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

Co-authored-by: Devin AI <158243242+devin-ai-integration[bot]@users.noreply.github.com>

.circleci/config.yml

@@ -1,68 +1,52 @@
 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@1.26.0
-executors:
-  # Custom executor to override Cypress config
-  deploy-to-prod-executor:
-    docker:
-      - image: cimg/node:16.14
-        environment:
-          CYPRESS_BASE_URL: https://ohif-staging.netlify.com/
-  chrome-and-pacs:
-    docker:
-      # Primary container image where all steps run.
-      - image: 'cypress/browsers:node16.14.2-slim-chrome103-ff102'
+  cypress: cypress-io/cypress@3.3.1
 
 defaults: &defaults
   docker:
-    - image: cimg/node:16.14-browsers
+    - image: cimg/node:20.18.1
       environment:
-        TERM: xterm # Enable colors in term
+        TERM: xterm
         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:
-      # Update yarn
-      - run: yarn -v
-      # Checkout code and ALL Git Tags
+      - install_bun
+      - run: node --version
       - 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: yarn install --frozen-lockfile
-      - save_cache:
-          name: Save Yarn Package Cache
-          paths:
-            - ~/.cache ## Cache yarn and Cypress
-          key: yarn-packages-{{ checksum "yarn.lock" }}
+          command: bun install --no-save
       # RUN TESTS
       - run:
           name: 'JavaScript Test Suite'
-          command: yarn run test:unit:ci
+          command: bun run test:unit:ci
       # platform/app
       - run:
           name: 'VIEWER: Combine report output'
@@ -90,72 +74,23 @@ jobs:
           file: '/home/circleci/repo/platform/core/coverage/reports'
           flags: 'core'
 
-  ###
-  # Workflow: PR_OPTIONAL_DOCKER_PUBLISH
-  ###
-  DOCKER_PR_PUBLISH:
-    <<: *defaults
-    steps:
-      # Enable yarn workspaces
-      - run: yarn config set workspaces-experimental true
-
-      # 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: yarn install --frozen-lockfile
-
-      - setup_remote_docker:
-          docker_layer_caching: false
-
-      - run:
-          name: Build and push Docker image
-          command: |
-            # Remove npm config
-            rm -f ./.npmrc
-            # Set our version number using vars
-            echo $CIRCLE_BUILD_NUM
-            # Build our image, auth, and push
-            docker build --tag ohif/app:PR_BUILD-$CIRCLE_BUILD_NUM .
-            echo $DOCKER_PWD | docker login -u $DOCKER_LOGIN --password-stdin
-            docker push ohif/app:PR_BUILD-$CIRCLE_BUILD_NUM
-
-  ###
-  # Workflow: DEPLOY
-  ###
   BUILD:
     <<: *defaults
+    resource_class: large
     steps:
       # 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-
+      - install_bun
       - run:
           name: Install Dependencies
-          command: yarn install --frozen-lockfile
-      - save_cache:
-          name: Save Yarn Package Cache
-          paths:
-            - ~/.cache ## Cache yarn and Cypress
-          key: yarn-packages-{{ checksum "yarn.lock" }}
+          command: bun install --no-save
       # Build & Test
       - run:
           name: 'Perform the versioning before build'
-          command: node ./version.mjs
+          command: bun ./version.mjs
       - run:
           name: 'Build the OHIF Viewer'
-          command: yarn run build
+          command: bun run build
           no_output_timeout: 45m
       - run:
           name: 'Upload SourceMaps, Send Deploy Notification'
@@ -177,88 +112,18 @@ jobs:
             - commit.txt
             - version.json
 
-  # DEPLOY_TO_DEV:
-  #   docker:
-  #     - image: circleci/node:16.14.0
-  #       environment:
-  #         TERM: xterm
-  #         NETLIFY_SITE_ID: 32708787-c9b0-4634-b50f-7ca41952da77
-  #   working_directory: ~/repo
-  #   steps:
-  #     - attach_workspace:
-  #         at: ~/repo
-  #     - run: cd .netlify && npm install
-  #     - run: cp .netlify/deploy-workflow/_redirects platform/app/dist/_redirects
-  #     - run: cd .netlify && npm run deploy
-
-  # DEPLOY_TO_STAGING:
-  #   docker:
-  #     - image: circleci/node:16.14.0
-  #       environment:
-  #         TERM: xterm
-  #         NETLIFY_SITE_ID: c7502ae3-b150-493c-8422-05701e44a969
-  #   working_directory: ~/repo
-  #   steps:
-  #     - attach_workspace:
-  #         at: ~/repo
-  #     - run: cd .netlify && npm install
-  #     - run: cp .netlify/deploy-workflow/_redirects platform/app/dist/_redirects
-  #     - run: cd .netlify && npm run deploy
-
-  # DEPLOY_TO_PRODUCTION:
-  #   docker:
-  #     - image: circleci/node:16.14.0
-  #       environment:
-  #         TERM: xterm
-  #         NETLIFY_SITE_ID: 79c4a5da-5c95-4dc9-84f7-45fd9dfe21b0
-  #   working_directory: ~/repo
-  #   steps:
-  #     - attach_workspace:
-  #         at: ~/repo
-  #     - run: cd .netlify && npm install
-  #     - run: cp .netlify/deploy-workflow/_redirects platform/app/dist/_redirects
-  #     - run: cd .netlify && npm run deploy
-
-  #   DEPLOY_TO_RELEASE_DEV:
-  #     docker:
-  #       - image: circleci/node:16.14.0
-  #         environment:
-  #           TERM: xterm
-  #           NETLIFY_SITE_ID: 3270878-22
-  #     working_directory: ~/repo
-  #     steps:
-  #       - attach_workspace:
-  #           at: ~/repo
-  #       - run: cd .netlify && npm install
-  #       - run:
-  #           cp .netlify/deploy-workflow/_redirects platform/app/dist/_redirects
-  #       - run: cd .netlify && npm run deploy
-
-  ###
-  # Workflow: RELEASE
-  ###
-  NPM_PUBLISH:
+  BUILD_PACKAGES_QUICK:
     <<: *defaults
+    resource_class: large
     steps:
-      - run: yarn -v
+      - install_bun
       # 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: yarn install --frozen-lockfile
-      - save_cache:
-          name: Save Yarn Package Cache
-          paths:
-            - ~/.cache/yarn
-          key: yarn-packages-{{ checksum "yarn.lock" }}
+          command: bun install --frozen-lockfile
       - run:
           name: Avoid hosts unknown for github
           command: |
@@ -270,29 +135,65 @@ jobs:
       - run:
           name: Authenticate with NPM registry
           command: echo "//registry.npmjs.org/:_authToken=$NPM_TOKEN" > ~/repo/.npmrc
-      - run:
-          name: Increase the event emitter limit
-          command: |
-            node ./increaseEventEmitterLimit.mjs
       - run:
           name: build half of the packages (to avoid out of memory in circleci)
           command: |
-            yarn run build:package-all
+            bun run build:package-all
       - run:
           name: build the other half of the packages
           command: |
-            yarn run build:package-all-1
+            bun run build:package-all-1
+
+  NPM_PUBLISH:
+    <<: *defaults
+    resource_class: large
+    steps:
+      - install_bun
+      # Checkout code and ALL Git Tags
+      - checkout
+      - attach_workspace:
+          at: ~/repo
+      - run:
+          name: Install Dependencies
+          command: bun install --no-save
+      - run:
+          name: Avoid hosts unknown for github
+          command: |
+            rm -rf ~/.ssh
+            mkdir ~/.ssh/
+            echo -e "Host github.com\n\tStrictHostKeyChecking no\n" > ~/.ssh/config
+            git config --global user.email "danny.ri.brown+ohif-bot@gmail.com"
+            git config --global user.name "ohif-bot"
+      - run:
+          name: Authenticate with NPM registry
+          command: echo "//registry.npmjs.org/:_authToken=$NPM_TOKEN" > ~/repo/.npmrc
+      - run:
+          name: build half of the packages (to avoid out of memory in circleci)
+          command: |
+            bun run build:package-all
+      - run:
+          name: build the other half of the packages
+          command: |
+            bun run build:package-all-1
+      - run:
+          name: increase min time out
+          command: |
+            npm config set fetch-retry-mintimeout 20000
+      - run:
+          name: increase max time out
+          command: |
+            npm config set fetch-retry-maxtimeout 120000
       - run:
           name: publish package versions
           command: |
-            node ./publish-version.mjs
+            bun ./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: |
-            node ./publish-package.mjs
+            bun ./publish-package.mjs
       - persist_to_workspace:
           root: ~/repo
           paths:
@@ -300,13 +201,14 @@ jobs:
 
   DOCKER_RELEASE_PUBLISH:
     <<: *defaults
+    resource_class: large
     steps:
       - attach_workspace:
           at: ~/repo
       - setup_remote_docker:
           docker_layer_caching: false
       - run:
-          name: Build and push Docker image from the release branch
+          name: Build Docker image for amd64
           command: |
             # This file will exist if a new version was published by
             # our command in the previous job.
@@ -320,22 +222,61 @@ jobs:
               export IMAGE_VERSION_FULL=v$IMAGE_VERSION
               echo $IMAGE_VERSION
               echo $IMAGE_VERSION_FULL
-              # Build our image, auth, and push
-              docker build --tag ohif/app:$IMAGE_VERSION_FULL --tag ohif/app:latest .
+              # Build our amd64 image, auth, and push
+              docker build --platform linux/amd64 --tag ohif/app:$IMAGE_VERSION_FULL-amd64 --tag ohif/app:latest-amd64 .
               echo $DOCKER_PWD | docker login -u $DOCKER_LOGIN --password-stdin
-              docker push ohif/app:$IMAGE_VERSION_FULL
-              docker push ohif/app:latest
+              docker push ohif/app:$IMAGE_VERSION_FULL-amd64
+              docker push ohif/app:latest-amd64
             fi
+      - persist_to_workspace:
+          root: ~/repo
+          paths:
+            - .
 
-  DOCKER_BETA_PUBLISH:
+  DOCKER_RELEASE_PUBLISH_ARM:
     <<: *defaults
+    resource_class: arm.large
     steps:
       - attach_workspace:
           at: ~/repo
       - setup_remote_docker:
           docker_layer_caching: false
       - run:
-          name: Build and push Docker image from the master branch (beta releases)
+          name: Build Docker image for arm64
+          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)
           command: |
             echo $(ls -l)
 
@@ -347,89 +288,169 @@ 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 $IMAGE_VERSION_FULL
-              # Build our image, auth, and push
+              # Build our amd64 image, auth, and push
+              docker build --platform linux/amd64 --tag ohif/app:$IMAGE_VERSION_FULL-amd64 --tag ohif/app:latest-beta-amd64 .
+              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
+            fi
 
-              echo "starting docker build"
-              docker build --tag ohif/app:$IMAGE_VERSION_FULL .
+  DOCKER_BETA_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 (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:
+      - install_bun
+      - run:
+          name: Install Xvfb
+          command: sudo apt-get update && sudo apt-get install -y xvfb
+      - run:
+          name: Start Xvfb
+          command: Xvfb :99 -screen 0 1920x1080x24 &
+          background: true
+      - run:
+          name: Export Display Variable
+          command: export DISPLAY=:99
+      - cypress/install:
+          install-browsers: true
+          install-command: bun install --no-save
+          package-manager: yarn
+      - cypress/run-tests:
+          cypress-command:
+            npx wait-on@latest http://localhost:3000 && cd platform/app &&  npx cypress run --record
+            --browser chrome --parallel
+          start-command: bun run test:data && bun 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
+          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
 
-              echo "starting docker push"
-              docker push ohif/app:$IMAGE_VERSION_FULL
+              # Create and push manifest for specific version
+              docker manifest create ohif/app:$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
 
 workflows:
-  version: 2
-
   PR_CHECKS:
     jobs:
+      - BUILD_PACKAGES_QUICK:
+          filters:
+            branches:
+              ignore: master
       - UNIT_TESTS
+      - CYPRESS:
+          name: 'Cypress Tests'
+          context: cypress
 
