Checks if the given `displaySet`can be rehydrated into the `measurementService`.

extensions/cornerstone-dynamic-volume/CHANGELOG.md

@@ -3,6 +3,463 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [3.9.3](https://github.com/OHIF/Viewers/compare/v3.9.2...v3.9.3) (2025-01-21)
+
+
+### Bug Fixes
+
+* OHIF 3.9 Recovery 3 ([#4697](https://github.com/OHIF/Viewers/issues/4697)) ([5d4f2e2](https://github.com/OHIF/Viewers/commit/5d4f2e2a8e62f8de97d56a4e3f17be6018e9f2eb))
+
+
+
+
+
+## [3.9.2](https://github.com/OHIF/Viewers/compare/v3.9.1...v3.9.2) (2024-12-03)
+
+
+### Bug Fixes
+
+* **multiframe:** metadata handling of NM studies and loading order ([#4540](https://github.com/OHIF/Viewers/issues/4540)) ([71f06dc](https://github.com/OHIF/Viewers/commit/71f06dcd3e6d24f1e3d931f7db756c26038927da))
+
+
+
+
+
+## [3.9.1](https://github.com/OHIF/Viewers/compare/v3.9.0...v3.9.1) (2024-11-13)
+
+
+### Bug Fixes
+
+* video playback ([#4497](https://github.com/OHIF/Viewers/issues/4497)) ([610faa5](https://github.com/OHIF/Viewers/commit/610faa5a2738da5eabc40e57e338c359f481e852))
+
+
+
+
+
+# [3.9.0](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.111...v3.9.0) (2024-11-12)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.111](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.110...v3.9.0-beta.111) (2024-11-12)
+
+
+### Bug Fixes
+
+* Measurement Tracking: Various UI and functionality improvements ([#4481](https://github.com/OHIF/Viewers/issues/4481)) ([62b2748](https://github.com/OHIF/Viewers/commit/62b27488471c9d5979142e2d15872a85778b90ed))
+
+
+
+
+
+# [3.9.0-beta.110](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.109...v3.9.0-beta.110) (2024-11-11)
+
+
+### Bug Fixes
+
+* **bugs:** Update dependencies and enhance UI components ([#4478](https://github.com/OHIF/Viewers/issues/4478)) ([05d41c5](https://github.com/OHIF/Viewers/commit/05d41c52068a3b7ba249f15ecdf71838c352fd30))
+
+
+
+
+
+# [3.9.0-beta.109](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.108...v3.9.0-beta.109) (2024-11-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.108](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.107...v3.9.0-beta.108) (2024-11-07)
+
+
+### Bug Fixes
+
+* **tmtv:** fix toggle one up weird behaviours ([#4473](https://github.com/OHIF/Viewers/issues/4473)) ([aa2b649](https://github.com/OHIF/Viewers/commit/aa2b649444eb4fe5422e72ea7830a709c4d24a90))
+
+
+
+
+
+# [3.9.0-beta.107](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.106...v3.9.0-beta.107) (2024-11-06)
+
+
+### Bug Fixes
+
+* build ([#4471](https://github.com/OHIF/Viewers/issues/4471)) ([3d11ef2](https://github.com/OHIF/Viewers/commit/3d11ef28f213361ec7586809317bd219fa70e742))
+
+
+
+
+
+# [3.9.0-beta.106](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.105...v3.9.0-beta.106) (2024-11-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.105](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.104...v3.9.0-beta.105) (2024-11-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.104](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.103...v3.9.0-beta.104) (2024-10-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.103](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.102...v3.9.0-beta.103) (2024-10-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.102](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.101...v3.9.0-beta.102) (2024-10-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.101](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.100...v3.9.0-beta.101) (2024-10-18)
+
+
+### Features
+
+* **new-study-panel:** default to list view for non thumbnail series, change default fitler to all, and add more menu to thumbnail items with a dicom tag browser ([#4417](https://github.com/OHIF/Viewers/issues/4417)) ([a7fd9fa](https://github.com/OHIF/Viewers/commit/a7fd9fa5bfff7a1b533d99cb96f7147a35fd528f))
+
+
+
+
+
+# [3.9.0-beta.100](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.99...v3.9.0-beta.100) (2024-10-17)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.99](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.98...v3.9.0-beta.99) (2024-10-17)
+
+
+### Features
+
+* **SR:** SCOORD3D point annotations support for stack viewports ([#4315](https://github.com/OHIF/Viewers/issues/4315)) ([ac1cad2](https://github.com/OHIF/Viewers/commit/ac1cad25af12ee0f7d508647e3134ed724d9b4d3))
+
+
+
+
+
+# [3.9.0-beta.98](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.97...v3.9.0-beta.98) (2024-10-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.97](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.96...v3.9.0-beta.97) (2024-10-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.96](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.95...v3.9.0-beta.96) (2024-10-10)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.95](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.94...v3.9.0-beta.95) (2024-10-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.94](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.93...v3.9.0-beta.94) (2024-10-04)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.93](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.92...v3.9.0-beta.93) (2024-10-04)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.92](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.91...v3.9.0-beta.92) (2024-10-01)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.91](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.90...v3.9.0-beta.91) (2024-10-01)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.90](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.89...v3.9.0-beta.90) (2024-09-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.89](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.88...v3.9.0-beta.89) (2024-09-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.88](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.87...v3.9.0-beta.88) (2024-09-24)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.87](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.86...v3.9.0-beta.87) (2024-09-19)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.86](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.85...v3.9.0-beta.86) (2024-09-19)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.85](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.84...v3.9.0-beta.85) (2024-09-17)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.84](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.83...v3.9.0-beta.84) (2024-09-12)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.83](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.82...v3.9.0-beta.83) (2024-09-11)
+
+
+### Features
+
+* **studies-panel:** New OHIF study panel - under experimental flag ([#4254](https://github.com/OHIF/Viewers/issues/4254)) ([7a96406](https://github.com/OHIF/Viewers/commit/7a96406a116e46e62c396855fa64f434e2984b58))
+
+
+
+
+
+# [3.9.0-beta.82](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.81...v3.9.0-beta.82) (2024-09-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.81](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.80...v3.9.0-beta.81) (2024-08-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.80](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.79...v3.9.0-beta.80) (2024-08-16)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.79](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.78...v3.9.0-beta.79) (2024-08-16)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.78](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.77...v3.9.0-beta.78) (2024-08-15)
+
+
+### Features
+
+* Add CS3D WSI and Video Viewports and add annotation navigation for MPR ([#4182](https://github.com/OHIF/Viewers/issues/4182)) ([7599ec9](https://github.com/OHIF/Viewers/commit/7599ec9421129dcade94e6fa6ec7908424ab3134))
+
+
+
+
+
+# [3.9.0-beta.77](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.76...v3.9.0-beta.77) (2024-08-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.76](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.75...v3.9.0-beta.76) (2024-08-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.75](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.74...v3.9.0-beta.75) (2024-08-07)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.74](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.73...v3.9.0-beta.74) (2024-08-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.73](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.72...v3.9.0-beta.73) (2024-08-02)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.72](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.71...v3.9.0-beta.72) (2024-07-31)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.71](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.70...v3.9.0-beta.71) (2024-07-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.70](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.69...v3.9.0-beta.70) (2024-07-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.69](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.68...v3.9.0-beta.69) (2024-07-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.68](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.67...v3.9.0-beta.68) (2024-07-26)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.67](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.66...v3.9.0-beta.67) (2024-07-26)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.66](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.65...v3.9.0-beta.66) (2024-07-24)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.65](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.64...v3.9.0-beta.65) (2024-07-23)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.64](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.63...v3.9.0-beta.64) (2024-07-19)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
+# [3.9.0-beta.63](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.62...v3.9.0-beta.63) (2024-07-10)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume
+
+
+
+
+
 # [3.9.0-beta.62](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.61...v3.9.0-beta.62) (2024-07-09)
 
 **Note:** Version bump only for package @ohif/extension-cornerstone-dynamic-volume

extensions/cornerstone-dynamic-volume/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone-dynamic-volume",
-  "version": "3.9.0-beta.62",
+  "version": "3.9.3",
   "description": "OHIF extension for 4D volumes data",
   "author": "OHIF",
   "license": "MIT",
@@ -29,11 +29,11 @@
     "test:unit:ci": "jest --ci --runInBand --collectCoverage --passWithNoTests"
   },
   "peerDependencies": {
-    "@ohif/core": "3.9.0-beta.62",
-    "@ohif/extension-cornerstone": "3.9.0-beta.62",
-    "@ohif/extension-default": "3.9.0-beta.62",
-    "@ohif/i18n": "3.9.0-beta.62",
-    "@ohif/ui": "3.9.0-beta.62",
+    "@ohif/core": "3.9.3",
+    "@ohif/extension-cornerstone": "3.9.3",
+    "@ohif/extension-default": "3.9.3",
+    "@ohif/i18n": "3.9.3",
+    "@ohif/ui": "3.9.3",
     "dcmjs": "*",
     "dicom-parser": "^1.8.21",
     "hammerjs": "^2.0.8",
@@ -42,9 +42,8 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/core": "^1.82.0",
-    "@cornerstonejs/streaming-image-volume-loader": "^1.82.0",
-    "@cornerstonejs/tools": "^1.82.0",
+    "@cornerstonejs/core": "^2.2.20",
+    "@cornerstonejs/tools": "^2.2.20",
     "classnames": "^2.3.2"
   }
 }

extensions/cornerstone-dynamic-volume/src/actions/updateSegmentationsChartDisplaySet.ts

@@ -110,7 +110,12 @@ function _getTimePointsData(volume) {
   return { timePoints, timePointsUnit };
 }
 
-function _getSegmentationData(segmentation, volumesTimePointsCache, displaySetService) {
+function _getSegmentationData(
+  segmentation,
+  volumesTimePointsCache,
+  { servicesManager }: { servicesManager: AppTypes.ServicesManager }
+) {
+  const { displaySetService, segmentationService, viewportGridService } = servicesManager.services;
   const displaySets = displaySetService.getActiveDisplaySets();
 
   const dynamic4DDisplaySet = displaySets.find(displaySet => {
@@ -145,8 +150,11 @@ function _getSegmentationData(segmentation, volumesTimePointsCache, displaySetSe
     referencedDynamicVolume.imageIds[0]
   );
 
+  const segmentationVolume = segmentationService.getLabelmapVolume(segmentation.segmentationId);
+  const maskVolumeId = segmentationVolume?.volumeId;
+
   const [timeData, _] = csToolsUtils.dynamicVolume.getDataInTime(referencedDynamicVolume, {
-    maskVolumeId: segmentation.id,
+    maskVolumeId,
   }) as number[][];
 
   const pixelCount = timeData.length;
@@ -155,27 +163,15 @@ function _getSegmentationData(segmentation, volumesTimePointsCache, displaySetSe
     return [];
   }
 
-  // since we only use one segmentation representation per segmentationId
-  // it is fine to pick the first one
-  const segmentationRepresentations = csTools.segmentation.state.getSegmentationIdRepresentations(
-    segmentation.id
-  );
-
-  const segmentationRepresentationUID =
-    segmentationRepresentations[0].segmentationRepresentationUID;
-
-  const toolGroupId = csTools.segmentation.state.getToolGroupIdFromSegmentationRepresentationUID(
-    segmentationRepresentationUID
-  );
-
   // Todo: this is useless we should be able to grab color with just segRepUID and segmentIndex
-  const color = csTools.segmentation.config.color.getColorForSegmentIndex(
-    toolGroupId,
-    segmentationRepresentationUID,
-    1 // segmentIndex
-  );
+  // const color = csTools.segmentation.config.color.getSegmentIndexColor(
+  //   segmentationRepresentationUID,
+  //   1 // segmentIndex
+  // );
+  const viewportId = viewportGridService.getActiveViewportId();
+  const color = segmentationService.getSegmentColor(viewportId, segmentation.segmentationId, 1);
 
-  const hexColor = cs.utilities.color.rgbToHex(...color);
+  const hexColor = cs.utilities.color.rgbToHex(color[0], color[1], color[2]);
   let timePointsData = volumesTimePointsCache.get(referencedDynamicVolume);
 
   if (!timePointsData) {
@@ -219,14 +215,14 @@ function _getSegmentationData(segmentation, volumesTimePointsCache, displaySetSe
   };
 }
 
-function _getInstanceFromSegmentations(segmentations, displaySetService) {
+function _getInstanceFromSegmentations(segmentations, { servicesManager }) {
   if (!segmentations.length) {
     return;
   }
 
   const volumesTimePointsCache = new WeakMap();
   const segmentationsData = segmentations.map(segmentation =>
-    _getSegmentationData(segmentation, volumesTimePointsCache, displaySetService)
+    _getSegmentationData(segmentation, volumesTimePointsCache, { servicesManager })
   );
 
   const { date: seriesDate, time: seriesTime } = _getDateTimeStr();
@@ -266,10 +262,10 @@ function _getInstanceFromSegmentations(segmentations, displaySetService) {
 }
 
 function updateSegmentationsChartDisplaySet({ servicesManager }: withAppTypes): void {
-  const { segmentationService, displaySetService } = servicesManager.services;
+  const { segmentationService } = servicesManager.services;
   const segmentations = segmentationService.getSegmentations();
   const { seriesMetadata, instance } =
-    _getInstanceFromSegmentations(segmentations, displaySetService) ?? {};
+    _getInstanceFromSegmentations(segmentations, { servicesManager }) ?? {};
 
   if (seriesMetadata && instance) {
     // An event is triggered after adding the instance and the displaySet is created

extensions/cornerstone-dynamic-volume/src/commandsModule.ts

@@ -84,11 +84,11 @@ const commandsModule = ({ commandsManager, servicesManager }: withAppTypes) => {
         const stdDeviation = Math.sqrt(variance);
         return stdDeviation;
       }
-
       // Iterate through each segmentation to get the timeData and ijkCoords
-      segmentations.forEach((segmentation, segmentationIndex) => {
+      segmentations.forEach(segmentation => {
+        const volume = segmentationService.getLabelmapVolume(segmentation.segmentationId);
         const [timeData, ijkCoords] = utilities.dynamicVolume.getDataInTime(dynamicVolume, {
-          maskVolumeId: segmentation.id,
+          maskVolumeId: volume.volumeId,
         }) as number[][];
 
         if (summaryStats) {
@@ -113,17 +113,33 @@ const commandsModule = ({ commandsManager, servicesManager }: withAppTypes) => {
           for (let timeIndex = 0; timeIndex < maxLength; timeIndex++) {
             // for each voxel in the ROI, get the value at the current time point
             const voxelValues = [];
+            let sum = 0;
+            let minValue = Infinity;
+            let maxValue = -Infinity;
+            let minIndex = 0;
+            let maxIndex = 0;
+
+            // Single pass through the data to collect all needed values
             for (let voxelIndex = 0; voxelIndex < numVoxels; voxelIndex++) {
-              voxelValues.push(timeData[voxelIndex][timeIndex]);
+              const value = timeData[voxelIndex][timeIndex];
+              voxelValues.push(value);
+              sum += value;
+
+              if (value < minValue) {
+                minValue = value;
+                minIndex = voxelIndex;
+              }
+              if (value > maxValue) {
+                maxValue = value;
+                maxIndex = voxelIndex;
+              }
             }
 
