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

Co-authored-by: Alireza <ar.sedghi@gmail.com>

.circleci/config.yml

@@ -1,52 +1,71 @@
 version: 2.1
 
+### ABOUT
+#
+# This configuration powers our Circleci.io integration
+#
+# Note:
+# Netlify works independently from this configuration to
+# create pull request previews and to update `https://docs.ohif.org`
+###
+
+## https://github.com/cypress-io/circleci-orb
+##
 orbs:
   codecov: codecov/codecov@1.0.5
-  cypress: cypress-io/cypress@3.4.2
+  cypress: cypress-io/cypress@3.3.1
+
+executors:
+  cypress-custom:
+    description: |
+      Single Docker container used to run Cypress Tests
+    docker:
+      - image: cimg/node:<< parameters.node-version >>-browsers
+    parameters:
+      node-version:
+        default: '18.16.1'
+        description: |
+          The version of Node to run your tests with.
+        type: string
 
 defaults: &defaults
   docker:
-    - image: cimg/node:20.18.1
+    - image: cimg/node:18.18
       environment:
-        TERM: xterm
+        TERM: xterm # Enable colors in term
         QUICK_BUILD: true
   working_directory: ~/repo
 
-commands:
-  install_bun:
-    steps:
-      - restore_cache:
-          keys:
-            - bun-cache-v2-{{ arch }}-latest
-      - run:
-          name: Install Bun
-          command: |
-            if [ ! -d "$HOME/.bun" ]; then
-              curl -fsSL https://bun.sh/install | bash
-            fi
-            echo 'export BUN_INSTALL="$HOME/.bun"' >> $BASH_ENV
-            echo 'export PATH="$BUN_INSTALL/bin:$PATH"' >> $BASH_ENV
-            source $BASH_ENV
-      - save_cache:
-          key: bun-cache-v2-{{ arch }}-latest
-          paths:
-            - ~/.bun
-
 jobs:
+  ###
+  # Workflow: PR_CHECKS
+  ###
   UNIT_TESTS:
     <<: *defaults
-    resource_class: large
     steps:
-      - install_bun
+      # Update yarn
+      - run: yarn -v
       - run: node --version
+      # Checkout code and ALL Git Tags
       - checkout
+      - restore_cache:
+          name: Restore Yarn and Cypress Package Cache
+          keys:
+            # when lock file changes, use increasingly general patterns to restore cache
+            - yarn-packages-{{ checksum "yarn.lock" }}
+            - yarn-packages-
       - run:
           name: Install Dependencies
-          command: bun install --no-save
+          command: yarn install --frozen-lockfile
+      - save_cache:
+          name: Save Yarn Package Cache
+          paths:
+            - ~/.cache ## Cache yarn and Cypress
+          key: yarn-packages-{{ checksum "yarn.lock" }}
       # RUN TESTS
       - run:
           name: 'JavaScript Test Suite'
-          command: bun run test:unit:ci
+          command: yarn run test:unit:ci
       # platform/app
       - run:
           name: 'VIEWER: Combine report output'
@@ -74,23 +93,35 @@ jobs:
           file: '/home/circleci/repo/platform/core/coverage/reports'
           flags: 'core'
 
+  ###
+  # Workflow: DEPLOY
+  ###
   BUILD:
     <<: *defaults
-    resource_class: large
     steps:
       # Checkout code and ALL Git Tags
       - checkout
-      - install_bun
+      - restore_cache:
+          name: Restore Yarn and Cypress Package Cache
+          keys:
+            # when lock file changes, use increasingly general patterns to restore cache
+            - yarn-packages-{{ checksum "yarn.lock" }}
+            - yarn-packages-
       - run:
           name: Install Dependencies
-          command: bun install --no-save
+          command: yarn install --frozen-lockfile
+      - save_cache:
+          name: Save Yarn Package Cache
+          paths:
+            - ~/.cache ## Cache yarn and Cypress
+          key: yarn-packages-{{ checksum "yarn.lock" }}
       # Build & Test
       - run:
           name: 'Perform the versioning before build'
-          command: bun ./version.mjs
+          command: node ./version.mjs
       - run:
           name: 'Build the OHIF Viewer'
-          command: bun run build
+          command: yarn run build
           no_output_timeout: 45m
       - run:
           name: 'Upload SourceMaps, Send Deploy Notification'
@@ -112,18 +143,29 @@ jobs:
             - commit.txt
             - version.json
 
+  # just to make sure later on we can publish them
   BUILD_PACKAGES_QUICK:
     <<: *defaults
-    resource_class: large
     steps:
-      - install_bun
+      - run: yarn -v
       # Checkout code and ALL Git Tags
       - checkout
       - attach_workspace:
           at: ~/repo
+      # Use increasingly general patterns to restore cache
+      - restore_cache:
+          name: Restore Yarn and Cypress Package Cache
+          keys:
+            - yarn-packages-{{ checksum "yarn.lock" }}
+            - yarn-packages-
       - run:
           name: Install Dependencies
-          command: bun install --frozen-lockfile
+          command: yarn install --frozen-lockfile
+      - save_cache:
+          name: Save Yarn Package Cache
+          paths:
+            - ~/.cache/yarn
+          key: yarn-packages-{{ checksum "yarn.lock" }}
       - run:
           name: Avoid hosts unknown for github
           command: |
@@ -135,27 +177,44 @@ 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: |
-            bun run build:package-all
+            yarn run build:package-all
       - run:
           name: build the other half of the packages
           command: |
-            bun run build:package-all-1
+            yarn run build:package-all-1
 
+  ###
+  # Workflow: RELEASE
+  ###
   NPM_PUBLISH:
     <<: *defaults
-    resource_class: large
     steps:
-      - install_bun
+      - run: yarn -v
       # Checkout code and ALL Git Tags
       - checkout
       - attach_workspace:
           at: ~/repo
+      # Use increasingly general patterns to restore cache
+      - restore_cache:
+          name: Restore Yarn and Cypress Package Cache
+          keys:
+            - yarn-packages-{{ checksum "yarn.lock" }}
+            - yarn-packages-
       - run:
           name: Install Dependencies
-          command: bun install --no-save
+          command: yarn install --frozen-lockfile
+      - save_cache:
+          name: Save Yarn Package Cache
+          paths:
+            - ~/.cache/yarn
+          key: yarn-packages-{{ checksum "yarn.lock" }}
       - run:
           name: Avoid hosts unknown for github
           command: |
@@ -167,14 +226,18 @@ jobs:
       - run:
           name: Authenticate with NPM registry
           command: echo "//registry.npmjs.org/:_authToken=$NPM_TOKEN" > ~/repo/.npmrc
+      - run:
+          name: Increase the event emitter limit
+          command: |
+            node ./increaseEventEmitterLimit.mjs
       - run:
           name: build half of the packages (to avoid out of memory in circleci)
           command: |
-            bun run build:package-all
+            yarn run build:package-all
       - run:
           name: build the other half of the packages
           command: |
-            bun run build:package-all-1
+            yarn run build:package-all-1
       - run:
           name: increase min time out
           command: |
@@ -186,14 +249,14 @@ jobs:
       - run:
           name: publish package versions
           command: |
-            bun ./publish-version.mjs
+            node ./publish-version.mjs
       - run:
           name: Again set the NPM registry (was deleted in the version script)
           command: echo "//registry.npmjs.org/:_authToken=$NPM_TOKEN" > ~/repo/.npmrc
       - run:
           name: publish package dist
           command: |
-            bun ./publish-package.mjs
+            node ./publish-package.mjs
       - persist_to_workspace:
           root: ~/repo
           paths:
@@ -201,14 +264,13 @@ jobs:
 
   DOCKER_RELEASE_PUBLISH:
     <<: *defaults
-    resource_class: large
     steps:
       - attach_workspace:
           at: ~/repo
       - setup_remote_docker:
           docker_layer_caching: false
       - run:
-          name: Build Docker image for amd64
+          name: Build and push Docker image from the release branch
           command: |
             # This file will exist if a new version was published by
             # our command in the previous job.
@@ -222,61 +284,22 @@ jobs:
               export IMAGE_VERSION_FULL=v$IMAGE_VERSION
               echo $IMAGE_VERSION
               echo $IMAGE_VERSION_FULL
-              # Build our amd64 image, auth, and push
-              docker build --platform linux/amd64 --tag ohif/app:$IMAGE_VERSION_FULL-amd64 --tag ohif/app:latest-amd64 .
+              # Build our image, auth, and push
+              docker build --tag ohif/app:$IMAGE_VERSION_FULL --tag ohif/app:latest .
               echo $DOCKER_PWD | docker login -u $DOCKER_LOGIN --password-stdin
-              docker push ohif/app:$IMAGE_VERSION_FULL-amd64
-              docker push ohif/app:latest-amd64
+              docker push ohif/app:$IMAGE_VERSION_FULL
+              docker push ohif/app:latest
             fi
-      - persist_to_workspace:
-          root: ~/repo
-          paths:
-            - .
-
-  DOCKER_RELEASE_PUBLISH_ARM:
-    <<: *defaults
-    resource_class: arm.large
-    steps:
-      - attach_workspace:
-          at: ~/repo
-      - setup_remote_docker:
-          docker_layer_caching: false
-      - run:
-          name: Build Docker image for arm64 (Release)
-          command: |
-            # This file will exist if a new version was published by
-            # our command in the previous job.
-            if [[ ! -e version.txt ]]; then
-              exit 0
-            else
-              # Remove npm config
-              rm -f ./.npmrc
-              # Set our version number using vars
-              export IMAGE_VERSION=$(cat version.txt)
-              export IMAGE_VERSION_FULL=v$IMAGE_VERSION
-              echo $IMAGE_VERSION
-              echo $IMAGE_VERSION_FULL
-              # Build our arm64 image, auth, and push
-              docker build --platform linux/arm64 --tag ohif/app:$IMAGE_VERSION_FULL-arm64 --tag ohif/app:latest-arm64 .
-              echo $DOCKER_PWD | docker login -u $DOCKER_LOGIN --password-stdin
-              docker push ohif/app:$IMAGE_VERSION_FULL-arm64
-              docker push ohif/app:latest-arm64
-            fi
-      - persist_to_workspace:
-          root: ~/repo
-          paths:
-            - .
 
   DOCKER_BETA_PUBLISH:
     <<: *defaults
-    resource_class: large
     steps:
       - attach_workspace:
           at: ~/repo
       - setup_remote_docker:
           docker_layer_caching: false
       - run:
-          name: Build Docker image for amd64 (Beta)
+          name: Build and push Docker image from the master branch (beta releases)
           command: |
             echo $(ls -l)
 
@@ -288,153 +311,107 @@ jobs:
             else
               echo "Building and pushing Docker image from the master branch (beta releases)"
               rm -f ./.npmrc
-
               # Set our version number using vars
               export IMAGE_VERSION=$(cat version.txt)
               export IMAGE_VERSION_FULL=v$IMAGE_VERSION
               echo $IMAGE_VERSION
               echo $IMAGE_VERSION_FULL
-              # Build our amd64 image, auth, and push
-              docker build --platform linux/amd64 --tag ohif/app:$IMAGE_VERSION_FULL-amd64 --tag ohif/app:latest-beta-amd64 .
+              # Build our image, auth, and push
+
+              echo "starting docker build"
+              docker build --tag ohif/app:$IMAGE_VERSION_FULL .
               echo $DOCKER_PWD | docker login -u $DOCKER_LOGIN --password-stdin
-              docker push ohif/app:$IMAGE_VERSION_FULL-amd64
-              docker push ohif/app:latest-beta-amd64
+
+              echo "starting docker push"
+              docker push ohif/app:$IMAGE_VERSION_FULL
             fi
 
-  DOCKER_BETA_PUBLISH_ARM:
-    <<: *defaults
-    resource_class: arm.large
+  # This is copied from the Cypress orb since the default for cypress/run is node 16 and
+  # we migrated to 18
+  CYPRESS_CUSTOM_RUN:
+    description: |
+      A single, complete job to run Cypress end-to-end tests in your application.
+    executor: cypress-custom
+    parallelism: << parameters.parallelism >>
+    parameters:
+      cypress-cache-key:
+        default: cypress-cache-{{ arch }}-{{ checksum "package.json" }}
+        description: Cache key used to cache the Cypress binary.
+        type: string
+      cypress-cache-path:
+        default: ~/.cache/Cypress
+        description: |
+          By default, this will cache the '~/.cache/Cypress' directory so that the Cypress binary is cached. You can override this by providing your own cache path.
+        type: string
+      cypress-command:
+        default: npx cypress run
+        description: Command used to run your Cypress tests
+        type: string
+      include-branch-in-node-cache-key:
+        default: false
+        description: |
+          If true, this cache will only apply to runs within the same branch. (Adds -{{ .Branch }}- to the node cache key)
+        type: boolean
+      install-browsers:
+        default: false
+        description: |
+          Cypress runs by default in the Electron browser. Use this flag to install additional browsers to run your tests in.
+          This is only needed if you are passing the `--browser` flag in your `cypress-command`.
+          This parameter leverages the `circleci/browser-tools` orb and includes Chrome and FireFox.
+          If you need additional browser support you can set this to false and use an executor with a docker image
+          that includes the browsers of your choosing. See https://hub.docker.com/r/cypress/browsers/tags
+        type: boolean
+      install-command:
+        default: ''
+        description: Overrides the default NPM command (npm ci)
+        type: string
+      node-cache-version:
+        default: v1
+        description:
+          Change the default node cache version if you need to clear the cache for any reason.
+        type: string
+      package-manager:
+        default: npm
+        description: Select the default node package manager to use. NPM v5+ Required.
+        enum:
+          - npm
+          - yarn
+          - yarn-berry
+        type: enum
+      parallelism:
+        default: 1
+        description: |
+          Number of Circle machines to use for load balancing, min 1
+          (requires `parallel` and `record` flags in your `cypress-command`)
+        type: integer
+      post-install:
+        default: ''
+        description: |
+          Additional commands to run after running install but before verifying Cypress and saving cache.
+        type: string
+      start-command:
+        default: ''
+        description: Command used to start your local dev server for Cypress to tests against
+        type: string
+      working-directory:
+        default: ''
+        description: Directory containing package.json
+        type: string
     steps:
-      - attach_workspace:
-          at: ~/repo
-      - setup_remote_docker:
-          docker_layer_caching: false
-      - run:
-          name: Build Docker image for arm64 (Beta)
-          command: |
-            echo $(ls -l)
-
-            # This file will exist if a new version was published by
-            # our command in the previous job.
-            if [[ ! -e version.txt ]]; then
-              echo "don't have version txt"
-              exit 0
-            else
-              echo "Building and pushing ARM64 Docker image from the master branch (beta releases)"
-              rm -f ./.npmrc
-              # Set our version number using vars
-              export IMAGE_VERSION=$(cat version.txt)
-              export IMAGE_VERSION_FULL=v$IMAGE_VERSION
-              echo $IMAGE_VERSION
-              echo $IMAGE_VERSION_FULL
-              # Build our arm64 image, auth, and push
-              docker build --platform linux/arm64 --tag ohif/app:$IMAGE_VERSION_FULL-arm64 --tag ohif/app:latest-beta-arm64 .
-              echo $DOCKER_PWD | docker login -u $DOCKER_LOGIN --password-stdin
-              docker push ohif/app:$IMAGE_VERSION_FULL-arm64
-              docker push ohif/app:latest-beta-arm64
-            fi
-
-  CYPRESS:
-    <<: *defaults
-    resource_class: large
-    parallelism: 8
-    steps:
-      - run:
-          name: Install System Dependencies
-          command: |
-            sudo apt-get update
-            sudo apt-get install -y xvfb libgtk2.0-0 libgtk-3-0 libgbm-dev libnotify-dev libgconf-2-4 libnss3 libxss1 libasound2 libxtst6
-      - run:
-          name: Start Xvfb
-          command: Xvfb :99 -screen 0 1920x1080x24 &
-          background: true
-      - run:
-          name: Export Display Variable
-          command: export DISPLAY=:99
       - cypress/install:
-          install-command: yarn install --no-save
+          cypress-cache-key: << parameters.cypress-cache-key >>
+          cypress-cache-path: << parameters.cypress-cache-path >>
+          include-branch-in-node-cache-key: << parameters.include-branch-in-node-cache-key >>
+          install-browsers: << parameters.install-browsers >>
+          install-command: << parameters.install-command >>
+          node-cache-version: << parameters.node-cache-version >>
+          package-manager: << parameters.package-manager >>
+          post-install: << parameters.post-install >>
+          working-directory: << parameters.working-directory >>
       - cypress/run-tests:
-          cypress-command: |
-            npx wait-on@latest http://localhost:3000 && cd platform/app && npx cypress run --record --parallel
-          start-command: yarn run test:data && yarn run test:e2e:serve
-
-  DOCKER_MULTIARCH_MANIFEST:
-    <<: *defaults
-    resource_class: large
-    steps:
-      - attach_workspace:
-          at: ~/repo
-      - setup_remote_docker:
-          docker_layer_caching: false
-      - run:
-          name: Create and push multi-architecture manifest (Release)
-          command: |
-            # This file will exist if a new version was published by
-            # our command in the previous job.
-            if [[ ! -e version.txt ]]; then
-              exit 0
-            else
-              echo "Building and pushing multi-architecture manifest from the master branch (release releases)"
-              rm -f ./.npmrc
-              # Set our version number using vars
-              export IMAGE_VERSION=$(cat version.txt)
-              export IMAGE_VERSION_FULL=v$IMAGE_VERSION
-              echo $IMAGE_VERSION
-              echo $IMAGE_VERSION_FULL
-              echo $DOCKER_PWD | docker login -u $DOCKER_LOGIN --password-stdin
-
-              # Create and push manifest for specific version
-              docker manifest create ohif/app:$IMAGE_VERSION_FULL \
-                --amend ohif/app:$IMAGE_VERSION_FULL-amd64 \
-                --amend ohif/app:$IMAGE_VERSION_FULL-arm64
-              docker manifest push ohif/app:$IMAGE_VERSION_FULL
-
-              # Create and push manifest for "latest" tag
-              docker manifest create ohif/app:latest \
-                --amend ohif/app:latest-amd64 \
-                --amend ohif/app:latest-arm64
-              docker manifest push ohif/app:latest
-            fi
-
-  DOCKER_BETA_MULTIARCH_MANIFEST:
-    <<: *defaults
-    resource_class: large
-    steps:
-      - attach_workspace:
-          at: ~/repo
-      - setup_remote_docker:
-          docker_layer_caching: false
-      - run:
-          name: Create and push multi-architecture manifest (Beta)
-          command: |
-            echo $(ls -l)
-
-            # This file will exist if a new version was published by
-            # our command in the previous job.
-            if [[ ! -e version.txt ]]; then
-              exit 0
-            else
-              echo "Building and pushing multi-architecture manifest from the master branch (beta releases)"
-              rm -f ./.npmrc
-              # Set our version number using vars
-              export IMAGE_VERSION=$(cat version.txt)
-              export IMAGE_VERSION_FULL=v$IMAGE_VERSION
-              echo $IMAGE_VERSION
-              echo $IMAGE_VERSION_FULL
-              echo $DOCKER_PWD | docker login -u $DOCKER_LOGIN --password-stdin
-
-              # Create and push manifest for specific beta version
-              docker manifest create ohif/app:$IMAGE_VERSION_FULL \
-                --amend ohif/app:$IMAGE_VERSION_FULL-amd64 \
-                --amend ohif/app:$IMAGE_VERSION_FULL-arm64
-              docker manifest push ohif/app:$IMAGE_VERSION_FULL
-
-              # Create and push manifest for "latest-beta" tag
-              docker manifest create ohif/app:latest-beta \
-                --amend ohif/app:latest-beta-amd64 \
-                --amend ohif/app:latest-beta-arm64
-              docker manifest push ohif/app:latest-beta
-            fi
+          cypress-command: << parameters.cypress-command >>
+          start-command: << parameters.start-command >>
+          working-directory: << parameters.working-directory >>
 
 workflows:
   PR_CHECKS:
@@ -443,12 +420,61 @@ workflows:
           filters:
             branches:
               ignore: master
-      - UNIT_TESTS
-      - CYPRESS:
+      - UNIT_TESTS:
+          requires:
+            - BUILD_PACKAGES_QUICK
+      - CYPRESS_CUSTOM_RUN:
           name: 'Cypress Tests'
           context: cypress
+          matrix:
+            parameters:
+              start-command:
+                - yarn run test:data && yarn run test:e2e:serve
+              install-browsers:
+                - true
+              cypress-command:
+                - 'npx wait-on@latest http://localhost:3000 && cd platform/app &&  npx cypress run
+                  --record --browser chrome --parallel'
+              package-manager:
+                - 'yarn'
+              cypress-cache-key:
+                - 'yarn-packages-{{ checksum "yarn.lock" }}'
+              cypress-cache-path:
+                - '~/.cache/Cypress'
+          requires:
+            - BUILD_PACKAGES_QUICK
 
-  # viewer-dev.ohif.org
+  # PR_OPTIONAL_VISUAL_TESTS:
+  #   jobs:
+  #     - AWAIT_APPROVAL:
+  #         type: approval
+  #     # Update hub.docker.org
+  #     - cypress/run:
+  #         name: 'Generate Percy Snapshots'
+  #         executor: cypress/browsers-chrome76
+  #         browser: chrome
+  #         pre-steps:
+  #           - run: 'rm -rf ~/.yarn && yarn -v && yarn global add wait-on'
+  #         yarn: true
+  #         store_artifacts: false
+  #         working_directory: platform/app
+  #         build:
+  #           yarn test:data && npx cross-env QUICK_BUILD=true APP_CONFIG=config/dicomweb-server.js
+  #           yarn run build
+  #         # start server --> verify running --> percy + chrome + cypress
+  #         command: yarn run test:e2e:dist
+  #         cache-key: 'yarn-packages-{{ checksum "yarn.lock" }}'
+  #         no-workspace: true # Don't persist workspace
+  #         post-steps:
+  #           - store_artifacts:
+  #               path: platform/app/cypress/screenshots
+  #           - store_artifacts:
+  #               path: platform/app/cypress/videos
+  #         requires:
+  #           - AWAIT_APPROVAL
+
+  # Our master branch deploys to viewer-dev.ohif.org, the viewer.ohif.org is
+  # deployed from the release branch which is more stable and less frequently updated.
   DEPLOY_MASTER:
     jobs:
       - BUILD:
@@ -461,14 +487,9 @@ workflows:
       - DOCKER_BETA_PUBLISH:
           requires:
             - NPM_PUBLISH
-      - DOCKER_BETA_PUBLISH_ARM:
-          requires:
-            - DOCKER_BETA_PUBLISH
-      - DOCKER_BETA_MULTIARCH_MANIFEST:
-          requires:
-            - DOCKER_BETA_PUBLISH_ARM
 