-      # E2E: PWA
-      - cypress/run:
-          name: 'E2E: PWA'
-          executor: chrome-and-pacs
-          browser: chrome
-          pre-steps:
-            - run: |
-                # Clear yarn cache; use yarn from image (update image to update yarn)
-                rm -rf ~/.yarn
-                yarn -v
-          yarn: true
-          record: true
-          store_artifacts: true
-          working_directory: platform/app
-          build: yarn test:data
-          start: yarn run test:e2e:serve
-          spec: 'cypress/integration/**/*'
-          wait-on: 'http://localhost:3000'
-          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
-          requires:
-            - UNIT_TESTS
-
-  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.
+  # viewer-dev.ohif.org
   DEPLOY_MASTER:
     jobs:
       - BUILD:
@@ -442,64 +463,35 @@ workflows:
       - DOCKER_BETA_PUBLISH:
           requires:
             - NPM_PUBLISH
+      - DOCKER_BETA_PUBLISH_ARM:
+          requires:
+            - NPM_PUBLISH
+      - DOCKER_BETA_MULTIARCH_MANIFEST:
+          requires:
+            - DOCKER_BETA_PUBLISH
+            - DOCKER_BETA_PUBLISH_ARM
 
-  # Our release branch deploys to viewer.ohif.org and is more stable and less
-  # frequently updated after being tested in the staging environment.
+  # viewer.ohif.org
   DEPLOY_RELEASE:
     jobs:
       - BUILD:
           filters:
             branches:
-              only: release
-      - NPM_PUBLISH:
+              only: /^release\/.*/
+      - HOLD_FOR_APPROVAL:
+          type: approval
           requires:
             - BUILD
+      - NPM_PUBLISH:
+          requires:
+            - HOLD_FOR_APPROVAL
       - DOCKER_RELEASE_PUBLISH:
           requires:
             - NPM_PUBLISH
-  ###
-  # 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_RELEASE_PUBLISH_ARM:
+          requires:
+            - NPM_PUBLISH
+      - DOCKER_MULTIARCH_MANIFEST:
+          requires:
+            - DOCKER_RELEASE_PUBLISH
+            - DOCKER_RELEASE_PUBLISH_ARM

.codecov.yml

@@ -1,25 +0,0 @@
-# ABOUT:
-# https://docs.codecov.io/docs/codecov-yaml
-#
-#
-# COMMIT STATUS:
-# https://docs.codecov.io/docs/commit-status
-coverage:
-  status:
-    project:
-      default:
-        threshold: 0.5%
-      core:
-        flags: core
-        threshold: 0.5%
-      viewer:
-        flags: viewer
-        threshold: 0.5%
-    patch: off
-flags:
-  core:
-    paths:
-      - platform/core
-  viewer:
-    paths:
-      - platform/app

.codespellrc

@@ -0,0 +1,6 @@
+[codespell]
+skip = .git,*.pdf,*.svg,yarn.lock,*.min.js,locales
+# ignore words ending with … and some camelcased variables and names
+ignore-regex = \b\S+…\S*|\b(doubleClick|afterAll|PostgresSQL)\b|\bWee, L\.|.*te.*Telugu.*
+# some odd variables
+ignore-words-list = datea,ser,childrens

.docker/Nginx-Orthanc/config/nginx.conf

@@ -1,48 +0,0 @@
-worker_processes 1;
-
-events { worker_connections 1024; }
-
-http {
-
-    upstream orthanc-server {
-        server orthanc:8042;
-    }
-
-    server {
-        listen [::]:80 default_server;
-        listen 80;
-
-        # CORS Magic
-        add_header 'Access-Control-Allow-Origin' '*';
-        add_header 'Access-Control-Allow_Credentials' 'true';
-        add_header 'Access-Control-Allow-Headers' 'Authorization,Accept,Origin,DNT,X-CustomHeader,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Content-Range,Range';
-        add_header 'Access-Control-Allow-Methods' 'GET,POST,OPTIONS,PUT,DELETE,PATCH';
-
-        location / {
-
-            if ($request_method = 'OPTIONS') {
-                add_header 'Access-Control-Allow-Origin' '*';
-                add_header 'Access-Control-Allow_Credentials' 'true';
-                add_header 'Access-Control-Allow-Headers' 'Authorization,Accept,Origin,DNT,X-CustomHeader,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Content-Range,Range';
-                add_header 'Access-Control-Allow-Methods' 'GET,POST,OPTIONS,PUT,DELETE,PATCH';
-                add_header 'Access-Control-Max-Age' 1728000;
-                add_header 'Content-Type' 'text/plain charset=UTF-8';
-                add_header 'Content-Length' 0;
-                return 204;
-            }
-
-            proxy_pass         http://orthanc:8042;
-            proxy_redirect     off;
-            proxy_set_header   Host $host;
-            proxy_set_header   X-Real-IP $remote_addr;
-            proxy_set_header   X-Forwarded-For $proxy_add_x_forwarded_for;
-            proxy_set_header   X-Forwarded-Host $server_name;
-
-            # CORS Magic
-            add_header 'Access-Control-Allow-Origin' '*';
-            add_header 'Access-Control-Allow_Credentials' 'true';
-            add_header 'Access-Control-Allow-Headers' 'Authorization,Accept,Origin,DNT,X-CustomHeader,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Content-Range,Range';
-            add_header 'Access-Control-Allow-Methods' 'GET,POST,OPTIONS,PUT,DELETE,PATCH';
-        }
-    }
-}

.docker/Nginx-Orthanc/docker-compose.yml

@@ -1,23 +0,0 @@
-version: '3.5'
-
-services:
-  orthanc:
-    image: jodogne/orthanc-plugins:1.11.0
-    hostname: orthanc
-    volumes:
-      # Config
-      - ./config/orthanc.json:/etc/orthanc/orthanc.json:ro
-      # Persist data
-      - ./volumes/orthanc-db/:/var/lib/orthanc/db/
-    ports:
-      - '4242:4242' # DICOM
-      - '8042:8042' # Web
-    restart: unless-stopped
-  nginx:
-    image: nginx:latest
-    volumes:
-      - ./config/nginx.conf:/etc/nginx/nginx.conf
-    ports:
-      - '80:80' #ngnix proxy
-    depends_on:
-      - orthanc

.docker/Nginx-Orthanc/volumes/orthanc-db/.gitignore

@@ -1,2 +0,0 @@
-*
-!.gitignore

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

@@ -1,12 +1,13 @@
 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/ /index.html;
-    add_header Cross-Origin-Opener-Policy same-origin;
-    add_header Cross-Origin-Embedder-Policy require-corp;
     add_header Cross-Origin-Resource-Policy same-origin;
     proxy_set_header Host $host;
     proxy_set_header X-Real-IP $remote_addr;

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

@@ -7,8 +7,6 @@ server {
     root   /usr/share/nginx/html;
     index  index.html index.htm;
     try_files $uri $uri/ /index.html;
-    add_header Cross-Origin-Opener-Policy same-origin;
-    add_header Cross-Origin-Embedder-Policy require-corp;
     add_header Cross-Origin-Resource-Policy same-origin;
     proxy_set_header Host $host;
     proxy_set_header X-Real-IP $remote_addr;

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

@@ -7,9 +7,18 @@ if [ -n "$SSL_PORT" ]
     envsubst '${PORT}' < /usr/src/default.conf.template > /etc/nginx/conf.d/default.conf
 fi
 
-if [ -n "$APP_CONFIG" ]
+if [ -n "$APP_CONFIG" ] ; then
+  echo "$APP_CONFIG" > /usr/share/nginx/html${PUBLIC_URL}app-config.js
+  # Removes the old compressed app-config file, then compresses the replacement
+  # and finally creates a new empty file so that gunzip works correctly.
+  # This code is correct despite the AI warning otherwise about order of create/delete
+  rm /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${PUBLIC_URL}app-config.js
+fi
+if [ ! -n "$APP_CONFIG" ]
   then
-    echo "$APP_CONFIG" > /usr/share/nginx/html/app-config.js
+    echo "Not using custom app config"
 fi
 
 if [ -n "$CLIENT_ID" ] || [ -n "$HEALTHCARE_API_ENDPOINT" ]
@@ -40,6 +49,6 @@ 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..."
+echo "Starting Nginx to serve the OHIF Viewer on ${PUBLIC_URL}"
 
 exec "$@"

.docker/compressDist.sh

@@ -0,0 +1,4 @@
+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/
-docs/
+platform/docs/
 testdata/

.env.example

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

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -64,7 +64,7 @@ body:
     attributes:
       label: 'Node version'
       description: 'Your Node.js version.'
-      placeholder: 'e.g., 16.14.0'
+      placeholder: 'e.g., 20.18.1'
     validations:
       required: true
   - type: input

.github/pull_request_template.md

@@ -83,7 +83,7 @@ after the commits are squashed.
 #### Tested Environment
 
 - [] OS: <!--[e.g. Windows 10, macOS 10.15.4]-->
-- [] Node version: <!--[e.g. 16.14.0]-->
+- [] Node version: <!--[e.g. 18.16.1]-->
 - [] Browser:
   <!--[e.g. Chrome 83.0.4103.116, Firefox 77.0.1, Safari 13.1.1]-->
 

.github/workflows/playwright.yml

@@ -0,0 +1,76 @@
+name: Playwright Tests
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+jobs:
+  playwright-tests:
+    timeout-minutes: 60
+    runs-on: ubuntu-latest
+    container:
+      image: mcr.microsoft.com/playwright:v1.49.0-noble
+    strategy:
+      fail-fast: false
+      matrix:
+        shardIndex: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
+        shardTotal: [10]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install unzip
+        run: apt-get update && apt-get install -y unzip
+      - uses: oven-sh/setup-bun@v2
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 20
+      - name: Install dependencies
+        run: bun install --frozen-lockfile
+      - name: Set up Git safe directory
+        run: git config --global --add safe.directory /__w/Viewers/Viewers
+      - name: Run Playwright tests
+        run:
+          export NODE_OPTIONS="--max_old_space_size=8192" && bun x playwright test --shard=${{
+          matrix.shardIndex }}/${{ matrix.shardTotal }}
+
+      - name: Upload blob report to GitHub Actions Artifacts
+        if: ${{ !cancelled() }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: blob-report-${{ matrix.shardIndex }}
+          path: blob-report
+          retention-days: 1
+
+  merge-reports:
+    if: ${{ !cancelled() }}
+    needs: [playwright-tests]
+    runs-on: ubuntu-latest
+    container:
+      image: mcr.microsoft.com/playwright:v1.48.1-focal
+    steps:
+      - name: Install unzip
+        run: apt-get update && apt-get install -y unzip
+      - uses: oven-sh/setup-bun@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 20
+      - name: Install dependencies
+        run: bun install --frozen-lockfile
+      - name: Set up Git safe directory
+        run: git config --global --add safe.directory /__w/Viewers/Viewers
+      - name: Download blob reports from GitHub Actions Artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: all-blob-reports
+          pattern: blob-report-*
+          merge-multiple: true
+
+      - name: Merge into HTML Report
+        run: bun x playwright merge-reports --reporter html ./all-blob-reports
+
+      - name: Upload HTML report
+        uses: actions/upload-artifact@v4
+        with:
+          name: html-report--attempt-${{ github.run_attempt }}
+          path: playwright-report
+          retention-days: 14