-            mean.push(voxelValues.reduce((acc, value) => acc + value, 0) / numVoxels);
-            const minimum = Math.min(...voxelValues);
-            min.push(minimum);
-            minIJK.push(ijkCoords[voxelValues.indexOf(minimum)]);
-            const maximum = Math.max(...voxelValues);
-            max.push(maximum);
-            maxIJK.push(ijkCoords[voxelValues.indexOf(maximum)]);
+            mean.push(sum / numVoxels);
+            min.push(minValue);
+            minIJK.push(ijkCoords[minIndex]);
+            max.push(maxValue);
+            maxIJK.push(ijkCoords[maxIndex]);
             std.push(calculateStandardDeviation(voxelValues));
           }
 
@@ -340,30 +356,19 @@ const commandsModule = ({ commandsManager, servicesManager }: withAppTypes) => {
         throw new Error('No reference display set found based on the dynamic data');
       }
 
-      const segmentationId = await segmentationService.createSegmentationForDisplaySet(
-        referenceDisplaySet.displaySetInstanceUID,
-        { label }
+      const displaySet = displaySetService.getDisplaySetByUID(
+        referenceDisplaySet.displaySetInstanceUID
       );
 
-      // Add Segmentation to all toolGroupIds in the viewer
-      const toolGroupIds = Array.from(
-        viewports.values(),
-        viewport => viewport.viewportOptions.toolGroupId
-      );
+      const segmentationId = await segmentationService.createLabelmapForDisplaySet(displaySet, {
+        label,
+      });
 
-      const representationType = LABELMAP;
+      const firstViewport = viewports.values().next().value;
 
-      for (const toolGroupId of toolGroupIds) {
-        const hydrateSegmentation = true;
-        await segmentationService.addSegmentationRepresentationToToolGroup(
-          toolGroupId,
-          segmentationId,
-          hydrateSegmentation,
-          representationType
-        );
-
-        segmentationService.setActiveSegmentationForToolGroup(segmentationId, toolGroupId);
-      }
+      await segmentationService.addSegmentationRepresentation(firstViewport.viewportId, {
+        segmentationId,
+      });
 
       return segmentationId;
     },

extensions/cornerstone-dynamic-volume/src/getHangingProtocolModule.ts

@@ -147,8 +147,8 @@ function getFusionViewports() {
       name: DEFAULT_COLORMAP,
       opacity: [
         { value: 0, opacity: 0 },
-        { value: 0.1, opacity: 0.3 },
-        { value: 1, opacity: 0.3 },
+        { value: 0.1, opacity: 0.8 },
+        { value: 1, opacity: 0.8 },
       ],
     },
   };
@@ -191,6 +191,15 @@ function getFusionViewports() {
               syncInvertState: false,
             },
           },
+          {
+            type: 'hydrateseg',
+            id: 'sameFORId',
+            source: true,
+            target: true,
+            options: {
+              matchingRules: ['sameFOR'],
+            },
+          },
         ],
       },
       displaySets: [
@@ -240,6 +249,15 @@ function getFusionViewports() {
               syncInvertState: false,
             },
           },
+          {
+            type: 'hydrateseg',
+            id: 'sameFORId',
+            source: true,
+            target: true,
+            options: {
+              matchingRules: ['sameFOR'],
+            },
+          },
         ],
       },
       displaySets: [
@@ -289,6 +307,15 @@ function getFusionViewports() {
               syncInvertState: false,
             },
           },
+          {
+            type: 'hydrateseg',
+            id: 'sameFORId',
+            source: true,
+            target: true,
+            options: {
+              matchingRules: ['sameFOR'],
+            },
+          },
         ],
       },
       displaySets: [

extensions/cornerstone-dynamic-volume/src/getPanelModule.tsx

@@ -1,9 +1,10 @@
 import React from 'react';
 import { DynamicDataPanel } from './panels';
-import { Toolbox } from '@ohif/ui';
+import { Toolbox } from '@ohif/ui-next';
+import { PanelSegmentation } from '@ohif/extension-cornerstone';
 import DynamicExport from './panels/DynamicExport';
 
-function getPanelModule({ commandsManager, extensionManager, servicesManager }) {
+function getPanelModule({ commandsManager, extensionManager, servicesManager, configuration }) {
   const wrappedDynamicDataPanel = () => {
     return (
       <DynamicDataPanel
@@ -14,7 +15,7 @@ function getPanelModule({ commandsManager, extensionManager, servicesManager })
     );
   };
 
-  const wrappedDynamicToolbox = () => {
+  const wrappedDynamicSegmentation = () => {
     return (
       <>
         <Toolbox
@@ -24,18 +25,17 @@ function getPanelModule({ commandsManager, extensionManager, servicesManager })
           buttonSectionId="dynamic-toolbox"
           title="Threshold Tools"
         />
-      </>
-    );
-  };
-
-  const wrappedDynamicExport = () => {
-    return (
-      <>
-        <DynamicExport
-          commandsManager={commandsManager}
+        <PanelSegmentation
           servicesManager={servicesManager}
+          commandsManager={commandsManager}
           extensionManager={extensionManager}
-        />
+          configuration={configuration}
+        >
+          <DynamicExport
+            servicesManager={servicesManager}
+            commandsManager={commandsManager}
+          />
+        </PanelSegmentation>
       </>
     );
   };
@@ -49,18 +49,11 @@ function getPanelModule({ commandsManager, extensionManager, servicesManager })
       component: wrappedDynamicDataPanel,
     },
     {
-      name: 'dynamic-toolbox',
-      iconName: 'tab-4d',
-      iconLabel: '4D Workflow',
-      label: 'Dynamic Toolbox',
-      component: wrappedDynamicToolbox,
-    },
-    {
-      name: 'dynamic-export',
-      iconName: 'tab-4d',
-      iconLabel: '4D Workflow',
-      label: '4D Workflow',
-      component: wrappedDynamicExport,
+      name: 'dynamic-segmentation',
+      iconName: 'tab-segmentation',
+      iconLabel: 'Segmentation',
+      label: 'Segmentation',
+      component: wrappedDynamicSegmentation,
     },
   ];
 }

extensions/cornerstone-dynamic-volume/src/panels/DynamicDataPanel.tsx

@@ -1,17 +1,19 @@
 import React from 'react';
 import PanelGenerateImage from './PanelGenerateImage';
 
-function DynamicDataPanel({ servicesManager, commandsManager }) {
+function DynamicDataPanel({ servicesManager, commandsManager, tab }: withAppTypes) {
   return (
-    <div
-      className="flex flex-col text-white"
-      data-cy={'dynamic-volume-panel'}
-    >
-      <PanelGenerateImage
-        commandsManager={commandsManager}
-        servicesManager={servicesManager}
-      ></PanelGenerateImage>
-    </div>
+    <>
+      <div
+        className="flex flex-col text-white"
+        data-cy={'dynamic-volume-panel'}
+      >
+        <PanelGenerateImage
+          commandsManager={commandsManager}
+          servicesManager={servicesManager}
+        ></PanelGenerateImage>
+      </div>
+    </>
   );
 }
 

extensions/cornerstone-dynamic-volume/src/panels/DynamicExport.tsx

@@ -1,73 +1,52 @@
-import React, { useState, useEffect } from 'react';
-import { ActionButtons } from '@ohif/ui';
-import { useTranslation } from 'react-i18next';
+import React from 'react';
+import { Button, Icons } from '@ohif/ui-next';
+import { useSegmentations } from '@ohif/extension-cornerstone';
 
-function DynamicExport({ commandsManager, servicesManager, extensionManager }: withAppTypes) {
-  const { segmentationService } = servicesManager.services;
-  const { t } = useTranslation('dynamicExport');
+function DynamicExport({ commandsManager, servicesManager }: withAppTypes) {
+  const segmentations = useSegmentations({ servicesManager });
 
-  const [segmentations, setSegmentations] = useState(() => segmentationService.getSegmentations());
-
-  const actions = [
-    {
-      label: 'Export Time Data',
-      onClick: () => {
-        commandsManager.runCommand('exportTimeReportCSV', {
-          segmentations,
-          options: {
-            filename: 'TimeData.csv',
-          },
-        });
-      },
-      disabled: !segmentations?.length,
-    },
-    {
-      label: 'Export ROI Stats',
-      onClick: () => {
-        commandsManager.runCommand('exportTimeReportCSV', {
-          segmentations,
-          summaryStats: true,
-          options: {
-            filename: 'ROIStats.csv',
-          },
-        });
-      },
-      disabled: !segmentations?.length,
-    },
-  ];
-
-  /**
-   * Update UI based on segmentation changes (added, removed, updated)
-   */
-  useEffect(() => {
-    // ~~ Subscription
-    const added = segmentationService.EVENTS.SEGMENTATION_ADDED;
-    const updated = segmentationService.EVENTS.SEGMENTATION_UPDATED;
-    const removed = segmentationService.EVENTS.SEGMENTATION_REMOVED;
-    const subscriptions = [];
-
-    [added, updated, removed].forEach(evt => {
-      const { unsubscribe } = segmentationService.subscribe(evt, () => {
-        const segmentations = segmentationService.getSegmentations();
-        setSegmentations(segmentations);
-      });
-      subscriptions.push(unsubscribe);
-    });
-
-    return () => {
-      subscriptions.forEach(unsub => {
-        unsub();
-      });
-    };
-  }, []);
+  if (!segmentations?.length) {
+    return null;
+  }
 
   return (
-    <div>
-      <div className="mt-3 flex justify-center px-2">
-        <ActionButtons
-          actions={actions}
-          t={t}
-        />
+    <div className="flex gap-2">
+      <div className="flex h-8 w-full items-center rounded pr-0.5">
+        <Button
+          size="sm"
+          variant="ghost"
+          className="pl-1.5"
+          onClick={() => {
+            commandsManager.runCommand('exportTimeReportCSV', {
+              segmentations,
+              options: {
+                filename: 'TimeData.csv',
+              },
+            });
+          }}
+        >
+          <Icons.Export />
+          <span className="pl-1">Time Data</span>
+        </Button>
+      </div>
+      <div className="flex h-8 w-full items-center rounded pr-0.5">
+        <Button
+          size="sm"
+          variant="ghost"
+          className="pl-1.5"
+          onClick={() => {
+            commandsManager.runCommand('exportTimeReportCSV', {
+              segmentations,
+              summaryStats: true,
+              options: {
+                filename: 'ROIStats.csv',
+              },
+            });
+          }}
+        >
+          <Icons.Export />
+          <span className="pl-1">ROI Stats</span>
+        </Button>
       </div>
     </div>
   );

extensions/cornerstone-dynamic-volume/src/panels/DynamicVolumeControls.tsx

@@ -1,6 +1,5 @@
 import React, { useEffect, useState } from 'react';
 import {
-  InputDoubleRange,
   Button,
   PanelSection,
   ButtonGroup,
@@ -10,6 +9,8 @@ import {
   Tooltip,
 } from '@ohif/ui';
 
+import { DoubleSlider } from '@ohif/ui-next';
+
 import { Enums } from '@cornerstonejs/core';
 
 const controlClassNames = {
@@ -55,21 +56,15 @@ const DynamicVolumeControls = ({
 
   const [computeViewMode, setComputeViewMode] = useState(Enums.DynamicOperatorType.SUM);
 
-  const [sliderRangeValues, setSliderRangeValues] = useState([framesLength / 4, framesLength / 2]);
-
-  useEffect(() => {
-    setSliderRangeValues([framesLength / 4, framesLength / 2]);
-  }, [framesLength]);
+  const [sliderRangeValues, setSliderRangeValues] = useState([0, framesLength - 1]);
 
   const handleSliderChange = newValues => {
     onDoubleRangeChange(newValues);
-
-    if (newValues[0] === sliderRangeValues[0] && newValues[1] === sliderRangeValues[1]) {
-      return;
-    }
     setSliderRangeValues(newValues);
   };
 
+  const formatLabel = value => Math.round(value);
+
   return (
     <div className="flex select-none flex-col">
       <PanelSection
@@ -134,7 +129,7 @@ const DynamicVolumeControls = ({
             }
           />
           <ButtonGroup
-            className={`mt-2 w-full `}
+            className={`mt-2 w-full`}
             separated={true}
           >
             <button
@@ -156,15 +151,15 @@ const DynamicVolumeControls = ({
               {Enums.DynamicOperatorType.SUBTRACT.toString().toUpperCase()}
             </button>
           </ButtonGroup>
-          <div className="w-ful mt-2">
-            <InputDoubleRange
-              values={sliderRangeValues}
-              onChange={handleSliderChange}
-              minValue={0}
-              showLabel={true}
-              allowNumberEdit={true}
-              maxValue={framesLength}
+          <div className="mt-2 w-full">
+            <DoubleSlider
+              min={0}
+              max={framesLength - 1}
               step={1}
+              defaultValue={sliderRangeValues}
+              onValueChange={handleSliderChange}
+              formatLabel={formatLabel}
+              className="w-full"
             />
           </div>
           <Button
@@ -216,14 +211,14 @@ function FrameControls({
         >
           <Icon
             name={getPlayPauseIconName()}
-            className=" active:text-primary-light hover:bg-customblue-300 h-[24px] w-[24px] cursor-pointer text-white"
+            className="active:text-primary-light hover:bg-customblue-300 h-[24px] w-[24px] cursor-pointer text-white"
           />
         </IconButton>
         <InputNumber
           value={currentFrameIndex}
           onChange={onFrameChange}
           minValue={0}
-          maxValue={framesLength}
+          maxValue={framesLength - 1}
           label="Frame"
           {...controlClassNames}
         />

extensions/cornerstone-dynamic-volume/src/panels/PanelGenerateImage.tsx

@@ -1,8 +1,6 @@
 import React, { useEffect, useState, useRef } from 'react';
-import PropTypes from 'prop-types';
 import { useCine, useViewportGrid } from '@ohif/ui';
-import { cache, utilities as csUtils, volumeLoader, eventTarget } from '@cornerstonejs/core';
-import { Enums } from '@cornerstonejs/streaming-image-volume-loader';
+import { utilities as csUtils, volumeLoader, eventTarget, Enums, cache } from '@cornerstonejs/core';
 import { utilities as cstUtils } from '@cornerstonejs/tools';
 import DynamicVolumeControls from './DynamicVolumeControls';
 