-  # viewer.ohif.org
+  # Our release branch deploys to viewer.ohif.org and is more stable and less
+  # frequently updated after being tested in the staging environment.
   DEPLOY_RELEASE:
     jobs:
       - BUILD:
@@ -485,9 +506,50 @@ workflows:
       - DOCKER_RELEASE_PUBLISH:
           requires:
             - NPM_PUBLISH
-      - DOCKER_RELEASE_PUBLISH_ARM:
-          requires:
-            - DOCKER_RELEASE_PUBLISH
-      - DOCKER_MULTIARCH_MANIFEST:
-          requires:
-            - DOCKER_RELEASE_PUBLISH_ARM
+
+  ###
+  # Unit and E2E tests have already run for PR_CHECKS
+  # Re-running should not gain us any confidence here
+  ###
+  # RELEASE:
+  #   jobs:
+  #     - NPM_PUBLISH:
+  #         filters:
+  #           branches:
+  #             only: master
+  #     - DOCS_PUBLISH:
+  #         filters:
+  #           branches:
+  #             only: master
+  #     # Update base branch snapshots
+  #     # and record a Cypress dashboard test run
+  #     - cypress/run:
+  #         name: 'Generate Percy Snapshots'
+  #         executor: cypress/browsers-chrome76
+  #         browser: chrome
+  #         pre-steps:
+  #           - run: 'rm -rf ~/.yarn && npm i -g yarn && yarn -v && yarn global
+  #               add wait-on' # Use yarn latest
+  #         yarn: true
+  #         store_artifacts: false
+  #         working_directory: platform/app
+  #         build:
+  #           npx cross-env QUICK_BUILD=true APP_CONFIG=config/e2e.js yarn run
+  #           build
+  #         # start server --> verify running --> percy + chrome + cypress
+  #         command: yarn run test:e2e:dist
+  #         cache-key: 'yarn-packages-{{ checksum "yarn.lock" }}'
+  #         no-workspace: true # Don't persist workspace
+  #         post-steps:
+  #           - store_artifacts:
+  #               path: platform/app/cypress/screenshots
+  #           - store_artifacts:
+  #               path: platform/app/cypress/videos
+  #           - store_test_results:
+  #               path: platform/app/cypress/results
+  #         filters:
+  #           branches:
+  #             only: master
+  #     - DOCKER_MASTER_PUBLISH:
+  #         requires:
+  #           - NPM_PUBLISH

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

@@ -1,13 +1,12 @@
 server {
-  gzip_static  always;
-  gzip_proxied expired no-cache no-store private auth;
-  gunzip       on;
   listen ${PORT} default_server;
   listen [::]:${PORT} default_server;
   location / {
     root   /usr/share/nginx/html;
     index  index.html index.htm;
-    try_files $uri $uri/ ${PUBLIC_URL}index.html;
+    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

@@ -7,6 +7,8 @@ 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/entrypoint.sh

@@ -2,34 +2,16 @@
 
 if [ -n "$SSL_PORT" ]
   then
-    envsubst '${SSL_PORT}:${PORT}' < /usr/src/default.ssl.conf.template | envsubst '${PUBLIC_URL}' > /etc/nginx/conf.d/default.conf
+    envsubst '${SSL_PORT}:${PORT}' < /usr/src/default.ssl.conf.template > /etc/nginx/conf.d/default.conf
   else
-    envsubst '${PORT}:${PUBLIC_URL}' < /usr/src/default.conf.template  > /etc/nginx/conf.d/default.conf
+    envsubst '${PORT}' < /usr/src/default.conf.template > /etc/nginx/conf.d/default.conf
 fi
 
-if [ -n "$APP_CONFIG" ]; then
-  echo "$APP_CONFIG" > /usr/share/nginx/html${PUBLIC_URL}app-config.js
-  echo "Using custom APP_CONFIG environment variable"
-else
-  echo "Not using custom APP_CONFIG"
+if [ -n "$APP_CONFIG" ]
+  then
+    echo "$APP_CONFIG" > /usr/share/nginx/html/app-config.js
 fi
 
-if [ -f /usr/share/nginx/html${PUBLIC_URL}app-config.js ]; then
-  if [ -s /usr/share/nginx/html${PUBLIC_URL}app-config.js ]; then
-    echo "Detected non-empty app-config.js. Ensuring .gz file is updated..."
-    rm -f /usr/share/nginx/html${PUBLIC_URL}app-config.js.gz
-    gzip /usr/share/nginx/html${PUBLIC_URL}app-config.js
-    touch /usr/share/nginx/html${PUBLIC_URL}app-config.js
-    echo "Compressed app-config.js to app-config.js.gz"
-  else
-    echo "app-config.js is empty. Skipping compression."
-  fi
-else
-  echo "No app-config.js file found. Skipping compression."
-fi
-
-
-
 if [ -n "$CLIENT_ID" ] || [ -n "$HEALTHCARE_API_ENDPOINT" ]
   then
     # If CLIENT_ID is specified, use the google.js configuration with the modified ID
@@ -58,6 +40,6 @@ if [ -n "$CLIENT_ID" ] || [ -n "$HEALTHCARE_API_ENDPOINT" ]
 	  cp /usr/share/nginx/html/google.js /usr/share/nginx/html/app-config.js
 fi
 
-echo "Starting Nginx to serve the OHIF Viewer on ${PUBLIC_URL}"
+echo "Starting Nginx to serve the OHIF Viewer..."
 
 exec "$@"

.docker/compressDist.sh

@@ -1,4 +0,0 @@
-find platform/app/dist -name "*.js" -exec gzip -9 "{}" \; -exec touch "{}" \;
-find platform/app/dist -name "*.map" -exec gzip -9 "{}" \; -exec touch "{}" \;
-find platform/app/dist -name "*.css" -exec gzip -9 "{}" \; -exec touch "{}" \;
-find platform/app/dist -name "*.svg" -exec gzip -9 "{}" \; -exec touch "{}" \;

.dockerignore

@@ -8,11 +8,11 @@
 # have this file as their .dockerignore.
 
 # Output
-**/dist/
-**/build/
+dist/
+build/
 
 # Dependencies
-**/node_modules/
+node_modules/
 
 # Root
 README.md
@@ -33,5 +33,5 @@ dockerfile
 .scripts/
 .vscode/
 coverage/
-platform/docs/
+docs/
 testdata/

.env.example

@@ -0,0 +1 @@
+PERCY_TOKEN=<your token here>

.eslintrc.json

@@ -18,8 +18,7 @@
   },
   "rules": {
     // Enforce consistent brace style for all control statements for readability
-    "curly": "error",
-    "import/no-anonymous-default-export": "off"
+    "curly": "error"
   },
   "globals": {
     "cy": true,

.github/.dependabot.yaml

@@ -1,19 +0,0 @@
-version: 2
-enable-beta-ecosystems: true
-updates:
-  - package-ecosystem: 'bun'
-    directory: '/'
-    schedule:
-      interval: 'daily'
-    labels: ['dependencies']
-    commit-message:
-      prefix: 'chore'
-      include: 'scope'
-  - package-ecosystem: 'npm'
-    directory: '/'
-    schedule:
-      interval: 'daily'
-    labels: ['dependencies']
-    commit-message:
-      prefix: 'chore'
-      include: 'scope'

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -64,7 +64,7 @@ body:
     attributes:
       label: 'Node version'
       description: 'Your Node.js version.'
-      placeholder: 'e.g., 20.18.1'
+      placeholder: 'e.g., 18.16.1'
     validations:
       required: true
   - type: input

.github/workflows/build-docs.yml

@@ -1,108 +0,0 @@
-name: Build and Deploy Docs
-
-on:
-  push:
-    branches: [master]
-
-env:
-  ACTIONS_STEP_DEBUG: true
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
-
-jobs:
-  build-and-deploy-docs:
-    timeout-minutes: 60
-    runs-on: ubuntu-latest
-    # Need permissions to read actions and pull requests
-    permissions:
-      actions: read
-      contents: read
-      pull-requests: read
-    steps:
-      - uses: actions/checkout@v4
-      - uses: oven-sh/setup-bun@v2
-      - uses: actions/setup-node@v4
-        with:
-          node-version: 20 # Or your desired Node version
-
-      - name: Install root dependencies
-        run: bun install --frozen-lockfile
-
-      # Removed Playwright tests and coverage generation steps
-
-      - name: Find PR and associated workflow run
-        id: find_pr_run
-        env:
-          GH_TOKEN: ${{ github.token }}
-          MERGE_COMMIT_SHA: ${{ github.sha }}
-        run: |
-          # Find the PR associated with the merge commit SHA
-          # Note: This relies on the merge commit being directly pushed to main
-          PR_DATA=$(gh pr list --state merged --search "$MERGE_COMMIT_SHA" --json number,headRefOid --jq '.[0]')
-          if [ -z "$PR_DATA" ]; then
-            echo "Could not find merged PR for commit $MERGE_COMMIT_SHA."
-            # Decide how to handle - fail, or maybe generate coverage now?
-            # For now, let's fail.
-            exit 1
-          fi
-          PR_HEAD_SHA=$(echo "$PR_DATA" | jq -r '.headRefOid')
-          PR_NUMBER=$(echo "$PR_DATA" | jq -r '.number')
-          echo "Found PR Number: $PR_NUMBER"
-          echo "Found PR Head SHA: $PR_HEAD_SHA"
-
-          # Find the latest workflow run ID for the playwright workflow on the PR head commit
-          # Uses the workflow file name 'playwright.yml'
-          # Remove the --status success flag to find any run
-          RUN_ID=$(gh run list --workflow playwright.yml --commit "$PR_HEAD_SHA" --event pull_request --json databaseId --jq '.[0].databaseId')
-
-          if [ -z "$RUN_ID" ]; then
-            echo "Could not find any 'playwright.yml' run for PR $PR_NUMBER (Head SHA: $PR_HEAD_SHA)."
-            # Decide how to handle - maybe try finding the artifact from the merge commit run if that exists?
-            # For now, let's fail.
-            exit 1
-          fi
-          echo "Found Run ID: $RUN_ID"
-          echo "run_id=$RUN_ID" >> $GITHUB_OUTPUT
-
-      - name: Download coverage artifact from PR run
-        env:
-          GH_TOKEN: ${{ github.token }}
-        run: |
-          mkdir -p ./coverage-artifact
-          gh run download ${{ steps.find_pr_run.outputs.run_id }} -n coverage-report-pr --dir ./coverage-artifact
-          # Check if download was successful (e.g., check if files exist)
-          if [ ! -f ./coverage-artifact/base.css ]; then
-            echo "Failed to download or find expected files in artifact 'coverage-report-pr' from run ${{ steps.find_pr_run.outputs.run_id }}."
-            exit 1
-          fi
-          echo "Artifact downloaded successfully."
-
-      - name: Install docs dependencies
-        run: cd platform/docs && bun install
-
-      - name: Copy coverage to docs static directory
-        run: |
-          # Copy files from the downloaded artifact directory
-          mkdir -p platform/docs/static/coverage
-          cp -r ./coverage-artifact/* platform/docs/static/coverage/
-          # Copy specific asset files from the downloaded artifact root to static root
-          cp ./coverage-artifact/base.css platform/docs/static/
-          cp ./coverage-artifact/block-navigation.js platform/docs/static/
-          cp ./coverage-artifact/prettify.css platform/docs/static/
-          cp ./coverage-artifact/prettify.js platform/docs/static/
-          cp ./coverage-artifact/favicon.png platform/docs/static/
-          cp ./coverage-artifact/sort-arrow-sprite.png platform/docs/static/
-          cp ./coverage-artifact/sorter.js platform/docs/static/
-
-      - name: Build docs
-        run: cd platform/docs && bun run build
-
-      - name: Deploy to Netlify
-        run: |
-          cd platform/docs
-          npx netlify-cli deploy --dir=./build --prod
-        env:
-          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
-          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}

.github/workflows/codeql.yml

@@ -1,98 +0,0 @@
-# For most projects, this workflow file will not need changing; you simply need
-# to commit it to your repository.
-#
-# You may wish to alter this file to override the set of languages analyzed,
-# or to provide custom queries or build logic.
-#
-# ******** NOTE ********
-# We have attempted to detect the languages in your repository. Please check
-# the `language` matrix defined below to confirm you have the correct set of
-# supported CodeQL languages.
-#
-name: "CodeQL Advanced"
-
-on:
-  pull_request:
-    branches: [ "main" ]
-  schedule:
-    - cron: '15 1 * * 5'
-
-jobs:
-  analyze:
-    name: Analyze (${{ matrix.language }})
-    # Runner size impacts CodeQL analysis time. To learn more, please see:
-    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
-    #   - https://gh.io/supported-runners-and-hardware-resources
-    #   - https://gh.io/using-larger-runners (GitHub.com only)
-    # Consider using larger runners or machines with greater resources for possible analysis time improvements.
-    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
-    permissions:
-      # required for all workflows
-      security-events: write
-
-      # required to fetch internal or private CodeQL packs
-      packages: read
-
-      # only required for workflows in private repositories
-      actions: read
-      contents: read
-
-    strategy:
-      fail-fast: false
-      matrix:
-        include:
-        - language: actions
-          build-mode: none
-        - language: javascript-typescript
-          build-mode: none
-        # CodeQL supports the following values keywords for 'language': 'actions', 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift'
-        # Use `c-cpp` to analyze code written in C, C++ or both
-        # Use 'java-kotlin' to analyze code written in Java, Kotlin or both
-        # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
-        # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
-        # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
-        # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
-        # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v4
-
-    # Add any setup steps before running the `github/codeql-action/init` action.
-    # This includes steps like installing compilers or runtimes (`actions/setup-node`
-    # or others). This is typically only required for manual builds.
-    # - name: Setup runtime (example)
-    #   uses: actions/setup-example@v1
-
-    # Initializes the CodeQL tools for scanning.
-    - name: Initialize CodeQL
-      uses: github/codeql-action/init@v3
-      with:
-        languages: ${{ matrix.language }}
-        build-mode: ${{ matrix.build-mode }}
-        # If you wish to specify custom queries, you can do so here or in a config file.
-        # By default, queries listed here will override any specified in a config file.
-        # Prefix the list here with "+" to use these queries and those in the config file.
-
-        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
-        # queries: security-extended,security-and-quality
-
-    # If the analyze step fails for one of the languages you are analyzing with
-    # "We were unable to automatically build your code", modify the matrix above
-    # to set the build mode to "manual" for that language. Then modify this step
-    # to build your code.
-    # ℹ️ Command-line programs to run using the OS shell.
-    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
-    - if: matrix.build-mode == 'manual'
-      shell: bash
-      run: |
-        echo 'If you are using a "manual" build mode for one or more of the' \
-          'languages you are analyzing, replace this with the commands to build' \
-          'your code, for example:'
-        echo '  make bootstrap'
-        echo '  make release'
-        exit 1
-
-    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v3
-      with:
-        category: "/language:${{matrix.language}}"

.github/workflows/playwright.yml

@@ -1,54 +0,0 @@
-name: Playwright Tests
-on:
-  pull_request:
-    branches: [master]
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
-
-jobs:
-  playwright-tests:
-    timeout-minutes: 60
-    runs-on: self-hosted
-    strategy:
-      fail-fast: false
-      matrix:
-        node-version: [20]
-    steps:
-      - uses: actions/checkout@v4
-      - uses: oven-sh/setup-bun@v2
-      - uses: actions/setup-node@v4
-        with:
-          node-version: ${{ matrix.node-version }}
-      - name: Install dependencies
-        run: bun install --frozen-lockfile
-      - name: Install Playwright browsers
-        run: npx playwright install
-      - name: Run Playwright tests
-        run: |
-          export NODE_OPTIONS="--max_old_space_size=10192"
-          bun run test:e2e:coverage
-      - name: Create directory of test results
-        if: ${{ !cancelled() }}
-        run: |
-          mkdir -p packaged-test-results
-          cp -r ./tests/test-results packaged-test-results/ || true
-          cp ./tests/playwright-report.json packaged-test-results/ || true
-      - name: Upload directory of test results artifact
-        if: ${{ !cancelled() }}
-        uses: actions/upload-artifact@v4
-        with:
-          name: playwright-results
-          path: packaged-test-results/
-          retention-days: 5
-      - name: create the coverage report
-        run: |
-          bun nyc report --reporter=lcov --reporter=text
-      - name: Upload the coverage report to GitHub Actions Artifacts
-        if: ${{ !cancelled() }}
-        uses: actions/upload-artifact@v4
-        with:
-          name: coverage-report-pr
-          path: coverage
-          retention-days: 3

.gitignore

@@ -1,7 +1,6 @@
 # Packages
 node_modules
-.cursor/
-.nyc_output/
+
 # Output
 build
 dist
@@ -11,9 +10,6 @@ junit.xml
 coverage/
 .docz/
 .yarn/
-.nx/
-addOns/yarn.lock
-playwright-report/
 
 # YALC (for Erik)
 .yalc
@@ -37,7 +33,7 @@ docker/dcm4che/dcm4che-arc
 
 # Cypress test results
 videos/
-
+screenshots/
 
 # Locize settings
 .locize
@@ -45,18 +41,8 @@ videos/
 # autogenerated files
 platform/app/src/pluginImports.js
 /Viewers.iml
-platform/app/.recipes/Nginx-Dcm4Chee/logs/*
+platform/app/.recipes/Nginx-Dcm4Che/dcm4che/dcm4che-arc/*
 platform/app/.recipes/OpenResty-Orthanc/logs/*
 .vercel
 
 .vs
-
-# PlayWright
-
-node_modules/
-tests/test-results/
-tests/playwright-report/
-/blob-report/
-/playwright/.cache/
-
-**/.claude/settings.local.json

.node-version

@@ -1 +1 @@
-20.9.0
+18.16.1

.nycrc.json

@@ -1,24 +0,0 @@
-{
-  "extends": "@istanbuljs/nyc-config-typescript",
-  "instrument": true,
-  "sourceMap": true,
-  "cache": false,
-  "all": true,
-  "include": [
-    "platform/*/src/**/*.ts",
-    "platform/*/src/**/*.js",
-    "extensions/*/src/**/*.ts",
-    "extensions/*/src/**/*.js",
-    "modes/*/src/**/*.ts",
-    "modes/*/src/**/*.js"
-  ],
-  "exclude": [
-    "**/*.spec.ts",
-    "**/*.test.ts",
-    "**/test/**",
-    "**/tests/**",
-    "**/examples/**",
-    "**/stories/**",
-    "platform/docs/**"
-  ]
-}

.scripts/dicom-json-generator.js

@@ -4,34 +4,26 @@
  * 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 dicom-json-generator.js <studyFolder> <urlPrefix> <outputJSONPath> <optional scheme>
+ * Usage: node dicomStudyToJSONLaunch.js <studyFolder> <urlPrefix> <outputJSONPath>
  *
  * params:
- * - studyFolder: path to the study folder which contains the DICOM files
+ * - studyFolder: path to the study folder
  * - 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, scheme = 'dicomweb'] = args;
+const [studyDirectory, urlPrefix, outputPath] = args;
 
-if (args.length < 3 || args.length > 4) {
-  console.error(
-    'Usage: node dicom-json-generator.js <studyFolder> <urlPrefix> <outputJSONPath> [scheme]'
-  );
+if (args.length !== 3) {
+  console.error('Usage: node dicomStudyToJSONLaunch.js <studyFolder> <urlPrefix> <outputJSONPath>');
   process.exit(1);
 }
 
@@ -39,7 +31,7 @@ const model = {
   studies: [],
 };
 
-async function convertDICOMToJSON(studyDirectory, urlPrefix, outputPath, scheme) {
+async function convertDICOMToJSON(studyDirectory, urlPrefix, outputPath) {
   try {
     const files = await recursiveReadDir(studyDirectory);
     console.debug('Processing...');
@@ -50,7 +42,7 @@ async function convertDICOMToJSON(studyDirectory, urlPrefix, outputPath, scheme)
         const dicomDict = dcmjs.data.DicomMessage.readFile(arrayBuffer.buffer);
         const instance = dcmjs.data.DicomMetaDictionary.naturalizeDataset(dicomDict.dict);
 
-        instance.fileLocation = createImageId(file, urlPrefix, studyDirectory, scheme);
+        instance.fileLocation = createImageId(file, urlPrefix, studyDirectory);
         processInstance(instance);
       }
     }
@@ -85,10 +77,10 @@ async function recursiveReadDir(dir) {
   return results;
 }
 
-function createImageId(fileLocation, urlPrefix, studyDirectory, scheme) {
+function createImageId(fileLocation, urlPrefix, studyDirectory) {
   const relativePath = path.relative(studyDirectory, fileLocation);
   const normalizedPath = path.normalize(relativePath).replace(/\\/g, '/');
-  return `${scheme}:${urlPrefix}${normalizedPath}`;
+  return `dicomweb:${urlPrefix}${normalizedPath}`;
 }
 
 function processInstance(instance) {
@@ -270,4 +262,4 @@ function createInstanceMetaDataMultiFrame(instance) {
   return instances;
 }
 
-convertDICOMToJSON(studyDirectory, urlPrefix, outputPath, scheme);
+convertDICOMToJSON(studyDirectory, urlPrefix, outputPath);

.vscode/extensions.json

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

.vscode/settings.json

@@ -1,5 +1,4 @@
 {
-  "editor.defaultFormatter": "esbenp.prettier-vscode",
   "editor.rulers": [80, 120],
   // ===
   // Spacing
@@ -15,103 +14,23 @@
   // 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",
-    "rtstruct",
-    "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",
-    "Colorbar",
-    "Colorbars"
-  ]
+  }
 }

.webpack/webpack.base.js

@@ -7,26 +7,23 @@ const fs = require('fs');
 const webpack = require('webpack');
 
 // ~~ PLUGINS
-// const BundleAnalyzerPlugin = require('webpack-bundle-analyzer').BundleAnalyzerPlugin;
+const BundleAnalyzerPlugin = require('webpack-bundle-analyzer').BundleAnalyzerPlugin;
 const TerserJSPlugin = require('terser-webpack-plugin');
 
 // ~~ PackageJSON
 // 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');
-// Only uncomment for old v2 stylus
-// const stylusToJavaScript = require('./rules/stylusToJavaScript.js');
-const ReactRefreshWebpackPlugin = require('@pmmmwh/react-refresh-webpack-plugin');
+const stylusToJavaScript = require('./rules/stylusToJavaScript.js');
 