.gitignore

@@ -10,6 +10,8 @@ junit.xml
 coverage/
 .docz/
 .yarn/
+.nx/
+addOns/yarn.lock
 
 # YALC (for Erik)
 .yalc
@@ -24,6 +26,7 @@ yarn-error.log
 .DS_Store
 .env
 *.code-workspace
+.directory
 
 # Common Example Data Directories
 sampledata/
@@ -32,7 +35,7 @@ docker/dcm4che/dcm4che-arc
 
 # Cypress test results
 videos/
-screenshots/
+
 
 # Locize settings
 .locize
@@ -40,5 +43,16 @@ screenshots/
 # autogenerated files
 platform/app/src/pluginImports.js
 /Viewers.iml
-platform/app/.recipes/Nginx-Dcm4Che/dcm4che/dcm4che-arc/*
+platform/app/.recipes/Nginx-Dcm4Chee/logs/*
 platform/app/.recipes/OpenResty-Orthanc/logs/*
+.vercel
+
+.vs
+
+# PlayWright
+
+node_modules/
+tests/test-results/
+tests/playwright-report/
+/blob-report/
+/playwright/.cache/

.node-version

@@ -1 +1 @@
-16.14.0
+20.9.0

.prettierrc

@@ -7,5 +7,6 @@
   "semi": true,
   "singleQuote": true,
   "arrowParens": "avoid",
-  "singleAttributePerLine": true
+  "singleAttributePerLine": true,
+  "endOfLine": "auto"
 }

.scripts/dicom-json-generator.js

@@ -0,0 +1,273 @@
+/*
+ * This script uses nodejs to generate a JSON file from a DICOM study folder.
+ * You need to have dcmjs installed in your project.
+ * 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>
+ *
+ * params:
+ * - studyFolder: path to the study folder which contains the DICOM files
+ * - urlPrefix: prefix to the url that will be used to load the study into the viewer. For instance
+ *   we use https://ohif-assets.s3.us-east-2.amazonaws.com/dicom-json/data as the urlPrefix for the
+ *   example since the data is hosted on S3 and each study is in a folder. So the url in the generated
+ *   json file for the first instance of the first series of the first study will be
+ *   dicomweb:https://ohif-assets.s3.us-east-2.amazonaws.com/dicom-json/data/Series1/Instance1
+ *
+ *   as you see the dicomweb is a prefix that is used to load the data into the viewer, which is suited when
+ *   the .dcm file is hosted statically and can be accessed via a URL (like our example above)
+ *   However, you can specify a new scheme bellow.
+ *
+ * - outputJSONPath: path to the output JSON file
+ * - scheme: default dicomweb if not provided
+ */
+const dcmjs = require('dcmjs');
+const path = require('path');
+const fs = require('fs').promises;
+
+const args = process.argv.slice(2);
+const [studyDirectory, urlPrefix, outputPath, scheme = 'dicomweb'] = args;
+
+if (args.length < 3 || args.length > 4) {
+  console.error(
+    'Usage: node dicom-json-generator.js <studyFolder> <urlPrefix> <outputJSONPath> [scheme]'
+  );
+  process.exit(1);
+}
+
+const model = {
+  studies: [],
+};
+
+async function convertDICOMToJSON(studyDirectory, urlPrefix, outputPath, scheme) {
+  try {
+    const files = await recursiveReadDir(studyDirectory);
+    console.debug('Processing...');
+
+    for (const file of files) {
+      if (!file.includes('.DS_Store') && !file.includes('.xml')) {
+        const arrayBuffer = await fs.readFile(file);
+        const dicomDict = dcmjs.data.DicomMessage.readFile(arrayBuffer.buffer);
+        const instance = dcmjs.data.DicomMetaDictionary.naturalizeDataset(dicomDict.dict);
+
+        instance.fileLocation = createImageId(file, urlPrefix, studyDirectory, scheme);
+        processInstance(instance);
+      }
+    }
+
+    console.log('Successfully loaded data');
+
+    model.studies.forEach(study => {
+      study.NumInstances = findInstancesNumber(study);
+      study.Modalities = findModalities(study).join('/');
+    });
+
+    await fs.writeFile(outputPath, JSON.stringify(model, null, 2));
+    console.log('JSON saved');
+  } catch (error) {
+    console.error(error);
+  }
+}
+
+async function recursiveReadDir(dir) {
+  let results = [];
+  const list = await fs.readdir(dir);
+  for (const file of list) {
+    const filePath = path.resolve(dir, file);
+    const stat = await fs.stat(filePath);
+    if (stat.isDirectory()) {
+      const res = await recursiveReadDir(filePath);
+      results = results.concat(res);
+    } else {
+      results.push(filePath);
+    }
+  }
+  return results;
+}
+
+function createImageId(fileLocation, urlPrefix, studyDirectory, scheme) {
+  const relativePath = path.relative(studyDirectory, fileLocation);
+  const normalizedPath = path.normalize(relativePath).replace(/\\/g, '/');
+  return `${scheme}:${urlPrefix}${normalizedPath}`;
+}
+
+function processInstance(instance) {
+  const { StudyInstanceUID, SeriesInstanceUID } = instance;
+  let study = getStudy(StudyInstanceUID);
+
+  if (!study) {
+    study = createStudyMetadata(StudyInstanceUID, instance);
+    model.studies.push(study);
+  }
+
+  let series = getSeries(StudyInstanceUID, SeriesInstanceUID);
+
+  if (!series) {
+    series = createSeriesMetadata(instance);
+    study.series.push(series);
+  }
+
+  const instanceMetaData =
+    instance.NumberOfFrames > 1
+      ? createInstanceMetaDataMultiFrame(instance)
+      : createInstanceMetaData(instance);
+
+  series.instances.push(...[].concat(instanceMetaData));
+}
+
+function getStudy(StudyInstanceUID) {
+  return model.studies.find(study => study.StudyInstanceUID === StudyInstanceUID);
+}
+
+function getSeries(StudyInstanceUID, SeriesInstanceUID) {
+  const study = getStudy(StudyInstanceUID);
+  return study
+    ? study.series.find(series => series.SeriesInstanceUID === SeriesInstanceUID)
+    : undefined;
+}
+
+const findInstancesNumber = study => {
+  let numInstances = 0;
+  study.series.forEach(aSeries => {
+    numInstances = numInstances + aSeries.instances.length;
+  });
+  return numInstances;
+};
+
+const findModalities = study => {
+  let modalities = new Set();
+  study.series.forEach(aSeries => {
+    modalities.add(aSeries.Modality);
+  });
+  return Array.from(modalities);
+};
+
+function createStudyMetadata(StudyInstanceUID, instance) {
+  return {
+    StudyInstanceUID,
+    StudyDescription: instance.StudyDescription,
+    StudyDate: instance.StudyDate,
+    StudyTime: instance.StudyTime,
+    PatientName: instance.PatientName,
+    PatientID: instance.PatientID || '1234', // this is critical to have
+    AccessionNumber: instance.AccessionNumber,
+    PatientAge: instance.PatientAge,
+    PatientSex: instance.PatientSex,
+    PatientWeight: instance.PatientWeight,
+    series: [],
+  };
+}
+function createSeriesMetadata(instance) {
+  return {
+    SeriesInstanceUID: instance.SeriesInstanceUID,
+    SeriesDescription: instance.SeriesDescription,
+    SeriesNumber: instance.SeriesNumber,
+    SeriesTime: instance.SeriesTime,
+    Modality: instance.Modality,
+    SliceThickness: instance.SliceThickness,
+    instances: [],
+  };
+}
+function commonMetaData(instance) {
+  return {
+    Columns: instance.Columns,
+    Rows: instance.Rows,
+    InstanceNumber: instance.InstanceNumber,
+    SOPClassUID: instance.SOPClassUID,
+    AcquisitionNumber: instance.AcquisitionNumber,
+    PhotometricInterpretation: instance.PhotometricInterpretation,
+    BitsAllocated: instance.BitsAllocated,
+    BitsStored: instance.BitsStored,
+    PixelRepresentation: instance.PixelRepresentation,
+    SamplesPerPixel: instance.SamplesPerPixel,
+    PixelSpacing: instance.PixelSpacing,
+    HighBit: instance.HighBit,
+    ImageOrientationPatient: instance.ImageOrientationPatient,
+    ImagePositionPatient: instance.ImagePositionPatient,
+    FrameOfReferenceUID: instance.FrameOfReferenceUID,
+    ImageType: instance.ImageType,
+    Modality: instance.Modality,
+    SOPInstanceUID: instance.SOPInstanceUID,
+    SeriesInstanceUID: instance.SeriesInstanceUID,
+    StudyInstanceUID: instance.StudyInstanceUID,
+    WindowCenter: instance.WindowCenter,
+    WindowWidth: instance.WindowWidth,
+    RescaleIntercept: instance.RescaleIntercept,
+    RescaleSlope: instance.RescaleSlope,
+  };
+}
+
+function conditionalMetaData(instance) {
+  return {
+    ...(instance.ConceptNameCodeSequence && {
+      ConceptNameCodeSequence: instance.ConceptNameCodeSequence,
+    }),
+    ...(instance.SeriesDate && { SeriesDate: instance.SeriesDate }),
+    ...(instance.ReferencedSeriesSequence && {
+      ReferencedSeriesSequence: instance.ReferencedSeriesSequence,
+    }),
+    ...(instance.SharedFunctionalGroupsSequence && {
+      SharedFunctionalGroupsSequence: instance.SharedFunctionalGroupsSequence,
+    }),
+    ...(instance.PerFrameFunctionalGroupsSequence && {
+      PerFrameFunctionalGroupsSequence: instance.PerFrameFunctionalGroupsSequence,
+    }),
+    ...(instance.ContentSequence && { ContentSequence: instance.ContentSequence }),
+    ...(instance.ContentTemplateSequence && {
+      ContentTemplateSequence: instance.ContentTemplateSequence,
+    }),
+    ...(instance.CurrentRequestedProcedureEvidenceSequence && {
+      CurrentRequestedProcedureEvidenceSequence: instance.CurrentRequestedProcedureEvidenceSequence,
+    }),
+    ...(instance.CodingSchemeIdentificationSequence && {
+      CodingSchemeIdentificationSequence: instance.CodingSchemeIdentificationSequence,
+    }),
+    ...(instance.RadiopharmaceuticalInformationSequence && {
+      RadiopharmaceuticalInformationSequence: instance.RadiopharmaceuticalInformationSequence,
+    }),
+    ...(instance.ROIContourSequence && {
+      ROIContourSequence: instance.ROIContourSequence,
+    }),
+    ...(instance.StructureSetROISequence && {
+      StructureSetROISequence: instance.StructureSetROISequence,
+    }),
+    ...(instance.ReferencedFrameOfReferenceSequence && {
+      ReferencedFrameOfReferenceSequence: instance.ReferencedFrameOfReferenceSequence,
+    }),
+    ...(instance.CorrectedImage && { CorrectedImage: instance.CorrectedImage }),
+    ...(instance.Units && { Units: instance.Units }),
+    ...(instance.DecayCorrection && { DecayCorrection: instance.DecayCorrection }),
+    ...(instance.AcquisitionDate && { AcquisitionDate: instance.AcquisitionDate }),
+    ...(instance.AcquisitionTime && { AcquisitionTime: instance.AcquisitionTime }),
+    ...(instance.PatientWeight && { PatientWeight: instance.PatientWeight }),
+    ...(instance.NumberOfFrames && { NumberOfFrames: instance.NumberOfFrames }),
+    ...(instance.FrameTime && { FrameTime: instance.FrameTime }),
+    ...(instance.EncapsulatedDocument && { EncapsulatedDocument: instance.EncapsulatedDocument }),
+    ...(instance.SequenceOfUltrasoundRegions && {
+      SequenceOfUltrasoundRegions: instance.SequenceOfUltrasoundRegions,
+    }),
+  };
+}
+
+function createInstanceMetaData(instance) {
+  const metadata = {
+    ...commonMetaData(instance),
+    ...conditionalMetaData(instance),
+  };
+  return { metadata, url: instance.fileLocation };
+}
+
+function createInstanceMetaDataMultiFrame(instance) {
+  const instances = [];
+  const commonData = commonMetaData(instance);
+  const conditionalData = conditionalMetaData(instance);
+
+  for (let i = 1; i <= instance.NumberOfFrames; i++) {
+    const metadata = { ...commonData, ...conditionalData };
+    const result = { metadata, url: instance.fileLocation + `?frame=${i}` };
+    instances.push(result);
+  }
+  return instances;
+}
+
+convertDICOMToJSON(studyDirectory, urlPrefix, outputPath, scheme);