@@ -16,8 +14,8 @@ export default function PanelGenerateImage({ servicesManager, commandsManager }:
   const [{ activeViewportId }] = useViewportGrid();
 
   //
-  const [timePointsRange, setTimePointsRange] = useState([]);
-  const [timePointsRangeToUseForGenerate, setTimePointsRangeToUseForGenerate] = useState([]);
+  const [timePointsRange, setTimePointsRange] = useState([0, 0]);
+  const [timePointsRangeToUseForGenerate, setTimePointsRangeToUseForGenerate] = useState([0, 0]);
   const [computedDisplaySet, setComputedDisplaySet] = useState(null);
   const [dynamicVolume, setDynamicVolume] = useState(null);
   const [frameRate, setFrameRate] = useState(20);
@@ -31,47 +29,62 @@ export default function PanelGenerateImage({ servicesManager, commandsManager }:
   const computedVolumeId = `cornerstoneStreamingImageVolume:${uuidComputedVolume.current}`;
 
   useEffect(() => {
-    const evt = cornerstoneViewportService.EVENTS.VIEWPORT_DATA_CHANGED;
+    const viewportDataChangedEvt = cornerstoneViewportService.EVENTS.VIEWPORT_DATA_CHANGED;
+    const cineStateChangedEvt = servicesManager.services.cineService.EVENTS.CINE_STATE_CHANGED;
 
-    const { unsubscribe } = cornerstoneViewportService.subscribe(evt, evtDetails => {
+    const viewportDataChangedCallback = evtDetails => {
       evtDetails.viewportData.data.forEach(volumeData => {
-        if (volumeData.volume.isDynamicVolume()) {
+        if (volumeData.volume?.isDynamicVolume()) {
           setDynamicVolume(volumeData.volume);
           uuidDynamicVolume.current = volumeData.displaySetInstanceUID;
-          setTimePointsRange([1, volumeData.volume.numTimePoints]);
+          const newRange = [1, volumeData.volume.numTimePoints];
+          setTimePointsRange(newRange);
+          setTimePointsRangeToUseForGenerate(newRange);
         }
       });
-    });
+    };
+
+    const cineStateChangedCallback = evt => {
+      setIsPlaying(evt.isPlaying);
+    };
+
+    const { unsubscribe: unsubscribeViewportData } = cornerstoneViewportService.subscribe(
+      viewportDataChangedEvt,
+      viewportDataChangedCallback
+    );
+    const { unsubscribe: unsubscribeCineState } = servicesManager.services.cineService.subscribe(
+      cineStateChangedEvt,
+      cineStateChangedCallback
+    );
 
     return () => {
-      unsubscribe();
+      unsubscribeViewportData();
+      unsubscribeCineState();
+    };
+  }, [cornerstoneViewportService, cineService, servicesManager.services.cineService]);
+
+  useEffect(() => {
+    const evt = Enums.Events.DYNAMIC_VOLUME_TIME_POINT_INDEX_CHANGED;
+
+    const callback = evt => {
+      setTimePointRendered(evt.detail.timePointIndex);
+    };
+
+    eventTarget.addEventListener(evt, callback);
+
+    return () => {
+      eventTarget.removeEventListener(evt, callback);
     };
   }, [cornerstoneViewportService]);
 
-  useEffect(() => {
-    const { unsubscribe } = servicesManager.services.cineService.subscribe(
-      servicesManager.services.cineService.EVENTS.CINE_STATE_CHANGED,
-      evt => {
-        setIsPlaying(evt.isPlaying);
-      }
-    );
-
-    return () => {
-      unsubscribe();
-    };
-  }, [cineService]);
-
   useEffect(() => {
     const displaySetUIDs = viewportGridService.getDisplaySetsUIDsForViewport(activeViewportId);
 
-    if (!displaySetUIDs || displaySetUIDs.length === 0) {
+    if (!displaySetUIDs?.length) {
       return;
     }
 
-    const displaySets = displaySetUIDs.map(displaySetUID =>
-      displaySetService.getDisplaySetByUID(displaySetUID)
-    );
-
+    const displaySets = displaySetUIDs.map(displaySetService.getDisplaySetByUID);
     const dynamicVolumeDisplaySet = displaySets.find(displaySet => displaySet.isDynamicVolume);
 
     if (!dynamicVolumeDisplaySet) {
@@ -88,23 +101,16 @@ export default function PanelGenerateImage({ servicesManager, commandsManager }:
 
     setDynamicVolume(dynamicVolume);
     uuidDynamicVolume.current = dynamicVolumeDisplaySet.displaySetInstanceUID;
-    setTimePointsRange([1, dynamicVolume.numTimePoints]);
-  }, [activeViewportId, cornerstoneViewportService]);
-
-  useEffect(() => {
-    // ~~ Subscription
-    const evt = Enums.Events.DYNAMIC_VOLUME_TIME_POINT_INDEX_CHANGED;
-
-    const callback = evt => {
-      setTimePointRendered(evt.detail.timePointIndex);
-    };
-
-    eventTarget.addEventListener(evt, callback);
-
-    return () => {
-      eventTarget.removeEventListener(evt, callback);
-    };
-  }, [cornerstoneViewportService]);
+    const newRange = [1, dynamicVolume.numTimePoints];
+    setTimePointsRange(newRange);
+    setTimePointsRangeToUseForGenerate(newRange);
+  }, [
+    activeViewportId,
+    viewportGridService,
+    displaySetService,
+    cornerstoneViewportService,
+    cineService,
+  ]);
 
   function renderGeneratedImage(displaySet) {
     commandsManager.runCommand('swapDynamicWithComputedDisplaySet', {
@@ -130,26 +136,19 @@ export default function PanelGenerateImage({ servicesManager, commandsManager }:
     let computedVolume = cache.getVolume(computedVolumeId);
 
     if (!computedVolume) {
-      await createComputedVolume(dynamicVolumeId, computedVolumeId);
-      computedVolume = cache.getVolume(computedVolumeId);
+      computedVolume = await volumeLoader.createAndCacheDerivedVolume(dynamicVolumeId, {
+        volumeId: computedVolumeId,
+      });
     }
+    const [start, end] = timePointsRangeToUseForGenerate;
+    const frameNumbers = Array.from({ length: end - start + 1 }, (_, i) => i + start - 1);
 
-    const vals = timePointsRangeToUseForGenerate;
+    const options = {
+      frameNumbers: operationName === 'SUBTRACT' ? [start, end - 1] : frameNumbers,
+      targetVolume: computedVolume,
+    };
 
-    const targets = Array.from({ length: vals[1] - vals[0] + 1 }, (_, i) => i + vals[0]);
-
-    const dataInTime = cstUtils.dynamicVolume.generateImageFromTimeData(
-      dynamicVolume,
-      operationName,
-      operationName === 'SUBTRACT' ? vals : targets
-    );
-
-    // Add loadStatus.loaded to computed volume and set to true
-    computedVolume.loadStatus = {};
-    computedVolume.loadStatus.loaded = true;
-    // Set computed scalar data to volume
-    const scalarData = computedVolume.getScalarData();
-    scalarData.set(dataInTime);
+    cstUtils.dynamicVolume.updateVolumeFromTimeData(dynamicVolume, operationName, options);
 
     // If computed display set does not exist, create an object to be used as
     // the displaySet. If it does exist, update the image data and vtkTexture
@@ -166,6 +165,7 @@ export default function PanelGenerateImage({ servicesManager, commandsManager }:
         madeInClient: true,
         FrameOfReferenceUID: dynamicVolume.metadata.FrameOfReferenceUID,
         isDerived: true,
+        imageIds: computedVolume.imageIds,
       };
       setComputedDisplaySet(displaySet);
       renderGeneratedImage(displaySet);
@@ -173,19 +173,8 @@ export default function PanelGenerateImage({ servicesManager, commandsManager }:
       commandsManager.runCommand('updateVolumeData', {
         volume: computedVolume,
       });
-      // Check if viewport is currently displaying the computed volume, if so,
-      // call render on the viewports to update the image, if not, call
-      // renderGeneratedImage
-      // if (!cache.getVolume(dynamicVolumeId)) {
-      //   for (const viewportId of viewports.keys()) {
-      //     const viewportForRendering =
-      //       cornerstoneViewportService.getCornerstoneViewport(viewportId);
-      //     viewportForRendering.render();
-      //   }
-      // } else {
       cornerstoneViewportService.getRenderingEngine().render();
       renderGeneratedImage(computedDisplaySet);
-      // }
     }
   }
 
@@ -248,28 +237,7 @@ export default function PanelGenerateImage({ servicesManager, commandsManager }:
       onGenerate={onGenerateImage}
       onDynamicClick={displayingComputed ? () => renderDynamicImage(computedDisplaySet) : null}
       onDoubleRangeChange={handleSliderChange}
+      initialRangeValues={timePointsRangeToUseForGenerate}
     />
   );
 }
-
-async function createComputedVolume(dynamicVolumeId, computedVolumeId) {
-  if (!cache.getVolume(computedVolumeId)) {
-    const computedVolume = await volumeLoader.createAndCacheDerivedVolume(dynamicVolumeId, {
-      volumeId: computedVolumeId,
-    });
-    return computedVolume;
-  }
-}
-
-PanelGenerateImage.propTypes = {
-  servicesManager: PropTypes.shape({
-    services: PropTypes.shape({
-      measurementService: PropTypes.shape({
-        getMeasurements: PropTypes.func.isRequired,
-        subscribe: PropTypes.func.isRequired,
-        EVENTS: PropTypes.object.isRequired,
-        VALUE_TYPES: PropTypes.object.isRequired,
-      }).isRequired,
-    }).isRequired,
-  }).isRequired,
-};