 // ~~ ENV VARS
 const NODE_ENV = process.env.NODE_ENV;
 const QUICK_BUILD = process.env.QUICK_BUILD;
 const BUILD_NUM = process.env.CIRCLE_BUILD_NUM || '0';
-const IS_COVERAGE = process.env.COVERAGE === 'true';
 
 // read from ../version.txt
 const VERSION_NUMBER = fs.readFileSync(path.join(__dirname, '../version.txt'), 'utf8') || '';
@@ -50,7 +47,6 @@ const defineValues = {
   'process.env.LOCIZE_PROJECTID': JSON.stringify(process.env.LOCIZE_PROJECTID || ''),
   'process.env.LOCIZE_API_KEY': JSON.stringify(process.env.LOCIZE_API_KEY || ''),
   'process.env.REACT_APP_I18N_DEBUG': JSON.stringify(process.env.REACT_APP_I18N_DEBUG || ''),
-  'process.env.TEST_ENV': JSON.stringify(process.env.TEST_ENV || ''),
 };
 
 // Only redefine updated values.  This avoids warning messages in the logs
@@ -59,6 +55,10 @@ 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';
@@ -96,67 +96,12 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
       type: 'filesystem',
     },
     module: {
-      noParse: [/(dicomicc)/],
+      noParse: [/(codec)/, /(dicomicc)/],
       rules: [
-        ...(isProdBuild
-          ? []
-          : [
-              ...(IS_COVERAGE
-                ? [
-                    {
-                      test: /\.[jt]sx?$/,
-                      exclude: /node_modules/,
-                      use: {
-                        loader: 'babel-loader',
-                        options: {
-                          presets: ['@babel/preset-typescript', '@babel/preset-react'],
-                          plugins: ['istanbul'],
-                        },
-                      },
-                    },
-                  ]
-                : [
-                    {
-                      test: /\.[jt]sx?$/,
-                      exclude: /node_modules/,
-                      loader: 'babel-loader',
-                      options: {
-                        plugins: isProdBuild ? [] : ['react-refresh/babel'],
-                      },
-                    },
-                  ]),
-            ]),
         {
-          test: /\.svg?$/,
-          oneOf: [
-            {
-              use: [
-                {
-                  loader: '@svgr/webpack',
-                  options: {
-                    svgoConfig: {
-                      plugins: [
-                        {
-                          name: 'preset-default',
-                          params: {
-                            overrides: {
-                              removeViewBox: false,
-                            },
-                          },
-                        },
-                      ],
-                    },
-                    prettier: false,
-                    svgo: true,
-                    titleProp: true,
-                  },
-                },
-              ],
-              issuer: {
-                and: [/\.(ts|tsx|js|jsx|md|mdx)$/],
-              },
-            },
-          ],
+          test: /\.js$/,
+          enforce: 'pre',
+          use: 'source-map-loader',
         },
         transpileJavaScriptRule(mode),
         loadWebWorkersRule,
@@ -186,10 +131,6 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
             },
           ],
         },
-        {
-          test: /\.(woff|woff2|eot|ttf|otf)$/i,
-          type: 'asset/resource',
-        },
       ], //.concat(vtkRules),
     },
     resolve: {
@@ -203,6 +144,8 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
         '@state': path.resolve(__dirname, '../platform/app/src/state'),
         'dicom-microscopy-viewer':
           'dicom-microscopy-viewer/dist/dynamic-import/dicomMicroscopyViewer.min.js',
+        '@cornerstonejs/dicom-image-loader':
+          '@cornerstonejs/dicom-image-loader/dist/dynamic-import/cornerstoneDICOMImageLoader.min.js',
       },
       // Which directories to search when resolving modules
       modules: [
@@ -230,7 +173,6 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
       new webpack.ProvidePlugin({
         Buffer: ['buffer', 'Buffer'],
       }),
-      ...(isProdBuild ? [] : [new ReactRefreshWebpackPlugin({ overlay: false })]),
       // Uncomment to generate bundle analyzer
       // new BundleAnalyzerPlugin(),
     ],

DATACITATION.md

@@ -10,7 +10,6 @@ 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.
@@ -148,150 +147,3 @@ 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

Dockerfile

@@ -1,4 +1,3 @@
-# syntax=docker/dockerfile:1.7-labs
 # This dockerfile is used to publish the `ohif/app` image on dockerhub.
 #
 # It's a good example of how to build our static application and package it
@@ -20,85 +19,61 @@
 #
 
 
-# syntax=docker/dockerfile:1.7-labs
-# This dockerfile is used to publish the `ohif/app` image on dockerhub.
-#
-# It's a good example of how to build our static application and package it
-# with a web server capable of hosting it as static content.
-#
-# docker build
-# --------------
-# If you would like to use this dockerfile to build and tag an image, make sure
-# you set the context to the project's root directory:
-# https://docs.docker.com/engine/reference/commandline/build/
-#
-#
-# SUMMARY
-# --------------
-# This dockerfile is used as an input for a second stage to make things run faster.
-#
-
-
 # Stage 1: Build the application
 # docker build -t ohif/viewer:latest .
-# Copy Files
-FROM node:20.18.1-slim as builder
-
-RUN apt-get update && apt-get install -y build-essential python3
-
+FROM node:18.16.1-slim as json-copier
 
 RUN mkdir /usr/src/app
 WORKDIR /usr/src/app
-RUN npm install -g bun
-# RUN npm install -g lerna@7.4.2
-ENV PATH=/usr/src/app/node_modules/.bin:$PATH
 
-# Do an initial install and then a final install
-COPY package.json yarn.lock preinstall.js lerna.json ./
-COPY --parents ./addOns/package.json ./addOns/*/*/package.json ./extensions/*/package.json ./modes/*/package.json ./platform/*/package.json ./
+COPY ["package.json", "yarn.lock", "preinstall.js", "./"]
+COPY extensions /usr/src/app/extensions
+COPY modes /usr/src/app/modes
+COPY platform /usr/src/app/platform
+
+# Find and remove non-package.json files
+#RUN find extensions \! -name "package.json" -mindepth 2 -maxdepth 2 -print | xargs rm -rf
+#RUN find modes \! -name "package.json" -mindepth 2 -maxdepth 2 -print | xargs rm -rf
+#RUN find platform \! -name "package.json" -mindepth 2 -maxdepth 2 -print | xargs rm -rf
+
+# Copy Files
+FROM node:18.16.1-slim as builder
+RUN apt-get update && apt-get install -y build-essential python3
+RUN mkdir /usr/src/app
+WORKDIR /usr/src/app
+
+COPY --from=json-copier /usr/src/app .
+
 # Run the install before copying the rest of the files
+RUN yarn config set workspaces-experimental true
+RUN yarn install --frozen-lockfile --verbose
 
-RUN bun pm cache rm
-RUN bun install
-# Copy the local directory
-COPY --link --exclude=yarn.lock --exclude=package.json --exclude=Dockerfile . .
+COPY . .
 
-# Build here
-# After install it should hopefully be stable until the local directory changes
+# To restore workspaces symlinks
+RUN yarn install --frozen-lockfile --verbose
+
+ENV PATH /usr/src/app/node_modules/.bin:$PATH
 ENV QUICK_BUILD true
 # ENV GENERATE_SOURCEMAP=false
-ARG APP_CONFIG=config/default.js
-ARG PUBLIC_URL=/
-ENV PUBLIC_URL=${PUBLIC_URL}
+# ENV REACT_APP_CONFIG=config/default.js
 
-RUN bun run show:config
-RUN bun run build
-
-# Precompress files
-RUN chmod u+x .docker/compressDist.sh
-RUN ./.docker/compressDist.sh
+RUN yarn run build
 
 # Stage 3: Bundle the built application into a Docker container
 # which runs Nginx using Alpine Linux
-FROM nginxinc/nginx-unprivileged:1.27-alpine as final
+FROM nginxinc/nginx-unprivileged:1.25-alpine as final
 #RUN apk add --no-cache bash
-ARG PUBLIC_URL=/
-ENV PUBLIC_URL=${PUBLIC_URL}
-ARG PORT=80
-ENV PORT=${PORT}
+ENV PORT=80
 RUN rm /etc/nginx/conf.d/default.conf
 USER nginx
 COPY --chown=nginx:nginx .docker/Viewer-v3.x /usr/src
 RUN chmod 777 /usr/src/entrypoint.sh
-COPY --from=builder /usr/src/app/platform/app/dist /usr/share/nginx/html${PUBLIC_URL}
-# Copy paths that are renamed/redirected generally
-# Microscopy libraries depend on root level include, so must be copied
-COPY --from=builder /usr/src/app/platform/app/dist/dicom-microscopy-viewer /usr/share/nginx/html/dicom-microscopy-viewer
-
+COPY --from=builder /usr/src/app/platform/app/dist /usr/share/nginx/html
 # In entrypoint.sh, app-config.js might be overwritten, so chmod it to be writeable.
 # The nginx user cannot chmod it, so change to root.
 USER root
-RUN chown -R nginx:nginx /usr/share/nginx/html
+RUN chmod 666 /usr/share/nginx/html/app-config.js
 USER nginx
 ENTRYPOINT ["/usr/src/entrypoint.sh"]
 CMD ["nginx", "-g", "daemon off;"]

README.md

@@ -1,4 +1,5 @@
 <!-- prettier-ignore-start -->
+<!-- markdownlint-disable -->
 <div align="center">
   <h1>OHIF Medical Imaging Viewer</h1>
   <p><strong>The OHIF Viewer</strong> is a zero-footprint medical image viewer
@@ -50,9 +51,10 @@ provided by the <a href="https://ohif.org/">Open Health Imaging Foundation (OHIF
 | <img src="https://github.com/OHIF/Viewers/blob/master/platform/docs/docs/assets/img/demo-video.webp?raw=true" alt="VIDEO" width="350"/> | Video  | [Demo](https://viewer.ohif.org/viewer?StudyInstanceUIDs=2.25.96975534054447904995905761963464388233) |
 | <img src="https://github.com/OHIF/Viewers/blob/master/platform/docs/docs/assets/img/microscopy.webp?raw=true" alt="microscopy" width="350"/> | Slide Microscopy  | [Demo](https://viewer.ohif.org/microscopy?StudyInstanceUIDs=2.25.141277760791347900862109212450152067508) |
 
+
 ## About
 
-The OHIF Viewer can retrieve
+The OHIF Medical Imaging Viewer is for viewing medical images. It can retrieve
 and load images from most sources and formats; render sets in 2D, 3D, and
 reconstructed representations; allows for the manipulation, annotation, and
 serialization of observations; supports internationalization, OpenID Connect,
@@ -117,16 +119,19 @@ This is typically where the latest development happens. Code that is in the mast
 
 Each package is tagged with beta version numbers, and published to npm such as `@ohif/ui@3.6.0-beta.1`
 
-### `release/*` branches - The latest stable releases
-Once the `master` branch code reaches a stable, release-ready state, we conduct a comprehensive code review and QA testing. Upon approval, we create a new release branch from `master`. These branches represent the latest stable version considered ready for production.
+### `release` branch - The latest stable release
 
-For example, `release/3.5` is the branch for version 3.5.0, and `release/3.6` is for version 3.6.0. After each release, we wait a few days to ensure no critical bugs. If any are found, we fix them in the release branch and create a new release with a minor version bump, e.g., 3.5.1 in the `release/3.5` branch.
+This branch represents the latest stable version of the project that is considered ready for production. The code in this branch should be fully tested and vetted for release. Once the code in the master branch reaches a state where it's stable and ready to be released to users,
+we do a comprehensive code review and QA testing. Once the code is approved,
+we merge it into the release branch and tag a new release.
 
-Each package is tagged with version numbers and published to npm, such as `@ohif/ui@3.5.0`. Note that `master` is always ahead of the `release` branch. We publish docker builds for both beta and stable releases.
+Each package is tagged with version numbers, and published to npm such as `@ohif/ui@3.5.0`
+
+Note: `master` is always ahead of `release` branch. We publish both docker builds for beta and stable releases.
 
 Here is a schematic representation of our development workflow:
 
-![alt text](platform/docs/docs/assets/img/github-readme-branches-Jun2024.png)
+![Alt text](platform/docs/docs/assets/img/github-readme-branches.png)
 
 
 
@@ -134,8 +139,8 @@ Here is a schematic representation of our development workflow:
 
 ### Requirements
 
-- [Yarn 1.20.0+](https://yarnpkg.com/en/docs/install)
-- [Node 18+](https://nodejs.org/en/)
+- [Yarn 1.17.3+](https://yarnpkg.com/en/docs/install)
+- [Node 16+](https://nodejs.org/en/)
 - Yarn Workspaces should be enabled on your machine:
   - `yarn config set workspaces-experimental true`
 
@@ -170,13 +175,12 @@ also supports a number of commands that can be found in their respective
 | Yarn Commands                | Description                                                   |
 | ---------------------------- | ------------------------------------------------------------- |
 | **Develop**                  |                                                               |
-| `dev`              | Default development experience for Viewer                     |
-| `dev:fast`             | Our experimental fast dev mode that uses rsbuild instead of webpack                     |
+| `dev` or `start`             | Default development experience for Viewer                     |
 | `test:unit`                  | Jest multi-project test runner; overall coverage              |
 | **Deploy**                   |                                                               |
 | `build`\*                    | Builds production output for our PWA Viewer                   |  |
 
-\* - For more information on different builds, check out our [Deploy
+\* - For more information on our different builds, check out our [Deploy
 Docs][deployment-docs]
 
 ## Project
@@ -333,4 +337,4 @@ MIT © [OHIF](https://github.com/OHIF)
 [vtk-npm]: https://www.npmjs.com/package/@ohif/extension-vtk
 <!-- prettier-ignore-end -->
 
-[![FOSSA Status](https://app.fossa.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)
+[![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)

addOns/README.md

@@ -1,3 +0,0 @@
-# External Dependencies
-
-This module contains optional dependencies and external dependencies for including in OHIF, such as the DICOM Microscopy Viewer component.  

addOns/externals/devDependencies/package.json

@@ -1,97 +0,0 @@
-{
-  "name": "@externals/devDependencies",
-  "description": "External dev dependencies - put dev build dependencies here",
-  "version": "3.11.0-beta.95",
-  "license": "MIT",
-  "private": true,
-  "engines": {
-    "node": ">=12",
-    "yarn": ">=1.19.1"
-  },
-  "dependencies": {
-    "@babel/runtime": "^7.20.13",
-    "@kitware/vtk.js": "32.12.0",
-    "clsx": "^2.1.1",
-    "core-js": "^3.2.1",
-    "moment": "^2.30.1"
-  },
-  "peerDependencies": {
-    "react": "^18.3.1",
-    "react-dom": "^18.3.1"
-  },
-  "devDependencies": {
-    "@babel/eslint-parser": "7.28.0",
-    "@pmmmwh/react-refresh-webpack-plugin": "^0.5.15",
-    "@rsbuild/core": "^1.3.16",
-    "@rsbuild/plugin-node-polyfill": "^1.3.0",
-    "@rsbuild/plugin-react": "^1.3.1",
-    "@svgr/webpack": "^8.1.0",
-    "@swc/helpers": "^0.5.15",
-    "@types/jest": "^27.5.0",
-    "@typescript-eslint/eslint-plugin": "^6.3.0",
-    "@typescript-eslint/parser": "^6.3.0",
-    "autoprefixer": "^10.4.4",
-    "babel-loader": "^8.2.4",
-    "babel-plugin-module-resolver": "^5.0.0",
-    "clean-webpack-plugin": "^3.0.0",
-    "copy-webpack-plugin": "^9.0.1",
-    "cross-env": "^5.2.0",
-    "css-loader": "^6.8.1",
-    "dotenv": "^8.1.0",
-    "eslint": "^8.39.0",
-    "eslint-config-prettier": "7.2.0",
-    "eslint-config-react-app": "^6.0.0",
-    "eslint-plugin-cypress": "^2.12.1",
-    "eslint-plugin-flowtype": "^7.0.0",
-    "eslint-plugin-import": "^2.26.0",
-    "eslint-plugin-jsx-a11y": "^6.5.1",
-    "eslint-plugin-node": "^11.1.0",
-    "eslint-plugin-prettier": "5.5.1",
-    "eslint-plugin-promise": "^5.2.0",
-    "eslint-plugin-react": "^7.29.4",
-    "eslint-plugin-react-hooks": "^4.4.0",
-    "eslint-plugin-tsdoc": "^0.2.11",
-    "eslint-webpack-plugin": "^2.5.3",
-    "execa": "^8.0.1",
-    "extract-css-chunks-webpack-plugin": "^4.5.4",
-    "html-webpack-plugin": "^5.3.2",
-    "husky": "^3.0.0",
-    "jest": "^29.5.0",
-    "jest-canvas-mock": "^2.1.0",
-    "jest-environment-jsdom": "^29.5.0",
-    "jest-junit": "^6.4.0",
-    "lerna": "^7.2.0",
-    "lint-staged": "^9.0.2",
-    "mini-css-extract-plugin": "^2.1.0",
-    "optimize-css-assets-webpack-plugin": "^6.0.1",
-    "postcss": "^8.3.5",
-    "postcss-import": "^14.0.2",
-    "postcss-loader": "^6.1.1",
-    "postcss-preset-env": "^7.4.3",
-    "prettier": "3.6.2",
-    "prettier-plugin-tailwindcss": "0.6.9",
-    "react-refresh": "^0.14.2",
-    "semver": "^7.5.1",
-    "serve": "^14.2.4",
-    "shader-loader": "^1.3.1",
-    "shx": "^0.3.3",
-    "source-map-loader": "^4.0.1",
-    "style-loader": "^1.0.0",
-    "stylus": "^0.59.0",
-    "stylus-loader": "^7.1.3",
-    "terser-webpack-plugin": "^5.1.4",
-    "typescript": "5.5.4",
-    "unused-webpack-plugin": "2.4.0",
-    "webpack": "^5.94.0",
-    "webpack-bundle-analyzer": "^4.8.0",
-    "webpack-cli": "^5.0.1",
-    "webpack-dev-server": "5.2.2",
-    "webpack-hot-middleware": "^2.25.0",
-    "webpack-merge": "^5.7.3",
-    "workbox-webpack-plugin": "^6.1.5",
-    "worker-loader": "^3.0.8"
-  },
-  "scripts": {
-    "build": "Included as direct dependency"
-  }
-}

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

@@ -1,9 +0,0 @@
-{
-  "name": "@externals/dicom-microscopy-viewer",
-  "description": "External reference to dicom-microscopy-viewer",
-  "version": "3.11.0-beta.95",
-  "license": "MIT",
-  "dependencies": {
-    "dicom-microscopy-viewer": "^0.46.1"
-  }
-}

addOns/package.json

@@ -1,51 +0,0 @@
-{
-  "name": "ohif-monorepo-root",
-  "private": true,
-  "packageManager": "yarn@1.22.22",
-  "workspaces": {
-    "packages": [
-      "../platform/i18n",
-      "../platform/core",
-      "../platform/ui",
-      "../platform/ui-next",
-      "../platform/app",
-      "../extensions/*",
-      "../modes/*",
-      "../addOns/externals/*"
-    ],
-    "nohoist": [
-      "**/html-minifier-terser"
-    ]
-  },
-  "scripts": {
-    "preinstall": "cd .. && node preinstall.js"
-  },
-  "devDependencies": {
-    "@babel/core": "7.28.0",
-    "@babel/plugin-transform-class-properties": "^7.27.1",
-    "@babel/plugin-transform-object-rest-spread": "^7.28.0",
-    "@babel/plugin-transform-private-methods": "^7.27.1",
-    "@babel/plugin-transform-private-property-in-object": "^7.27.1",
-    "@babel/plugin-syntax-dynamic-import": "^7.8.3",
-    "@babel/plugin-transform-arrow-functions": "^7.16.7",
-    "@babel/plugin-transform-regenerator": "^7.16.7",
-    "@babel/plugin-transform-runtime": "7.28.0",
-    "@babel/plugin-transform-typescript": "^7.28.0",
-    "@babel/preset-env": "7.28.0",
-    "@babel/preset-react": "^7.27.1",
-    "@babel/preset-typescript": "^7.27.1"
-  },
-  "resolutions": {
-    "**/@babel/runtime": "^7.20.13",
-    "commander": "8.3.0",
-    "dcmjs": "^0.42.0",
-    "dicomweb-client": ">=0.10.4",
-    "nth-check": "^2.1.1",
-    "trim-newlines": "^5.0.0",
-    "glob-parent": "^6.0.2",
-    "trim": "^1.0.0",
-    "package-json": "^8.1.0",
-    "typescript": "5.5.4",
-    "sharp": "^0.32.6"
-  }
-}

babel.config.js

@@ -1,12 +1,31 @@
 // https://babeljs.io/docs/en/options#babelrcroots
+const { extendDefaultPlugins } = require('svgo');
+
 module.exports = {
   babelrcRoots: ['./platform/*', './extensions/*', './modes/*'],
   presets: ['@babel/preset-env', '@babel/preset-react', '@babel/preset-typescript'],
   plugins: [
-    ['@babel/plugin-transform-class-properties', { loose: true }],
+    [
+      'inline-react-svg',
+      {
+        svgo: {
+          plugins: [
+            {
+              name: 'preset-default',
+              params: {
+                overrides: {
+                  removeViewBox: false,
+                },
+              },
+            },
+          ],
+        },
+      },
+    ],
+    ['@babel/plugin-proposal-class-properties', { loose: true }],
     '@babel/plugin-transform-typescript',
-    ['@babel/plugin-transform-private-property-in-object', { loose: true }],
-    ['@babel/plugin-transform-private-methods', { loose: true }],
+    ['@babel/plugin-proposal-private-property-in-object', { loose: true }],
+    ['@babel/plugin-proposal-private-methods', { loose: true }],
     '@babel/plugin-transform-class-static-block',
   ],
   env: {
@@ -18,23 +37,18 @@ module.exports = {
           {
             modules: 'commonjs',
             debug: false,
-            targets: { node: 'current' },
-            bugfixes: true,
           },
         ],
         '@babel/preset-react',
         '@babel/preset-typescript',
       ],
       plugins: [
-        'babel-plugin-istanbul',
-        '@babel/plugin-transform-object-rest-spread',
+        '@babel/plugin-proposal-object-rest-spread',
         '@babel/plugin-syntax-dynamic-import',
         '@babel/plugin-transform-regenerator',
         '@babel/transform-destructuring',
         '@babel/plugin-transform-runtime',
         '@babel/plugin-transform-typescript',
-        '@babel/plugin-transform-class-static-block',
-        '@babel/plugin-transform-for-of',
       ],
     },
     production: {
@@ -53,6 +67,7 @@ module.exports = {
         '@babel/preset-react',
         '@babel/preset-typescript',
       ],
+      plugins: ['react-hot-loader/babel'],
       ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
     },
   },