.vscode/extensions.json

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

.vscode/settings.json

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

.webpack/rules/stylusToJavaScript.js

@@ -0,0 +1,10 @@
+const stylusToJavaScript = {
+  test: /\.styl$/,
+  use: [
+    { loader: 'style-loader' }, // 3. Style nodes from JS Strings
+    { loader: 'css-loader' }, // 2. CSS to CommonJS
+    { loader: 'stylus-loader' }, // 1. Stylus to CSS
+  ],
+};
+
+module.exports = stylusToJavaScript;

.webpack/webpack.base.js

@@ -7,17 +7,20 @@ 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');
 
 // ~~ ENV VARS
 const NODE_ENV = process.env.NODE_ENV;
@@ -32,11 +35,28 @@ const COMMIT_HASH = fs.readFileSync(path.join(__dirname, '../commit.txt'), 'utf8
 //
 dotenv.config();
 
-module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
-  if (!process.env.NODE_ENV) {
-    throw new Error('process.env.NODE_ENV not set');
-  }
+const defineValues = {
+  /* Application */
+  'process.env.NODE_ENV': JSON.stringify(process.env.NODE_ENV),
+  'process.env.NODE_DEBUG': JSON.stringify(process.env.NODE_DEBUG),
+  'process.env.DEBUG': JSON.stringify(process.env.DEBUG),
+  'process.env.PUBLIC_URL': JSON.stringify(process.env.PUBLIC_URL || '/'),
+  'process.env.BUILD_NUM': JSON.stringify(BUILD_NUM),
+  'process.env.VERSION_NUMBER': JSON.stringify(VERSION_NUMBER),
+  'process.env.COMMIT_HASH': JSON.stringify(COMMIT_HASH),
+  /* i18n */
+  'process.env.USE_LOCIZE': JSON.stringify(process.env.USE_LOCIZE || ''),
+  'process.env.LOCIZE_PROJECTID': JSON.stringify(process.env.LOCIZE_PROJECTID || ''),
+  'process.env.LOCIZE_API_KEY': JSON.stringify(process.env.LOCIZE_API_KEY || ''),
+  'process.env.REACT_APP_I18N_DEBUG': JSON.stringify(process.env.REACT_APP_I18N_DEBUG || ''),
+};
 
+// Only redefine updated values.  This avoids warning messages in the logs
+if (!process.env.APP_CONFIG) {
+  defineValues['process.env.APP_CONFIG'] = '';
+}
+
+module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
   const mode = NODE_ENV === 'production' ? 'production' : 'development';
   const isProdBuild = NODE_ENV === 'production';
   const isQuickBuild = QUICK_BUILD === 'true';
@@ -74,12 +94,51 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
       type: 'filesystem',
     },
     module: {
-      noParse: [/(codec)/, /(dicomicc)/],
+      noParse: [/(dicomicc)/],
       rules: [
+        ...(isProdBuild
+          ? []
+          : [
+              {
+                test: /\.[jt]sx?$/,
+                exclude: /node_modules/,
+                loader: 'babel-loader',
+                options: {
+                  plugins: isProdBuild ? [] : ['react-refresh/babel'],
+                },
+              },
+            ]),
         {
-          test: /\.js$/,
-          enforce: 'pre',
-          use: 'source-map-loader',
+          test: /\.svg?$/,
+          oneOf: [
+            {
+              use: [
+                {
+                  loader: '@svgr/webpack',
+                  options: {
+                    svgoConfig: {
+                      plugins: [
+                        {
+                          name: 'preset-default',
+                          params: {
+                            overrides: {
+                              removeViewBox: false,
+                            },
+                          },
+                        },
+                      ],
+                    },
+                    prettier: false,
+                    svgo: true,
+                    titleProp: true,
+                  },
+                },
+              ],
+              issuer: {
+                and: [/\.(ts|tsx|js|jsx|md|mdx)$/],
+              },
+            },
+          ],
         },
         transpileJavaScriptRule(mode),
         loadWebWorkersRule,
@@ -91,10 +150,24 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
           },
         },
         cssToJavaScript,
+        // Note: Only uncomment the following if you are using the old style of stylus in v2
+        // Also you need to uncomment this platform/app/.webpack/rules/extractStyleChunks.js
+        // stylusToJavaScript,
         {
           test: /\.wasm/,
           type: 'asset/resource',
         },
+        {
+          test: /\.(png|jpe?g|gif|svg)$/i,
+          use: [
+            {
+              loader: 'file-loader',
+              options: {
+                name: 'assets/images/[name].[ext]',
+              },
+            },
+          ],
+        },
       ], //.concat(vtkRules),
     },
     resolve: {
@@ -108,8 +181,6 @@ 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: [
@@ -133,24 +204,11 @@ module.exports = (env, argv, { SRC_DIR, ENTRY }) => {
       },
     },
     plugins: [
-      new webpack.DefinePlugin({
-        /* Application */
-        'process.env.NODE_ENV': JSON.stringify(process.env.NODE_ENV),
-        'process.env.DEBUG': JSON.stringify(process.env.DEBUG),
-        'process.env.APP_CONFIG': JSON.stringify(process.env.APP_CONFIG || ''),
-        'process.env.PUBLIC_URL': JSON.stringify(process.env.PUBLIC_URL || '/'),
-        'process.env.BUILD_NUM': JSON.stringify(BUILD_NUM),
-        'process.env.VERSION_NUMBER': JSON.stringify(VERSION_NUMBER),
-        'process.env.COMMIT_HASH': JSON.stringify(COMMIT_HASH),
-        /* i18n */
-        'process.env.USE_LOCIZE': JSON.stringify(process.env.USE_LOCIZE || ''),
-        'process.env.LOCIZE_PROJECTID': JSON.stringify(process.env.LOCIZE_PROJECTID || ''),
-        'process.env.LOCIZE_API_KEY': JSON.stringify(process.env.LOCIZE_API_KEY || ''),
-        'process.env.REACT_APP_I18N_DEBUG': JSON.stringify(process.env.REACT_APP_I18N_DEBUG || ''),
-      }),
+      new webpack.DefinePlugin(defineValues),
       new webpack.ProvidePlugin({
         Buffer: ['buffer', 'Buffer'],
       }),
+      ...(isProdBuild ? [] : [new ReactRefreshWebpackPlugin({ overlay: false })]),
       // Uncomment to generate bundle analyzer
       // new BundleAnalyzerPlugin(),
     ],

DATACITATION.md

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

Dockerfile

@@ -1,3 +1,4 @@
+# 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
@@ -19,61 +20,79 @@
 #
 
 
+# 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 .
-FROM node:16.15.0-slim as json-copier
-
-RUN mkdir /usr/src/app
-WORKDIR /usr/src/app
-
-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:16.15.0-slim as builder
+FROM node:20.18.1-slim as builder
 RUN apt-get update && apt-get install -y build-essential python3
 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
 
-COPY --from=json-copier /usr/src/app .
-
+# 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 ./
 # 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 install
+# Copy the local directory
+COPY --link --exclude=yarn.lock --exclude=package.json --exclude=Dockerfile . .
+# Do a second install to finalize things after the copy
+RUN bun run show:config
+RUN bun install
 
-COPY . .
-
-# To restore workspaces symlinks
-RUN yarn install --frozen-lockfile --verbose
-
-ENV PATH /usr/src/app/node_modules/.bin:$PATH
+# Build here
+# After install it should hopefully be stable until the local directory changes
 ENV QUICK_BUILD true
 # ENV GENERATE_SOURCEMAP=false
-# ENV REACT_APP_CONFIG=config/default.js
+ARG APP_CONFIG=config/default.js
+ARG PUBLIC_URL=/
 
-RUN yarn run build
+RUN bun run show:config
+RUN bun run build
+
+# Precompress files
+RUN chmod u+x .docker/compressDist.sh
+RUN ./.docker/compressDist.sh
 
 # Stage 3: Bundle the built application into a Docker container
 # which runs Nginx using Alpine Linux
-FROM nginxinc/nginx-unprivileged:1.25-alpine as final
+FROM nginxinc/nginx-unprivileged:1.27-alpine as final
 #RUN apk add --no-cache bash
-ENV PORT=80
+ARG PORT=80
+ENV PORT=${PORT}
+ARG PUBLIC_URL=/
+ENV PUBLIC_URL=${PUBLIC_URL}
 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
+COPY --from=builder /usr/src/app/platform/app/dist /usr/share/nginx/html${PUBLIC_URL}
+COPY --from=builder /usr/src/app/platform/app/dist/index.html /usr/share/nginx/html
 # In entrypoint.sh, app-config.js might be overwritten, so chmod it to be writeable.
 # The nginx user cannot chmod it, so change to root.
 USER root
-RUN chmod 666 /usr/share/nginx/html/app-config.js
+RUN chown -R nginx:nginx /usr/share/nginx/html
 USER nginx
 ENTRYPOINT ["/usr/src/entrypoint.sh"]
 CMD ["nginx", "-g", "daemon off;"]

README.md

@@ -17,6 +17,10 @@ provided by the <a href="https://ohif.org/">Open Health Imaging Foundation (OHIF
 <div align="center">
   📰 <a href="https://ohif.org/news/"><strong>Join OHIF Newsletter</strong></a> 📰
 </div>
+<div align="center">
+  📰 <a href="https://ohif.org/news/"><strong>Join OHIF Newsletter</strong></a> 📰
+</div>
+
 
 
 <hr />
@@ -37,17 +41,19 @@ provided by the <a href="https://ohif.org/">Open Health Imaging Foundation (OHIF
 