extensions/cornerstone/CHANGELOG.md

@@ -3,6 +3,479 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [3.9.3](https://github.com/OHIF/Viewers/compare/v3.9.2...v3.9.3) (2025-01-21)
+
+
+### Bug Fixes
+
+* OHIF 3.9 Recovery 3 ([#4697](https://github.com/OHIF/Viewers/issues/4697)) ([5d4f2e2](https://github.com/OHIF/Viewers/commit/5d4f2e2a8e62f8de97d56a4e3f17be6018e9f2eb))
+
+
+
+
+
+## [3.9.2](https://github.com/OHIF/Viewers/compare/v3.9.1...v3.9.2) (2024-12-03)
+
+
+### Bug Fixes
+
+* **modes:** don't attempt to retrieve a stage index if HPs  ([#4552](https://github.com/OHIF/Viewers/issues/4552)) ([e5286d9](https://github.com/OHIF/Viewers/commit/e5286d9fc2449da50b738e7e6208d489cce1633e))
+* **multiframe:** metadata handling of NM studies and loading order ([#4540](https://github.com/OHIF/Viewers/issues/4540)) ([71f06dc](https://github.com/OHIF/Viewers/commit/71f06dcd3e6d24f1e3d931f7db756c26038927da))
+
+
+
+
+
+## [3.9.1](https://github.com/OHIF/Viewers/compare/v3.9.0...v3.9.1) (2024-11-13)
+
+
+### Bug Fixes
+
+* video playback ([#4497](https://github.com/OHIF/Viewers/issues/4497)) ([610faa5](https://github.com/OHIF/Viewers/commit/610faa5a2738da5eabc40e57e338c359f481e852))
+
+
+
+
+
+# [3.9.0](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.111...v3.9.0) (2024-11-12)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.111](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.110...v3.9.0-beta.111) (2024-11-12)
+
+
+### Bug Fixes
+
+* Measurement Tracking: Various UI and functionality improvements ([#4481](https://github.com/OHIF/Viewers/issues/4481)) ([62b2748](https://github.com/OHIF/Viewers/commit/62b27488471c9d5979142e2d15872a85778b90ed))
+
+
+
+
+
+# [3.9.0-beta.110](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.109...v3.9.0-beta.110) (2024-11-11)
+
+
+### Bug Fixes
+
+* **bugs:** Update dependencies and enhance UI components ([#4478](https://github.com/OHIF/Viewers/issues/4478)) ([05d41c5](https://github.com/OHIF/Viewers/commit/05d41c52068a3b7ba249f15ecdf71838c352fd30))
+
+
+
+
+
+# [3.9.0-beta.109](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.108...v3.9.0-beta.109) (2024-11-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.108](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.107...v3.9.0-beta.108) (2024-11-07)
+
+
+### Bug Fixes
+
+* **tmtv:** fix toggle one up weird behaviours ([#4473](https://github.com/OHIF/Viewers/issues/4473)) ([aa2b649](https://github.com/OHIF/Viewers/commit/aa2b649444eb4fe5422e72ea7830a709c4d24a90))
+
+
+
+
+
+# [3.9.0-beta.107](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.106...v3.9.0-beta.107) (2024-11-06)
+
+
+### Bug Fixes
+
+* build ([#4471](https://github.com/OHIF/Viewers/issues/4471)) ([3d11ef2](https://github.com/OHIF/Viewers/commit/3d11ef28f213361ec7586809317bd219fa70e742))
+
+
+
+
+
+# [3.9.0-beta.106](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.105...v3.9.0-beta.106) (2024-11-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.105](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.104...v3.9.0-beta.105) (2024-11-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.104](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.103...v3.9.0-beta.104) (2024-10-30)
+
+
+### Bug Fixes
+
+* **ui:** show ui notification on displaySet load error ([#4447](https://github.com/OHIF/Viewers/issues/4447)) ([4f20523](https://github.com/OHIF/Viewers/commit/4f20523109ecbb7ec5a6d5f2c97f7e73f81cda09))
+
+
+
+
+
+# [3.9.0-beta.103](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.102...v3.9.0-beta.103) (2024-10-29)
+
+
+### Bug Fixes
+
+* **ui:** display error in ui while loading seg ([#4433](https://github.com/OHIF/Viewers/issues/4433)) ([2e96371](https://github.com/OHIF/Viewers/commit/2e96371b0631a9e5d411b0142300708ab8ba7d27))
+
+
+
+
+
+# [3.9.0-beta.102](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.101...v3.9.0-beta.102) (2024-10-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.101](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.100...v3.9.0-beta.101) (2024-10-18)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.100](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.99...v3.9.0-beta.100) (2024-10-17)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.99](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.98...v3.9.0-beta.99) (2024-10-17)
+
+
+### Bug Fixes
+
+* **3d-viewport:** exception was being thrown and 3d viewpot not getting resized. ([#4366](https://github.com/OHIF/Viewers/issues/4366)) ([433cc80](https://github.com/OHIF/Viewers/commit/433cc8089db6aa218c9075bd0eeb7952a7e4f028))
+* **hp-presets:** select the active displaySet when toggling an HP preset, not a random one from the series panel ([#4365](https://github.com/OHIF/Viewers/issues/4365)) ([ace67b3](https://github.com/OHIF/Viewers/commit/ace67b3bbb6be4e8c78e613e20d3e10b93762bf7))
+* **tools:** check if seriesNumber is an undefined properly ([#4338](https://github.com/OHIF/Viewers/issues/4338)) ([307b144](https://github.com/OHIF/Viewers/commit/307b14476be41b10b861d6a8474f7386b5107618))
+* **typo:** type in fourup preset ([#4426](https://github.com/OHIF/Viewers/issues/4426)) ([03aad4e](https://github.com/OHIF/Viewers/commit/03aad4eba24e33a266a6d91eaf74df52dc2a550e))
+* **updateIndex:** getNumberOfSlices is defined when used with a 3D viewport ([#4424](https://github.com/OHIF/Viewers/issues/4424)) ([d5bcf54](https://github.com/OHIF/Viewers/commit/d5bcf54e23ef68abd85c5f0ea671feca637c4f49))
+
+
+### Features
+
+* **SR:** SCOORD3D point annotations support for stack viewports ([#4315](https://github.com/OHIF/Viewers/issues/4315)) ([ac1cad2](https://github.com/OHIF/Viewers/commit/ac1cad25af12ee0f7d508647e3134ed724d9b4d3))
+
+
+
+
+
+# [3.9.0-beta.98](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.97...v3.9.0-beta.98) (2024-10-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.97](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.96...v3.9.0-beta.97) (2024-10-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.96](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.95...v3.9.0-beta.96) (2024-10-10)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.95](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.94...v3.9.0-beta.95) (2024-10-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.94](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.93...v3.9.0-beta.94) (2024-10-04)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.93](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.92...v3.9.0-beta.93) (2024-10-04)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.92](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.91...v3.9.0-beta.92) (2024-10-01)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.91](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.90...v3.9.0-beta.91) (2024-10-01)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.90](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.89...v3.9.0-beta.90) (2024-09-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.89](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.88...v3.9.0-beta.89) (2024-09-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.88](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.87...v3.9.0-beta.88) (2024-09-24)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.87](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.86...v3.9.0-beta.87) (2024-09-19)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.86](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.85...v3.9.0-beta.86) (2024-09-19)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.85](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.84...v3.9.0-beta.85) (2024-09-17)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.84](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.83...v3.9.0-beta.84) (2024-09-12)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.83](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.82...v3.9.0-beta.83) (2024-09-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.82](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.81...v3.9.0-beta.82) (2024-09-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.81](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.80...v3.9.0-beta.81) (2024-08-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.80](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.79...v3.9.0-beta.80) (2024-08-16)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.79](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.78...v3.9.0-beta.79) (2024-08-16)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.78](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.77...v3.9.0-beta.78) (2024-08-15)
+
+
+### Features
+
+* Add CS3D WSI and Video Viewports and add annotation navigation for MPR ([#4182](https://github.com/OHIF/Viewers/issues/4182)) ([7599ec9](https://github.com/OHIF/Viewers/commit/7599ec9421129dcade94e6fa6ec7908424ab3134))
+
+
+
+
+
+# [3.9.0-beta.77](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.76...v3.9.0-beta.77) (2024-08-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.76](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.75...v3.9.0-beta.76) (2024-08-08)
+
+
+### Bug Fixes
+
+* unexpected mpr measurements ([#4332](https://github.com/OHIF/Viewers/issues/4332)) ([ab6e341](https://github.com/OHIF/Viewers/commit/ab6e341731652a4fa894fcb576eb23dc95aefa11))
+
+
+
+
+
+# [3.9.0-beta.75](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.74...v3.9.0-beta.75) (2024-08-07)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.74](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.73...v3.9.0-beta.74) (2024-08-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.73](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.72...v3.9.0-beta.73) (2024-08-02)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.72](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.71...v3.9.0-beta.72) (2024-07-31)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.71](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.70...v3.9.0-beta.71) (2024-07-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.70](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.69...v3.9.0-beta.70) (2024-07-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.69](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.68...v3.9.0-beta.69) (2024-07-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.68](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.67...v3.9.0-beta.68) (2024-07-26)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.67](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.66...v3.9.0-beta.67) (2024-07-26)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.66](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.65...v3.9.0-beta.66) (2024-07-24)
+
+
+### Features
+
+* **pmap:** added support for parametric map ([#4284](https://github.com/OHIF/Viewers/issues/4284)) ([fc0064f](https://github.com/OHIF/Viewers/commit/fc0064fd9d8cdc8fde81b81f0e71fd5d077ca22b))
+
+
+
+
+
+# [3.9.0-beta.65](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.64...v3.9.0-beta.65) (2024-07-23)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.64](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.63...v3.9.0-beta.64) (2024-07-19)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [3.9.0-beta.63](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.62...v3.9.0-beta.63) (2024-07-10)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
 # [3.9.0-beta.62](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.61...v3.9.0-beta.62) (2024-07-09)
 
 **Note:** Version bump only for package @ohif/extension-cornerstone

extensions/cornerstone/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone",
-  "version": "3.9.0-beta.62",
+  "version": "3.9.3",
   "description": "OHIF extension for Cornerstone",
   "author": "OHIF",
   "license": "MIT",
@@ -36,12 +36,12 @@
   "peerDependencies": {
     "@cornerstonejs/codec-charls": "^1.2.3",
     "@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2",
-    "@cornerstonejs/codec-openjpeg": "^1.2.2",
-    "@cornerstonejs/codec-openjph": "^2.4.2",
-    "@cornerstonejs/dicom-image-loader": "^1.82.0",
+    "@cornerstonejs/codec-openjpeg": "^1.2.4",
+    "@cornerstonejs/codec-openjph": "^2.4.5",
+    "@cornerstonejs/dicom-image-loader": "^2.2.20",
     "@icr/polyseg-wasm": "^0.4.0",
-    "@ohif/core": "3.9.0-beta.62",
-    "@ohif/ui": "3.9.0-beta.62",
+    "@ohif/core": "3.9.3",
+    "@ohif/ui": "3.9.3",
     "dcmjs": "*",
     "dicom-parser": "^1.8.21",
     "hammerjs": "^2.0.8",
@@ -55,12 +55,11 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/adapters": "^1.82.0",
-    "@cornerstonejs/core": "^1.82.0",
-    "@cornerstonejs/streaming-image-volume-loader": "^1.82.0",
-    "@cornerstonejs/tools": "^1.82.0",
+    "@cornerstonejs/adapters": "^2.2.20",
+    "@cornerstonejs/core": "^2.2.20",
+    "@cornerstonejs/tools": "^2.2.20",
     "@icr/polyseg-wasm": "^0.4.0",
-    "@kitware/vtk.js": "30.4.1",
+    "@kitware/vtk.js": "32.1.1",
     "html2canvas": "^1.4.1",
     "lodash.debounce": "^4.0.8",
     "lodash.merge": "^4.6.2",

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

@@ -2,15 +2,17 @@ import React, { useCallback, useEffect, useMemo, useState } from 'react';
 import { vec3 } from 'gl-matrix';
 import PropTypes from 'prop-types';
 import { metaData, Enums, utilities } from '@cornerstonejs/core';
-import { ImageSliceData } from '@cornerstonejs/core/dist/esm/types';
+import type { ImageSliceData } from '@cornerstonejs/core/types';
 import { ViewportOverlay } from '@ohif/ui';
-import { InstanceMetadata } from '@ohif/core/src/types';
-import { formatPN, formatDICOMDate, formatDICOMTime, formatNumberPrecision } from './utils';
+import type { InstanceMetadata } from '@ohif/core/src/types';
+import { formatDICOMDate, formatDICOMTime, formatNumberPrecision } from './utils';
+import { utils } from '@ohif/core';
 import { StackViewportData, VolumeViewportData } from '../../types/CornerstoneCacheService';
 
 import './CustomizableViewportOverlay.css';
 
 const EPSILON = 1e-4;
+const { formatPN } = utils;
 
 type ViewportData = StackViewportData | VolumeViewportData;
 
@@ -45,14 +47,14 @@ const OverlayItemComponents = {
   'ohif.overlayItem.instanceNumber': InstanceNumberOverlayItem,
 };
 
-
 const studyDateItem = {
   id: 'StudyDate',
   customizationType: 'ohif.overlayItem',
   label: '',
   title: 'Study date',
   condition: ({ referenceInstance }) => referenceInstance?.StudyDate,
-  contentF: ({ referenceInstance, formatters: { formatDate } }) => formatDate(referenceInstance.StudyDate),
+  contentF: ({ referenceInstance, formatters: { formatDate } }) =>
+    formatDate(referenceInstance.StudyDate),
 };
 
 const seriesDescriptionItem = {
@@ -63,15 +65,19 @@ const seriesDescriptionItem = {
   condition: ({ referenceInstance }) => {
     return referenceInstance && referenceInstance.SeriesDescription;
   },
-  contentF: ({ referenceInstance }) => referenceInstance.SeriesDescription
+  contentF: ({ referenceInstance }) => referenceInstance.SeriesDescription,
 };
 
-const topLeftItems = { id: 'cornerstoneOverlayTopLeft', items: [studyDateItem, seriesDescriptionItem] };
+const topLeftItems = {
+  id: 'cornerstoneOverlayTopLeft',
+  items: [studyDateItem, seriesDescriptionItem],
+};
 
 const topRightItems = { id: 'cornerstoneOverlayTopRight', items: [] };
 
 const bottomLeftItems = {
-  id: 'cornerstoneOverlayBottomLeft', items: [
+  id: 'cornerstoneOverlayBottomLeft',
+  items: [
     {
       id: 'WindowLevel',
       customizationType: 'ohif.overlayItem.windowLevel',
@@ -79,12 +85,12 @@ const bottomLeftItems = {
     {
       id: 'ZoomLevel',
       customizationType: 'ohif.overlayItem.zoomLevel',
-      condition: (props) => {
+      condition: props => {
         const activeToolName = props.toolGroupService.getActiveToolForViewport(props.viewportId);
         return activeToolName === 'Zoom';
       },
     },
-  ]
+  ],
 };
 
 const bottomRightItems = {
@@ -94,7 +100,7 @@ const bottomRightItems = {
       id: 'InstanceNumber',
       customizationType: 'ohif.overlayItem.instanceNumber',
     },
-  ]
+  ],
 };
 
 /**
@@ -145,19 +151,18 @@ function CustomizableViewportOverlay({
   // append functionality.  This code enables the historical usage, but
   // the recommended functionality is to append to the default values in
   // cornerstoneOverlay rather than defining individual items.
-  const topLeftCustomization = customizationService.getCustomization(
-    'cornerstoneOverlayTopLeft'
-  ) || cornerstoneOverlay?.topLeftItems;
-  const topRightCustomization = customizationService.getCustomization(
-    'cornerstoneOverlayTopRight'
-  ) || cornerstoneOverlay?.topRightItems;
-  const bottomLeftCustomization = customizationService.getCustomization(
-    'cornerstoneOverlayBottomLeft'
-  ) || cornerstoneOverlay?.bottomLeftItems;
-  const bottomRightCustomization = customizationService.getCustomization(
-    'cornerstoneOverlayBottomRight'
-  ) || cornerstoneOverlay?.bottomRightItems;
-
+  const topLeftCustomization =
+    customizationService.getCustomization('cornerstoneOverlayTopLeft') ||
+    cornerstoneOverlay?.topLeftItems;
+  const topRightCustomization =
+    customizationService.getCustomization('cornerstoneOverlayTopRight') ||
+    cornerstoneOverlay?.topRightItems;
+  const bottomLeftCustomization =
+    customizationService.getCustomization('cornerstoneOverlayBottomLeft') ||
+    cornerstoneOverlay?.bottomLeftItems;
+  const bottomRightCustomization =
+    customizationService.getCustomization('cornerstoneOverlayBottomRight') ||
+    cornerstoneOverlay?.bottomRightItems;
 
   const instanceNumber = useMemo(
     () =>
@@ -177,13 +182,12 @@ function CustomizableViewportOverlay({
     return {
       displaySets,
       displaySet,
-      instance: instances[imageIndex],
+      instance: instances?.[imageIndex],
       instances,
       referenceInstance,
     };
   }, [viewportData, viewportId, instanceNumber, cornerstoneViewportService]);
 
-
   /**
    * Updating the VOI when the viewport changes its voi
    */
@@ -307,7 +311,8 @@ function CustomizableViewportOverlay({
         <>
           {items.map((item, index) => (
             <div key={`${keyPrefix}_${index}`}>
-              {(!item?.condition || item.condition(props)) && _renderOverlayItem(item, props) || null}
+              {((!item?.condition || item.condition(props)) && _renderOverlayItem(item, props)) ||
+                null}
             </div>
           ))}
         </>
@@ -316,7 +321,6 @@ function CustomizableViewportOverlay({
     [_renderOverlayItem]
   );
 