commit.txt

@@ -1 +1 @@
-bde0eb1f07698b7375f7c4a58753d0368703e5bf
+339299113c65b5ce4032b02b5b4043a8968107ed

diff.txt

@@ -1,118 +0,0 @@
-diff --git a/extensions/cornerstone/src/components/ViewportOrientationMenu/ViewportOrientationMenu.tsx b/extensions/cornerstone/src/components/ViewportOrientationMenu/ViewportOrientationMenu.tsx
-index 6c1e4f8f6..56dac15b5 100644
---- a/extensions/cornerstone/src/components/ViewportOrientationMenu/ViewportOrientationMenu.tsx
-+++ b/extensions/cornerstone/src/components/ViewportOrientationMenu/ViewportOrientationMenu.tsx
-@@ -156,65 +156,65 @@ function ViewportOrientationMenu({
-       >
-         <Button
-           variant="ghost"
--          className="flex h-[28px] flex-shrink-0 items-center justify-start self-stretch"
-+          className="flex h-7 w-full flex-shrink-0 items-center justify-start self-stretch px-1 py-0"
-           onClick={() => handleOrientationChange('axial')}
-         >
--          <span className="mr-0 flex w-4 items-center justify-center">
-+          <div className="mr-1 flex w-6 items-center justify-start">
-             {currentOrientation === 'axial' ? (
--              <Icons.Checked className="text-primary h-5 w-5" />
-+              <Icons.Checked className="text-primary h-6 w-6" />
-             ) : null}
--          </span>
--          <span className="flex-1 text-left">Axial</span>
-+          </div>
-+          <div className="flex-1 text-left">Axial</div>
-         </Button>
-         <Button
-           variant="ghost"
--          className="flex h-[28px] flex-shrink-0 items-center justify-start self-stretch"
-+          className="flex h-7 w-full flex-shrink-0 items-center justify-start self-stretch px-1 py-0"
-           onClick={() => handleOrientationChange('sagittal')}
-         >
--          <span className="mr-0 flex w-4 items-center justify-center">
-+          <div className="mr-1 flex w-6 items-center justify-start">
-             {currentOrientation === 'sagittal' ? (
--              <Icons.Checked className="text-primary h-5 w-5" />
-+              <Icons.Checked className="text-primary h-6 w-6" />
-             ) : null}
--          </span>
--          <span className="flex-1 text-left">Sagittal</span>
-+          </div>
-+          <div className="flex-1 text-left">Sagittal</div>
-         </Button>
-         <Button
-           variant="ghost"
--          className="flex h-[28px] flex-shrink-0 items-center justify-start self-stretch"
-+          className="flex h-7 w-full flex-shrink-0 items-center justify-start self-stretch px-1 py-0"
-           onClick={() => handleOrientationChange('coronal')}
-         >
--          <span className="mr-0 flex w-4 items-center justify-center">
-+          <div className="mr-1 flex w-6 items-center justify-start">
-             {currentOrientation === 'coronal' ? (
--              <Icons.Checked className="text-primary h-5 w-5" />
-+              <Icons.Checked className="text-primary h-6 w-6" />
-             ) : null}
--          </span>
--          <span className="flex-1 text-left">Coronal</span>
-+          </div>
-+          <div className="flex-1 text-left">Coronal</div>
-         </Button>
-         <Button
-           variant="ghost"
--          className="flex h-[28px] flex-shrink-0 items-center justify-start self-stretch"
-+          className="flex h-7 w-full flex-shrink-0 items-center justify-start self-stretch px-1 py-0"
-           onClick={() => handleOrientationChange('acquisition')}
-         >
--          <span className="mr-0 flex w-4 items-center justify-center">
-+          <div className="mr-1 flex w-6 items-center justify-start">
-             {currentOrientation === 'acquisition' ? (
--              <Icons.Checked className="text-primary h-5 w-5" />
-+              <Icons.Checked className="text-primary h-6 w-6" />
-             ) : null}
--          </span>
--          <span className="flex-1 text-left">Acquisition</span>
-+          </div>
-+          <div className="flex-1 text-left">Acquisition</div>
-         </Button>
-         {/* Divider */}
--        <div className="my-2 border-t border-white/20" />
-+        <div className="mx-1 my-2 border-t border-white/20" />
-         <Button
-           variant="ghost"
--          className="flex h-[28px] flex-shrink-0 items-center justify-start self-stretch"
-+          className="flex h-7 w-full flex-shrink-0 items-center justify-start self-stretch px-1 py-0"
-           onClick={() => handleOrientationChange('reformat')}
-         >
--          <span className="mr-0 flex w-4 items-center justify-center">
-+          <div className="mr-1 flex w-6 items-center justify-start">
-             {currentOrientation === 'reformat' ? (
--              <Icons.Checked className="text-primary h-5 w-5" />
-+              <Icons.Checked className="text-primary h-6 w-6" />
-             ) : null}
--          </span>
--          <span className="flex-1 text-left">Reformat</span>
-+          </div>
-+          <div className="flex-1 text-left">Reformat</div>
-         </Button>
-       </PopoverContent>
-     </Popover>
-diff --git a/platform/ui-next/src/components/Icons/Sources/Checked.tsx b/platform/ui-next/src/components/Icons/Sources/Checked.tsx
-index 83c8fc57e..c88b75e0d 100644
---- a/platform/ui-next/src/components/Icons/Sources/Checked.tsx
-+++ b/platform/ui-next/src/components/Icons/Sources/Checked.tsx
-@@ -4,14 +4,14 @@ import type { IconProps } from '../types';
- export const Checked = (props: IconProps) => (
-   <svg
-     {...props}
--    width="24"
-+    width="20"
-     height="24"
--    viewBox="0 0 24 24"
-+    viewBox="0 0 20 24"
-     fill="none"
-     xmlns="http://www.w3.org/2000/svg"
-   >
-     <path
--      d="M16 9L11.3333 15L8 12.4737"
-+      d="M14 9L9.3333 15L6 12.4737"
-       stroke="currentColor"
-       strokeWidth="1.5"
-       strokeLinecap="round"

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

@@ -1,12 +0,0 @@
-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

@@ -1,54 +0,0 @@
-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/LICENSE

@@ -1,20 +0,0 @@
-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

@@ -1,12 +0,0 @@
-# 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

@@ -1,44 +0,0 @@
-module.exports = {
-  plugins: ['@babel/plugin-transform-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-transform-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

@@ -1,54 +0,0 @@
-{
-  "name": "@ohif/extension-cornerstone-dicom-pmap",
-  "version": "3.11.0-beta.95",
-  "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": "3.11.0-beta.95",
-    "@ohif/extension-cornerstone": "3.11.0-beta.95",
-    "@ohif/extension-default": "3.11.0-beta.95",
-    "@ohif/i18n": "3.11.0-beta.95",
-    "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": "^3.30.3",
-    "@cornerstonejs/core": "^3.30.3",
-    "@kitware/vtk.js": "32.12.0",
-    "react-color": "^2.19.3"
-  }
-}

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

@@ -1,245 +0,0 @@
-import { utils, Types as OhifTypes } from '@ohif/core';
-import i18n from '@ohif/i18n';
-import { metaData, cache, utilities as csUtils, volumeLoader } from '@cornerstonejs/core';
-import { adaptersPMAP } from '@cornerstonejs/adapters';
-import { SOPClassHandlerId } from './id';
-import { dicomLoaderService, VOLUME_LOADER_SCHEME } from '@ohif/extension-cornerstone';
-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.${utils.guid()}`,
-    SeriesDescription,
-    SeriesNumber,
-    SeriesDate,
-    SOPInstanceUID,
-    SeriesInstanceUID,
-    StudyInstanceUID,
-    SOPClassHandlerId,
-    SOPClassUID,
-    referencedImages: null,
-    referencedSeriesInstanceUID: null,
-    referencedDisplaySetInstanceUID: null,
-    referencedVolumeURI: null,
-    referencedVolumeId: null,
-    isDerivedDisplaySet: true,
-    loadStatus: {
-      loading: false,
-      loaded: false,
-    },
-    sopClassUids,
-    instance,
-    instances: [instance],
-    wadoRoot,
-    wadoUriRoot,
-    wadoUri,
-    supportsWindowLevel: true,
-    label: SeriesDescription || `${i18n.t('Series')} ${SeriesNumber} - ${i18n.t('PMAP')}`,
-  };
-
-  const referencedSeriesSequence = instance.ReferencedSeriesSequence;
-
-  if (!referencedSeriesSequence) {
-    console.error('ReferencedSeriesSequence is missing for the parametric map');
-    return;
-  }
-
-  const referencedSeries = referencedSeriesSequence[0] || referencedSeriesSequence;
-
-  displaySet.referencedImages = instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
-  displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID;
-
-  // Does not get the referenced displaySet during parametric displaySet creation
-  // because it is still not available (getDisplaySetByUID returns `undefined`).
-  displaySet.getReferenceDisplaySet = () => {
-    const { displaySetService } = servicesManager.services;
-
-    if (displaySet.referencedDisplaySetInstanceUID) {
-      return displaySetService.getDisplaySetByUID(displaySet.referencedDisplaySetInstanceUID);
-    }
-
-    const referencedDisplaySets = displaySetService.getDisplaySetsForSeries(
-      displaySet.referencedSeriesInstanceUID
-    );
-
-    if (!referencedDisplaySets || referencedDisplaySets.length === 0) {
-      throw new Error('Referenced displaySet is missing for the parametric map');
-    }
-
-    const referencedDisplaySet = referencedDisplaySets[0];
-
-    displaySet.referencedDisplaySetInstanceUID = referencedDisplaySet.displaySetInstanceUID;
-
-    return referencedDisplaySet;
-  };
-
-  // Does not get the referenced volumeId during parametric displaySet creation because the
-  // referenced displaySet is still not available  (getDisplaySetByUID returns `undefined`).
-  displaySet.getReferencedVolumeId = () => {
-    if (displaySet.referencedVolumeId) {
-      return displaySet.referencedVolumeId;
-    }
-
-    const referencedDisplaySet = displaySet.getReferenceDisplaySet();
-    const referencedVolumeURI = referencedDisplaySet.displaySetInstanceUID;
-    const referencedVolumeId = `${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(params: OhifTypes.Extensions.ExtensionParams) {
-  const { servicesManager, extensionManager } = params;
-  const getDisplaySetsFromSeries = instances => {
-    return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
-  };
-
-  return [
-    {
-      name: 'dicom-pmap',
-      sopClassUids,
-      getDisplaySetsFromSeries,
-    },
-  ];
-}
-
-export default getSopClassHandlerModule;

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

@@ -1,7 +0,0 @@
-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

@@ -1,39 +0,0 @@
-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

@@ -1,202 +0,0 @@
-import PropTypes from 'prop-types';
-import React, { useCallback, useEffect, useRef, useState } from 'react';
-import { useViewportGrid } from '@ohif/ui-next';
-import { OHIFCornerstoneViewport } from '@ohif/extension-cornerstone';
-
-function OHIFCornerstonePMAPViewport(props: withAppTypes) {
-  const { displaySets, children, viewportOptions, displaySetOptions, servicesManager } = props;
-  const viewportId = viewportOptions.viewportId;
-  const { displaySetService, segmentationService, uiNotificationService, customizationService } =
-    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 LoadingIndicatorTotalPercent = customizationService.getCustomization(
-    'ui.loadingIndicatorTotalPercent'
-  );
-
-  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;
-
-    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 (
-      <OHIFCornerstoneViewport
-        {...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]}
-      />
-    );
-  }, [
-    displaySetOptions,
-    props,
-    pmapDisplaySet,
-    viewportOptions.orientation,
-    viewportOptions.viewportId,
-    viewportOptions.presentationIds,
-    uiNotificationService,
-  ]);
-
-  // 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/babel.config.js

@@ -1,5 +1,5 @@
 module.exports = {
-  plugins: ['@babel/plugin-transform-class-properties'],
+  plugins: ['inline-react-svg', '@babel/plugin-proposal-class-properties'],
   env: {
     test: {
       presets: [
@@ -15,7 +15,7 @@ module.exports = {
         '@babel/preset-react',
       ],
       plugins: [
-        '@babel/plugin-transform-object-rest-spread',
+        '@babel/plugin-proposal-object-rest-spread',
         '@babel/plugin-syntax-dynamic-import',
         '@babel/plugin-transform-regenerator',
         '@babel/plugin-transform-runtime',
@@ -37,6 +37,7 @@ module.exports = {
         '@babel/preset-react',
         '@babel/preset-typescript',
       ],
+      plugins: ['react-hot-loader/babel'],
       ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
     },
   },

extensions/cornerstone-dicom-rt/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone-dicom-rt",
-  "version": "3.11.0-beta.95",
+  "version": "3.8.2",
   "description": "DICOM RT read workflow",
   "author": "OHIF",
   "license": "MIT",
@@ -33,16 +33,16 @@
     "start": "yarn run dev"
   },
   "peerDependencies": {
-    "@ohif/core": "3.11.0-beta.95",
-    "@ohif/extension-cornerstone": "3.11.0-beta.95",
-    "@ohif/extension-default": "3.11.0-beta.95",
-    "@ohif/i18n": "3.11.0-beta.95",
+    "@ohif/core": "3.8.2\n",
+    "@ohif/extension-cornerstone": "3.8.2\n",
+    "@ohif/extension-default": "3.8.2\n",
+    "@ohif/i18n": "3.8.2\n",
     "prop-types": "^15.6.2",
-    "react": "^18.3.1",
-    "react-dom": "^18.3.1",
+    "react": "^17.0.2",
+    "react-dom": "^17.0.2",
     "react-i18next": "^10.11.0",
-    "react-router": "^6.23.1",
-    "react-router-dom": "^6.23.1"
+    "react-router": "^6.3.0",
+    "react-router-dom": "^6.3.0"
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",

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

@@ -1,55 +0,0 @@
-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,
-        displaySetInstanceUIDs: [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

@@ -1,5 +1,4 @@
-import { utils, Types as OhifTypes } from '@ohif/core';
-import i18n from '@ohif/i18n';
+import { utils } from '@ohif/core';
 
 import { SOPClassHandlerId } from './id';
 import loadRTStruct from './loadRTStruct';
@@ -31,7 +30,7 @@ function _getDisplaySetsFromSeries(
   const displaySet = {
     Modality: 'RTSTRUCT',
     loading: false,
-    isReconstructable: false,
+    isReconstructable: false, // by default for now since it is a volumetric SEG currently
     displaySetInstanceUID: utils.guid(),
     SeriesDescription,
     SeriesNumber,
@@ -54,7 +53,6 @@ function _getDisplaySetsFromSeries(
     wadoUriRoot,
     wadoUri,
     isOverlayDisplaySet: true,
-    label: SeriesDescription || `${i18n.t('Series')} ${SeriesNumber} - ${i18n.t('RTSTRUCT')}`,
   };
 
   let referencedSeriesSequence = instance.ReferencedSeriesSequence;
@@ -74,43 +72,29 @@ function _getDisplaySetsFromSeries(
   displaySet.referencedImages = instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
   displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID;
 
-  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;
-          displaySet.isReconstructable = addedDisplaySet.isReconstructable;
-          unsubscribe();
-        }
-      }
+  displaySet.getReferenceDisplaySet = () => {
+    const { displaySetService } = servicesManager.services;
+    const referencedDisplaySets = displaySetService.getDisplaySetsForSeries(
+      displaySet.referencedSeriesInstanceUID
     );
-  } else {
-    const referencedDisplaySet = referencedDisplaySets[0];
-    displaySet.referencedDisplaySetInstanceUID = referencedDisplaySet.displaySetInstanceUID;
-    displaySet.isReconstructable = referencedDisplaySet.isReconstructable;
-  }
 
-  displaySet.load = ({ headers, createSegmentation = true }) =>
-    _load(displaySet, servicesManager, extensionManager, headers, createSegmentation);
+    if (!referencedDisplaySets || referencedDisplaySets.length === 0) {
+      throw new Error('Referenced DisplaySet is missing for the RT');
+    }
+
+    const referencedDisplaySet = referencedDisplaySets[0];
+
+    displaySet.referencedDisplaySetInstanceUID = referencedDisplaySet.displaySetInstanceUID;
+
+    return referencedDisplaySet;
+  };
+
+  displaySet.load = ({ headers }) => _load(displaySet, servicesManager, extensionManager, headers);
 
   return [displaySet];
 }
 
-function _load(
-  rtDisplaySet,
-  servicesManager: AppTypes.ServicesManager,
-  extensionManager,
-  headers,
-  createSegmentation = true
-) {
+function _load(rtDisplaySet, servicesManager: AppTypes.ServicesManager, extensionManager, headers) {
   const { SOPInstanceUID } = rtDisplaySet;
   const { segmentationService } = servicesManager.services;
   if (
@@ -127,26 +111,27 @@ function _load(
   // 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, headers);
+      const structureSet = await loadRTStruct(
+        extensionManager,
+        rtDisplaySet,
+        rtDisplaySet.getReferenceDisplaySet(),
+        headers
+      );
 
       rtDisplaySet.structureSet = structureSet;
     }
 
-    if (createSegmentation) {
-      segmentationService
-        .createSegmentationForRTDisplaySet(rtDisplaySet)
-        .then(() => {
-          rtDisplaySet.loading = false;
-          resolve();
-        })
-        .catch(error => {
-          rtDisplaySet.loading = false;
-          reject(error);
-        });
-    } else {
-      rtDisplaySet.loading = false;
-      resolve();
-    }
+    const suppressEvents = true;
+    segmentationService
+      .createSegmentationForRTDisplaySet(rtDisplaySet, null, suppressEvents)
+      .then(() => {
+        rtDisplaySet.loading = false;
+        resolve();
+      })
+      .catch(error => {
+        rtDisplaySet.loading = false;
+        reject(error);
+      });
   });
 
   return loadPromises[SOPInstanceUID];
@@ -187,14 +172,20 @@ function _deriveReferencedSeriesSequenceFromFrameOfReferenceSequence(
   return ReferencedSeriesSequence;
 }
 
-function _segmentationExistsInCache() {
+function _segmentationExistsInCache(
+  rtDisplaySet,
+  segmentationService: AppTypes.SegmentationService
+) {
   // Todo: fix this
   return false;
+  // This should be abstracted with the CornerstoneCacheService
+  const rtContourId = rtDisplaySet.displaySetInstanceUID;
+  const contour = segmentationService.getContour(rtContourId);
+
+  return contour !== undefined;
 }
 
-function getSopClassHandlerModule(params: OhifTypes.Extensions.ExtensionParams) {
-  const { servicesManager, extensionManager } = params;
-
+function getSopClassHandlerModule({ servicesManager, extensionManager }) {
   return [
     {
       name: 'dicom-rt',

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

@@ -2,7 +2,6 @@ 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');
@@ -25,7 +24,6 @@ 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

@@ -89,7 +89,12 @@ async function checkAndLoadContourData(instance, datasource) {
   });
 }
 
-export default async function loadRTStruct(extensionManager, rtStructDisplaySet, headers) {
+export default async function loadRTStruct(
+  extensionManager,
+  rtStructDisplaySet,
+  referencedDisplaySet,
+  headers
+) {
   const utilityModule = extensionManager.getModuleEntry(
     '@ohif/extension-cornerstone.utilityModule.common'
   );
@@ -97,6 +102,8 @@ export default async function loadRTStruct(extensionManager, rtStructDisplaySet,
   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.
@@ -126,7 +133,6 @@ export default async function loadRTStruct(extensionManager, rtStructDisplaySet,
     SeriesInstanceUID: instance.SeriesInstanceUID,
     ROIContours: [],
     visible: true,
-    ReferencedSOPInstanceUIDsSet: new Set(),
   };
 
   for (let i = 0; i < ROIContourSequence.length; i++) {
@@ -143,7 +149,7 @@ export default async function loadRTStruct(extensionManager, rtStructDisplaySet,
 
     const contourPoints = [];
     for (let c = 0; c < ContourSequenceArray.length; c++) {
-      const { ContourData, NumberOfContourPoints, ContourGeometricType, ContourImageSequence } =
+      const { ContourImageSequence, ContourData, NumberOfContourPoints, ContourGeometricType } =
         ContourSequenceArray[c];
 
       let isSupported = false;
@@ -174,12 +180,6 @@ export default async function loadRTStruct(extensionManager, rtStructDisplaySet,
         type: ContourGeometricType,
         isSupported,
       });
-
-      if (ContourImageSequence?.ReferencedSOPInstanceUID) {
-        structureSet.ReferencedSOPInstanceUIDsSet.add(
-          ContourImageSequence?.ReferencedSOPInstanceUID
-        );
-      }
     }
 
     _setROIContourMetadata(
@@ -194,6 +194,24 @@ export default async function loadRTStruct(extensionManager, rtStructDisplaySet,
   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/initRTToolGroup.ts

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

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

@@ -1,25 +1,78 @@
-import { utils, Types } from '@ohif/extension-cornerstone';
+import { ButtonEnums } from '@ohif/ui';
+
+const RESPONSE = {
+  NO_NEVER: -1,
+  CANCEL: 0,
+  HYDRATE_SEG: 5,
+};
 
 function promptHydrateRT({
   servicesManager,
   rtDisplaySet,
   viewportId,
+  toolGroupId = 'default',
   preHydrateCallbacks,
   hydrateRTDisplaySet,
-}: {
-  servicesManager: AppTypes.ServicesManager;
-  rtDisplaySet: AppTypes.DisplaySet;
-  viewportId: string;
-  preHydrateCallbacks?: Types.HydrationCallback[];
-  hydrateRTDisplaySet: Types.HydrationCallback;
-}) {
-  return utils.promptHydrationDialog({
-    servicesManager,
-    viewportId,
-    displaySet: rtDisplaySet,
-    preHydrateCallbacks,
-    hydrateCallback: hydrateRTDisplaySet,
-    type: 'RTSTRUCT',
+}: withAppTypes) {
+  const { uiViewportDialogService } = servicesManager.services;
+
+  return new Promise(async function (resolve, reject) {
+    const promptResult = await _askHydrate(uiViewportDialogService, viewportId);
+
+    if (promptResult === RESPONSE.HYDRATE_SEG) {
+      preHydrateCallbacks?.forEach(callback => {
+        callback();
+      });
+
+      const isHydrated = await hydrateRTDisplaySet({
+        rtDisplaySet,
+        viewportId,
+        toolGroupId,
+        servicesManager,
+      });
+
+      resolve(isHydrated);
+    }
+  });
+}
+
+function _askHydrate(uiViewportDialogService: AppTypes.UIViewportDialogService, viewportId) {
+  return new Promise(function (resolve, reject) {
+    const message = 'Do you want to open this Segmentation?';
+    const actions = [
+      {
+        type: ButtonEnums.type.secondary,
+        text: 'No',
+        value: RESPONSE.CANCEL,
+      },
+      {
+        type: ButtonEnums.type.primary,
+        text: 'Yes',
+        value: RESPONSE.HYDRATE_SEG,
+      },
+    ];
+    const onSubmit = result => {
+      uiViewportDialogService.hide();
+      resolve(result);
+    };
+
+    uiViewportDialogService.show({
+      id: 'promptHydrateRT',
+      viewportId,
+      type: 'info',
+      message,
+      actions,
+      onSubmit,
+      onOutsideClick: () => {
+        uiViewportDialogService.hide();
+        resolve(RESPONSE.CANCEL);
+      },
+      onKeyPress: event => {
+        if (event.key === 'Enter') {
+          onSubmit(RESPONSE.HYDRATE_SEG);
+        }
+      },
+    });
   });
 }
 