 |     |  | |
 | :-: | :---  | :--- |
-| <img src="platform/docs/docs/assets/img/demo-measurements.jpg" alt="Measurement tracking" width="350"/> | Measurement Tracking | [Demo](https://viewer.ohif.org/viewer?StudyInstanceUIDs=1.3.6.1.4.1.25403.345050719074.3824.20170125095438.5) |
-| <img src="platform/docs/docs/assets/img/demo-segmentation.png" alt="Segmentations" width="350"/> | Labelmap Segmentations  | [Demo](https://viewer.ohif.org/viewer?StudyInstanceUIDs=1.3.12.2.1107.5.2.32.35162.30000015050317233592200000046) |
-| <img src="platform/docs/docs/assets/img/demo-ptct.png" alt="Hanging Protocols" width="350"/> | Fusion and Custom Hanging protocols  | [Demo](https://viewer.ohif.org/tmtv?StudyInstanceUIDs=1.3.6.1.4.1.14519.5.2.1.7009.2403.334240657131972136850343327463) |
-| <img src="platform/docs/docs/assets/img/demo-microscopy.png" alt="Microscopy" width="350"/> | Slide Microscopy  | [Demo](https://viewer.ohif.org/microscopy?StudyInstanceUIDs=2.25.275741864483510678566144889372061815320) |
-| <img src="platform/docs/docs/assets/img/demo-volumeRendering.png" alt="Volume Rendering" width="350"/> | Volume Rendering  | [Demo](https://viewer.ohif.org/viewer?StudyInstanceUIDs=1.3.6.1.4.1.25403.345050719074.3824.20170125095438.5&hangingprotocolId=mprAnd3DVolumeViewport) |
-
-
+| <img src="https://github.com/OHIF/Viewers/blob/master/platform/docs/docs/assets/img/demo-measurements.webp?raw=true" alt="Measurement tracking" width="350"/> | Measurement Tracking | [Demo](https://viewer.ohif.org/viewer?StudyInstanceUIDs=1.3.6.1.4.1.25403.345050719074.3824.20170125095438.5) |
+| <img src="https://github.com/OHIF/Viewers/blob/master/platform/docs/docs/assets/img/demo-segmentation.webp?raw=true" alt="Segmentations" width="350"/> | Labelmap Segmentations  | [Demo](https://viewer.ohif.org/viewer?StudyInstanceUIDs=1.3.12.2.1107.5.2.32.35162.30000015050317233592200000046) |
+| <img src="https://github.com/OHIF/Viewers/blob/master/platform/docs/docs/assets/img/demo-ptct.webp?raw=true" alt="Hanging Protocols" width="350"/> | Fusion and Custom Hanging protocols  | [Demo](https://viewer.ohif.org/tmtv?StudyInstanceUIDs=1.3.6.1.4.1.14519.5.2.1.7009.2403.334240657131972136850343327463) |
+| <img src="https://github.com/OHIF/Viewers/blob/master/platform/docs/docs/assets/img/demo-volume-rendering.webp?raw=true" alt="Volume Rendering" width="350"/> | Volume Rendering  | [Demo](https://viewer.ohif.org/viewer?StudyInstanceUIDs=1.3.6.1.4.1.25403.345050719074.3824.20170125095438.5&hangingprotocolId=mprAnd3DVolumeViewport) |
+| <img src="https://github.com/OHIF/Viewers/blob/master/platform/docs/docs/assets/img/demo-pdf.webp?raw=true" alt="PDF" width="350"/> | PDF  | [Demo](https://viewer.ohif.org/viewer?StudyInstanceUIDs=2.25.317377619501274872606137091638706705333) |
+| <img src="https://github.com/OHIF/Viewers/blob/master/platform/docs/docs/assets/img/demo-rtstruct.webp?raw=true" alt="RTSTRUCT" width="350"/> | RT STRUCT  | [Demo](https://viewer.ohif.org/viewer?StudyInstanceUIDs=1.3.6.1.4.1.5962.99.1.2968617883.1314880426.1493322302363.3.0) |
+| <img src="https://github.com/OHIF/Viewers/blob/master/platform/docs/docs/assets/img/demo-4d.webp?raw=true" alt="4D" width="350"/> | 4D  | [Demo](https://viewer.ohif.org/dynamic-volume?StudyInstanceUIDs=2.25.232704420736447710317909004159492840763) |
+| <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 Medical Imaging Viewer is for viewing medical images. It can retrieve
+The OHIF Viewer 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,
@@ -112,19 +118,16 @@ 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` branch - The latest stable release
+### `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.
 
-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.
+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.
 
-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.
+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.
 
 Here is a schematic representation of our development workflow:
 
-![Alt text](platform/docs/docs/assets/img/github-readme-branches.png)
+![alt text](platform/docs/docs/assets/img/github-readme-branches-Jun2024.png)
 
 
 
@@ -133,7 +136,7 @@ Here is a schematic representation of our development workflow:
 ### Requirements
 
 - [Yarn 1.17.3+](https://yarnpkg.com/en/docs/install)
-- [Node 16+](https://nodejs.org/en/)
+- [Node 18+](https://nodejs.org/en/)
 - Yarn Workspaces should be enabled on your machine:
   - `yarn config set workspaces-experimental true`
 
@@ -173,7 +176,7 @@ also supports a number of commands that can be found in their respective
 | **Deploy**                   |                                                               |
 | `build`\*                    | Builds production output for our PWA Viewer                   |  |
 
-\* - For more information on our different builds, check out our [Deploy
+\* - For more information on different builds, check out our [Deploy
 Docs][deployment-docs]
 
 ## Project
@@ -330,4 +333,4 @@ MIT © [OHIF](https://github.com/OHIF)
 [vtk-npm]: https://www.npmjs.com/package/@ohif/extension-vtk
 <!-- prettier-ignore-end -->
 
-[![FOSSA Status](https://app.fossa.io/api/projects/git%2Bgithub.com%2FOHIF%2FViewers.svg?type=large)](https://app.fossa.io/projects/git%2Bgithub.com%2FOHIF%2FViewers?ref=badge_large)
+[![FOSSA Status](https://app.fossa.com/api/projects/git%2Bgithub.com%2FOHIF%2FViewers.svg?type=large&issueType=license)](https://app.fossa.com/projects/git%2Bgithub.com%2FOHIF%2FViewers?ref=badge_large&issueType=license)

addOns/README.md

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

addOns/externals/devDependencies/CHANGELOG.md

@@ -0,0 +1,846 @@
+# Change Log
+
+All notable changes to this project will be documented in this file.
+See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+# [3.10.0-beta.39](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.38...v3.10.0-beta.39) (2025-01-08)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.38](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.37...v3.10.0-beta.38) (2025-01-07)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.37](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.36...v3.10.0-beta.37) (2025-01-06)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.36](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.35...v3.10.0-beta.36) (2025-01-03)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.35](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.34...v3.10.0-beta.35) (2025-01-03)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.34](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.33...v3.10.0-beta.34) (2025-01-02)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.33](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.32...v3.10.0-beta.33) (2024-12-20)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.32](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.31...v3.10.0-beta.32) (2024-12-20)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.31](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.30...v3.10.0-beta.31) (2024-12-20)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.30](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.29...v3.10.0-beta.30) (2024-12-18)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.29](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.28...v3.10.0-beta.29) (2024-12-18)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.28](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.27...v3.10.0-beta.28) (2024-12-18)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.27](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.26...v3.10.0-beta.27) (2024-12-18)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.26](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.25...v3.10.0-beta.26) (2024-12-18)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.25](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.24...v3.10.0-beta.25) (2024-12-17)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.24](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.23...v3.10.0-beta.24) (2024-12-17)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.23](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.22...v3.10.0-beta.23) (2024-12-17)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.22](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.21...v3.10.0-beta.22) (2024-12-13)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.21](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.20...v3.10.0-beta.21) (2024-12-11)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.20](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.19...v3.10.0-beta.20) (2024-12-11)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.19](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.18...v3.10.0-beta.19) (2024-12-11)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.18](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.17...v3.10.0-beta.18) (2024-12-06)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.17](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.16...v3.10.0-beta.17) (2024-12-06)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.16](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.15...v3.10.0-beta.16) (2024-12-05)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.15](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.14...v3.10.0-beta.15) (2024-12-05)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.14](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.13...v3.10.0-beta.14) (2024-12-03)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.13](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.12...v3.10.0-beta.13) (2024-12-02)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.12](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.11...v3.10.0-beta.12) (2024-11-29)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.11](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.10...v3.10.0-beta.11) (2024-11-28)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.10](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.9...v3.10.0-beta.10) (2024-11-28)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.9](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.8...v3.10.0-beta.9) (2024-11-22)
+
+
+### Bug Fixes
+
+* **colorlut:** use the correct colorlut index and update vtk ([#4544](https://github.com/OHIF/Viewers/issues/4544)) ([b9c26e7](https://github.com/OHIF/Viewers/commit/b9c26e775a49044673473418dd5bdee2e5562ab9))
+
+
+
+
+
+# [3.10.0-beta.8](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.7...v3.10.0-beta.8) (2024-11-22)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.7](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.6...v3.10.0-beta.7) (2024-11-22)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.6](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.5...v3.10.0-beta.6) (2024-11-22)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.5](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.4...v3.10.0-beta.5) (2024-11-15)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.4](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.3...v3.10.0-beta.4) (2024-11-15)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.3](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.2...v3.10.0-beta.3) (2024-11-14)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.2](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.1...v3.10.0-beta.2) (2024-11-13)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.1](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.0...v3.10.0-beta.1) (2024-11-12)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.10.0-beta.0](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.111...v3.10.0-beta.0) (2024-11-12)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.111](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.110...v3.9.0-beta.111) (2024-11-12)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.110](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.109...v3.9.0-beta.110) (2024-11-11)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.109](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.108...v3.9.0-beta.109) (2024-11-08)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.108](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.107...v3.9.0-beta.108) (2024-11-07)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.107](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.106...v3.9.0-beta.107) (2024-11-06)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.106](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.105...v3.9.0-beta.106) (2024-11-06)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.105](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.104...v3.9.0-beta.105) (2024-11-05)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.104](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.103...v3.9.0-beta.104) (2024-10-30)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.103](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.102...v3.9.0-beta.103) (2024-10-29)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.102](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.101...v3.9.0-beta.102) (2024-10-29)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.101](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.100...v3.9.0-beta.101) (2024-10-18)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.100](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.99...v3.9.0-beta.100) (2024-10-17)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.99](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.98...v3.9.0-beta.99) (2024-10-17)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.98](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.97...v3.9.0-beta.98) (2024-10-15)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.97](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.96...v3.9.0-beta.97) (2024-10-11)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.96](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.95...v3.9.0-beta.96) (2024-10-10)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.95](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.94...v3.9.0-beta.95) (2024-10-08)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.94](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.93...v3.9.0-beta.94) (2024-10-04)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.93](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.92...v3.9.0-beta.93) (2024-10-04)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.92](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.91...v3.9.0-beta.92) (2024-10-01)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.91](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.90...v3.9.0-beta.91) (2024-10-01)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.90](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.89...v3.9.0-beta.90) (2024-09-30)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.89](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.88...v3.9.0-beta.89) (2024-09-27)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.88](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.87...v3.9.0-beta.88) (2024-09-24)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.87](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.86...v3.9.0-beta.87) (2024-09-19)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.86](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.85...v3.9.0-beta.86) (2024-09-19)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.85](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.84...v3.9.0-beta.85) (2024-09-17)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.84](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.83...v3.9.0-beta.84) (2024-09-12)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.83](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.82...v3.9.0-beta.83) (2024-09-11)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.82](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.81...v3.9.0-beta.82) (2024-09-05)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.81](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.80...v3.9.0-beta.81) (2024-08-27)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.80](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.79...v3.9.0-beta.80) (2024-08-16)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.79](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.78...v3.9.0-beta.79) (2024-08-16)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.78](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.77...v3.9.0-beta.78) (2024-08-15)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.77](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.76...v3.9.0-beta.77) (2024-08-15)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.76](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.75...v3.9.0-beta.76) (2024-08-08)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.75](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.74...v3.9.0-beta.75) (2024-08-07)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.74](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.73...v3.9.0-beta.74) (2024-08-06)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.73](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.72...v3.9.0-beta.73) (2024-08-02)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.72](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.71...v3.9.0-beta.72) (2024-07-31)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.71](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.70...v3.9.0-beta.71) (2024-07-30)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.70](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.69...v3.9.0-beta.70) (2024-07-30)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.69](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.68...v3.9.0-beta.69) (2024-07-27)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.68](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.67...v3.9.0-beta.68) (2024-07-26)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.67](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.66...v3.9.0-beta.67) (2024-07-26)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.66](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.65...v3.9.0-beta.66) (2024-07-24)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.65](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.64...v3.9.0-beta.65) (2024-07-23)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.64](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.63...v3.9.0-beta.64) (2024-07-19)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.63](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.62...v3.9.0-beta.63) (2024-07-10)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.62](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.61...v3.9.0-beta.62) (2024-07-09)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.61](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.60...v3.9.0-beta.61) (2024-07-09)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.60](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.59...v3.9.0-beta.60) (2024-07-09)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.59](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.58...v3.9.0-beta.59) (2024-07-05)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.58](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.57...v3.9.0-beta.58) (2024-07-04)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.57](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.56...v3.9.0-beta.57) (2024-07-02)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.56](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.55...v3.9.0-beta.56) (2024-07-02)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.55](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.54...v3.9.0-beta.55) (2024-06-28)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.54](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.53...v3.9.0-beta.54) (2024-06-28)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.53](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.52...v3.9.0-beta.53) (2024-06-28)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.52](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.51...v3.9.0-beta.52) (2024-06-27)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.51](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.50...v3.9.0-beta.51) (2024-06-27)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.50](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.49...v3.9.0-beta.50) (2024-06-26)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.49](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.48...v3.9.0-beta.49) (2024-06-26)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.48](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.47...v3.9.0-beta.48) (2024-06-25)
+
+**Note:** Version bump only for package @externals/devDependencies
+
+
+
+
+
+# [3.9.0-beta.47](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.46...v3.9.0-beta.47) (2024-06-21)
+
+
+### Bug Fixes
+
+* Allow the mode setup/creation to be async, and provide a few more values to extension/app config/mode setup. ([#4016](https://github.com/OHIF/Viewers/issues/4016)) ([88575c6](https://github.com/OHIF/Viewers/commit/88575c6c09fd778a31b2f91524163ce65d1639dd))