-
   return (
     <ViewportOverlay
       topLeft={getContent(topLeftCustomization, 'topLeftOverlayItem')}
@@ -335,7 +339,9 @@ function getDisplaySets(viewportData, displaySetService) {
   if (!viewportData?.data?.length) {
     return null;
   }
-  const displaySets = viewportData.data.map(datum => displaySetService.getDisplaySetByUID(datum.displaySetInstanceUID)).filter(it => !!it);
+  const displaySets = viewportData.data
+    .map(datum => displaySetService.getDisplaySetByUID(datum.displaySetInstanceUID))
+    .filter(it => !!it);
   if (!displaySets.length) {
     return null;
   }
@@ -382,7 +388,6 @@ function _getInstanceNumberFromStack(viewportData, imageIndex) {
   return parseInt(instanceNumber);
 }
 
-
 // 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
@@ -400,6 +405,11 @@ function _getInstanceNumberFromVolume(
 
   // Todo: support fusion of acquisition plane which has instanceNumber
   const { volume } = volumes[0];
+
+  if (!volume) {
+    return;
+  }
+
   const { direction, imageIds } = volume;
 
   const cornerstoneViewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
@@ -443,9 +453,10 @@ function OverlayItem(props) {
       style={{ color, background }}
       title={title}
     >
-      {label ? (<span className="mr-1 shrink-0">{label}</span>) : null}
+      {label ? <span className="mr-1 shrink-0">{label}</span> : null}
       <span className="ml-1 mr-2 shrink-0">{value}</span>
-    </div>);
+    </div>
+  );
 }
 
 /**

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

@@ -1,7 +1,6 @@
 import React, { useEffect } from 'react';
 import PropTypes from 'prop-types';
-import { Enums, Types, utilities } from '@cornerstonejs/core';
-import { utilities as csToolsUtils } from '@cornerstonejs/tools';
+import { Enums, VolumeViewport3D, utilities as csUtils } from '@cornerstonejs/core';
 import { ImageScrollbar } from '@ohif/ui';
 
 function CornerstoneImageScrollbar({
@@ -12,7 +11,9 @@ function CornerstoneImageScrollbar({
   setImageSliceData,
   scrollbarHeight,
   servicesManager,
-}: withAppTypes) {
+}: withAppTypes<{
+  element: HTMLElement;
+}>) {
   const { cineService, cornerstoneViewportService } = servicesManager.services;
 
   const onImageScrollbarChange = (imageIndex, viewportId) => {
@@ -26,7 +27,7 @@ function CornerstoneImageScrollbar({
       cineService.setCine({ id: viewportId, isPlaying: false });
     }
 
-    csToolsUtils.jumpToSlice(viewport.element, {
+    csUtils.jumpToSlice(viewport.element, {
       imageIndex,
       debounceLoading: true,
     });
@@ -39,71 +40,47 @@ function CornerstoneImageScrollbar({
 
     const viewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
 
-    if (!viewport) {
+    if (!viewport || viewport instanceof VolumeViewport3D) {
       return;
     }
 
-    if (viewportData.viewportType === Enums.ViewportType.STACK) {
-      const imageIndex = viewport.getCurrentImageIdIndex();
+    const imageIndex = viewport.getCurrentImageIdIndex();
+    const numberOfSlices = viewport.getNumberOfSlices();
 
-      setImageSliceData({
-        imageIndex: imageIndex,
-        numberOfSlices: viewportData.data[0].imageIds.length,
-      });
-
-      return;
-    }
-
-    if (viewportData.viewportType === Enums.ViewportType.ORTHOGRAPHIC) {
-      const sliceData = utilities.getImageSliceDataForVolumeViewport(
-        viewport as Types.IVolumeViewport
-      );
-
-      if (!sliceData) {
-        return;
-      }
-
-      const { imageIndex, numberOfSlices } = sliceData;
-      setImageSliceData({ imageIndex, numberOfSlices });
-    }
+    setImageSliceData({
+      imageIndex: imageIndex,
+      numberOfSlices,
+    });
   }, [viewportId, viewportData]);
 
   useEffect(() => {
-    if (viewportData?.viewportType !== Enums.ViewportType.STACK) {
+    if (!viewportData) {
       return;
     }
+    const { viewportType } = viewportData;
+    const eventId =
+      (viewportType === Enums.ViewportType.STACK && Enums.Events.STACK_VIEWPORT_SCROLL) ||
+      (viewportType === Enums.ViewportType.ORTHOGRAPHIC && Enums.Events.VOLUME_NEW_IMAGE) ||
+      Enums.Events.IMAGE_RENDERED;
 
-    const updateStackIndex = event => {
-      const { newImageIdIndex } = event.detail;
+    const updateIndex = event => {
+      const viewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
+      if (!viewport || viewport instanceof VolumeViewport3D) {
+        return;
+      }
+      const { imageIndex, newImageIdIndex = imageIndex } = event.detail;
+      const numberOfSlices = viewport.getNumberOfSlices();
       // find the index of imageId in the imageIds
       setImageSliceData({
         imageIndex: newImageIdIndex,
-        numberOfSlices: viewportData.data[0].imageIds.length,
+        numberOfSlices,
       });
     };
 
-    element.addEventListener(Enums.Events.STACK_VIEWPORT_SCROLL, updateStackIndex);
+    element.addEventListener(eventId, updateIndex);
 
     return () => {
-      element.removeEventListener(Enums.Events.STACK_VIEWPORT_SCROLL, updateStackIndex);
-    };
-  }, [viewportData, element]);
-
-  useEffect(() => {
-    if (viewportData?.viewportType !== Enums.ViewportType.ORTHOGRAPHIC) {
-      return;
-    }
-
-    const updateVolumeIndex = event => {
-      const { imageIndex, numberOfSlices } = event.detail;
-      // find the index of imageId in the imageIds
-      setImageSliceData({ imageIndex, numberOfSlices });
-    };
-
-    element.addEventListener(Enums.Events.VOLUME_NEW_IMAGE, updateVolumeIndex);
-
-    return () => {
-      element.removeEventListener(Enums.Events.VOLUME_NEW_IMAGE, updateVolumeIndex);
+      element.removeEventListener(eventId, updateIndex);
     };
   }, [viewportData, element]);
 
@@ -112,7 +89,7 @@ function CornerstoneImageScrollbar({
       onChange={evt => onImageScrollbarChange(evt, viewportId)}
       max={imageSliceData.numberOfSlices ? imageSliceData.numberOfSlices - 1 : 0}
       height={scrollbarHeight}
-      value={imageSliceData.imageIndex}
+      value={imageSliceData.imageIndex || 0}
     />
   );
 }

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

@@ -1,14 +1,7 @@
 import React, { useEffect, useState, useMemo } from 'react';
 import classNames from 'classnames';
-import {
-  metaData,
-  Enums,
-  Types,
-  getEnabledElement,
-  utilities as csUtils,
-} from '@cornerstonejs/core';
+import { metaData, Enums, Types, getEnabledElement } from '@cornerstonejs/core';
 import { utilities } from '@cornerstonejs/tools';
-import PropTypes from 'prop-types';
 import { vec3 } from 'gl-matrix';
 
 import './ViewportOrientationMarkers.css';
@@ -31,8 +24,9 @@ function ViewportOrientationMarkers({
 
   useEffect(() => {
     const cameraModifiedListener = (evt: Types.EventTypes.CameraModifiedEvent) => {
-      const { rotation, previousCamera, camera } = evt.detail;
+      const { previousCamera, camera } = evt.detail;
 
+      const { rotation } = camera;
       if (rotation !== undefined) {
         setRotation(rotation);
       }
@@ -74,7 +68,12 @@ function ViewportOrientationMarkers({
         return false;
       }
 
-      ({ rowCosines, columnCosines, isDefaultValueSetForColumnCosine, isDefaultValueSetForColumnCosine } = metaData.get('imagePlaneModule', imageId) || {});
+      ({
+        rowCosines,
+        columnCosines,
+        isDefaultValueSetForColumnCosine,
+        isDefaultValueSetForColumnCosine,
+      } = metaData.get('imagePlaneModule', imageId) || {});
     } else {
       if (!element || !getEnabledElement(element)) {
         return '';
@@ -90,7 +89,13 @@ function ViewportOrientationMarkers({
       rowCosines = viewRight;
     }
 
-    if (!rowCosines || !columnCosines || rotation === undefined || isDefaultValueSetForRowCosine || isDefaultValueSetForColumnCosine) {
+    if (
+      !rowCosines ||
+      !columnCosines ||
+      rotation === undefined ||
+      isDefaultValueSetForRowCosine ||
+      isDefaultValueSetForColumnCosine
+    ) {
       return '';
     }
 

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

@@ -52,31 +52,6 @@ export function formatDICOMTime(time, strFormat = 'HH:mm:ss') {
   return moment(time, 'HH:mm:ss').format(strFormat);
 }
 
-/**
- * Formats a patient name for display purposes
- *
- * @param {string} name
- * @returns {string} formatted name.
- */
-export function formatPN(name) {
-  if (!name) {
-    return '';
-  }
-  if (typeof name === 'object') {
-    name = name.Alphabetic;
-    if (!name) {
-      return '';
-    }
-  }
-
-  const cleaned = name
-    .split('^')
-    .filter(s => !!s)
-    .join(', ')
-    .trim();
-  return cleaned === ',' || cleaned === '' ? '' : cleaned;
-}
-
 /**
  * Gets compression type
  *

extensions/cornerstone/src/commandsModule.ts

@@ -12,15 +12,23 @@ import {
   utilities as cstUtils,
   ReferenceLinesTool,
 } from '@cornerstonejs/tools';
+
 import { Types as OhifTypes } from '@ohif/core';
+import {
+  callLabelAutocompleteDialog,
+  showLabelAnnotationPopup,
+  createReportAsync,
+  callInputDialog,
+  colorPickerDialog,
+} from '@ohif/extension-default';
 import { vec3, mat4 } from 'gl-matrix';
 
 import CornerstoneViewportDownloadForm from './utils/CornerstoneViewportDownloadForm';
-import { callLabelAutocompleteDialog, showLabelAnnotationPopup } from './utils/callInputDialog';
 import toggleImageSliceSync from './utils/imageSliceSync/toggleImageSliceSync';
 import { getFirstAnnotationSelected } from './utils/measurementServiceMappings/utils/selection';
 import getActiveViewportEnabledElement from './utils/getActiveViewportEnabledElement';
 import toggleVOISliceSync from './utils/toggleVOISliceSync';
+import { usePositionPresentationStore, useSegmentationPresentationStore } from './stores';
 
 const toggleSyncFunctions = {
   imageSlice: toggleImageSliceSync,
@@ -29,6 +37,7 @@ const toggleSyncFunctions = {
 
 function commandsModule({
   servicesManager,
+  extensionManager,
   commandsManager,
 }: OhifTypes.Extensions.ExtensionParams): OhifTypes.Extensions.CommandsModule {
   const {
@@ -101,7 +110,47 @@ function commandsModule({
 
       commandsManager.run(options, optionsToUse);
     },
+    updateStoredSegmentationPresentation: ({ displaySet, type }) => {
+      const { addSegmentationPresentationItem } = useSegmentationPresentationStore.getState();
 
+      const referencedDisplaySetInstanceUID = displaySet.referencedDisplaySetInstanceUID;
+      addSegmentationPresentationItem(referencedDisplaySetInstanceUID, {
+        segmentationId: displaySet.displaySetInstanceUID,
+        hydrated: true,
+        type,
+      });
+    },
+    updateStoredPositionPresentation: ({ viewportId, displaySetInstanceUID }) => {
+      const presentations = cornerstoneViewportService.getPresentations(viewportId);
+      const { positionPresentationStore, setPositionPresentation, getPositionPresentationId } =
+        usePositionPresentationStore.getState();
+
+      // Look inside positionPresentationStore and find the key that includes the displaySetInstanceUID
+      // and the value has viewportId as activeViewportId.
+      const previousReferencedDisplaySetStoreKey = Object.entries(positionPresentationStore).find(
+        ([key, value]) => key.includes(displaySetInstanceUID) && value.viewportId === viewportId
+      )?.[0];
+
+      if (previousReferencedDisplaySetStoreKey) {
+        setPositionPresentation(
+          previousReferencedDisplaySetStoreKey,
+          presentations.positionPresentation
+        );
+
+        return;
+      }
+
+      // if not found means we have not visited that referencedDisplaySetInstanceUID before
+      // so we need to grab the positionPresentationId directly from the store,
+      // Todo: this is really hacky, we should have a better way for this
+
+      const positionPresentationId = getPositionPresentationId({
+        displaySetInstanceUIDs: [displaySetInstanceUID],
+        viewportId,
+      });
+
+      setPositionPresentation(positionPresentationId, presentations.positionPresentation);
+    },
     getNearbyToolData({ nearbyToolData, element, canvasCoordinates }) {
       return nearbyToolData ?? cstUtils.getAnnotationNearPoint(element, canvasCoordinates);
     },
@@ -435,9 +484,10 @@ function commandsModule({
         viewport.setCamera({ viewUp: rotatedViewUp as CoreTypes.Point3 });
         viewport.render();
       } else if (viewport.getRotation !== undefined) {
-        const currentRotation = viewport.getRotation();
+        const presentation = viewport.getViewPresentation();
+        const { rotation: currentRotation } = presentation;
         const newRotation = (currentRotation + rotation) % 360;
-        viewport.setProperties({ rotation: newRotation });
+        viewport.setViewPresentation({ rotation: newRotation });
         viewport.render();
       }
     },
@@ -554,7 +604,7 @@ function commandsModule({
 
       // Set slice to last slice
       const options = { imageIndex: jumpIndex };
-      cstUtils.jumpToSlice(viewport.element, options);
+      csUtils.jumpToSlice(viewport.element, options);
     },
     scroll: ({ direction }) => {
       const enabledElement = _getActiveViewportEnabledElement();
@@ -566,7 +616,7 @@ function commandsModule({
       const { viewport } = enabledElement;
       const options = { delta: direction };
 