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

@@ -1,27 +1,31 @@
-import React, { Component, useCallback, useEffect, useRef, useState } from 'react';
+import React, { useCallback, useEffect, useRef, useState } from 'react';
 import PropTypes from 'prop-types';
-import { useViewportGrid } from '@ohif/ui-next';
-import {
-  utils,
-  usePositionPresentationStore,
-  OHIFCornerstoneViewport,
-} from '@ohif/extension-cornerstone';
+import { useViewportGrid, LoadingIndicatorTotalPercent, ViewportActionArrows } from '@ohif/ui';
 
 import promptHydrateRT from '../utils/promptHydrateRT';
+import _getStatusComponent from './_getStatusComponent';
 import createRTToolGroupAndAddTools from '../utils/initRTToolGroup';
-import { useSystem } from '@ohif/core/src';
+
 const RT_TOOLGROUP_BASE_NAME = 'RTToolGroup';
 
 function OHIFCornerstoneRTViewport(props: withAppTypes) {
-  const { servicesManager, commandsManager } = useSystem();
-  const { children, displaySets, viewportOptions } = props as {
-    children: React.ReactNode;
-    displaySets: AppTypes.DisplaySet[];
-    viewportOptions: AppTypes.ViewportOptions;
-  };
+  const {
+    children,
+    displaySets,
+    viewportOptions,
+    servicesManager,
+    extensionManager,
+    commandsManager,
+  } = props;
 
-  const { displaySetService, toolGroupService, segmentationService, customizationService } =
-    servicesManager.services;
+  const {
+    displaySetService,
+    toolGroupService,
+    segmentationService,
+    uiNotificationService,
+    customizationService,
+    viewportActionCornersService,
+  } = servicesManager.services;
 
   const viewportId = viewportOptions.viewportId;
 
@@ -32,59 +36,140 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
     throw new Error('RT viewport should only have a single display set');
   }
 
-  const LoadingIndicatorTotalPercent = customizationService.getCustomization(
-    'ui.loadingIndicatorTotalPercent'
-  );
-
   const rtDisplaySet = displaySets[0];
 
-  const [{ viewports, activeViewportId }, viewportGridService] = useViewportGrid();
+  const [viewportGrid, viewportGridService] = useViewportGrid();
 
   // States
-  const { setPositionPresentation } = usePositionPresentationStore();
+  const [isToolGroupCreated, setToolGroupCreated] = useState(false);
+  const [selectedSegment, setSelectedSegment] = useState(1);
+
+  // 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
+  // same frameOfReferenceUID as the referencedSeriesUID of the RT. However,
+  // loading basically means RT loading over network and bit unpacking of the
+  // RT data.
+  const [isHydrated, setIsHydrated] = useState(rtDisplaySet.isHydrated);
   const [rtIsLoading, setRtIsLoading] = useState(!rtDisplaySet.isLoaded);
+  const [element, setElement] = useState(null);
   const [processingProgress, setProcessingProgress] = useState({
     percentComplete: null,
     totalSegments: null,
   });
 
+  // refs
   const referencedDisplaySetRef = useRef(null);
 
-  const referencedDisplaySetInstanceUID = rtDisplaySet.referencedDisplaySetInstanceUID;
-  const referencedDisplaySet = displaySetService.getDisplaySetByUID(
-    referencedDisplaySetInstanceUID
-  );
+  const { viewports, activeViewportId } = viewportGrid;
+
+  const referencedDisplaySet = rtDisplaySet.getReferenceDisplaySet();
   const referencedDisplaySetMetadata = _getReferencedDisplaySetMetadata(referencedDisplaySet);
 
   referencedDisplaySetRef.current = {
     displaySet: referencedDisplaySet,
     metadata: referencedDisplaySetMetadata,
   };
+  /**
+   * OnElementEnabled callback which is called after the cornerstoneExtension
+   * has enabled the element. Note: we delegate all the image rendering to
+   * cornerstoneExtension, so we don't need to do anything here regarding
+   * the image rendering, element enabling etc.
+   */
+  const onElementEnabled = evt => {
+    setElement(evt.detail.element);
+  };
+
+  const onElementDisabled = () => {
+    setElement(null);
+  };
+
+  const storePresentationState = useCallback(() => {
+    viewportGrid?.viewports.forEach(({ viewportId }) => {
+      commandsManager.runCommand('storePresentation', {
+        viewportId,
+      });
+    });
+  }, [viewportGrid]);
+
+  const hydrateRTDisplaySet = ({ rtDisplaySet, viewportId }) => {
+    commandsManager.runCommand('loadSegmentationDisplaySetsForViewport', {
+      displaySets: [rtDisplaySet],
+      viewportId,
+    });
+  };
+
+  const getCornerstoneViewport = useCallback(() => {
+    const { component: Component } = extensionManager.getModuleEntry(
+      '@ohif/extension-cornerstone.viewportModule.cornerstone'
+    );
+
+    const { displaySet: referencedDisplaySet } = referencedDisplaySetRef.current;
+
+    // Todo: jump to the center of the first segment
+    return (
+      <Component
+        {...props}
+        displaySets={[referencedDisplaySet, rtDisplaySet]}
+        viewportOptions={{
+          viewportType: 'stack',
+          toolGroupId: toolGroupId,
+          orientation: viewportOptions.orientation,
+          viewportId: viewportOptions.viewportId,
+        }}
+        onElementEnabled={evt => {
+          props.onElementEnabled?.(evt);
+          onElementEnabled(evt);
+        }}
+        onElementDisabled={onElementDisabled}
+      ></Component>
+    );
+  }, [viewportId, rtDisplaySet, toolGroupId]);
+
+  const onSegmentChange = useCallback(
+    direction => {
+      const segmentationId = rtDisplaySet.displaySetInstanceUID;
+      const segmentation = segmentationService.getSegmentation(segmentationId);
+
+      const { segments } = segmentation;
+
+      const numberOfSegments = Object.keys(segments).length;
+
+      let newSelectedSegmentIndex = selectedSegment + direction;
+
+      // Segment 0 is always background
+      if (newSelectedSegmentIndex >= numberOfSegments - 1) {
+        newSelectedSegmentIndex = 1;
+      } else if (newSelectedSegmentIndex === 0) {
+        newSelectedSegmentIndex = numberOfSegments - 1;
+      }
+
+      segmentationService.jumpToSegmentCenter(segmentationId, newSelectedSegmentIndex, toolGroupId);
+      setSelectedSegment(newSelectedSegmentIndex);
+    },
+    [selectedSegment]
+  );
 
   useEffect(() => {
     if (rtIsLoading) {
       return;
     }
 
-    // if not active viewport, return
-    if (viewportId !== activeViewportId) {
-      return;
-    }
-
     promptHydrateRT({
       servicesManager,
       viewportId,
       rtDisplaySet,
-      hydrateRTDisplaySet: async () => {
-        return commandsManager.runCommand('hydrateSecondaryDisplaySet', {
-          displaySet: rtDisplaySet,
-          viewportId,
-        });
-      },
+      preHydrateCallbacks: [storePresentationState],
+      hydrateRTDisplaySet,
+    }).then(isHydrated => {
+      if (isHydrated) {
+        setIsHydrated(true);
+      }
     });
-  }, [servicesManager, viewportId, rtDisplaySet, rtIsLoading, commandsManager, activeViewportId]);
+  }, [servicesManager, viewportId, rtDisplaySet, rtIsLoading]);
 
   useEffect(() => {
+    // I'm not sure what is this, since in RT we support Overlapping segments
+    // via contours
     const { unsubscribe } = segmentationService.subscribe(
       segmentationService.EVENTS.SEGMENTATION_LOADING_COMPLETE,
       evt => {
@@ -92,16 +177,11 @@ 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',
+            message: 'Overlapping segments detected which is not currently supported',
+            type: 'warning',
           });
         }
       }
@@ -113,7 +193,7 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
   }, [rtDisplaySet]);
 
   useEffect(() => {
-    const segmentLoadingSubscription = segmentationService.subscribe(
+    const { unsubscribe } = segmentationService.subscribe(
       segmentationService.EVENTS.SEGMENT_LOADING_COMPLETE,
       ({ percentComplete, numSegments }) => {
         setProcessingProgress({
@@ -123,7 +203,16 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
       }
     );
 
-    const displaySetsRemovedSubscription = displaySetService.subscribe(
+    return () => {
+      unsubscribe();
+    };
+  }, [rtDisplaySet]);
+
+  /**
+   Cleanup the SEG viewport when the viewport is destroyed
+   */
+  useEffect(() => {
+    const onDisplaySetsRemovedSubscription = displaySetService.subscribe(
       displaySetService.EVENTS.DISPLAY_SETS_REMOVED,
       ({ displaySetInstanceUIDs }) => {
         const activeViewport = viewports.get(activeViewportId);
@@ -137,10 +226,9 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
     );
 
     return () => {
-      segmentLoadingSubscription.unsubscribe();
-      displaySetsRemovedSubscription.unsubscribe();
+      onDisplaySetsRemovedSubscription.unsubscribe();
     };
-  }, [rtDisplaySet, displaySetService, viewports, activeViewportId, viewportGridService]);
+  }, []);
 
   useEffect(() => {
     let toolGroup = toolGroupService.getToolGroup(toolGroupId);
@@ -151,36 +239,27 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
 
     toolGroup = createRTToolGroupAndAddTools(toolGroupService, customizationService, toolGroupId);
 
+    setToolGroupCreated(true);
+
     return () => {
       // remove the segmentation representations if seg displayset changed
-      segmentationService.removeSegmentationRepresentations(viewportId);
-      referencedDisplaySetRef.current = null;
+      segmentationService.removeSegmentationRepresentationFromToolGroup(toolGroupId);
+
       toolGroupService.destroyToolGroup(toolGroupId);
     };
   }, []);
 
-  const getCornerstoneViewport = useCallback(() => {
-    const { displaySet: referencedDisplaySet } = referencedDisplaySetRef.current;
+  useEffect(() => {
+    setIsHydrated(rtDisplaySet.isHydrated);
 
-    // Todo: jump to the center of the first segment
-    return (
-      <OHIFCornerstoneViewport
-        {...props}
-        displaySets={[referencedDisplaySet, rtDisplaySet]}
-        viewportOptions={{
-          viewportType: viewportOptions.viewportType,
-          toolGroupId: toolGroupId,
-          orientation: viewportOptions.orientation,
-          viewportId: viewportOptions.viewportId,
-          presentationIds: viewportOptions.presentationIds,
-        }}
-        onElementEnabled={evt => {
-          props.onElementEnabled?.(evt);
-        }}
-      />
-    );
-  }, [viewportId, rtDisplaySet, toolGroupId]);
+    return () => {
+      // remove the segmentation representations if seg displayset changed
+      segmentationService.removeSegmentationRepresentationFromToolGroup(toolGroupId);
+      referencedDisplaySetRef.current = null;
+    };
+  }, [rtDisplaySet]);
 
+  // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   let childrenWithProps = null;
 
   if (
@@ -203,6 +282,59 @@ 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([
+      {
+        viewportId,
+        id: 'viewportStatusComponent',
+        component: _getStatusComponent({
+          isHydrated,
+          onStatusClick,
+        }),
+        indexPriority: -100,
+        location: viewportActionCornersService.LOCATIONS.topLeft,
+      },
+      {
+        viewportId,
+        id: 'viewportActionArrowsComponent',
+        component: (
+          <ViewportActionArrows
+            key="actionArrows"
+            onArrowsClick={onSegmentChange}
+            className={
+              viewportId === activeViewportId ? 'visible' : 'invisible group-hover:visible'
+            }
+          ></ViewportActionArrows>
+        ),
+        indexPriority: 0,
+        location: viewportActionCornersService.LOCATIONS.topRight,
+      },
+    ]);
+  }, [
+    activeViewportId,
+    isHydrated,
+    onSegmentChange,
+    onStatusClick,
+    viewportActionCornersService,
+    viewportId,
+  ]);
+
   return (
     <>
       <div className="relative flex h-full w-full flex-row overflow-hidden">
@@ -226,6 +358,11 @@ OHIFCornerstoneRTViewport.propTypes = {
   viewportId: PropTypes.string.isRequired,
   dataSource: PropTypes.object,
   children: PropTypes.node,
+  customProps: PropTypes.object,
+};
+
+OHIFCornerstoneRTViewport.defaultProps = {
+  customProps: {},
 };
 
 function _getReferencedDisplaySetMetadata(referencedDisplaySet) {

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

@@ -0,0 +1,62 @@
+import React from 'react';
+import { useTranslation } from 'react-i18next';
+import { Icon, Tooltip } from '@ohif/ui';
+
+export default function _getStatusComponent({ isHydrated, onStatusClick }) {
+  let ToolTipMessage = null;
+  let StatusIcon = null;
+
+  switch (isHydrated) {
+    case true:
+      StatusIcon = () => <Icon name="status-alert" />;
+
+      ToolTipMessage = () => <div>This Segmentation is loaded in the segmentation panel</div>;
+      break;
+    case false:
+      StatusIcon = () => (
+        <Icon
+          className="text-aqua-pale"
+          name="status-untracked"
+        />
+      );
+
+      ToolTipMessage = () => <div>Click LOAD to load RTSTRUCT.</div>;
+  }
+
+  const StatusArea = () => {
+    const { t } = useTranslation('Common');
+    const loadStr = t('LOAD');
+
+    return (
+      <div className="flex h-6 cursor-default text-sm leading-6 text-white">
+        <div className="bg-customgray-100 flex min-w-[45px] items-center rounded-l-xl rounded-r p-1">
+          <StatusIcon />
+          <span className="ml-1">RTSTRUCT</span>
+        </div>
+        {!isHydrated && (
+          <div
+            className="bg-primary-main hover:bg-primary-light ml-1 cursor-pointer rounded px-1.5 hover:text-black"
+            // Using onMouseUp here because onClick is not working when the viewport is not active and is styled with pointer-events:none
+            onMouseUp={onStatusClick}
+          >
+            {loadStr}
+          </div>
+        )}
+      </div>
+    );
+  };
+
+  return (
+    <>
+      {ToolTipMessage && (
+        <Tooltip
+          content={<ToolTipMessage />}
+          position="bottom-left"
+        >
+          <StatusArea />
+        </Tooltip>
+      )}
+      {!ToolTipMessage && <StatusArea />}
+    </>
+  );
+}

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

@@ -1,5 +1,5 @@
 module.exports = {
-  plugins: ['@babel/plugin-transform-class-properties'],
+  plugins: ['inline-react-svg', '@babel/plugin-proposal-class-properties'],
   env: {
     test: {
       presets: [
@@ -15,7 +15,7 @@ module.exports = {
         '@babel/preset-react',
       ],
       plugins: [
-        '@babel/plugin-transform-object-rest-spread',
+        '@babel/plugin-proposal-object-rest-spread',
         '@babel/plugin-syntax-dynamic-import',
         '@babel/plugin-transform-regenerator',
         '@babel/plugin-transform-runtime',
@@ -37,6 +37,7 @@ module.exports = {
         '@babel/preset-react',
         '@babel/preset-typescript',
       ],
+      plugins: ['react-hot-loader/babel'],
       ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
     },
   },

extensions/cornerstone-dicom-seg/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone-dicom-seg",
-  "version": "3.11.0-beta.95",
+  "version": "3.8.2",
   "description": "DICOM SEG read workflow",
   "author": "OHIF",
   "license": "MIT",
@@ -33,22 +33,22 @@
     "start": "yarn run dev"
   },
   "peerDependencies": {
-    "@ohif/core": "3.11.0-beta.95",
-    "@ohif/extension-cornerstone": "3.11.0-beta.95",
-    "@ohif/extension-default": "3.11.0-beta.95",
-    "@ohif/i18n": "3.11.0-beta.95",
+    "@ohif/core": "3.8.2\n",
+    "@ohif/extension-cornerstone": "3.8.2\n",
+    "@ohif/extension-default": "3.8.2\n",
+    "@ohif/i18n": "3.8.2\n",
     "prop-types": "^15.6.2",
-    "react": "^18.3.1",
-    "react-dom": "^18.3.1",
+    "react": "^17.0.2",
+    "react-dom": "^17.0.2",
     "react-i18next": "^12.2.2",
-    "react-router": "^6.23.1",
-    "react-router-dom": "^6.23.1"
+    "react-router": "^6.8.1",
+    "react-router-dom": "^6.8.1"
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/adapters": "^3.30.3",
-    "@cornerstonejs/core": "^3.30.3",
-    "@kitware/vtk.js": "32.12.0",
+    "@cornerstonejs/adapters": "^1.77.6",
+    "@cornerstonejs/core": "^1.77.6",
+    "@kitware/vtk.js": "30.4.1",
     "react-color": "^2.19.3"
   }
 }

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

@@ -1,27 +1,31 @@
 import dcmjs from 'dcmjs';
-import { classes, Types } from '@ohif/core';
-import { cache, metaData } from '@cornerstonejs/core';
-import { segmentation as cornerstoneToolsSegmentation } from '@cornerstonejs/tools';
-import { adaptersRT, helpers, adaptersSEG } from '@cornerstonejs/adapters';
 import { createReportDialogPrompt } from '@ohif/extension-default';
-import { DicomMetadataStore } from '@ohif/core';
+import { Types } from '@ohif/core';
+import { cache, metaData } from '@cornerstonejs/core';
+import {
+  segmentation as cornerstoneToolsSegmentation,
+  Enums as cornerstoneToolsEnums,
+  utilities,
+} from '@cornerstonejs/tools';
+import { adaptersRT, helpers, adaptersSEG } from '@cornerstonejs/adapters';
+import { classes, DicomMetadataStore } from '@ohif/core';
 
-import PROMPT_RESPONSES from '../../default/src/utils/_shared/PROMPT_RESPONSES';
+import vtkImageMarchingSquares from '@kitware/vtk.js/Filters/General/ImageMarchingSquares';
+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: { generateSegmentation },
+    Segmentation: { generateLabelMaps2DFrom3D, generateSegmentation },
   },
 } = adaptersSEG;
 
@@ -37,10 +41,87 @@ const commandsModule = ({
   servicesManager,
   extensionManager,
 }: Types.Extensions.ExtensionParams): Types.Extensions.CommandsModule => {
-  const { segmentationService, displaySetService, viewportGridService, toolGroupService } =
-    servicesManager.services as AppTypes.Services;
+  const {
+    uiNotificationService,
+    segmentationService,
+    uiDialogService,
+    displaySetService,
+    viewportGridService,
+    toolGroupService,
+  } = servicesManager.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.
@@ -52,30 +133,103 @@ 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 viewport = getTargetViewport({ viewportId, viewportGridService });
-      const displaySetInstanceUID = viewport.displaySetInstanceUIDs[0];
+      const displaySet = displaySets[0];
+      const referencedDisplaySet = displaySetService.getDisplaySetByUID(
+        displaySet.referencedDisplaySetInstanceUID
+      );
 
-      const segmentation = segmentations[0];
-      const segmentationId = segmentation.segmentationId;
-      const label = segmentation.config.label;
-      const segments = segmentation.config.segments;
+      updateViewportsForSegmentationRendering({
+        viewportId,
+        servicesManager,
+        displaySet,
+        loadFn: async () => {
+          const segDisplaySet = displaySet;
+          const suppressEvents = false;
+          const serviceFunction =
+            segDisplaySet.Modality === 'SEG'
+              ? 'createSegmentationForSEGDisplaySet'
+              : 'createSegmentationForRTDisplaySet';
 
-      const displaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
-
-      await segmentationService.createLabelmapForDisplaySet(displaySet, {
-        segmentationId,
-        segments,
-        label,
+          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;
+        },
       });
-
-      segmentationService.addOrUpdateSegmentation(segmentation);
-
-      await segmentationService.addSegmentationRepresentation(viewport.viewportId, {
-        segmentationId,
-      });
-
-      return segmentationId;
     },
     /**
      * Generates a segmentation from a given segmentation ID.
@@ -93,61 +247,22 @@ const commandsModule = ({
     generateSegmentation: ({ segmentationId, options = {} }) => {
       const segmentation = cornerstoneToolsSegmentation.state.getSegmentation(segmentationId);
 
-      const { imageIds } = segmentation.representationData.Labelmap;
+      const { referencedVolumeId } = segmentation.representationData.LABELMAP;
 
-      const segImages = imageIds.map(imageId => cache.getImage(imageId));
-      const referencedImages = segImages.map(image => cache.getImage(image.referencedImageId));
+      const segmentationVolume = cache.getVolume(segmentationId);
+      const referencedVolume = cache.getVolume(referencedVolumeId);
+      const referencedImages = referencedVolume.getCornerstoneImages();
 
-      const labelmaps2D = [];
+      const labelmapObj = generateLabelMaps2DFrom3D(segmentationVolume);
 