addOns/externals/devDependencies/package.json

@@ -0,0 +1,94 @@
+{
+  "name": "@externals/devDependencies",
+  "description": "External dev dependencies - put dev build dependencies here",
+  "version": "3.10.0-beta.39",
+  "license": "MIT",
+  "private": true,
+  "engines": {
+    "node": ">=12",
+    "yarn": ">=1.19.1"
+  },
+  "dependencies": {
+    "@babel/runtime": "^7.20.13",
+    "@kitware/vtk.js": "32.1.1",
+    "clsx": "^2.1.1",
+    "core-js": "^3.2.1",
+    "moment": "^2.9.4"
+  },
+  "peerDependencies": {
+    "react": "^18.3.1",
+    "react-dom": "^18.3.1"
+  },
+  "devDependencies": {
+    "@pmmmwh/react-refresh-webpack-plugin": "^0.5.15",
+    "@svgr/webpack": "^8.1.0",
+    "@types/jest": "^27.5.0",
+    "@typescript-eslint/eslint-plugin": "^6.3.0",
+    "@typescript-eslint/parser": "^6.3.0",
+    "autoprefixer": "^10.4.4",
+    "babel-eslint": "9.x",
+    "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": "^5.0.0",
+    "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": "^3.0.3",
+    "prettier-plugin-tailwindcss": "^0.5.4",
+    "react-refresh": "^0.14.2",
+    "semver": "^7.5.1",
+    "serve": "^14.2.0",
+    "shader-loader": "^1.3.1",
+    "shx": "^0.3.3",
+    "source-map-loader": "^4.0.1",
+    "start-server-and-test": "^1.10.0",
+    "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": "^4.7.2",
+    "webpack-dev-server": "4.7.3",
+    "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/CHANGELOG.md

@@ -0,0 +1,843 @@
+# Change Log
+
+All notable changes to this project will be documented in this file.
+See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+# [3.10.0-beta.39](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.38...v3.10.0-beta.39) (2025-01-08)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.38](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.37...v3.10.0-beta.38) (2025-01-07)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.37](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.36...v3.10.0-beta.37) (2025-01-06)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.36](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.35...v3.10.0-beta.36) (2025-01-03)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.35](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.34...v3.10.0-beta.35) (2025-01-03)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.34](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.33...v3.10.0-beta.34) (2025-01-02)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.33](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.32...v3.10.0-beta.33) (2024-12-20)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.32](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.31...v3.10.0-beta.32) (2024-12-20)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.31](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.30...v3.10.0-beta.31) (2024-12-20)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.30](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.29...v3.10.0-beta.30) (2024-12-18)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.29](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.28...v3.10.0-beta.29) (2024-12-18)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.28](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.27...v3.10.0-beta.28) (2024-12-18)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.27](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.26...v3.10.0-beta.27) (2024-12-18)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.26](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.25...v3.10.0-beta.26) (2024-12-18)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.25](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.24...v3.10.0-beta.25) (2024-12-17)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.24](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.23...v3.10.0-beta.24) (2024-12-17)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.23](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.22...v3.10.0-beta.23) (2024-12-17)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.22](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.21...v3.10.0-beta.22) (2024-12-13)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.21](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.20...v3.10.0-beta.21) (2024-12-11)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.20](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.19...v3.10.0-beta.20) (2024-12-11)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.19](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.18...v3.10.0-beta.19) (2024-12-11)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.18](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.17...v3.10.0-beta.18) (2024-12-06)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.17](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.16...v3.10.0-beta.17) (2024-12-06)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.16](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.15...v3.10.0-beta.16) (2024-12-05)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.15](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.14...v3.10.0-beta.15) (2024-12-05)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.14](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.13...v3.10.0-beta.14) (2024-12-03)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.13](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.12...v3.10.0-beta.13) (2024-12-02)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.12](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.11...v3.10.0-beta.12) (2024-11-29)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.11](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.10...v3.10.0-beta.11) (2024-11-28)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.10](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.9...v3.10.0-beta.10) (2024-11-28)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.9](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.8...v3.10.0-beta.9) (2024-11-22)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.8](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.7...v3.10.0-beta.8) (2024-11-22)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.7](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.6...v3.10.0-beta.7) (2024-11-22)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.6](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.5...v3.10.0-beta.6) (2024-11-22)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.5](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.4...v3.10.0-beta.5) (2024-11-15)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.4](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.3...v3.10.0-beta.4) (2024-11-15)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.3](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.2...v3.10.0-beta.3) (2024-11-14)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.2](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.1...v3.10.0-beta.2) (2024-11-13)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.1](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.0...v3.10.0-beta.1) (2024-11-12)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.10.0-beta.0](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.111...v3.10.0-beta.0) (2024-11-12)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.111](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.110...v3.9.0-beta.111) (2024-11-12)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.110](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.109...v3.9.0-beta.110) (2024-11-11)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.109](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.108...v3.9.0-beta.109) (2024-11-08)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.108](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.107...v3.9.0-beta.108) (2024-11-07)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.107](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.106...v3.9.0-beta.107) (2024-11-06)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.106](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.105...v3.9.0-beta.106) (2024-11-06)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.105](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.104...v3.9.0-beta.105) (2024-11-05)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.104](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.103...v3.9.0-beta.104) (2024-10-30)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.103](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.102...v3.9.0-beta.103) (2024-10-29)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.102](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.101...v3.9.0-beta.102) (2024-10-29)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.101](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.100...v3.9.0-beta.101) (2024-10-18)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.100](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.99...v3.9.0-beta.100) (2024-10-17)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.99](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.98...v3.9.0-beta.99) (2024-10-17)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.98](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.97...v3.9.0-beta.98) (2024-10-15)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.97](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.96...v3.9.0-beta.97) (2024-10-11)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.96](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.95...v3.9.0-beta.96) (2024-10-10)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.95](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.94...v3.9.0-beta.95) (2024-10-08)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.94](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.93...v3.9.0-beta.94) (2024-10-04)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.93](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.92...v3.9.0-beta.93) (2024-10-04)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.92](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.91...v3.9.0-beta.92) (2024-10-01)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.91](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.90...v3.9.0-beta.91) (2024-10-01)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.90](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.89...v3.9.0-beta.90) (2024-09-30)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.89](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.88...v3.9.0-beta.89) (2024-09-27)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.88](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.87...v3.9.0-beta.88) (2024-09-24)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.87](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.86...v3.9.0-beta.87) (2024-09-19)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.86](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.85...v3.9.0-beta.86) (2024-09-19)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.85](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.84...v3.9.0-beta.85) (2024-09-17)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.84](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.83...v3.9.0-beta.84) (2024-09-12)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.83](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.82...v3.9.0-beta.83) (2024-09-11)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.82](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.81...v3.9.0-beta.82) (2024-09-05)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.81](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.80...v3.9.0-beta.81) (2024-08-27)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.80](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.79...v3.9.0-beta.80) (2024-08-16)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.79](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.78...v3.9.0-beta.79) (2024-08-16)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.78](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.77...v3.9.0-beta.78) (2024-08-15)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.77](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.76...v3.9.0-beta.77) (2024-08-15)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.76](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.75...v3.9.0-beta.76) (2024-08-08)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.75](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.74...v3.9.0-beta.75) (2024-08-07)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.74](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.73...v3.9.0-beta.74) (2024-08-06)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.73](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.72...v3.9.0-beta.73) (2024-08-02)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.72](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.71...v3.9.0-beta.72) (2024-07-31)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.71](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.70...v3.9.0-beta.71) (2024-07-30)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.70](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.69...v3.9.0-beta.70) (2024-07-30)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.69](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.68...v3.9.0-beta.69) (2024-07-27)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.68](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.67...v3.9.0-beta.68) (2024-07-26)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.67](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.66...v3.9.0-beta.67) (2024-07-26)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.66](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.65...v3.9.0-beta.66) (2024-07-24)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.65](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.64...v3.9.0-beta.65) (2024-07-23)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.64](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.63...v3.9.0-beta.64) (2024-07-19)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.63](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.62...v3.9.0-beta.63) (2024-07-10)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.62](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.61...v3.9.0-beta.62) (2024-07-09)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.61](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.60...v3.9.0-beta.61) (2024-07-09)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.60](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.59...v3.9.0-beta.60) (2024-07-09)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.59](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.58...v3.9.0-beta.59) (2024-07-05)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.58](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.57...v3.9.0-beta.58) (2024-07-04)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.57](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.56...v3.9.0-beta.57) (2024-07-02)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.56](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.55...v3.9.0-beta.56) (2024-07-02)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.55](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.54...v3.9.0-beta.55) (2024-06-28)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.54](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.53...v3.9.0-beta.54) (2024-06-28)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.53](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.52...v3.9.0-beta.53) (2024-06-28)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.52](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.51...v3.9.0-beta.52) (2024-06-27)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.51](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.50...v3.9.0-beta.51) (2024-06-27)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.50](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.49...v3.9.0-beta.50) (2024-06-26)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.49](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.48...v3.9.0-beta.49) (2024-06-26)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.48](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.47...v3.9.0-beta.48) (2024-06-25)
+
+**Note:** Version bump only for package @externals/dicom-microscopy-viewer
+
+
+
+
+
+# [3.9.0-beta.47](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.46...v3.9.0-beta.47) (2024-06-21)
+
+
+### Bug Fixes
+
+* Allow the mode setup/creation to be async, and provide a few more values to extension/app config/mode setup. ([#4016](https://github.com/OHIF/Viewers/issues/4016)) ([88575c6](https://github.com/OHIF/Viewers/commit/88575c6c09fd778a31b2f91524163ce65d1639dd))

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

@@ -0,0 +1,9 @@
+{
+  "name": "@externals/dicom-microscopy-viewer",
+  "description": "External reference to dicom-microscopy-viewer",
+  "version": "3.10.0-beta.39",
+  "license": "MIT",
+  "dependencies": {
+    "dicom-microscopy-viewer": "^0.46.1"
+  }
+}

addOns/package.json

@@ -0,0 +1,51 @@
+{
+  "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": "7.24.7",
+    "@babel/plugin-proposal-class-properties": "^7.16.7",
+    "@babel/plugin-proposal-object-rest-spread": "^7.17.3",
+    "@babel/plugin-proposal-private-methods": "^7.18.6",
+    "@babel/plugin-proposal-private-property-in-object": "^7.21.11",
+    "@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": "7.24.7",
+    "@babel/plugin-transform-typescript": "^7.13.0",
+    "@babel/preset-env": "7.24.7",
+    "@babel/preset-react": "^7.16.7",
+    "@babel/preset-typescript": "^7.13.0"
+  },
+  "resolutions": {
+    "**/@babel/runtime": "^7.20.13",
+    "commander": "8.3.0",
+    "dcmjs": ">=0.33.0",
+    "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