-      cstUtils.scroll(viewport, options);
+      csUtils.scroll(viewport, options);
     },
     setViewportColormap: ({
       viewportId,
@@ -577,7 +627,6 @@ function commandsModule({
     }) => {
       const viewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
 
-      const actorEntries = viewport.getActors();
       let hpOpacity;
       // Retrieve active protocol's viewport match details
       const { viewportMatchDetails } = hangingProtocolService.getActiveProtocol();
@@ -596,14 +645,8 @@ function commandsModule({
       // HP takes priority over the default opacity
       colormap = { ...colormap, opacity: hpOpacity || opacity };
 
-      const setViewportProperties = (viewport, uid) => {
-        const actorEntry = actorEntries.find(entry => entry.uid.includes(uid));
-        const { actor: volumeActor, uid: volumeId } = actorEntry;
-        viewport.setProperties({ colormap, volumeActor }, volumeId);
-      };
-
       if (viewport instanceof StackViewport) {
-        setViewportProperties(viewport, viewportId);
+        viewport.setProperties({ colormap });
       }
 
       if (viewport instanceof VolumeViewport) {
@@ -611,7 +654,9 @@ function commandsModule({
           const { viewports } = viewportGridService.getState();
           displaySetInstanceUID = viewports.get(viewportId)?.displaySetInstanceUIDs[0];
         }
-        setViewportProperties(viewport, displaySetInstanceUID);
+
+        const volumeId = viewport.getVolumeId();
+        viewport.setProperties({ colormap }, volumeId);
       }
 
       if (immediate) {
@@ -824,9 +869,352 @@ function commandsModule({
       }
 
       crosshairInstances.forEach(ins => {
-        ins?.resetCrosshairs();
+        ins?.computeToolCenter();
       });
     },
+    /**
+     * Creates a labelmap for the active viewport
+     */
+    createLabelmapForViewport: async ({ viewportId, options = {} }) => {
+      const { viewportGridService, displaySetService, segmentationService } =
+        servicesManager.services;
+      const { viewports } = viewportGridService.getState();
+      const targetViewportId = viewportId;
+
+      const viewport = viewports.get(targetViewportId);
+
+      // Todo: add support for multiple display sets
+      const displaySetInstanceUID =
+        options.displaySetInstanceUID || viewport.displaySetInstanceUIDs[0];
+
+      const segs = segmentationService.getSegmentations();
+
+      const label = options.label || `Segmentation ${segs.length + 1}`;
+      const segmentationId = options.segmentationId || `${csUtils.uuidv4()}`;
+
+      const displaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
+
+      const generatedSegmentationId = await segmentationService.createLabelmapForDisplaySet(
+        displaySet,
+        {
+          label,
+          segmentationId,
+          segments: options.createInitialSegment
+            ? {
+                1: {
+                  label: 'Segment 1',
+                  active: true,
+                },
+              }
+            : {},
+        }
+      );
+
+      await segmentationService.addSegmentationRepresentation(viewportId, {
+        segmentationId,
+        type: Enums.SegmentationRepresentations.Labelmap,
+      });
+
+      return generatedSegmentationId;
+    },
+
+    /**
+     * Sets the active segmentation for a viewport
+     * @param props.segmentationId - The ID of the segmentation to set as active
+     */
+    setActiveSegmentation: ({ segmentationId }) => {
+      const { viewportGridService, segmentationService } = servicesManager.services;
+      segmentationService.setActiveSegmentation(
+        viewportGridService.getActiveViewportId(),
+        segmentationId
+      );
+    },
+
+    /**
+     * Adds a new segment to a segmentation
+     * @param props.segmentationId - The ID of the segmentation to add the segment to
+     */
+    addSegmentCommand: ({ segmentationId }) => {
+      const { segmentationService } = servicesManager.services;
+      segmentationService.addSegment(segmentationId);
+    },
+
+    /**
+     * Sets the active segment and jumps to its center
+     * @param props.segmentationId - The ID of the segmentation
+     * @param props.segmentIndex - The index of the segment to activate
+     */
+    setActiveSegmentAndCenterCommand: ({ segmentationId, segmentIndex }) => {
+      const { segmentationService } = servicesManager.services;
+      segmentationService.setActiveSegment(segmentationId, segmentIndex);
+      segmentationService.jumpToSegmentCenter(segmentationId, segmentIndex);
+    },
+
+    /**
+     * Toggles the visibility of a segment
+     * @param props.segmentationId - The ID of the segmentation
+     * @param props.segmentIndex - The index of the segment
+     * @param props.type - The type of visibility to toggle
+     */
+    toggleSegmentVisibilityCommand: ({ segmentationId, segmentIndex, type }) => {
+      const { segmentationService, viewportGridService } = servicesManager.services;
+      segmentationService.toggleSegmentVisibility(
+        viewportGridService.getActiveViewportId(),
+        segmentationId,
+        segmentIndex,
+        type
+      );
+    },
+
+    /**
+     * Toggles the lock state of a segment
+     * @param props.segmentationId - The ID of the segmentation
+     * @param props.segmentIndex - The index of the segment
+     */
+    toggleSegmentLockCommand: ({ segmentationId, segmentIndex }) => {
+      const { segmentationService } = servicesManager.services;
+      segmentationService.toggleSegmentLocked(segmentationId, segmentIndex);
+    },
+
+    /**
+     * Toggles the visibility of a segmentation representation
+     * @param props.segmentationId - The ID of the segmentation
+     * @param props.type - The type of representation
+     */
+    toggleSegmentationVisibilityCommand: ({ segmentationId, type }) => {
+      const { segmentationService, viewportGridService } = servicesManager.services;
+      segmentationService.toggleSegmentationRepresentationVisibility(
+        viewportGridService.getActiveViewportId(),
+        { segmentationId, type }
+      );
+    },
+
+    /**
+     * Downloads a segmentation
+     * @param props.segmentationId - The ID of the segmentation to download
+     */
+    downloadSegmentationCommand: ({ segmentationId }) => {
+      const { segmentationService } = servicesManager.services;
+      segmentationService.downloadSegmentation(segmentationId);
+    },
+
+    /**
+     * Stores a segmentation and shows it in the viewport
+     * @param props.segmentationId - The ID of the segmentation to store
+     */
+    storeSegmentationCommand: async ({ segmentationId }) => {
+      const { segmentationService, viewportGridService } = servicesManager.services;
+      const datasources = extensionManager.getActiveDataSource();
+
+      const displaySetInstanceUIDs = await createReportAsync({
+        servicesManager,
+        getReport: () =>
+          commandsManager.runCommand('storeSegmentation', {
+            segmentationId,
+            dataSource: datasources[0],
+          }),
+        reportType: 'Segmentation',
+      });
+
+      if (displaySetInstanceUIDs) {
+        segmentationService.remove(segmentationId);
+        viewportGridService.setDisplaySetsForViewport({
+          viewportId: viewportGridService.getActiveViewportId(),
+          displaySetInstanceUIDs,
+        });
+      }
+    },
+
+    /**
+     * Downloads a segmentation as RTSS
+     * @param props.segmentationId - The ID of the segmentation
+     */
+    downloadRTSSCommand: ({ segmentationId }) => {
+      const { segmentationService } = servicesManager.services;
+      segmentationService.downloadRTSS(segmentationId);
+    },
+
+    /**
+     * Sets the style for a segmentation
+     * @param props.segmentationId - The ID of the segmentation
+     * @param props.type - The type of style
+     * @param props.key - The style key to set
+     * @param props.value - The style value
+     */
+    setSegmentationStyleCommand: ({ type, key, value }) => {
+      const { segmentationService } = servicesManager.services;
+      segmentationService.setStyle({ type }, { [key]: value });
+    },
+
+    /**
+     * Deletes a segment from a segmentation
+     * @param props.segmentationId - The ID of the segmentation
+     * @param props.segmentIndex - The index of the segment to delete
+     */
+    deleteSegmentCommand: ({ segmentationId, segmentIndex }) => {
+      const { segmentationService } = servicesManager.services;
+      segmentationService.removeSegment(segmentationId, segmentIndex);
+    },
+
+    /**
+     * Deletes an entire segmentation
+     * @param props.segmentationId - The ID of the segmentation to delete
+     */
+    deleteSegmentationCommand: ({ segmentationId }) => {
+      const { segmentationService } = servicesManager.services;
+      segmentationService.remove(segmentationId);
+    },
+
+    /**
+     * Removes a segmentation from the viewport
+     * @param props.segmentationId - The ID of the segmentation to remove
+     */
+    removeSegmentationFromViewportCommand: ({ segmentationId }) => {
+      const { segmentationService, viewportGridService } = servicesManager.services;
+      segmentationService.removeSegmentationRepresentations(
+        viewportGridService.getActiveViewportId(),
+        { segmentationId }
+      );
+    },
+
+    /**
+     * Toggles rendering of inactive segmentations
+     */
+    toggleRenderInactiveSegmentationsCommand: () => {
+      const { segmentationService, viewportGridService } = servicesManager.services;
+      const viewportId = viewportGridService.getActiveViewportId();
+      const renderInactive = segmentationService.getRenderInactiveSegmentations(viewportId);
+      segmentationService.setRenderInactiveSegmentations(viewportId, !renderInactive);
+    },
+
+    /**
+     * Sets the fill alpha value for a segmentation type
+     * @param props.type - The type of segmentation
+     * @param props.value - The alpha value to set
+     */
+    setFillAlphaCommand: ({ type, value }) => {
+      const { segmentationService } = servicesManager.services;
+      segmentationService.setStyle({ type }, { fillAlpha: value });
+    },
+
+    /**
+     * Sets the outline width for a segmentation type
+     * @param props.type - The type of segmentation
+     * @param props.value - The width value to set
+     */
+    setOutlineWidthCommand: ({ type, value }) => {
+      const { segmentationService } = servicesManager.services;
+      segmentationService.setStyle({ type }, { outlineWidth: value });
+    },
+
+    /**
+     * Sets whether to render fill for a segmentation type
+     * @param props.type - The type of segmentation
+     * @param props.value - Whether to render fill
+     */
+    setRenderFillCommand: ({ type, value }) => {
+      const { segmentationService } = servicesManager.services;
+      segmentationService.setStyle({ type }, { renderFill: value });
+    },
+
+    /**
+     * Sets whether to render outline for a segmentation type
+     * @param props.type - The type of segmentation
+     * @param props.value - Whether to render outline
+     */
+    setRenderOutlineCommand: ({ type, value }) => {
+      const { segmentationService } = servicesManager.services;
+      segmentationService.setStyle({ type }, { renderOutline: value });
+    },
+
+    /**
+     * Sets the fill alpha for inactive segmentations
+     * @param props.type - The type of segmentation
+     * @param props.value - The alpha value to set
+     */
+    setFillAlphaInactiveCommand: ({ type, value }) => {
+      const { segmentationService } = servicesManager.services;
+      segmentationService.setStyle({ type }, { fillAlphaInactive: value });
+    },
+
+    editSegmentLabel: ({ segmentationId, segmentIndex }) => {
+      const { segmentationService, uiDialogService } = servicesManager.services;
+      const segmentation = segmentationService.getSegmentation(segmentationId);
+
+      if (!segmentation) {
+        return;
+      }
+
+      const segment = segmentation.segments[segmentIndex];
+      const { label } = segment;
+
+      const callback = (label, actionId) => {
+        if (label === '') {
+          return;
+        }
+
+        segmentationService.setSegmentLabel(segmentationId, segmentIndex, label);
+      };
+
+      callInputDialog(uiDialogService, label, callback, false, {
+        dialogTitle: 'Edit Segment Label',
+        inputLabel: 'Enter new label',
+      });
+    },
+
+    editSegmentationLabel: ({ segmentationId }) => {
+      const { segmentationService, uiDialogService } = servicesManager.services;
+      const segmentation = segmentationService.getSegmentation(segmentationId);
+
+      if (!segmentation) {
+        return;
+      }
+
+      const { label } = segmentation;
+
+      const callback = (label, actionId) => {
+        if (label === '') {
+          return;
+        }
+
+        segmentationService.addOrUpdateSegmentation({ segmentationId, label });
+      };
+
+      callInputDialog(uiDialogService, label, callback, false, {
+        dialogTitle: 'Edit Segmentation Label',
+        inputLabel: 'Enter new label',
+      });
+    },
+
+    editSegmentColor: ({ segmentationId, segmentIndex }) => {
+      const { segmentationService, uiDialogService, viewportGridService } =
+        servicesManager.services;
+      const viewportId = viewportGridService.getActiveViewportId();
+      const color = segmentationService.getSegmentColor(viewportId, segmentationId, segmentIndex);
+
+      const rgbaColor = {
+        r: color[0],
+        g: color[1],
+        b: color[2],
+        a: color[3] / 255.0,
+      };
+
+      colorPickerDialog(uiDialogService, rgbaColor, (newRgbaColor, actionId) => {
+        if (actionId === 'cancel') {
+          return;
+        }
+
+        const color = [newRgbaColor.r, newRgbaColor.g, newRgbaColor.b, newRgbaColor.a * 255.0];
+        segmentationService.setSegmentColor(viewportId, segmentationId, segmentIndex, color);
+      });
+    },
+
+    getRenderInactiveSegmentations: () => {
+      const { segmentationService, viewportGridService } = servicesManager.services;
+      return segmentationService.getRenderInactiveSegmentations(
+        viewportGridService.getActiveViewportId()
+      );
+    },
   };
 