-      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,
-      };
+      // Generate fake metadata as an example
+      labelmapObj.metadata = [];
 
       const segmentationInOHIF = segmentationService.getSegmentation(segmentationId);
-      const representations = segmentationService.getRepresentationsForSegmentation(segmentationId);
-
-      Object.entries(segmentationInOHIF.segments).forEach(([segmentIndex, segment]) => {
+      labelmapObj.segmentsOnLabelmap.forEach(segmentIndex => {
         // segmentation service already has a color for each segment
-        if (!segment) {
-          return;
-        }
-
-        const { label } = segment;
-
-        const firstRepresentation = representations[0];
-        const color = segmentationService.getSegmentColor(
-          firstRepresentation.viewportId,
-          segmentationId,
-          segment.segmentIndex
-        );
+        const segment = segmentationInOHIF?.segments[segmentIndex];
+        const { label, color } = segment;
 
         const RecommendedDisplayCIELabValue = dcmjs.data.Colors.rgb2DICOMLAB(
           color.slice(0, 3).map(value => value / 255)
@@ -156,8 +271,8 @@ const commandsModule = ({
         const segmentMetadata = {
           SegmentNumber: segmentIndex.toString(),
           SegmentLabel: label,
-          SegmentAlgorithmType: segment?.algorithmType || 'MANUAL',
-          SegmentAlgorithmName: segment?.algorithmName || 'OHIF Brush',
+          SegmentAlgorithmType: 'MANUAL',
+          SegmentAlgorithmName: 'OHIF Brush',
           RecommendedDisplayCIELabValue,
           SegmentedPropertyCategoryCodeSequence: {
             CodeValue: 'T-D0050',
@@ -170,12 +285,12 @@ const commandsModule = ({
             CodeMeaning: 'Tissue',
           },
         };
-        labelmap3D.metadata[segmentIndex] = segmentMetadata;
+        labelmapObj.metadata[segmentIndex] = segmentMetadata;
       });
 
       const generatedSegmentation = generateSegmentation(
         referencedImages,
-        labelmap3D,
+        labelmapObj,
         metaData,
         options
       );
@@ -213,6 +328,14 @@ const commandsModule = ({
      * otherwise throws an error.
      */
     storeSegmentation: async ({ segmentationId, dataSource }) => {
+      const promptResult = await createReportDialogPrompt(uiDialogService, {
+        extensionManager,
+      });
+
+      if (promptResult.action !== 1 && promptResult.value) {
+        return;
+      }
+
       const segmentation = segmentationService.getSegmentation(segmentationId);
 
       if (!segmentation) {
@@ -220,55 +343,33 @@ const commandsModule = ({
       }
 
       const { label } = segmentation;
-      const defaultDataSource = dataSource ?? extensionManager.getActiveDataSource()[0];
+      const SeriesDescription = promptResult.value || label || 'Research Derived Series';
 
-      const {
-        value: reportName,
-        dataSourceName: selectedDataSource,
-        action,
-      } = await createReportDialogPrompt({
-        servicesManager,
-        extensionManager,
-        title: 'Store Segmentation',
+      const generatedData = actions.generateSegmentation({
+        segmentationId,
+        options: {
+          SeriesDescription,
+        },
       });
 
-      if (action === PROMPT_RESPONSES.CREATE_REPORT) {
-        try {
-          const selectedDataSourceConfig = selectedDataSource
-            ? extensionManager.getDataSources(selectedDataSource)[0]
-            : defaultDataSource;
-
-          const generatedData = actions.generateSegmentation({
-            segmentationId,
-            options: {
-              SeriesDescription: reportName || label || 'Research Derived Series',
-            },
-          });
-
-          if (!generatedData || !generatedData.dataset) {
-            throw new Error('Error during segmentation generation');
-          }
-
-          const { dataset: naturalizedReport } = generatedData;
-
-          // DCMJS assigns a dummy study id during creation, and this can cause problems, so clearing it out
-          if (naturalizedReport.StudyID === 'No Study ID') {
-            naturalizedReport.StudyID = '';
-          }
-
-          await selectedDataSourceConfig.store.dicom(naturalizedReport);
-
-          // add the information for where we stored it to the instance as well
-          naturalizedReport.wadoRoot = selectedDataSourceConfig.getConfig().wadoRoot;
-
-          DicomMetadataStore.addInstances([naturalizedReport], true);
-
-          return naturalizedReport;
-        } catch (error) {
-          console.debug('Error storing segmentation:', error);
-          throw error;
-        }
+      if (!generatedData || !generatedData.dataset) {
+        throw new Error('Error during segmentation generation');
       }
+
+      const { dataset: naturalizedReport } = generatedData;
+
+      await dataSource.store.dicom(naturalizedReport);
+
+      // The "Mode" route listens for DicomMetadataStore changes
+      // When a new instance is added, it listens and
+      // automatically calls makeDisplaySets
+
+      // add the information for where we stored it to the instance as well
+      naturalizedReport.wadoRoot = dataSource.getConfig().wadoRoot;
+
+      DicomMetadataStore.addInstances([naturalizedReport], true);
+
+      return naturalizedReport;
     },
     /**
      * Converts segmentations into RTSS for download.
@@ -277,24 +378,21 @@ const commandsModule = ({
      * converts dataset to downloadable blob.
      *
      */
-    downloadRTSS: async ({ segmentationId }) => {
+    downloadRTSS: ({ segmentationId }) => {
       const segmentations = segmentationService.getSegmentation(segmentationId);
+      const vtkUtils = {
+        vtkImageMarchingSquares,
+        vtkDataArray,
+        vtkImageData,
+      };
 
-      // inject colors to the segmentIndex
-      const firstRepresentation =
-        segmentationService.getRepresentationsForSegmentation(segmentationId)[0];
-      Object.entries(segmentations.segments).forEach(([segmentIndex, segment]) => {
-        segment.color = segmentationService.getSegmentColor(
-          firstRepresentation.viewportId,
-          segmentationId,
-          segmentIndex
-        );
-      });
-
-      const RTSS = await generateRTSSFromSegmentations(
+      const RTSS = generateRTSSFromSegmentations(
         segmentations,
         classes.MetadataProvider,
-        DicomMetadataStore
+        DicomMetadataStore,
+        cache,
+        cornerstoneToolsEnums,
+        vtkUtils
       );
 
       try {
@@ -307,13 +405,51 @@ const commandsModule = ({
         console.warn(e);
       }
     },
+    setBrushSize: ({ value, toolNames }) => {
+      const brushSize = Number(value);
+
+      toolGroupService.getToolGroupIds()?.forEach(toolGroupId => {
+        if (toolNames?.length === 0) {
+          segmentationUtils.setBrushSizeForToolGroup(toolGroupId, brushSize);
+        } else {
+          toolNames?.forEach(toolName => {
+            segmentationUtils.setBrushSizeForToolGroup(toolGroupId, brushSize, toolName);
+          });
+        }
+      });
+    },
+    setThresholdRange: ({
+      value,
+      toolNames = ['ThresholdCircularBrush', 'ThresholdSphereBrush'],
+    }) => {
+      toolGroupService.getToolGroupIds()?.forEach(toolGroupId => {
+        const toolGroup = toolGroupService.getToolGroup(toolGroupId);
+        toolNames?.forEach(toolName => {
+          toolGroup.setToolConfiguration(toolName, {
+            strategySpecificConfiguration: {
+              THRESHOLD: {
+                threshold: value,
+              },
+            },
+          });
+        });
+      });
+    },
   };
 
   const definitions = {
+    getUpdatedViewportsForSegmentation: {
+      commandFn: actions.getUpdatedViewportsForSegmentation,
+    },
+    loadSegmentationDisplaySetsForViewport: {
+      commandFn: actions.loadSegmentationDisplaySetsForViewport,
+    },
     loadSegmentationsForViewport: {
       commandFn: actions.loadSegmentationsForViewport,
     },
-
+    createEmptySegmentationForViewport: {
+      commandFn: actions.createEmptySegmentationForViewport,
+    },
     generateSegmentation: {
       commandFn: actions.generateSegmentation,
     },
@@ -326,6 +462,12 @@ const commandsModule = ({
     downloadRTSS: {
       commandFn: actions.downloadRTSS,
     },
+    setBrushSize: {
+      commandFn: actions.setBrushSize,
+    },
+    setThresholdRange: {
+      commandFn: actions.setThresholdRange,
+    },
   };
 
   return {

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

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

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

@@ -0,0 +1,80 @@
+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

@@ -1,13 +1,12 @@
-import { utils, Types as OhifTypes } from '@ohif/core';
-import i18n from '@ohif/i18n';
-import { metaData, eventTarget } from '@cornerstonejs/core';
-import { CONSTANTS, segmentation as cstSegmentation } from '@cornerstonejs/tools';
+import { utils } from '@ohif/core';
+import { metaData, cache, triggerEvent, eventTarget } from '@cornerstonejs/core';
+import { CONSTANTS } from '@cornerstonejs/tools';
 import { adaptersSEG, Enums } from '@cornerstonejs/adapters';
 
 import { SOPClassHandlerId } from './id';
 import { dicomlabToRGB } from './utils/dicomlabToRGB';
 
-const sopClassUids = ['1.2.840.10008.5.1.4.1.1.66.4', '1.2.840.10008.5.1.4.1.1.66.7'];
+const sopClassUids = ['1.2.840.10008.5.1.4.1.1.66.4'];
 
 const loadPromises = {};
 
@@ -34,7 +33,7 @@ function _getDisplaySetsFromSeries(
   const displaySet = {
     Modality: 'SEG',
     loading: false,
-    isReconstructable: false,
+    isReconstructable: true, // by default for now since it is a volumetric SEG currently
     displaySetInstanceUID: utils.guid(),
     SeriesDescription,
     SeriesNumber,
@@ -58,7 +57,6 @@ function _getDisplaySetsFromSeries(
     wadoUriRoot,
     wadoUri,
     isOverlayDisplaySet: true,
-    label: SeriesDescription || `${i18n.t('Series')} ${SeriesNumber} - ${i18n.t('SEG')}`,
   };
 
   const referencedSeriesSequence = instance.ReferencedSeriesSequence;
@@ -72,34 +70,28 @@ function _getDisplaySetsFromSeries(
 
   displaySet.referencedImages = instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
   displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID;
-  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;
-          displaySet.isReconstructable = addedDisplaySet.isReconstructable;
-          unsubscribe();
-        }
-      }
+  displaySet.getReferenceDisplaySet = () => {
+    const { displaySetService } = servicesManager.services;
+    const referencedDisplaySets = displaySetService.getDisplaySetsForSeries(
+      displaySet.referencedSeriesInstanceUID
     );
-  } else {
+
+    if (!referencedDisplaySets || referencedDisplaySets.length === 0) {
+      throw new Error('Referenced DisplaySet is missing for the SEG');
+    }
+
+    const referencedDisplaySet = referencedDisplaySets[0];
+
     displaySet.referencedDisplaySetInstanceUID = referencedDisplaySet.displaySetInstanceUID;
-    displaySet.isReconstructable = referencedDisplaySet.isReconstructable;
-  }
+
+    // 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);
@@ -119,7 +111,7 @@ function _load(
   if (
     (segDisplaySet.loading || segDisplaySet.isLoaded) &&
     loadPromises[SOPInstanceUID] &&
-    _segmentationExists(segDisplaySet)
+    _segmentationExists(segDisplaySet, segmentationService)
   ) {
     return loadPromises[SOPInstanceUID];
   }
@@ -130,21 +122,17 @@ 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) {
-      try {
-        await _loadSegments({
-          extensionManager,
-          servicesManager,
-          segDisplaySet,
-          headers,
-        });
-      } catch (e) {
-        segDisplaySet.loading = false;
-        return reject(e);
-      }
+      await _loadSegments({
+        extensionManager,
+        servicesManager,
+        segDisplaySet,
+        headers,
+      });
     }
 
+    const suppressEvents = true;
     segmentationService
-      .createSegmentationForSEGDisplaySet(segDisplaySet)
+      .createSegmentationForSEGDisplaySet(segDisplaySet, null, suppressEvents)
       .then(() => {
         segDisplaySet.loading = false;
         resolve();
@@ -173,24 +161,20 @@ async function _loadSegments({
   const { dicomLoaderService } = utilityModule.exports;
   const arrayBuffer = await dicomLoaderService.findDicomDataPromise(segDisplaySet, null, headers);
 
-  const referencedDisplaySet = servicesManager.services.displaySetService.getDisplaySetByUID(
-    segDisplaySet.referencedDisplaySetInstanceUID
-  );
+  const cachedReferencedVolume = cache.getVolume(segDisplaySet.referencedVolumeId);
 
-  if (!referencedDisplaySet) {
-    throw new Error('referencedDisplaySet is missing for SEG');
+  if (!cachedReferencedVolume) {
+    throw new Error(
+      'Referenced Volume is missing for the SEG, and stack viewport SEG is not supported yet'
+    );
   }
 
-  let { imageIds } = referencedDisplaySet;
-
-  if (!imageIds) {
-    // try images
-    const { images } = referencedDisplaySet;
-    imageIds = images.map(image => image.imageId);
-  }
+  const { imageIds } = cachedReferencedVolume;
 
   // Todo: what should be defaults here
   const tolerance = 0.001;
+  const skipOverlapping = true;
+
   eventTarget.addEventListener(Enums.Events.SEGMENTATION_LOAD_PROGRESS, evt => {
     const { percentComplete } = evt.detail;
     segmentationService._broadcastEvent(segmentationService.EVENTS.SEGMENT_LOADING_COMPLETE, {
@@ -198,10 +182,11 @@ async function _loadSegments({
     });
   });
 
-  const results = await adaptersSEG.Cornerstone3D.Segmentation.createFromDICOMSegBuffer(
+  const results = await adaptersSEG.Cornerstone3D.Segmentation.generateToolState(
     imageIds,
     arrayBuffer,
-    { metadataProvider: metaData, tolerance }
+    metaData,
+    { skipOverlapping, tolerance, eventTarget, triggerEvent }
   );
 
   let usedRecommendedDisplayCIELabValue = true;
@@ -218,6 +203,15 @@ async function _loadSegments({
     }
   });
 
+  if (results.overlappingSegments) {
+    uiNotificationService.show({
+      title: 'Overlapping Segments',
+      message:
+        'Unsupported overlapping segments detected, segmentation rendering results may be incorrect.',
+      type: 'warning',
+    });
+  }
+
   if (!usedRecommendedDisplayCIELabValue) {
     // Display a notification about the non-utilization of RecommendedDisplayCIELabValue
     uiNotificationService.show({
@@ -232,12 +226,12 @@ async function _loadSegments({
   Object.assign(segDisplaySet, results);
 }
 
-function _segmentationExists(segDisplaySet) {
-  return cstSegmentation.state.getSegmentation(segDisplaySet.displaySetInstanceUID);
+function _segmentationExists(segDisplaySet, segmentationService: AppTypes.SegmentationService) {
+  // This should be abstracted with the CornerstoneCacheService
+  return segmentationService.getSegmentation(segDisplaySet.displaySetInstanceUID);
 }
 
-function getSopClassHandlerModule(params: OhifTypes.Extensions.ExtensionParams) {
-  const { servicesManager, extensionManager } = params;
+function getSopClassHandlerModule({ servicesManager, extensionManager }) {
   const getDisplaySetsFromSeries = instances => {
     return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
   };

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

@@ -1,15 +1,6 @@
 export function getToolbarModule({ servicesManager }: withAppTypes) {
   const { segmentationService, toolbarService, toolGroupService } = servicesManager.services;
   return [
-    {
-      name: 'evaluate.cornerstone.hasSegmentation',
-      evaluate: ({ viewportId }) => {
-        const segmentations = segmentationService.getSegmentationRepresentations(viewportId);
-        return {
-          disabled: !segmentations?.length,
-        };
-      },
-    },
     {
       name: 'evaluate.cornerstone.segmentation',
       evaluate: ({ viewportId, button, toolNames, disabledText }) => {
@@ -17,43 +8,31 @@ 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.getSegmentationRepresentations(viewportId);
+        const segmentations = segmentationService.getSegmentations();
         if (!segmentations?.length) {
           return {
             disabled: true,
+            className: '!text-common-bright !bg-black opacity-50',
             disabledText: disabledText ?? 'No segmentations available',
           };
         }
 
-        const activeSegmentation = segmentationService.getActiveSegmentation(viewportId);
-        if (!Object.keys(activeSegmentation.segments).length) {
-          return {
-            disabled: true,
-            disabledText: 'Add segment to enable this tool',
-          };
-        }
-
         const toolGroup = toolGroupService.getToolGroupForViewport(viewportId);
 
         if (!toolGroup) {
           return {
             disabled: true,
+            className: '!text-common-bright ohif-disabled',
             disabledText: disabledText ?? 'Not available on the current viewport',
           };
         }
 
-        if (!toolNames) {
-          return {
-            disabled: false,
-            // isActive: false,
-          };
-        }
-
         const toolName = toolbarService.getToolNameForButton(button);
 
         if (!toolGroup.hasTool(toolName) && !toolNames) {
           return {
             disabled: true,
+            className: '!text-common-bright ohif-disabled',
             disabledText: disabledText ?? 'Not available on the current viewport',
           };
         }
@@ -64,6 +43,12 @@ export function getToolbarModule({ servicesManager }: withAppTypes) {
 
         return {
           disabled: false,
+          className: isPrimaryActive
+            ? '!text-black !bg-primary-light hover:bg-primary-light hover-text-black hover:cursor-pointer'
+            : '!text-common-bright !bg-black hover:bg-primary-light hover:cursor-pointer hover:text-black',
+          // Todo: isActive right now is used for nested buttons where the primary
+          // button needs to be fully rounded (vs partial rounded) when active
+          // otherwise it does not have any other use
           isActive: isPrimaryActive,
         };
       },

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

@@ -3,6 +3,7 @@ import React from 'react';
 
 import getSopClassHandlerModule from './getSopClassHandlerModule';
 import getHangingProtocolModule from './getHangingProtocolModule';
+import getPanelModule from './getPanelModule';
 import getCommandsModule from './commandsModule';
 import { getToolbarModule } from './getToolbarModule';
 
@@ -27,6 +28,13 @@ 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

@@ -0,0 +1,386 @@
+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

@@ -0,0 +1,62 @@
+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/colorPickerDialog.tsx

@@ -0,0 +1,58 @@
+import React from 'react';
+import { Dialog } from '@ohif/ui';
+import { ChromePicker } from 'react-color';
+
+import './colorPickerDialog.css';
+
+function callColorPickerDialog(uiDialogService, rgbaColor, callback) {
+  const dialogId = 'pick-color';
+
+  const onSubmitHandler = ({ action, value }) => {
+    switch (action.id) {
+      case 'save':
+        callback(value.rgbaColor, 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 Color',
+        value: { rgbaColor },
+        noCloseButton: true,
+        onClose: () => uiDialogService.dismiss({ id: dialogId }),
+        actions: [
+          { id: 'cancel', text: 'Cancel', type: 'primary' },
+          { id: 'save', text: 'Save', type: 'secondary' },
+        ],
+        onSubmit: onSubmitHandler,
+        body: ({ value, setValue }) => {
+          const handleChange = color => {
+            setValue({ rgbaColor: color.rgb });
+          };
+
+          return (
+            <ChromePicker
+              color={value.rgbaColor}
+              onChange={handleChange}
+              presetColors={[]}
+              width={300}
+            />
+          );
+        },
+      },
+    });
+  }
+}
+
+export default callColorPickerDialog;

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

@@ -0,0 +1,33 @@
+// 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

@@ -0,0 +1,192 @@
+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.
+ *
+ * @returns Returns true upon successful update of viewports for segmentation rendering.
+ */
+async function updateViewportsForSegmentationRendering({
+  viewportId,
+  loadFn,
+  servicesManager,
+  displaySet,
+}: {
+  viewportId: string;
+  loadFn: () => Promise<string>;
+  servicesManager: AppTypes.ServicesManager;
+  displaySet?: any;
+}) {
+  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;
+
+    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/initSEGToolGroup.ts

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

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

@@ -1,25 +1,74 @@
-import { utils, Types } from '@ohif/extension-cornerstone';
+import { ButtonEnums } from '@ohif/ui';
+
+const RESPONSE = {
+  NO_NEVER: -1,
+  CANCEL: 0,
+  HYDRATE_SEG: 5,
+};
 
 function promptHydrateSEG({
   servicesManager,
   segDisplaySet,
   viewportId,
   preHydrateCallbacks,
-  hydrateCallback,
-}: {
-  servicesManager: AppTypes.ServicesManager;
-  segDisplaySet: AppTypes.DisplaySet;
-  viewportId: string;
-  preHydrateCallbacks?: Types.HydrationCallback[];
-  hydrateCallback: Types.HydrationCallback;
-}) {
-  return utils.promptHydrationDialog({
-    servicesManager,
-    viewportId,
-    displaySet: segDisplaySet as AppTypes.DisplaySet,
-    preHydrateCallbacks,
-    hydrateCallback,
-    type: 'SEG',
+  hydrateSEGDisplaySet,
+}: withAppTypes) {
+  const { uiViewportDialogService } = servicesManager.services;
+
+  return new Promise(async function (resolve, reject) {
+    const promptResult = await _askHydrate(uiViewportDialogService, viewportId);
+
+    if (promptResult === RESPONSE.HYDRATE_SEG) {
+      preHydrateCallbacks?.forEach(callback => {
+        callback();
+      });
+
+      const isHydrated = await hydrateSEGDisplaySet({
+        segDisplaySet,
+        viewportId,
+      });
+
+      resolve(isHydrated);
+    }
+  });
+}
+
+function _askHydrate(uiViewportDialogService, viewportId) {
+  return new Promise(function (resolve, reject) {
+    const message = 'Do you want to open this Segmentation?';
+    const actions = [
+      {
+        type: ButtonEnums.type.secondary,
+        text: 'No',
+        value: RESPONSE.CANCEL,
+      },
+      {
+        type: ButtonEnums.type.primary,
+        text: 'Yes',
+        value: RESPONSE.HYDRATE_SEG,
+      },
+    ];
+    const onSubmit = result => {
+      uiViewportDialogService.hide();
+      resolve(result);
+    };
+
+    uiViewportDialogService.show({
+      viewportId,
+      type: 'info',
+      message,
+      actions,
+      onSubmit,
+      onOutsideClick: () => {
+        uiViewportDialogService.hide();
+        resolve(RESPONSE.CANCEL);
+      },
+      onKeyPress: event => {
+        if (event.key === 'Enter') {
+          onSubmit(RESPONSE.HYDRATE_SEG);
+        }
+      },
+    });
   });
 }
 

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

@@ -1,28 +1,33 @@
+import PropTypes from 'prop-types';
 import React, { useCallback, useEffect, useRef, useState } from 'react';
-import { useViewportGrid } from '@ohif/ui-next';
+import { useTranslation } from 'react-i18next';
+import { LoadingIndicatorTotalPercent, useViewportGrid, ViewportActionArrows } from '@ohif/ui';
 import createSEGToolGroupAndAddTools from '../utils/initSEGToolGroup';
 import promptHydrateSEG from '../utils/promptHydrateSEG';
-import { usePositionPresentationStore, OHIFCornerstoneViewport } from '@ohif/extension-cornerstone';
-import { SegmentationRepresentations } from '@cornerstonejs/tools/enums';
-import { useSystem } from '@ohif/core/src/contextProviders/SystemProvider';
+import _getStatusComponent from './_getStatusComponent';
 
 const SEG_TOOLGROUP_BASE_NAME = 'SEGToolGroup';
 
 function OHIFCornerstoneSEGViewport(props: withAppTypes) {
-  const { servicesManager, commandsManager } = useSystem();
-  const { children, displaySets, viewportOptions } = props as {
-    children: React.ReactNode;
-    displaySets: AppTypes.DisplaySet[];
-    viewportOptions: AppTypes.ViewportOptions;
-  };
+  const {
+    children,
+    displaySets,
+    viewportOptions,
+    servicesManager,
+    extensionManager,
+    commandsManager,
+  } = props;
+
+  const { t } = useTranslation('SEGViewport');
   const viewportId = viewportOptions.viewportId;
 