@@ -5,27 +5,11 @@ module.exports = {
   babelrcRoots: ['./platform/*', './extensions/*', './modes/*'],
   presets: ['@babel/preset-env', '@babel/preset-react', '@babel/preset-typescript'],
   plugins: [
-    [
-      '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-proposal-private-property-in-object', { loose: true }],
     ['@babel/plugin-proposal-private-methods', { loose: true }],
+    '@babel/plugin-transform-class-static-block',
   ],
   env: {
     test: {
@@ -45,8 +29,10 @@ module.exports = {
         '@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',
       ],
     },
     production: {
@@ -65,7 +51,7 @@ module.exports = {
         '@babel/preset-react',
         '@babel/preset-typescript',
       ],
-      plugins: ['react-hot-loader/babel'],
+      plugins: ['react-refresh/babel'],
       ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
     },
   },

commit.txt

@@ -1 +1 @@
-3ce72254b390f32c9aa207a0589e688805e2659d
+836e67a6ab8de66d8908c75856774318729544f4

extensions/_example/src/index.js

@@ -1,134 +0,0 @@
-import ImageSet from '@ohif/core/src/classes/ImageSet';
-import { IWebApiDataSource } from '@ohif/core';
-
-/**
- *
- */
-export default {
-  id: '@ohif/extension-*',
-
-  /**
-   * LIFECYCLE HOOKS
-   */
-  preRegistration() {},
-  beforeExtInit() {},
-  beforeExtDestroy() {},
-
-  /**
-   * MODULES
-   */
-  getCommandsModule,
-  getContextModule,
-  getDataSourcesModule,
-  getLayoutTemplateModule,
-  getPanelModule,
-  getSopClassHandlerModule,
-  getToolbarModule() {},
-  getViewportModule,
-};
-
-// appConfig,
-// extensionConfig,
-// dataSources,
-// servicesManager,
-// extensionManager,
-// commandsManager,
-
-/**
- *
- */
-const getCommandsModule = () => ({
-  definitions: {
-    exampleActionDef: {
-      commandFn: ({ param1 }) => {
-        console.log(`param1's value is: ${param1}`);
-      },
-      // storeContexts: ['viewports'],
-      options: { param1: 'hello world' },
-      context: 'VIEWER', // optional
-    },
-  },
-  defaultContext: 'ACTIVE_VIEWPORT::DICOMSR',
-});
-
-const ExampleContext = React.createContext();
-
-function ExampleContextProvider({ children }) {
-  return <ExampleContext.Provider value={{ example: 'value' }}>{children}</ExampleContext.Provider>;
-}
-
-const getContextModule = () => [
-  {
-    name: 'ExampleContext',
-    context: ExampleContext,
-    provider: ExampleContextProvider,
-  },
-];
-
-const getDataSourcesModule = () => [
-  {
-    name: 'exampleDataSource',
-    type: 'webApi', // 'webApi' | 'local' | 'other'
-    createDataSource: dataSourceConfig => {
-      return IWebApiDataSource.create(/* */);
-    },
-  },
-];
-
-const getLayoutTemplateModule = (/* ... */) => [
-  {
-    id: 'exampleLayout',
-    name: 'exampleLayout',
-    component: ExampleLayoutComponent,
-  },
-];
-
-const getPanelModule = () => {
-  return [
-    {
-      name: 'exampleSidePanel',
-      iconName: 'info-circle-o',
-      iconLabel: 'Example',
-      label: 'Hello World',
-      isDisabled: studies => {}, // optional
-      component: ExamplePanelContentComponent,
-    },
-  ];
-};
-
-const getSopClassHandlerModule = (/* ... */) => {
-  const BASIC_TEXT_SR = '1.2.840.10008.5.1.4.1.1.88.11';
-
-  return [
-    {
-      name: 'ExampleSopClassHandle',
-      sopClassUids: [BASIC_TEXT_SR],
-      getDisplaySetsFromSeries: instances => {
-        const imageSet = new ImageSet(instances);
-
-        imageSet.setAttributes(/** */);
-        imageSet.sortBy((a, b) => 0);
-
-        return imageSet;
-      },
-    },
-  ];
-};
-
-const getToolbarModule = () => {};
-
-// displaySet, dataSource
-const getViewportModule = () => {
-  const wrappedViewport = props => {
-    return (
-      <ExampleViewport
-        {...props}
-        onEvent={data => {
-          commandsManager.runCommand('commandName', data);
-        }}
-      />
-    );
-  };
-
-  return [{ name: 'example', component: wrappedViewport }];
-};

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

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

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

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

extensions/cornerstone-dicom-pmap/CHANGELOG.md

@@ -0,0 +1,727 @@
+# Change Log
+
+All notable changes to this project will be documented in this file.
+See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+# [3.10.0-beta.39](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.38...v3.10.0-beta.39) (2025-01-08)
+
+
+### Bug Fixes
+
+* **docker:** publish manifest for multiarch and update cs3d ([#4650](https://github.com/OHIF/Viewers/issues/4650)) ([836e67a](https://github.com/OHIF/Viewers/commit/836e67a6ab8de66d8908c75856774318729544f4))
+
+
+
+
+
+# [3.10.0-beta.38](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.37...v3.10.0-beta.38) (2025-01-07)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.37](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.36...v3.10.0-beta.37) (2025-01-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.36](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.35...v3.10.0-beta.36) (2025-01-03)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.35](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.34...v3.10.0-beta.35) (2025-01-03)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.34](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.33...v3.10.0-beta.34) (2025-01-02)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.33](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.32...v3.10.0-beta.33) (2024-12-20)
+
+
+### Bug Fixes
+
+* **tools:** enable additional tools in volume viewport ([#4620](https://github.com/OHIF/Viewers/issues/4620)) ([1992002](https://github.com/OHIF/Viewers/commit/1992002d2dced171c17b9a0163baf707fc551e3d))
+
+
+
+
+
+# [3.10.0-beta.32](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.31...v3.10.0-beta.32) (2024-12-20)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.31](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.30...v3.10.0-beta.31) (2024-12-20)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.30](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.29...v3.10.0-beta.30) (2024-12-18)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.29](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.28...v3.10.0-beta.29) (2024-12-18)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.28](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.27...v3.10.0-beta.28) (2024-12-18)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.27](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.26...v3.10.0-beta.27) (2024-12-18)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.26](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.25...v3.10.0-beta.26) (2024-12-18)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.25](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.24...v3.10.0-beta.25) (2024-12-17)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.24](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.23...v3.10.0-beta.24) (2024-12-17)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.23](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.22...v3.10.0-beta.23) (2024-12-17)
+
+
+### Bug Fixes
+
+* **seg:** jump to the first slice in SEG and RT that has data ([#4605](https://github.com/OHIF/Viewers/issues/4605)) ([9bf24d6](https://github.com/OHIF/Viewers/commit/9bf24d6dc58ed8f65c90899a17c11044b792cf40))
+
+
+
+
+
+# [3.10.0-beta.22](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.21...v3.10.0-beta.22) (2024-12-13)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.21](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.20...v3.10.0-beta.21) (2024-12-11)
+
+
+### Features
+
+* **node:** move to node 20 ([#4594](https://github.com/OHIF/Viewers/issues/4594)) ([1f04d6c](https://github.com/OHIF/Viewers/commit/1f04d6c1be729a26fe7bcda923770a1cd461053c))
+
+
+
+
+
+# [3.10.0-beta.20](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.19...v3.10.0-beta.20) (2024-12-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.19](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.18...v3.10.0-beta.19) (2024-12-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.18](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.17...v3.10.0-beta.18) (2024-12-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.17](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.16...v3.10.0-beta.17) (2024-12-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.16](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.15...v3.10.0-beta.16) (2024-12-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.15](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.14...v3.10.0-beta.15) (2024-12-05)
+
+
+### Bug Fixes
+
+* **CinePlayer:** always show cine player for dynamic data ([#4575](https://github.com/OHIF/Viewers/issues/4575)) ([b8e8bbe](https://github.com/OHIF/Viewers/commit/b8e8bbe482b66e8cbe9167d03e9d8dedd2d3b6c5))
+
+
+
+
+
+# [3.10.0-beta.14](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.13...v3.10.0-beta.14) (2024-12-03)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.13](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.12...v3.10.0-beta.13) (2024-12-02)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.12](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.11...v3.10.0-beta.12) (2024-11-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.11](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.10...v3.10.0-beta.11) (2024-11-28)
+
+
+### Bug Fixes
+
+* **multiframe:** metadata handling of NM studies and loading order  ([#4554](https://github.com/OHIF/Viewers/issues/4554)) ([7624ccb](https://github.com/OHIF/Viewers/commit/7624ccb5e495c0a151227a458d8d5bfb8babb22c))
+
+
+
+
+
+# [3.10.0-beta.10](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.9...v3.10.0-beta.10) (2024-11-28)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.9](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.8...v3.10.0-beta.9) (2024-11-22)
+
+
+### Bug Fixes
+
+* **colorlut:** use the correct colorlut index and update vtk ([#4544](https://github.com/OHIF/Viewers/issues/4544)) ([b9c26e7](https://github.com/OHIF/Viewers/commit/b9c26e775a49044673473418dd5bdee2e5562ab9))
+
+
+
+
+
+# [3.10.0-beta.8](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.7...v3.10.0-beta.8) (2024-11-22)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.7](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.6...v3.10.0-beta.7) (2024-11-22)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.6](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.5...v3.10.0-beta.6) (2024-11-22)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.5](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.4...v3.10.0-beta.5) (2024-11-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.4](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.3...v3.10.0-beta.4) (2024-11-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.3](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.2...v3.10.0-beta.3) (2024-11-14)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.2](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.1...v3.10.0-beta.2) (2024-11-13)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.1](https://github.com/OHIF/Viewers/compare/v3.10.0-beta.0...v3.10.0-beta.1) (2024-11-12)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.10.0-beta.0](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.111...v3.10.0-beta.0) (2024-11-12)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.111](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.110...v3.9.0-beta.111) (2024-11-12)
+
+
+### Bug Fixes
+
+* Measurement Tracking: Various UI and functionality improvements ([#4481](https://github.com/OHIF/Viewers/issues/4481)) ([62b2748](https://github.com/OHIF/Viewers/commit/62b27488471c9d5979142e2d15872a85778b90ed))
+
+
+
+
+
+# [3.9.0-beta.110](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.109...v3.9.0-beta.110) (2024-11-11)
+
+
+### Bug Fixes
+
+* **bugs:** Update dependencies and enhance UI components ([#4478](https://github.com/OHIF/Viewers/issues/4478)) ([05d41c5](https://github.com/OHIF/Viewers/commit/05d41c52068a3b7ba249f15ecdf71838c352fd30))
+
+
+
+
+
+# [3.9.0-beta.109](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.108...v3.9.0-beta.109) (2024-11-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.108](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.107...v3.9.0-beta.108) (2024-11-07)
+
+
+### Bug Fixes
+
+* **tmtv:** fix toggle one up weird behaviours ([#4473](https://github.com/OHIF/Viewers/issues/4473)) ([aa2b649](https://github.com/OHIF/Viewers/commit/aa2b649444eb4fe5422e72ea7830a709c4d24a90))
+
+
+
+
+
+# [3.9.0-beta.107](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.106...v3.9.0-beta.107) (2024-11-06)
+
+
+### Bug Fixes
+
+* build ([#4471](https://github.com/OHIF/Viewers/issues/4471)) ([3d11ef2](https://github.com/OHIF/Viewers/commit/3d11ef28f213361ec7586809317bd219fa70e742))
+
+
+
+
+
+# [3.9.0-beta.106](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.105...v3.9.0-beta.106) (2024-11-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.105](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.104...v3.9.0-beta.105) (2024-11-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.104](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.103...v3.9.0-beta.104) (2024-10-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.103](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.102...v3.9.0-beta.103) (2024-10-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.102](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.101...v3.9.0-beta.102) (2024-10-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.101](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.100...v3.9.0-beta.101) (2024-10-18)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.100](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.99...v3.9.0-beta.100) (2024-10-17)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.99](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.98...v3.9.0-beta.99) (2024-10-17)
+
+
+### Features
+
+* **SR:** SCOORD3D point annotations support for stack viewports ([#4315](https://github.com/OHIF/Viewers/issues/4315)) ([ac1cad2](https://github.com/OHIF/Viewers/commit/ac1cad25af12ee0f7d508647e3134ed724d9b4d3))
+
+
+
+
+
+# [3.9.0-beta.98](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.97...v3.9.0-beta.98) (2024-10-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.97](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.96...v3.9.0-beta.97) (2024-10-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.96](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.95...v3.9.0-beta.96) (2024-10-10)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.95](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.94...v3.9.0-beta.95) (2024-10-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.94](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.93...v3.9.0-beta.94) (2024-10-04)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.93](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.92...v3.9.0-beta.93) (2024-10-04)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.92](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.91...v3.9.0-beta.92) (2024-10-01)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.91](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.90...v3.9.0-beta.91) (2024-10-01)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.90](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.89...v3.9.0-beta.90) (2024-09-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.89](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.88...v3.9.0-beta.89) (2024-09-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.88](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.87...v3.9.0-beta.88) (2024-09-24)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.87](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.86...v3.9.0-beta.87) (2024-09-19)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.86](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.85...v3.9.0-beta.86) (2024-09-19)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.85](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.84...v3.9.0-beta.85) (2024-09-17)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.84](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.83...v3.9.0-beta.84) (2024-09-12)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.83](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.82...v3.9.0-beta.83) (2024-09-11)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.82](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.81...v3.9.0-beta.82) (2024-09-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.81](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.80...v3.9.0-beta.81) (2024-08-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.80](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.79...v3.9.0-beta.80) (2024-08-16)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.79](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.78...v3.9.0-beta.79) (2024-08-16)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.78](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.77...v3.9.0-beta.78) (2024-08-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.77](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.76...v3.9.0-beta.77) (2024-08-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.76](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.75...v3.9.0-beta.76) (2024-08-08)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.75](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.74...v3.9.0-beta.75) (2024-08-07)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.74](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.73...v3.9.0-beta.74) (2024-08-06)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.73](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.72...v3.9.0-beta.73) (2024-08-02)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.72](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.71...v3.9.0-beta.72) (2024-07-31)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.71](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.70...v3.9.0-beta.71) (2024-07-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.70](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.69...v3.9.0-beta.70) (2024-07-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.69](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.68...v3.9.0-beta.69) (2024-07-27)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.68](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.67...v3.9.0-beta.68) (2024-07-26)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.67](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.66...v3.9.0-beta.67) (2024-07-26)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone-dicom-pmap
+
+
+
+
+
+# [3.9.0-beta.66](https://github.com/OHIF/Viewers/compare/v3.9.0-beta.65...v3.9.0-beta.66) (2024-07-24)
+
+
+### Features
+
+* **pmap:** added support for parametric map ([#4284](https://github.com/OHIF/Viewers/issues/4284)) ([fc0064f](https://github.com/OHIF/Viewers/commit/fc0064fd9d8cdc8fde81b81f0e71fd5d077ca22b))