   const definitions = {
@@ -988,6 +1376,84 @@ function commandsModule({
     toggleActiveDisabledToolbar: {
       commandFn: actions.toggleActiveDisabledToolbar,
     },
+    updateStoredPositionPresentation: {
+      commandFn: actions.updateStoredPositionPresentation,
+    },
+    updateStoredSegmentationPresentation: {
+      commandFn: actions.updateStoredSegmentationPresentation,
+    },
+    createLabelmapForViewport: {
+      commandFn: actions.createLabelmapForViewport,
+    },
+    setActiveSegmentation: {
+      commandFn: actions.setActiveSegmentation,
+    },
+    addSegment: {
+      commandFn: actions.addSegmentCommand,
+    },
+    setActiveSegmentAndCenter: {
+      commandFn: actions.setActiveSegmentAndCenterCommand,
+    },
+    toggleSegmentVisibility: {
+      commandFn: actions.toggleSegmentVisibilityCommand,
+    },
+    toggleSegmentLock: {
+      commandFn: actions.toggleSegmentLockCommand,
+    },
+    toggleSegmentationVisibility: {
+      commandFn: actions.toggleSegmentationVisibilityCommand,
+    },
+    downloadSegmentation: {
+      commandFn: actions.downloadSegmentationCommand,
+    },
+    storeSegmentation: {
+      commandFn: actions.storeSegmentationCommand,
+    },
+    downloadRTSS: {
+      commandFn: actions.downloadRTSSCommand,
+    },
+    setSegmentationStyle: {
+      commandFn: actions.setSegmentationStyleCommand,
+    },
+    deleteSegment: {
+      commandFn: actions.deleteSegmentCommand,
+    },
+    deleteSegmentation: {
+      commandFn: actions.deleteSegmentationCommand,
+    },
+    removeSegmentationFromViewport: {
+      commandFn: actions.removeSegmentationFromViewportCommand,
+    },
+    toggleRenderInactiveSegmentations: {
+      commandFn: actions.toggleRenderInactiveSegmentationsCommand,
+    },
+    setFillAlpha: {
+      commandFn: actions.setFillAlphaCommand,
+    },
+    setOutlineWidth: {
+      commandFn: actions.setOutlineWidthCommand,
+    },
+    setRenderFill: {
+      commandFn: actions.setRenderFillCommand,
+    },
+    setRenderOutline: {
+      commandFn: actions.setRenderOutlineCommand,
+    },
+    setFillAlphaInactive: {
+      commandFn: actions.setFillAlphaInactiveCommand,
+    },
+    editSegmentLabel: {
+      commandFn: actions.editSegmentLabel,
+    },
+    editSegmentationLabel: {
+      commandFn: actions.editSegmentationLabel,
+    },
+    editSegmentColor: {
+      commandFn: actions.editSegmentColor,
+    },
+    getRenderInactiveSegmentations: {
+      commandFn: actions.getRenderInactiveSegmentations,
+    },
   };
 
   return {

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

@@ -1,7 +1,6 @@
 import React, { useCallback, useEffect, useState, useRef } from 'react';
 import { CinePlayer, useCine } from '@ohif/ui';
 import { Enums, eventTarget, cache } from '@cornerstonejs/core';
-import { Enums as StreamingEnums } from '@cornerstonejs/streaming-image-volume-loader';
 import { useAppConfig } from '@state';
 
 function WrappedCinePlayer({
@@ -101,7 +100,7 @@ function WrappedCinePlayer({
       return;
     }
 
-    eventTarget.addEventListener(Enums.Events.STACK_VIEWPORT_NEW_STACK, newDisplaySetHandler);
+    enabledVPElement.addEventListener(Enums.Events.VIEWPORT_NEW_IMAGE_SET, newDisplaySetHandler);
     // this doesn't makes sense that we are listening to this event on viewport element
     enabledVPElement.addEventListener(
       Enums.Events.VOLUME_VIEWPORT_NEW_VOLUME,
@@ -111,7 +110,10 @@ function WrappedCinePlayer({
     return () => {
       cineService.setCine({ id: viewportId, isPlaying: false });
 
-      eventTarget.removeEventListener(Enums.Events.STACK_VIEWPORT_NEW_STACK, newDisplaySetHandler);
+      enabledVPElement.removeEventListener(
+        Enums.Events.VIEWPORT_NEW_IMAGE_SET,
+        newDisplaySetHandler
+      );
       enabledVPElement.removeEventListener(
         Enums.Events.VOLUME_VIEWPORT_NEW_VOLUME,
         newDisplaySetHandler
@@ -181,13 +183,13 @@ function RenderCinePlayer({
     };
 
     eventTarget.addEventListener(
-      StreamingEnums.Events.DYNAMIC_VOLUME_TIME_POINT_INDEX_CHANGED,
+      Enums.Events.DYNAMIC_VOLUME_TIME_POINT_INDEX_CHANGED,
       handleTimePointIndexChange
     );
 
     return () => {
       eventTarget.removeEventListener(
-        StreamingEnums.Events.DYNAMIC_VOLUME_TIME_POINT_INDEX_CHANGED,
+        Enums.Events.DYNAMIC_VOLUME_TIME_POINT_INDEX_CHANGED,
         handleTimePointIndexChange
       );
     };
@@ -199,7 +201,7 @@ function RenderCinePlayer({
     }
 
     const { volumeId, timePointIndex, numTimePoints, splittingTag } = dynamicInfo || {};
-    const volume = cache.getVolume(volumeId);
+    const volume = cache.getVolume(volumeId, true);
     volume.timePointIndex = timePointIndex;
 
     setDynamicInfo({ volumeId, timePointIndex, numTimePoints, label: splittingTag });
@@ -207,7 +209,7 @@ function RenderCinePlayer({
 
   const updateDynamicInfo = useCallback(props => {
     const { volumeId, timePointIndex } = props;
-    const volume = cache.getVolume(volumeId);
+    const volume = cache.getVolume(volumeId, true);
     volume.timePointIndex = timePointIndex;
   }, []);
 
@@ -223,6 +225,7 @@ function RenderCinePlayer({
           isPlaying: false,
         });
         cineService.setIsCineEnabled(false);
+        cineService.setViewportCineClosed(viewportId);
       }}
       onPlayPauseChange={isPlaying => {
         cineService.setCine({

extensions/cornerstone/src/components/ViewportDataOverlaySettingMenu/ViewportSegmentationMenu.tsx

@@ -0,0 +1,136 @@
+import React, { useEffect, useState } from 'react';
+import { Button, Icons, Separator } from '@ohif/ui-next';
+import { SegmentationRepresentations } from '@cornerstonejs/tools/enums';
+
+function ViewportSegmentationMenu({
+  viewportId,
+  servicesManager,
+}: withAppTypes<{ viewportId: string }>) {
+  const { segmentationService } = servicesManager.services;
+  const [activeSegmentations, setActiveSegmentations] = useState([]);
+  const [availableSegmentations, setAvailableSegmentations] = useState([]);
+
+  useEffect(() => {
+    const updateSegmentations = () => {
+      const active = segmentationService.getSegmentationRepresentations(viewportId);
+      setActiveSegmentations(active);
+
+      const all = segmentationService.getSegmentations();
+      const available = all.filter(
+        seg => !active.some(activeSeg => activeSeg.segmentationId === seg.segmentationId)
+      );
+      setAvailableSegmentations(available);
+    };
+
+    updateSegmentations();
+
+    const subscriptions = [
+      segmentationService.EVENTS.SEGMENTATION_MODIFIED,
+      segmentationService.EVENTS.SEGMENTATION_REMOVED,
+      segmentationService.EVENTS.SEGMENTATION_REPRESENTATION_MODIFIED,
+    ].map(event => segmentationService.subscribe(event, updateSegmentations));
+
+    return () => {
+      subscriptions.forEach(subscription => subscription.unsubscribe());
+    };
+  }, [segmentationService, viewportId]);
+
+  const toggleSegmentationRepresentationVisibility = (
+    segmentationId,
+    type = SegmentationRepresentations.Labelmap
+  ) => {
+    segmentationService.toggleSegmentationRepresentationVisibility(viewportId, {
+      segmentationId,
+      type,
+    });
+  };
+
+  const addSegmentationToViewport = segmentationId => {
+    segmentationService.addSegmentationRepresentation(viewportId, { segmentationId });
+  };
+
+  const removeSegmentationFromViewport = segmentationId => {
+    segmentationService.removeSegmentationRepresentations(viewportId, {
+      segmentationId,
+    });
+  };
+
+  return (
+    <div className="bg-muted flex h-full w-[262px] flex-col rounded p-3">
+      <span className="text-muted-foreground mb-2 text-xs font-semibold">Current Viewport</span>
+      <ul className="space-y-1">
+        {activeSegmentations.map(segmentation => (
+          <li
+            key={segmentation.id}
+            className="flex items-center text-sm"
+          >
+            <Button
+              variant="ghost"
+              size="icon"
+              className="text-muted-foreground mr-2"
+              onClick={() => removeSegmentationFromViewport(segmentation.segmentationId)}
+            >
+              <Icons.Minus className="h-6 w-6" />
+            </Button>
+            <span className="text-foreground flex-grow">{segmentation.label}</span>
+            {segmentation.visible ? (
+              <Button
+                variant="ghost"
+                size="icon"
+                className="text-muted-foreground"
+                onClick={() =>
+                  toggleSegmentationRepresentationVisibility(
+                    segmentation.segmentationId,
+                    segmentation.type
+                  )
+                }
+              >
+                <Icons.Hide className="h-6 w-6" />
+              </Button>
+            ) : (
+              <Button
+                variant="ghost"
+                size="icon"
+                className="text-muted-foreground"
+                onClick={() =>
+                  toggleSegmentationRepresentationVisibility(
+                    segmentation.segmentationId,
+                    segmentation.type
+                  )
+                }
+              >
+                <Icons.Show className="h-6 w-6" />
+              </Button>
+            )}
+          </li>
+        ))}
+      </ul>
+      {availableSegmentations.length > 0 && (
+        <>
+          <Separator className="bg-input mb-3" />
+          <span className="text-muted-foreground mb-2 text-xs font-semibold">Available</span>
+          <ul className="space-y-1">
+            {availableSegmentations.map(({segmentationId, label}) => (
+              <li
+                key={segmentationId}
+                className="flex items-center text-sm"
+              >
+                <Button
+                  variant="ghost"
+                  size="icon"
+                  className="text-muted-foreground mr-2"
+                  onClick={() => addSegmentationToViewport(segmentationId)}
+                >
+                  <Icons.Plus className="h-6 w-6" />
+                </Button>
+                <span className="text-foreground/60">{label}</span>
+              </li>
+            ))}
+          </ul>
+        </>
+      )}
+    </div>
+  );
+}
+
+export default ViewportSegmentationMenu;

extensions/cornerstone/src/components/ViewportDataOverlaySettingMenu/ViewportSegmentationMenuWrapper.tsx

@@ -0,0 +1,83 @@
+import React, { ReactNode, useEffect, useState } from 'react';
+import { Button, Icons, Popover, PopoverContent, PopoverTrigger } from '@ohif/ui-next';
+import ViewportSegmentationMenu from './ViewportSegmentationMenu';
+import classNames from 'classnames';
+import { useSegmentations } from '../../hooks/useSegmentations';
+
+export function ViewportSegmentationMenuWrapper({
+  viewportId,
+  displaySets,
+  servicesManager,
+  commandsManager,
+  location,
+}: withAppTypes<{
+  viewportId: string;
+  element: HTMLElement;
+}>): ReactNode {
+  const { viewportActionCornersService, viewportGridService } = servicesManager.services;
+
+  const segmentations = useSegmentations({ servicesManager });
+
+  const activeViewportId = viewportGridService.getActiveViewportId();
+  const isActiveViewport = viewportId === activeViewportId;
+
+  const { align, side } = getAlignAndSide(viewportActionCornersService, location);
+
+  if (!segmentations?.length) {
+    return null;
+  }
+
+  return (
+    <Popover>
+      <PopoverTrigger
+        asChild
+        className="flex items-center justify-center"
+      >
+        <Button
+          variant="ghost"
+          size="icon"
+        >
+          <Icons.ViewportViews
+            className={classNames(
+              'text-highlight',
+              isActiveViewport ? 'visible' : 'invisible group-hover/pane:visible'
+            )}
+          />
+        </Button>
+      </PopoverTrigger>
+      <PopoverContent
+        className="border-none bg-transparent p-0 shadow-none"
+        side={side}
+        align={align}
+        alignOffset={-15}
+        sideOffset={5}
+      >
+        <ViewportSegmentationMenu
+          className="w-full"
+          viewportId={viewportId}
+          displaySets={displaySets}
+          servicesManager={servicesManager}
+          commandsManager={commandsManager}
+        />
+      </PopoverContent>
+    </Popover>
+  );
+}
+
+const getAlignAndSide = (viewportActionCornersService, location) => {
+  const ViewportActionCornersLocations = viewportActionCornersService.LOCATIONS;
+
+  switch (location) {
+    case ViewportActionCornersLocations.topLeft:
+      return { align: 'start', side: 'bottom' };
+    case ViewportActionCornersLocations.topRight:
+      return { align: 'end', side: 'bottom' };
+    case ViewportActionCornersLocations.bottomLeft:
+      return { align: 'start', side: 'top' };
+    case ViewportActionCornersLocations.bottomRight:
+      return { align: 'end', side: 'top' };
+    default:
+      console.debug('Unknown location, defaulting to bottom-start');
+      return { align: 'start', side: 'bottom' };
+  }
+};

extensions/cornerstone/src/components/ViewportDataOverlaySettingMenu/index.tsx

@@ -0,0 +1,11 @@
+import React, { ReactNode } from 'react';
+import { ViewportSegmentationMenuWrapper } from './ViewportSegmentationMenuWrapper';
+
+export function getViewportDataOverlaySettingsMenu(
+  props: withAppTypes<{
+    viewportId: string;
+    element: HTMLElement;
+  }>
+): ReactNode {
+  return <ViewportSegmentationMenuWrapper {...props} />;
+}

extensions/cornerstone/src/components/ViewportWindowLevel/ViewportWindowLevel.tsx

@@ -1,10 +1,15 @@
-import React, { useEffect, useCallback, useState, ReactElement } from 'react';
+import React, { useEffect, useCallback, useState, ReactElement, useMemo } from 'react';
 import PropTypes from 'prop-types';
 import debounce from 'lodash.debounce';
 import { PanelSection, WindowLevel } from '@ohif/ui';
-import vtkColorMaps from '@kitware/vtk.js/Rendering/Core/ColorTransferFunction/ColorMaps';
-import { Enums, eventTarget, cache as cs3DCache, utilities as csUtils } from '@cornerstonejs/core';
-import { getViewportVolumeHistogram } from './getViewportVolumeHistogram';
+import { Enums, eventTarget } from '@cornerstonejs/core';
+import { useActiveViewportDisplaySets } from '@ohif/core';
+import {
+  getNodeOpacity,
+  isPetVolumeWithDefaultOpacity,
+  isVolumeWithConstantOpacity,
+  getWindowLevelsData,
+} from './utils';
 
 const { Events } = Enums;
 