-  const { displaySetService, toolGroupService, segmentationService, customizationService } =
-    servicesManager.services;
-
-  const LoadingIndicatorTotalPercent = customizationService.getCustomization(
-    'ui.loadingIndicatorTotalPercent'
-  );
+  const {
+    displaySetService,
+    toolGroupService,
+    segmentationService,
+    customizationService,
+    viewportActionCornersService,
+  } = servicesManager.services;
 
   const toolGroupId = `${SEG_TOOLGROUP_BASE_NAME}-${viewportId}`;
 
@@ -32,17 +37,20 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
   }
 
   const segDisplaySet = displaySets[0];
+
   const [viewportGrid, viewportGridService] = useViewportGrid();
 
   // States
-  const { setPositionPresentation } = usePositionPresentationStore();
+  const [selectedSegment, setSelectedSegment] = useState(1);
 
   // 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
   // same frameOfReferenceUID as the referencedSeriesUID of the SEG. However,
   // loading basically means SEG loading over network and bit unpacking of the
   // SEG data.
+  const [isHydrated, setIsHydrated] = useState(segDisplaySet.isHydrated);
   const [segIsLoading, setSegIsLoading] = useState(!segDisplaySet.isLoaded);
+  const [element, setElement] = useState(null);
   const [processingProgress, setProcessingProgress] = useState({
     percentComplete: null,
     totalSegments: null,
@@ -53,11 +61,7 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
 
   const { viewports, activeViewportId } = viewportGrid;
 
-  const referencedDisplaySetInstanceUID = segDisplaySet.referencedDisplaySetInstanceUID;
-  const referencedDisplaySet = displaySetService.getDisplaySetByUID(
-    referencedDisplaySetInstanceUID
-  );
-
+  const referencedDisplaySet = segDisplaySet.getReferenceDisplaySet();
   const referencedDisplaySetMetadata = _getReferencedDisplaySetMetadata(
     referencedDisplaySet,
     segDisplaySet
@@ -67,72 +71,105 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
     displaySet: referencedDisplaySet,
     metadata: referencedDisplaySetMetadata,
   };
+  /**
+   * OnElementEnabled callback which is called after the cornerstoneExtension
+   * has enabled the element. Note: we delegate all the image rendering to
+   * cornerstoneExtension, so we don't need to do anything here regarding
+   * the image rendering, element enabling etc.
+   */
+  const onElementEnabled = evt => {
+    setElement(evt.detail.element);
+  };
+
+  const onElementDisabled = () => {
+    setElement(null);
+  };
+
+  const storePresentationState = useCallback(() => {
+    viewportGrid?.viewports.forEach(({ viewportId }) => {
+      commandsManager.runCommand('storePresentation', {
+        viewportId,
+      });
+    });
+  }, [viewportGrid]);
 
   const getCornerstoneViewport = useCallback(() => {
+    const { component: Component } = extensionManager.getModuleEntry(
+      '@ohif/extension-cornerstone.viewportModule.cornerstone'
+    );
+
+    const { displaySet: referencedDisplaySet } = referencedDisplaySetRef.current;
+
+    // Todo: jump to the center of the first segment
     return (
-      <OHIFCornerstoneViewport
+      <Component
         {...props}
-        displaySets={[segDisplaySet]}
+        displaySets={[referencedDisplaySet, segDisplaySet]}
         viewportOptions={{
-          viewportType: viewportOptions.viewportType,
+          viewportType: 'volume',
           toolGroupId: toolGroupId,
           orientation: viewportOptions.orientation,
           viewportId: viewportOptions.viewportId,
-          presentationIds: viewportOptions.presentationIds,
         }}
         onElementEnabled={evt => {
           props.onElementEnabled?.(evt);
+          onElementEnabled(evt);
         }}
-      />
+        onElementDisabled={onElementDisabled}
+      ></Component>
     );
-  }, [viewportId, segDisplaySet, toolGroupId, props, viewportOptions]);
+  }, [viewportId, segDisplaySet, toolGroupId]);
+
+  const onSegmentChange = useCallback(
+    direction => {
+      const segmentationId = segDisplaySet.displaySetInstanceUID;
+      const segmentation = segmentationService.getSegmentation(segmentationId);
+
+      const { segments } = segmentation;
+
+      const numberOfSegments = Object.keys(segments).length;
+
+      let newSelectedSegmentIndex = selectedSegment + direction;
+
+      // Segment 0 is always background
+
+      if (newSelectedSegmentIndex > numberOfSegments - 1) {
+        newSelectedSegmentIndex = 1;
+      } else if (newSelectedSegmentIndex === 0) {
+        newSelectedSegmentIndex = numberOfSegments - 1;
+      }
+
+      segmentationService.jumpToSegmentCenter(segmentationId, newSelectedSegmentIndex, toolGroupId);
+      setSelectedSegment(newSelectedSegmentIndex);
+    },
+    [selectedSegment]
+  );
 
   useEffect(() => {
     if (segIsLoading) {
       return;
     }
 
-    // if not active viewport, return
-    if (viewportId !== activeViewportId) {
-      return;
-    }
-
     promptHydrateSEG({
       servicesManager,
       viewportId,
       segDisplaySet,
-      hydrateCallback: async () => {
-        await commandsManager.runCommand('hydrateSecondaryDisplaySet', {
-          displaySet: segDisplaySet,
-          viewportId,
-        });
-
-        return true;
-      },
+      preHydrateCallbacks: [storePresentationState],
+      hydrateSEGDisplaySet,
+    }).then(isHydrated => {
+      if (isHydrated) {
+        setIsHydrated(true);
+      }
     });
-  }, [servicesManager, viewportId, segDisplaySet, segIsLoading, commandsManager, activeViewportId]);
+  }, [servicesManager, viewportId, segDisplaySet, segIsLoading]);
 
   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,
-            },
-          });
-        }
       }
     );
 
@@ -186,31 +223,92 @@ 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
-      // e.g., another seg displayset is dragged into the viewport
-      segmentationService.clearSegmentationRepresentations(viewportId);
+      segmentationService.removeSegmentationRepresentationFromToolGroup(toolGroupId);
 
       // 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
+    // presentation state, so that we can restore it after hydrating the SEG. This is
+    // required if the user has changed the viewport (other viewport than SEG viewport)
+    // presentation state (w/l and invert) and then opens the SEG. If we don't store
+    // the presentation state, the viewport will be reset to the default presentation
+    storePresentationState();
+    const isHydrated = await hydrateSEGDisplaySet({
+      segDisplaySet,
+      viewportId,
+    });
+
+    setIsHydrated(isHydrated);
+  }, [hydrateSEGDisplaySet, segDisplaySet, storePresentationState, viewportId]);
+
+  useEffect(() => {
+    viewportActionCornersService.setComponents([
+      {
+        viewportId,
+        id: 'viewportStatusComponent',
+        component: _getStatusComponent({
+          isHydrated,
+          onStatusClick,
+        }),
+        indexPriority: -100,
+        location: viewportActionCornersService.LOCATIONS.topLeft,
+      },
+      {
+        viewportId,
+        id: 'viewportActionArrowsComponent',
+        component: (
+          <ViewportActionArrows
+            key="actionArrows"
+            onArrowsClick={onSegmentChange}
+            className={
+              viewportId === activeViewportId ? 'visible' : 'invisible group-hover:visible'
+            }
+          ></ViewportActionArrows>
+        ),
+        indexPriority: 0,
+        location: viewportActionCornersService.LOCATIONS.topRight,
+      },
+    ]);
+  }, [
+    activeViewportId,
+    isHydrated,
+    onSegmentChange,
+    onStatusClick,
+    viewportActionCornersService,
+    viewportId,
+  ]);
+
   // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   let childrenWithProps = null;
 
@@ -234,6 +332,18 @@ 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">
@@ -252,6 +362,18 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
   );
 }
 
+OHIFCornerstoneSEGViewport.propTypes = {
+  displaySets: PropTypes.arrayOf(PropTypes.object),
+  viewportId: PropTypes.string.isRequired,
+  dataSource: PropTypes.object,
+  children: PropTypes.node,
+  customProps: PropTypes.object,
+};
+
+OHIFCornerstoneSEGViewport.defaultProps = {
+  customProps: {},
+};
+
 function _getReferencedDisplaySetMetadata(referencedDisplaySet, segDisplaySet) {
   const { SharedFunctionalGroupsSequence } = segDisplaySet.instance;
 

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

@@ -0,0 +1,62 @@
+import React from 'react';
+import { useTranslation } from 'react-i18next';
+import { Icon, Tooltip } from '@ohif/ui';
+
+export default function _getStatusComponent({ isHydrated, onStatusClick }) {
+  let ToolTipMessage = null;
+  let StatusIcon = null;
+
+  switch (isHydrated) {
+    case true:
+      StatusIcon = () => <Icon name="status-alert" />;
+
+      ToolTipMessage = () => <div>This Segmentation is loaded in the segmentation panel</div>;
+      break;
+    case false:
+      StatusIcon = () => (
+        <Icon
+          className="text-aqua-pale"
+          name="status-untracked"
+        />
+      );
+
+      ToolTipMessage = () => <div>Click LOAD to load segmentation.</div>;
+  }
+
+  const StatusArea = () => {
+    const { t } = useTranslation('Common');
+    const loadStr = t('LOAD');
+
+    return (
+      <div className="flex h-6 cursor-default text-sm leading-6 text-white">
+        <div className="bg-customgray-100 flex min-w-[45px] items-center rounded-l-xl rounded-r p-1">
+          <StatusIcon />
+          <span className="ml-1">SEG</span>
+        </div>
+        {!isHydrated && (
+          <div
+            className="bg-primary-main hover:bg-primary-light ml-1 cursor-pointer rounded px-1.5 hover:text-black"
+            // Using onMouseUp here because onClick is not working when the viewport is not active and is styled with pointer-events:none
+            onMouseUp={onStatusClick}
+          >
+            {loadStr}
+          </div>
+        )}
+      </div>
+    );
+  };
+
+  return (
+    <>
+      {ToolTipMessage && (
+        <Tooltip
+          content={<ToolTipMessage />}
+          position="bottom-left"
+        >
+          <StatusArea />
+        </Tooltip>
+      )}
+      {!ToolTipMessage && <StatusArea />}
+    </>
+  );
+}

extensions/cornerstone-dicom-sr/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone-dicom-sr",
-  "version": "3.11.0-beta.95",
+  "version": "3.8.2",
   "description": "OHIF extension for an SR Cornerstone Viewport",
   "author": "OHIF",
   "license": "MIT",
@@ -34,21 +34,21 @@
     "test:unit:ci": "jest --ci --runInBand --collectCoverage --passWithNoTests"
   },
   "peerDependencies": {
-    "@ohif/core": "3.11.0-beta.95",
-    "@ohif/extension-cornerstone": "3.11.0-beta.95",
-    "@ohif/extension-measurement-tracking": "3.11.0-beta.95",
-    "@ohif/ui": "3.11.0-beta.95",
-    "dcmjs": "^0.42.0",
+    "@ohif/core": "3.8.2\n",
+    "@ohif/extension-cornerstone": "3.8.2\n",
+    "@ohif/extension-measurement-tracking": "3.8.2\n",
+    "@ohif/ui": "3.8.2\n",
+    "dcmjs": "^0.29.12",
     "dicom-parser": "^1.8.9",
     "hammerjs": "^2.0.8",
     "prop-types": "^15.6.2",
-    "react": "^18.3.1"
+    "react": "^17.0.2"
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/adapters": "^3.30.3",
-    "@cornerstonejs/core": "^3.30.3",
-    "@cornerstonejs/tools": "^3.30.3",
+    "@cornerstonejs/adapters": "^1.77.6",
+    "@cornerstonejs/core": "^1.77.6",
+    "@cornerstonejs/tools": "^1.77.6",
     "classnames": "^2.3.2"
   }
 }

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

@@ -5,28 +5,19 @@ import dcmjs from 'dcmjs';
 import { adaptersSR } from '@cornerstonejs/adapters';
 
 import getFilteredCornerstoneToolState from './utils/getFilteredCornerstoneToolState';
-import hydrateStructuredReport from './utils/hydrateStructuredReport';
 
 const { MeasurementReport } = adaptersSR.Cornerstone3D;
 const { log } = OHIF;
 
-interface Options {
-  SeriesDescription?: string;
-  SeriesInstanceUID?: string;
-  SeriesNumber?: number;
-  InstanceNumber?: number;
-  SeriesDate?: string;
-  SeriesTime?: string;
-}
-
 /**
+ *
  * @param measurementData An array of measurements from the measurements service
  * that you wish to serialize.
  * @param additionalFindingTypes toolTypes that should be stored with labels as Findings
  * @param options Naturalized DICOM JSON headers to merge into the displaySet.
  *
  */
-const _generateReport = (measurementData, additionalFindingTypes, options: Options = {}) => {
+const _generateReport = (measurementData, additionalFindingTypes, options = {}) => {
   const filteredToolState = getFilteredCornerstoneToolState(
     measurementData,
     additionalFindingTypes
@@ -46,37 +37,13 @@ const _generateReport = (measurementData, additionalFindingTypes, options: Optio
   if (typeof dataset.SpecificCharacterSet === 'undefined') {
     dataset.SpecificCharacterSet = 'ISO_IR 192';
   }
-
-  dataset.InstanceNumber = options.InstanceNumber ?? 1;
-
   return dataset;
 };
 
 const commandsModule = (props: withAppTypes) => {
-  const { servicesManager, extensionManager, commandsManager } = props;
-  const { customizationService, viewportGridService, displaySetService } = servicesManager.services;
-
+  const { servicesManager } = props;
+  const { customizationService } = servicesManager.services;
   const actions = {
-    changeColorMeasurement: ({ uid }) => {
-      // When this gets supported, it probably belongs in cornerstone, not sr
-      throw new Error('Unsupported operation: changeColorMeasurement');
-      // const { color } = measurementService.getMeasurement(uid);
-      // 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);
-      // });
-    },
-
     /**
      *
      * @param measurementData An array of measurements from the measurements service
@@ -86,7 +53,7 @@ const commandsModule = (props: withAppTypes) => {
      * that you wish to serialize.
      */
     downloadReport: ({ measurementData, additionalFindingTypes, options = {} }) => {
-      const srDataset = _generateReport(measurementData, additionalFindingTypes, options);
+      const srDataset = actions.generateReport(measurementData, additionalFindingTypes, options);
       const reportBlob = dcmjs.data.datasetToBlob(srDataset);
 
       //Create a URL for the binary.
@@ -130,11 +97,12 @@ const commandsModule = (props: withAppTypes) => {
           throw new Error('Invalid report, no content');
         }
 
-        const onBeforeDicomStore = customizationService.getCustomization('onBeforeDicomStore');
+        const onBeforeDicomStore =
+          customizationService.getModeCustomization('onBeforeDicomStore')?.value;
 
         let dicomDict;
         if (typeof onBeforeDicomStore === 'function') {
-          dicomDict = onBeforeDicomStore({ dicomDict, measurementData, naturalizedReport });
+          dicomDict = onBeforeDicomStore({ measurementData, naturalizedReport });
         }
 
         await dataSource.store.dicom(naturalizedReport, null, dicomDict);
@@ -155,23 +123,15 @@ const commandsModule = (props: withAppTypes) => {
         throw new Error(error.message || 'Error while saving the measurements.');
       }
     },
-
-    /**
-     * Loads measurements by hydrating and loading the SR for the given display set instance UID
-     * and displays it in the active viewport.
-     */
-    hydrateStructuredReport: ({ displaySetInstanceUID }) => {
-      return hydrateStructuredReport(
-        { servicesManager, extensionManager, commandsManager },
-        displaySetInstanceUID
-      );
-    },
   };
 
   const definitions = {
-    downloadReport: actions.downloadReport,
-    storeMeasurements: actions.storeMeasurements,
-    hydrateStructuredReport: actions.hydrateStructuredReport,
+    downloadReport: {
+      commandFn: actions.downloadReport,
+    },
+    storeMeasurements: {
+      commandFn: actions.storeMeasurements,
+    },
   };
 
   return {

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

@@ -1,78 +0,0 @@
-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

@@ -1,63 +0,0 @@
-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

@@ -1,280 +0,0 @@
-import PropTypes from 'prop-types';
-import React, { useCallback, useEffect, useState } from 'react';
-import { setTrackingUniqueIdentifiersForElement } from '../tools/modules/dicomSRModule';
-
-import createReferencedImageDisplaySet from '../utils/createReferencedImageDisplaySet';
-import { usePositionPresentationStore, OHIFCornerstoneViewport } from '@ohif/extension-cornerstone';
-import { useViewportGrid } from '@ohif/ui-next';
-import { useSystem } from '@ohif/core/src/contextProviders/SystemProvider';
-
-const SR_TOOLGROUP_BASE_NAME = 'SRToolGroup';
-
-function OHIFCornerstoneSRMeasurementViewport(props) {
-  const { servicesManager } = useSystem();
-  const { children, dataSource, displaySets, viewportOptions } = props as {
-    children: React.ReactNode;
-    dataSource: unknown;
-    displaySets: AppTypes.DisplaySet[];
-    viewportOptions: AppTypes.ViewportOptions;
-  };
-
-  const { displaySetService } = servicesManager.services;
-
-  const viewportId = viewportOptions.viewportId;
-
-  // SR viewport will always have a single display set
-  if (displaySets.length > 1) {
-    throw new Error('SR viewport should only have a single display set');
-  }
-
-  const srDisplaySet = displaySets[0];
-
-  const { setPositionPresentation } = usePositionPresentationStore();
-
-  const [viewportGrid, viewportGridService] = useViewportGrid();
-  const [measurementSelected, setMeasurementSelected] = useState(0);
-  const [activeImageDisplaySetData, setActiveImageDisplaySetData] = useState(null);
-  const [referencedDisplaySetMetadata, setReferencedDisplaySetMetadata] = useState(null);
-  const [element, setElement] = useState(null);
-  const { viewports, activeViewportId } = viewportGrid;
-
-  const setTrackingIdentifiers = useCallback(
-    measurementSelected => {
-      const { measurements } = srDisplaySet;
-
-      setTrackingUniqueIdentifiersForElement(
-        element,
-        measurements.map(measurement => measurement.TrackingUniqueIdentifier),
-        measurementSelected
-      );
-    },
-    [element, measurementSelected, srDisplaySet]
-  );
-
-  /**
-   * OnElementEnabled callback which is called after the cornerstoneExtension
-   * has enabled the element. Note: we delegate all the image rendering to
-   * cornerstoneExtension, so we don't need to do anything here regarding
-   * the image rendering, element enabling etc.
-   */
-  const onElementEnabled = evt => {
-    setElement(evt.detail.element);
-  };
-
-  const updateViewport = useCallback(
-    newMeasurementSelected => {
-      const { StudyInstanceUID, displaySetInstanceUID, sopClassUids } = srDisplaySet;
-
-      if (!StudyInstanceUID || !displaySetInstanceUID) {
-        return;
-      }
-
-      if (sopClassUids && sopClassUids.length > 1) {
-        // Todo: what happens if there are multiple SOP Classes? Why we are
-        // not throwing an error?
-        console.warn('More than one SOPClassUID in the same series is not yet supported.');
-      }
-
-      _getViewportReferencedDisplaySetData(
-        srDisplaySet,
-        newMeasurementSelected,
-        displaySetService
-      ).then(({ referencedDisplaySet, referencedDisplaySetMetadata }) => {
-        if (!referencedDisplaySet || !referencedDisplaySetMetadata) {
-          return;
-        }
-
-        setMeasurementSelected(newMeasurementSelected);
-
-        setActiveImageDisplaySetData(referencedDisplaySet);
-        setReferencedDisplaySetMetadata(referencedDisplaySetMetadata);
-
-        const { presentationIds } = viewportOptions;
-        const measurement = srDisplaySet.measurements[newMeasurementSelected];
-        setPositionPresentation(presentationIds.positionPresentationId, {
-          viewReference: {
-            referencedImageId: measurement.imageId,
-          },
-        });
-      });
-    },
-    [dataSource, srDisplaySet, activeImageDisplaySetData, viewportId]
-  );
-
-  const getCornerstoneViewport = useCallback(() => {
-    if (!activeImageDisplaySetData) {
-      return null;
-    }
-
-    const { measurements } = srDisplaySet;
-    const measurement = measurements[measurementSelected];
-
-    if (!measurement) {
-      return null;
-    }
-
-    return (
-      <OHIFCornerstoneViewport
-        {...props}
-        // should be passed second since we don't want SR displaySet to
-        // override the activeImageDisplaySetData
-        displaySets={[activeImageDisplaySetData]}
-        // It is possible that there is a hanging protocol applying viewportOptions
-        // for the SR, so inherit the viewport options
-        // TODO: Ensure the viewport options are set correctly with respect to
-        // stack etc, in the incoming viewport options.
-        viewportOptions={{
-          ...viewportOptions,
-          toolGroupId: `${SR_TOOLGROUP_BASE_NAME}`,
-          // viewportType should not be required, as the stack type should be
-          // required already in order to view SR, but sometimes segmentation
-          // views set the viewport type without fixing the allowed display
-          viewportType: 'stack',
-          // The positionIds for the viewport aren't meaningful for the child display sets
-          positionIds: null,
-        }}
-        onElementEnabled={evt => {
-          props.onElementEnabled?.(evt);
-          onElementEnabled(evt);
-        }}
-        isJumpToMeasurementDisabled={true}
-      />
-    );
-  }, [activeImageDisplaySetData, viewportId, measurementSelected]);
-
-  /**
-   Cleanup the SR 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();
-    };
-  }, []);
-
-  /**
-   * Loading the measurements from the SR viewport, which goes through the
-   * isHydratable check, the outcome for the isHydrated state here is always FALSE
-   * since we don't do the hydration here. Todo: can't we just set it as false? why
-   * we are changing the state here? isHydrated is always false at this stage, and
-   * if it is hydrated we don't even use the SR viewport.
-   */
-  useEffect(() => {
-    const loadSR = async () => {
-      if (!srDisplaySet.isLoaded) {
-        await srDisplaySet.load();
-      }
-      updateViewport(measurementSelected);
-    };
-    loadSR();
-  }, [srDisplaySet]);
-
-  /**
-   * Hook to update the tracking identifiers when the selected measurement changes or
-   * the element changes
-   */
-  useEffect(() => {
-    const updateSR = async () => {
-      if (!srDisplaySet.isLoaded) {
-        await srDisplaySet.load();
-      }
-      if (!element || !srDisplaySet.isLoaded) {
-        return;
-      }
-      setTrackingIdentifiers(measurementSelected);
-    };
-    updateSR();
-  }, [measurementSelected, element, setTrackingIdentifiers, srDisplaySet]);
-
-  // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-  let childrenWithProps = null;
-
-  if (!activeImageDisplaySetData || !referencedDisplaySetMetadata) {
-    return 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">
-        {getCornerstoneViewport()}
-        {childrenWithProps}
-      </div>
-    </>
-  );
-}
-
-OHIFCornerstoneSRMeasurementViewport.propTypes = {
-  displaySets: PropTypes.arrayOf(PropTypes.object),
-  viewportId: PropTypes.string.isRequired,
-  dataSource: PropTypes.object,
-  children: PropTypes.node,
-  viewportLabel: PropTypes.string,
-  viewportOptions: PropTypes.object,
-};
-
-async function _getViewportReferencedDisplaySetData(
-  displaySet,
-  measurementSelected,
-  displaySetService
-) {
-  const { measurements } = displaySet;
-  const measurement = measurements[measurementSelected];
-
-  const { displaySetInstanceUID } = measurement;
-  if (!displaySet.keyImageDisplaySet) {
-    // Create a new display set, and preserve a reference to it here,
-    // so that it can be re-displayed and shown inside the SR viewport.
-    // This is only for ease of redisplay - the display set is stored in the
-    // usual manner in the display set service.
-    displaySet.keyImageDisplaySet = createReferencedImageDisplaySet(displaySetService, displaySet);
-  }
-
-  if (!displaySetInstanceUID) {
-    return { referencedDisplaySetMetadata: null, referencedDisplaySet: null };
-  }
-
-  const referencedDisplaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
-
-  const image0 = referencedDisplaySet.images[0];
-  const referencedDisplaySetMetadata = {
-    PatientID: image0.PatientID,
-    PatientName: image0.PatientName,
-    PatientSex: image0.PatientSex,
-    PatientAge: image0.PatientAge,
-    SliceThickness: image0.SliceThickness,
-    StudyDate: image0.StudyDate,
-    SeriesDescription: image0.SeriesDescription,
-    SeriesInstanceUID: image0.SeriesInstanceUID,
-    SeriesNumber: image0.SeriesNumber,
-    ManufacturerModelName: image0.ManufacturerModelName,
-    SpacingBetweenSlices: image0.SpacingBetweenSlices,
-  };
-
-  return { referencedDisplaySetMetadata, referencedDisplaySet };
-}
-
-export default OHIFCornerstoneSRMeasurementViewport;