@@ -16,19 +21,16 @@ const ViewportWindowLevel = ({
 }>): ReactElement => {
   const { cornerstoneViewportService } = servicesManager.services;
   const [windowLevels, setWindowLevels] = useState([]);
-  const [cachedHistograms, setCachedHistograms] = useState({});
+  const [isLoading, setIsLoading] = useState(true);
+  const displaySets = useActiveViewportDisplaySets({ servicesManager });
 
-  /**
-   * Looks for all viewports that has exactly all volumeIds passed as parameter.
-   */
   const getViewportsWithVolumeIds = useCallback(
     (volumeIds: string[]) => {
       const renderingEngine = cornerstoneViewportService.getRenderingEngine();
       const viewports = renderingEngine.getVolumeViewports();
 
       return viewports.filter(vp => {
-        const viewportVolumeIds = vp.getActors().map(actor => actor.uid);
-
+        const viewportVolumeIds = vp.getActors().map(actor => actor.referencedId);
         return (
           volumeIds.length === viewportVolumeIds.length &&
           volumeIds.every(volumeId => viewportVolumeIds.includes(volumeId))
@@ -38,97 +40,10 @@ const ViewportWindowLevel = ({
     [cornerstoneViewportService]
   );
 
-  const getNodeOpacity = (volumeActor, nodeIndex) => {
-    const volumeOpacity = volumeActor.getProperty().getScalarOpacity(0);
-    const nodeValue = [];
-
-    volumeOpacity.getNodeValue(nodeIndex, nodeValue);
-
-    return nodeValue[1];
-  };
-
-  /**
-   * Checks if the opacity applied to the PET volume is something like
-   * [{x: 0, y: 0}, {x: 0.1, y: [C]}, {x: [ANY], y: [C]}] where C is a
-   * constant opacity value for all x's greater than 0.1
-   */
-  const isPetVolumeWithDefaultOpacity = (volumeId, volumeActor) => {
-    const volume = cs3DCache.getVolume(volumeId);
-
-    if (!volume) {
-      return false;
-    }
-
-    const modality = volume.metadata.Modality;
-
-    if (modality !== 'PT') {
-      return false;
-    }
-
-    const volumeOpacity = volumeActor.getProperty().getScalarOpacity(0);
-
-    // It must have at least two points (0 and 0.1)
-    if (volumeOpacity.getSize() < 2) {
-      return false;
-    }
-
-    const node1Value = [];
-    const node2Value = [];
-
-    volumeOpacity.getNodeValue(0, node1Value);
-    volumeOpacity.getNodeValue(1, node2Value);
-
-    // First node must be (x:0, y:0} and the second one {x:0.1, y:any}
-    if (node1Value[0] !== 0 || node1Value[1] !== 0 || node2Value[0] !== 0.1) {
-      return false;
-    }
-
-    const expectedOpacity = node2Value[1];
-    const opacitySize = volumeOpacity.getSize();
-    const currentNodeValue = [];
-
-    // Any point after 0.1 must have the same opacity
-    for (let i = 2; i < opacitySize; i++) {
-      volumeOpacity.getNodeValue(i, currentNodeValue);
-
-      if (currentNodeValue[1] !== expectedOpacity) {
-        return false;
-      }
-    }
-
-    return true;
-  };
-
-  /**
-   * Checks if the opacity function has a constance opacity value for all x's
-   */
-  const isVolumeWithConstantOpacity = volumeActor => {
-    const volumeOpacity = volumeActor.getProperty().getScalarOpacity(0);
-    const opacitySize = volumeOpacity.getSize();
-    const firstNodeValue = [];
-
-    volumeOpacity.getNodeValue(0, firstNodeValue);
-
-    const firstNodeOpacity = firstNodeValue[1];
-
-    for (let i = 0; i < opacitySize; i++) {
-      const currentNodeValue = [];
-
-      volumeOpacity.getNodeValue(0, currentNodeValue);
-
-      if (currentNodeValue[1] !== firstNodeOpacity) {
-        return false;
-      }
-    }
-
-    return true;
-  };
-
   const getVolumeOpacity = useCallback((viewport, volumeId) => {
-    const volumeActor = viewport.getActor(volumeId).actor;
+    const volumeActor = viewport.getActors().find(actor => actor.referencedId === volumeId)?.actor;
 
     if (isPetVolumeWithDefaultOpacity(volumeId, volumeActor)) {
-      // Get the opacity from the second node at 0.1
       return getNodeOpacity(volumeActor, 1);
     } else if (isVolumeWithConstantOpacity(volumeActor)) {
       return getNodeOpacity(volumeActor, 0);
@@ -137,85 +52,14 @@ const ViewportWindowLevel = ({
     return undefined;
   }, []);
 
-  const getWindowLevelsData = useCallback(
-    async (viewportId: number) => {
-      const viewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
-
-      if (!viewport) {
-        return [];
-      }
-
-      const viewportInfo = cornerstoneViewportService.getViewportInfo(viewportId);
-
-      const volumeIds = viewport.getActors().map(actor => actor.uid);
-      const viewportProperties = viewport.getProperties();
-      const { voiRange } = viewportProperties;
-      const viewportVoi = voiRange
-        ? {
-            windowWidth: voiRange.upper - voiRange.lower,
-            windowCenter: voiRange.lower + (voiRange.upper - voiRange.lower) / 2,
-          }
-        : undefined;
-
-      const windowLevels = await Promise.all(
-        volumeIds.map(async (volumeId, volumeIndex) => {
-          const volume = cs3DCache.getVolume(volumeId);
-
-          if (!volume) {
-            return null;
-          }
-
-          const opacity = getVolumeOpacity(viewport, volumeId);
-          const { metadata, scaling } = volume;
-          const modality = metadata.Modality;
-
-          // TODO: find a proper way to fix the histogram
-          const options = {
-            min: modality === 'PT' ? 0.1 : -999,
-            max: modality === 'PT' ? 5 : 10000,
-          };
-
-          const histogram =
-            cachedHistograms[volumeId] ??
-            (await getViewportVolumeHistogram(viewport, volume, options));
-          const { voi: displaySetVOI, colormap: displaySetColormap } =
-            viewportInfo.displaySetOptions[volumeIndex];
-          let colormap;
-          if (displaySetColormap) {
-            colormap =
-              csUtils.colormap.getColormap(displaySetColormap.name) ??
-              vtkColorMaps.getPresetByName(displaySetColormap.name);
-          }
-
-          const voi = !volumeIndex ? viewportVoi ?? displaySetVOI : displaySetVOI;
-
-          return {
-            viewportId,
-            modality,
-            volumeId,
-            volumeIndex,
-            voi,
-            histogram,
-            colormap,
-            step: scaling?.PT ? 0.05 : 1,
-            opacity,
-            showOpacitySlider: volumeIndex === 1 && opacity !== undefined,
-          };
-        })
-      );
-
-      const data = windowLevels.filter(Boolean);
-      return data;
-    },
-
-    [cachedHistograms, cornerstoneViewportService, getVolumeOpacity]
-  );
-
   const updateViewportHistograms = useCallback(() => {
-    getWindowLevelsData(viewportId).then(windowLevels => {
-      setWindowLevels(windowLevels);
+    const viewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
+    const viewportInfo = cornerstoneViewportService.getViewportInfo(viewportId);
+
+    getWindowLevelsData(viewport, viewportInfo, getVolumeOpacity).then(data => {
+      setWindowLevels(data);
     });
-  }, [viewportId, getWindowLevelsData]);
+  }, [viewportId, cornerstoneViewportService, getVolumeOpacity]);
 
   const handleCornerstoneVOIModified = useCallback(
     e => {
@@ -252,8 +96,8 @@ const ViewportWindowLevel = ({
     [windowLevels]
   );
 
-  const debouncedHandleCornerstoneVOIModified = useCallback(
-    debounce(handleCornerstoneVOIModified, 100),
+  const debouncedHandleCornerstoneVOIModified = useMemo(
+    () => debounce(handleCornerstoneVOIModified, 100),
     [handleCornerstoneVOIModified]
   );
 
@@ -280,7 +124,7 @@ const ViewportWindowLevel = ({
         return;
       }
 
-      const viewportVolumeIds = viewport.getActors().map(actor => actor.uid);
+      const viewportVolumeIds = viewport.getActors().map(actor => actor.referencedId);
       const viewports = getViewportsWithVolumeIds(viewportVolumeIds);
 
       viewports.forEach(vp => {
@@ -291,49 +135,50 @@ const ViewportWindowLevel = ({
     [getViewportsWithVolumeIds, cornerstoneViewportService]
   );
 
-  // Listen to windowLevels changes and caches all the new ones
+  // New function to handle image volume loading completion
+  const handleImageVolumeLoadingCompleted = useCallback(() => {
+    setIsLoading(false);
+    updateViewportHistograms();
+  }, [updateViewportHistograms]);
+
+  // Listen to cornerstone events and set up interval for histogram updates
   useEffect(() => {
-    const newVolumeHistograms = windowLevels
-      .filter(windowLevel => !cachedHistograms[windowLevel.volumeId] && windowLevel.histogram)
-      .reduce((volumeHistograms, windowLevel) => {
-        // If the histogram exists, add it to the volumeHistograms object
-        if (windowLevel?.histogram) {
-          volumeHistograms[windowLevel.volumeId] = windowLevel.histogram;
-        }
-        return volumeHistograms;
-      }, {});
-
-    if (Object.keys(newVolumeHistograms).length) {
-      setCachedHistograms(prev => ({ ...prev, ...newVolumeHistograms }));
-    }
-  }, [windowLevels, cachedHistograms]);
-
-  // Updates the histogram when the viewport index prop has changed
-  useEffect(() => updateViewportHistograms(), [viewportId, updateViewportHistograms]);
-
-  // Listen to cornerstone events on "eventTarget" and at the document level
-  useEffect(() => {
-    eventTarget.addEventListener(Events.IMAGE_VOLUME_LOADING_COMPLETED, updateViewportHistograms);
-
     document.addEventListener(Events.VOI_MODIFIED, debouncedHandleCornerstoneVOIModified, true);
+    eventTarget.addEventListener(
+      Events.IMAGE_VOLUME_LOADING_COMPLETED,
+      handleImageVolumeLoadingCompleted
+    );
+
+    const intervalId = setInterval(() => {
+      if (isLoading) {
+        updateViewportHistograms();
+      }
+    }, 1000);
 
     return () => {
-      eventTarget.removeEventListener(
-        Events.IMAGE_VOLUME_LOADING_COMPLETED,
-        updateViewportHistograms
-      );
-
       document.removeEventListener(
         Events.VOI_MODIFIED,
         debouncedHandleCornerstoneVOIModified,
         true
       );
+      eventTarget.removeEventListener(
+        Events.IMAGE_VOLUME_LOADING_COMPLETED,
+        handleImageVolumeLoadingCompleted
+      );
+      clearInterval(intervalId);
     };
-  }, [updateViewportHistograms, debouncedHandleCornerstoneVOIModified]);
+  }, [
+    updateViewportHistograms,
+    debouncedHandleCornerstoneVOIModified,
+    handleImageVolumeLoadingCompleted,
+    isLoading,
+  ]);
+
+  // Create a memoized version of displaySet IDs for comparison
+  const displaySetIds = useMemo(() => {
+    return displaySets?.map(ds => ds.displaySetInstanceUID).sort() || [];
+  }, [displaySets]);
 
-  // Updates the viewport when the context of the viewport has changed. This is
-  // necessary when moving across different stages because the viewport index
-  // may not change but the volumes loaded on it may change.
   useEffect(() => {
     const { unsubscribe } = cornerstoneViewportService.subscribe(
       cornerstoneViewportService.EVENTS.VIEWPORT_VOLUMES_CHANGED,
@@ -344,10 +189,15 @@ const ViewportWindowLevel = ({
       }
     );
 
+    // Only update if displaySets actually changed and are loaded
+    if (displaySetIds.length && !isLoading) {
+      updateViewportHistograms();
+    }
+
     return () => {
       unsubscribe();
     };
-  }, [viewportId, cornerstoneViewportService, updateViewportHistograms]);
+  }, [viewportId, cornerstoneViewportService, updateViewportHistograms, displaySetIds, isLoading]);
 
   return (
     <PanelSection title="Window Level">

extensions/cornerstone/src/components/ViewportWindowLevel/getViewportVolumeHistogram.ts

@@ -20,10 +20,6 @@ const workerFn = () => {
 const getViewportVolumeHistogram = async (viewport, volume, options?) => {
   workerManager.registerWorker('histogram-worker', workerFn, WorkerOptions);
 
-  if (!volume?.loadStatus.loaded) {
-    return undefined;
-  }
-
   const volumeImageData = viewport.getImageData(volume.volumeId);
 
   if (!volumeImageData) {
@@ -32,12 +28,15 @@ const getViewportVolumeHistogram = async (viewport, volume, options?) => {
 
   let scalarData = volume.scalarData;
 
-  let prevTimePoint;
   if (volume.numTimePoints > 1) {
-    prevTimePoint = volume.timePointIndex;
-    const middleTimePoint = Math.round(volume.numTimePoints / 2);
-    volume.timePointIndex = middleTimePoint;
-    scalarData = volume.getScalarData(middleTimePoint);
+    const targetTimePoint = volume.numTimePoints - 1; // or any other time point you need
+    scalarData = volume.voxelManager.getTimePointScalarData(targetTimePoint);
+  } else {
+    scalarData = volume.voxelManager.getCompleteScalarDataArray();
+  }
+
+  if (!scalarData?.length) {
+    return undefined;
   }
 
   const { dimensions, origin, direction, spacing } = volume;
@@ -50,11 +49,12 @@ const getViewportVolumeHistogram = async (viewport, volume, options?) => {
     scalarData,
   });
 
-  // after we calculate the range let's reset the timePointIndex
-  if (volume.numTimePoints > 1) {
-    volume.timePointIndex = prevTimePoint;
-  }
   const { minimum: min, maximum: max } = range;
+
+  if (min === Infinity || max === -Infinity) {
+    return undefined;
+  }
+
   const calcHistOptions = {
     numBins: 256,
     min: Math.max(min, options?.min ?? min),