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

@@ -1,32 +0,0 @@
-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

@@ -1,30 +0,0 @@
-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

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

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

@@ -1,44 +0,0 @@
-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

@@ -1,38 +1,30 @@
-import { utils, classes, DisplaySetService, Types as OhifTypes } from '@ohif/core';
-import i18n from '@ohif/i18n';
-import { Enums as CSExtensionEnums } from '@ohif/extension-cornerstone';
-import { adaptersSR } from '@cornerstonejs/adapters';
-
-import addSRAnnotation from './utils/addSRAnnotation';
+import { SOPClassHandlerName, SOPClassHandlerId } from './id';
+import { utils, classes, DisplaySetService, Types } from '@ohif/core';
+import addDICOMSRDisplayAnnotation from './utils/addDICOMSRDisplayAnnotation';
 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;
+import { adaptersSR } from '@cornerstonejs/adapters';
 
 type InstanceMetadata = Types.InstanceMetadata;
 
-/**
- * TODO
- * - [ ] Add SR thumbnail
- * - [ ] Make viewport
- * - [ ] Get stacks from referenced displayInstanceUID and load into wrapped CornerStone viewport
- */
+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.
 
 const sopClassUids = [
-  sopClassDictionary.BasicTextSR,
-  sopClassDictionary.EnhancedSR,
-  sopClassDictionary.ComprehensiveSR,
+  '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:
 ];
 
+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) {
@@ -42,6 +34,31 @@ 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
@@ -91,39 +108,45 @@ function _getDisplaySetsFromSeries(
     SeriesDescription,
     SeriesNumber,
     SeriesDate,
-    SeriesTime,
     ConceptNameCodeSequence,
     SOPClassUID,
   } = instance;
   validateSameStudyUID(instance.StudyInstanceUID, instances);
 
-  const is3DSR = SOPClassUID === sopClassDictionary.Comprehensive3DSR;
-
-  const isImagingMeasurementReport =
-    ConceptNameCodeSequence?.CodeValue === CodeNameCodeSequenceValues.ImagingMeasurementReport;
+  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 displaySet = {
+    //plugin: id,
     Modality: 'SR',
     displaySetInstanceUID: utils.guid(),
     SeriesDescription,
     SeriesNumber,
     SeriesDate,
-    SeriesTime,
     SOPInstanceUID,
     SeriesInstanceUID,
     StudyInstanceUID,
-    SOPClassHandlerId: is3DSR ? SOPClassHandlerId3D : SOPClassHandlerId,
+    SOPClassHandlerId,
     SOPClassUID,
     instances,
     referencedImages: null,
     measurements: null,
     isDerivedDisplaySet: true,
     isLoaded: false,
-    isImagingMeasurementReport,
     sopClassUids,
     instance,
     addInstances,
-    label: SeriesDescription || `${i18n.t('Series')} ${SeriesNumber} - ${i18n.t('SR')}`,
   };
 
   displaySet.load = () => _load(displaySet, servicesManager, extensionManager);
@@ -131,21 +154,12 @@ function _getDisplaySetsFromSeries(
   return [displaySet];
 }
 
-/**
- * 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
-) {
+async function _load(displaySet, servicesManager: AppTypes.ServicesManager, extensionManager) {
   const { displaySetService, measurementService } = servicesManager.services;
   const dataSources = extensionManager.getDataSources();
   const dataSource = dataSources[0];
-  const { ContentSequence } = srDisplaySet.instance;
+
+  const { ContentSequence } = displaySet.instance;
 
   async function retrieveBulkData(obj, parentObj = null, key = null) {
     for (const prop in obj) {
@@ -156,9 +170,9 @@ async function _load(
       } else if (prop === 'BulkDataURI') {
         const value = await dataSource.retrieve.bulkDataURI({
           BulkDataURI: obj[prop],
-          StudyInstanceUID: srDisplaySet.instance.StudyInstanceUID,
-          SeriesInstanceUID: srDisplaySet.instance.SeriesInstanceUID,
-          SOPInstanceUID: srDisplaySet.instance.SOPInstanceUID,
+          StudyInstanceUID: displaySet.instance.StudyInstanceUID,
+          SeriesInstanceUID: displaySet.instance.SeriesInstanceUID,
+          SOPInstanceUID: displaySet.instance.SOPInstanceUID,
         });
         if (parentObj && key) {
           parentObj[key] = new Float32Array(value);
@@ -167,47 +181,40 @@ async function _load(
     }
   }
 
-  if (srDisplaySet.isLoaded !== true) {
+  if (displaySet.isLoaded !== true) {
     await retrieveBulkData(ContentSequence);
   }
 
-  if (srDisplaySet.isImagingMeasurementReport) {
-    srDisplaySet.referencedImages = _getReferencedImagesList(ContentSequence);
-    srDisplaySet.measurements = _getMeasurements(ContentSequence);
-  } else {
-    srDisplaySet.referencedImages = [];
-    srDisplaySet.measurements = [];
-  }
+  displaySet.referencedImages = _getReferencedImagesList(ContentSequence);
+  displaySet.measurements = _getMeasurements(ContentSequence);
 
   const mappings = measurementService.getSourceMappings(
     CORNERSTONE_3D_TOOLS_SOURCE_NAME,
     CORNERSTONE_3D_TOOLS_SOURCE_VERSION
   );
 
-  srDisplaySet.isHydrated = false;
-  srDisplaySet.isRehydratable = isRehydratable(srDisplaySet, mappings);
-  srDisplaySet.isLoaded = true;
+  displaySet.isHydrated = false;
+  displaySet.isRehydratable = isRehydratable(displaySet, mappings);
+  displaySet.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(
-      srDisplaySet,
+      displaySet,
       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(
-        srDisplaySet,
+        displaySet,
         newDisplaySet,
         dataSource,
         servicesManager
@@ -216,14 +223,6 @@ async function _load(
   });
 }
 
-/**
- * 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,
@@ -231,103 +230,108 @@ function _checkIfCanAddMeasurementsToDisplaySet(
   servicesManager: AppTypes.ServicesManager
 ) {
   const { customizationService } = servicesManager.services;
-
-  const unloadedMeasurements = srDisplaySet.measurements.filter(
+  let unloadedMeasurements = srDisplaySet.measurements.filter(
     measurement => measurement.loaded === false
   );
 
-  if (
-    unloadedMeasurements.length === 0 ||
-    !(newDisplaySet instanceof ImageSet) ||
-    newDisplaySet.unsupported
-  ) {
+  if (unloadedMeasurements.length === 0) {
+    // All already loaded!
     return;
   }
 
-  // const { sopClassUids } = newDisplaySet;
-  // Create a Set for faster lookups
-  // const sopClassUidSet = new Set(sopClassUids);
+  if ((!newDisplaySet) instanceof ImageSet) {
+    // This also filters out _this_ displaySet, as it is not an ImageSet.
+    return;
+  }
 
-  // Create a Map to efficiently look up ImageIds by SOPInstanceUID and frame number
-  const imageIdMap = new Map<string, string>();
-  const imageIds = dataSource.getImageIdsForDisplaySet(newDisplaySet);
+  if (newDisplaySet.unsupported) {
+    return;
+  }
+
+  const { sopClassUids } = newDisplaySet;
+
+  // Check if any have the newDisplaySet is the correct SOPClass.
+  unloadedMeasurements = unloadedMeasurements.filter(measurement =>
+    measurement.coords.some(coord =>
+      sopClassUids.includes(coord.ReferencedSOPSequence.ReferencedSOPClassUID)
+    )
+  );
+
+  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;
+    }
 
-  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 (SOPInstanceUIDs.includes(SOPInstanceUID)) {
+      for (let j = unloadedMeasurements.length - 1; j >= 0; j--) {
+        let measurement = unloadedMeasurements[j];
 
-  const is3DSR = srDisplaySet.SOPClassUID === sopClassDictionary.Comprehensive3DSR;
+        const onBeforeSRAddMeasurement = customizationService.getModeCustomization(
+          'onBeforeSRAddMeasurement'
+        )?.value;
 
-  for (let j = unloadedMeasurements.length - 1; j >= 0; j--) {
-    let measurement = unloadedMeasurements[j];
+        if (typeof onBeforeSRAddMeasurement === 'function') {
+          measurement = onBeforeSRAddMeasurement({
+            measurement,
+            StudyInstanceUID: srDisplaySet.StudyInstanceUID,
+            SeriesInstanceUID: srDisplaySet.SeriesInstanceUID,
+          });
+        }
 
-    const onBeforeSRAddMeasurement = customizationService.getCustomization(
-      'onBeforeSRAddMeasurement'
-    );
+        if (_measurementReferencesSOPInstanceUID(measurement, SOPInstanceUID, frameNumber)) {
+          const frame =
+            (measurement.coords[0].ReferencedSOPSequence &&
+              measurement.coords[0].ReferencedSOPSequence?.ReferencedFrameNumber) ||
+            1;
 
-    if (typeof onBeforeSRAddMeasurement === 'function') {
-      measurement = onBeforeSRAddMeasurement({
-        measurement,
-        StudyInstanceUID: srDisplaySet.StudyInstanceUID,
-        SeriesInstanceUID: srDisplaySet.SeriesInstanceUID,
-      });
-    }
+          /** Add DICOMSRDisplay annotation for the SR viewport (only) */
+          addDICOMSRDisplayAnnotation(measurement, imageId, frame);
 
-    // if it is 3d SR we can just add the SR annotation
-    if (is3DSR) {
-      addSRAnnotation(measurement, null, null);
-      measurement.loaded = true;
-      continue;
-    }
+          /** 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;
 
-    const referencedSOPSequence = measurement.coords[0].ReferencedSOPSequence;
-    if (!referencedSOPSequence) {
-      continue;
-    }
-
-    const { ReferencedSOPInstanceUID } = referencedSOPSequence;
-    const frame = referencedSOPSequence.ReferencedFrameNumber || 1;
-    const key = `${ReferencedSOPInstanceUID}:${frame}`;
-    const imageId = imageIdMap.get(key);
-
-    if (
-      imageId &&
-      _measurementReferencesSOPInstanceUID(measurement, ReferencedSOPInstanceUID, frame)
-    ) {
-      addSRAnnotation(measurement, imageId, frame);
-
-      // Update measurement properties
-      measurement.loaded = true;
-      measurement.imageId = imageId;
-      measurement.displaySetInstanceUID = newDisplaySet.displaySetInstanceUID;
-      measurement.ReferencedSOPInstanceUID = ReferencedSOPInstanceUID;
-      measurement.frameNumber = frame;
-
-      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) ||
@@ -340,63 +344,40 @@ 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(params: OhifTypes.Extensions.ExtensionParams) {
-  const { servicesManager, extensionManager } = params;
+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(
@@ -405,6 +386,7 @@ function _getMeasurements(ImagingMeasurementReportContentSequence) {
         mergedContentSequencesByTrackingUniqueIdentifiers[trackingUniqueIdentifier];
 
       const measurement = _processMeasurement(mergedContentSequence);
+
       if (measurement) {
         measurements.push(measurement);
       }
@@ -414,12 +396,6 @@ 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 = {};
 
@@ -431,6 +407,7 @@ function _getMergedContentSequencesByTrackingUniqueIdentifiers(MeasurementGroups
         item.ConceptNameCodeSequence.CodeValue ===
         CodeNameCodeSequenceValues.TrackingUniqueIdentifier
     );
+
     if (!TrackingUniqueIdentifierItem) {
       console.warn('No Tracking Unique Identifier, skipping ambiguous measurement.');
     }
@@ -459,15 +436,6 @@ 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(
@@ -480,21 +448,11 @@ 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' || group.ValueType === 'SCOORD3D'
-  );
+  const graphicItem = mergedContentSequence.find(group => group.ValueType === 'SCOORD');
 
   const UIDREFContentItem = mergedContentSequence.find(group => group.ValueType === 'UIDREF');
 
@@ -521,6 +479,7 @@ function _processTID1410Measurement(mergedContentSequence) {
 
   NUMContentItems.forEach(item => {
     const { ConceptNameCodeSequence, MeasuredValueSequence } = item;
+
     if (MeasuredValueSequence) {
       measurement.labels.push(
         _getLabelFromMeasuredValueSequence(ConceptNameCodeSequence, MeasuredValueSequence)
@@ -528,29 +487,12 @@ 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(
@@ -580,10 +522,10 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
     CodingSchemeDesignators.CornerstoneCodeSchemes.includes(
       finding.ConceptCodeSequence.CodingSchemeDesignator
     ) &&
-    finding.ConceptCodeSequence.CodeValue === Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT
+    finding.ConceptCodeSequence.CodeValue === CodeNameCodeSequenceValues.CornerstoneFreeText
   ) {
     measurement.labels.push({
-      label: Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT,
+      label: CORNERSTONE_FREETEXT_CODE_VALUE,
       value: finding.ConceptCodeSequence.CodeMeaning,
     });
   }
@@ -595,13 +537,12 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
         CodingSchemeDesignators.CornerstoneCodeSchemes.includes(
           FindingSite.ConceptCodeSequence.CodingSchemeDesignator
         ) &&
-        FindingSite.ConceptCodeSequence.CodeValue ===
-          Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT
+        FindingSite.ConceptCodeSequence.CodeValue === CodeNameCodeSequenceValues.CornerstoneFreeText
     );
 
     if (cornerstoneFreeTextFindingSite) {
       measurement.labels.push({
-        label: Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT,
+        label: CORNERSTONE_FREETEXT_CODE_VALUE,
         value: cornerstoneFreeTextFindingSite.ConceptCodeSequence.CodeMeaning,
       });
     }
@@ -611,12 +552,15 @@ 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);
     }
@@ -631,62 +575,59 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
   return measurement;
 }
 
-/**
- * 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 };
-  coords.ReferencedSOPSequence = graphicItem.ContentSequence?.ReferencedSOPSequence;
-  coords.ReferencedFrameOfReferenceSequence =
-    graphicItem.ReferencedFrameOfReferenceUID ||
-    graphicItem.ContentSequence?.ReferencedFrameOfReferenceSequence;
-  return coords;
-};
+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;
+  }
+
+  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;
+  }
+
+  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 = [];
 
@@ -710,15 +651,6 @@ 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

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

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

@@ -8,10 +8,9 @@ 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 */ './components/OHIFCornerstoneSRViewport');
+  return import(/* webpackPrefetch: true */ './viewports/OHIFCornerstoneSRViewport');
 });
 
 const OHIFCornerstoneSRViewport = props => {
@@ -30,7 +29,6 @@ const dicomSRExtension = {
    * Only required property. Should be a unique value across all extensions.
    */
   id,
-
   onModeEnter,
 
   preRegistration,
@@ -72,4 +70,4 @@ const dicomSRExtension = {
 export default dicomSRExtension;
 
 // Put static exports here so they can be type checked
-export { hydrateStructuredReport, createReferencedImageDisplaySet, srProtocol, Enums, toolNames };
+export { hydrateStructuredReport, createReferencedImageDisplaySet, srProtocol };

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

@@ -9,28 +9,16 @@ 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 = {},
-  servicesManager,
-}: Types.Extensions.ExtensionParams): void {
-  const { measurementService, cornerstoneViewportService } = servicesManager.services;
-
+export default function init({ configuration = {} }: Types.Extensions.ExtensionParams): void {
   addToolInstance(toolNames.DICOMSRDisplay, DICOMSRDisplayTool);
   addToolInstance(toolNames.SRLength, LengthTool);
   addToolInstance(toolNames.SRBidirectional, BidirectionalTool);
@@ -40,26 +28,10 @@ export default function init({
   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',

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

@@ -0,0 +1,15 @@
+import { SOPClassHandlerId } from './id';
+
+export default function onModeEnter({ servicesManager }) {
+  const { displaySetService } = servicesManager.services;
+  const displaySetCache = displaySetService.getDisplaySetCache();
+
+  const srDisplaySets = [...displaySetCache.values()].filter(
+    ds => ds.SOPClassHandlerId === SOPClassHandlerId
+  );
+
+  srDisplaySets.forEach(ds => {
+    // New mode route, allow SRs to be hydrated again
+    ds.isHydrated = false;
+  });
+}

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

@@ -1,15 +0,0 @@
-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.SOPClassHandlerId === SOPClassHandlerId3D
-  );
-
-  srDisplaySets.forEach(ds => {
-    // New mode route, allow SRs to be hydrated again
-    ds.isHydrated = false;
-  });
-}

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

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

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

@@ -1,203 +0,0 @@
-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

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

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

@@ -1,62 +0,0 @@
-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/addDICOMSRDisplayAnnotation.ts

@@ -0,0 +1,204 @@
+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';
+
+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] = [];
+    }
+
+    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[];
+
+  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);
+      }
+
+      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);
+      }
+
+      // 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');
+      }
+
+      const {
+        columnCosines,
+        rowCosines,
+      }: {
+        columnCosines: csTypes.Point3;
+        rowCosines: csTypes.Point3;
+      } = imagePlaneModule;
+
+      // 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);
+
+      const secondAxisEnd = vec3.create();
+      vec3.scaleAndAdd(secondAxisEnd, center, rowCosines, -radius);
+
+      renderableData = [
+        firstAxisStart as csTypes.Point3,
+        firstAxisEnd as csTypes.Point3,
+        secondAxisStart as csTypes.Point3,
+        secondAxisEnd as csTypes.Point3,
+      ];
+
+      break;
+    }
+    case SCOORD_TYPES.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 majorAxisStart = vec3.fromValues(...pointsWorld[0]);
+      const majorAxisEnd = vec3.fromValues(...pointsWorld[1]);
+      const minorAxisStart = vec3.fromValues(...pointsWorld[2]);
+      const minorAxisEnd = vec3.fromValues(...pointsWorld[3]);
+
+      const majorAxisVec = vec3.create();
+      vec3.sub(majorAxisVec, majorAxisEnd, majorAxisStart);
+
+      // normalize majorAxisVec to avoid scaling issues
+      vec3.normalize(majorAxisVec, majorAxisVec);
+
+      const minorAxisVec = vec3.create();
+      vec3.sub(minorAxisVec, minorAxisEnd, minorAxisStart);
+      vec3.normalize(minorAxisVec, minorAxisVec);
+
+      const imagePlaneModule = metaData.get('imagePlaneModule', imageId);
+
+      if (!imagePlaneModule) {
+        throw new Error('imageId does not have imagePlaneModule metadata');
+      }
+
+      const { columnCosines }: { columnCosines: csTypes.Point3 } = imagePlaneModule;
+
+      // find which axis is parallel to the columnCosines
+      const columnCosinesVec = vec3.fromValues(...columnCosines);
+
+      const projectedMajorAxisOnColVec = Math.abs(vec3.dot(columnCosinesVec, majorAxisVec));
+      const projectedMinorAxisOnColVec = Math.abs(vec3.dot(columnCosinesVec, minorAxisVec));
+
+      const absoluteOfMajorDotProduct = Math.abs(projectedMajorAxisOnColVec);
+      const absoluteOfMinorDotProduct = Math.abs(projectedMinorAxisOnColVec);
+
+      renderableData = [];
+      if (Math.abs(absoluteOfMajorDotProduct - 1) < EPSILON) {
+        renderableData = [pointsWorld[0], pointsWorld[1], pointsWorld[2], pointsWorld[3]];
+      } else if (Math.abs(absoluteOfMinorDotProduct - 1) < EPSILON) {
+        renderableData = [pointsWorld[2], pointsWorld[3], pointsWorld[0], pointsWorld[1]];
+      } else {
+        console.warn('OBLIQUE ELLIPSE NOT YET SUPPORTED');
+      }
+      break;
+    }
+    default:
+      console.warn('Unsupported GraphicType:', GraphicType);
+  }
+
+  return renderableData;
+}

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

@@ -1,66 +0,0 @@
-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);
-}

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

@@ -1,14 +1,8 @@
 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

@@ -61,11 +61,6 @@ 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

@@ -1,67 +0,0 @@
-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 };