extensions/cornerstone-dicom-pmap/LICENSE

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

extensions/cornerstone-dicom-pmap/README.md

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

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

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

extensions/cornerstone-dicom-pmap/package.json

@@ -0,0 +1,54 @@
+{
+  "name": "@ohif/extension-cornerstone-dicom-pmap",
+  "version": "3.10.0-beta.39",
+  "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": "3.10.0-beta.39",
+    "@ohif/extension-cornerstone": "3.10.0-beta.39",
+    "@ohif/extension-default": "3.10.0-beta.39",
+    "@ohif/i18n": "3.10.0-beta.39",
+    "prop-types": "^15.6.2",
+    "react": "^18.3.1",
+    "react-dom": "^18.3.1",
+    "react-i18next": "^12.2.2",
+    "react-router": "^6.8.1",
+    "react-router-dom": "^6.8.1"
+  },
+  "dependencies": {
+    "@babel/runtime": "^7.20.13",
+    "@cornerstonejs/adapters": "^2.14.7",
+    "@cornerstonejs/core": "^2.14.7",
+    "@kitware/vtk.js": "32.1.1",
+    "react-color": "^2.19.3"
+  }
+}

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

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

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

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

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

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

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

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

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

@@ -1,5 +1,5 @@
 module.exports = {
-  plugins: ['inline-react-svg', '@babel/plugin-proposal-class-properties'],
+  plugins: ['@babel/plugin-proposal-class-properties'],
   env: {
     test: {
       presets: [
@@ -37,7 +37,7 @@ module.exports = {
         '@babel/preset-react',
         '@babel/preset-typescript',
       ],
-      plugins: ['react-hot-loader/babel'],
+      plugins: ['react-refresh/babel'],
       ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
     },
   },

extensions/cornerstone-dicom-rt/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone-dicom-rt",
-  "version": "3.7.0-beta.64",
+  "version": "3.10.0-beta.39",
   "description": "DICOM RT read workflow",
   "author": "OHIF",
   "license": "MIT",
@@ -24,6 +24,8 @@
     "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-seg": "yarn run dev",
     "build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
@@ -31,16 +33,16 @@
     "start": "yarn run dev"
   },
   "peerDependencies": {
-    "@ohif/core": "3.7.0-beta.64",
-    "@ohif/extension-cornerstone": "3.7.0-beta.64",
-    "@ohif/extension-default": "3.7.0-beta.64",
-    "@ohif/i18n": "3.7.0-beta.64",
+    "@ohif/core": "3.10.0-beta.39",
+    "@ohif/extension-cornerstone": "3.10.0-beta.39",
+    "@ohif/extension-default": "3.10.0-beta.39",
+    "@ohif/i18n": "3.10.0-beta.39",
     "prop-types": "^15.6.2",
-    "react": "^17.0.2",
-    "react-dom": "^17.0.2",
+    "react": "^18.3.1",
+    "react-dom": "^18.3.1",
     "react-i18next": "^10.11.0",
-    "react-router": "^6.3.0",
-    "react-router-dom": "^6.3.0"
+    "react-router": "^6.23.1",
+    "react-router-dom": "^6.23.1"
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",

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

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

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

@@ -5,9 +5,13 @@ import loadRTStruct from './loadRTStruct';
 
 const sopClassUids = ['1.2.840.10008.5.1.4.1.1.481.3'];
 
-let loadPromises = {};
+const loadPromises = {};
 
-function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager) {
+function _getDisplaySetsFromSeries(
+  instances,
+  servicesManager: AppTypes.ServicesManager,
+  extensionManager
+) {
   const instance = instances[0];
 
   const {
@@ -68,29 +72,34 @@ function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager)
   displaySet.referencedImages = instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
   displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID;
 
-  displaySet.getReferenceDisplaySet = () => {
-    const { DisplaySetService } = servicesManager.services;
-    const referencedDisplaySets = DisplaySetService.getDisplaySetsForSeries(
-      displaySet.referencedSeriesInstanceUID
+  const { displaySetService } = servicesManager.services;
+  const referencedDisplaySets = displaySetService.getDisplaySetsForSeries(
+    displaySet.referencedSeriesInstanceUID
+  );
+
+  if (!referencedDisplaySets || referencedDisplaySets.length === 0) {
+    // Instead of throwing error, subscribe to display sets added
+    const { unsubscribe } = displaySetService.subscribe(
+      displaySetService.EVENTS.DISPLAY_SETS_ADDED,
+      ({ displaySetsAdded }) => {
+        const addedDisplaySet = displaySetsAdded[0];
+        if (addedDisplaySet.SeriesInstanceUID === displaySet.referencedSeriesInstanceUID) {
+          displaySet.referencedDisplaySetInstanceUID = addedDisplaySet.displaySetInstanceUID;
+          unsubscribe();
+        }
+      }
     );
-
-    if (!referencedDisplaySets || referencedDisplaySets.length === 0) {
-      throw new Error('Referenced DisplaySet is missing for the RT');
-    }
-
+  } else {
     const referencedDisplaySet = referencedDisplaySets[0];
-
     displaySet.referencedDisplaySetInstanceUID = referencedDisplaySet.displaySetInstanceUID;
-
-    return referencedDisplaySet;
-  };
+  }
 
   displaySet.load = ({ headers }) => _load(displaySet, servicesManager, extensionManager, headers);
 
   return [displaySet];
 }
 
-function _load(rtDisplaySet, servicesManager, extensionManager, headers) {
+function _load(rtDisplaySet, servicesManager: AppTypes.ServicesManager, extensionManager, headers) {
   const { SOPInstanceUID } = rtDisplaySet;
   const { segmentationService } = servicesManager.services;
   if (
@@ -107,19 +116,13 @@ function _load(rtDisplaySet, servicesManager, extensionManager, headers) {
   // and also return the same promise to any other callers.
   loadPromises[SOPInstanceUID] = new Promise(async (resolve, reject) => {
     if (!rtDisplaySet.structureSet) {
-      const structureSet = await loadRTStruct(
-        extensionManager,
-        rtDisplaySet,
-        rtDisplaySet.getReferenceDisplaySet(),
-        headers
-      );
+      const structureSet = await loadRTStruct(extensionManager, rtDisplaySet, headers);
 
       rtDisplaySet.structureSet = structureSet;
     }
 
-    const suppressEvents = true;
     segmentationService
-      .createSegmentationForRTDisplaySet(rtDisplaySet, null, suppressEvents)
+      .createSegmentationForRTDisplaySet(rtDisplaySet)
       .then(() => {
         rtDisplaySet.loading = false;
         resolve();
@@ -168,7 +171,10 @@ function _deriveReferencedSeriesSequenceFromFrameOfReferenceSequence(
   return ReferencedSeriesSequence;
 }
 
-function _segmentationExistsInCache(rtDisplaySet, segmentationService) {
+function _segmentationExistsInCache(
+  rtDisplaySet,
+  segmentationService: AppTypes.SegmentationService
+) {
   // Todo: fix this
   return false;
   // This should be abstracted with the CornerstoneCacheService

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

@@ -2,7 +2,7 @@ import { id } from './id';
 import React from 'react';
 import { Types } from '@ohif/core';
 import getSopClassHandlerModule from './getSopClassHandlerModule';
-import hydrateRTDisplaySet from './utils/_hydrateRT';
+import getCommandsModule from './getCommandsModule';
 
 const Component = React.lazy(() => {
   return import(/* webpackPrefetch: true */ './viewports/OHIFCornerstoneRTViewport');
@@ -25,6 +25,7 @@ const extension: Types.Extensions.Extension = {
    * You ID can be anything you want, but it should be unique.
    */
   id,
+  getCommandsModule,
 
   /**
    * PanelModule should provide a list of panels that will be available in OHIF
@@ -60,4 +61,3 @@ const extension: Types.Extensions.Extension = {
 };
 
 export default extension;
-export { hydrateRTDisplaySet };

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

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

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

@@ -1,70 +0,0 @@
-async function _hydrateRTDisplaySet({ rtDisplaySet, viewportId, servicesManager }) {
-  const { segmentationService, hangingProtocolService, viewportGridService } =
-    servicesManager.services;
-
-  const displaySetInstanceUID = rtDisplaySet.referencedDisplaySetInstanceUID;
-
-  let segmentationId = null;
-
-  // We need the hydration to notify panels about the new segmentation added
-  const suppressEvents = false;
-
-  segmentationId = await segmentationService.createSegmentationForRTDisplaySet(
-    rtDisplaySet,
-    segmentationId,
-    suppressEvents
-  );
-
-  segmentationService.hydrateSegmentation(rtDisplaySet.displaySetInstanceUID);
-
-  const { viewports } = viewportGridService.getState();
-
-  const updatedViewports = hangingProtocolService.getViewportsRequireUpdate(
-    viewportId,
-    displaySetInstanceUID
-  );
-
-  viewportGridService.setDisplaySetsForViewports(updatedViewports);
-
-  // Todo: fix this after we have a better way for stack viewport segmentations
-
-  // check every viewport in the viewports to see if the displaySetInstanceUID
-  // is being displayed, if so we need to update the viewport to use volume viewport
-  // (if already is not using it) since Cornerstone3D currently only supports
-  // volume viewport for segmentation
-  viewports.forEach(viewport => {
-    if (viewport.viewportId === viewportId) {
-      return;
-    }
-
-    const shouldDisplaySeg = segmentationService.shouldRenderSegmentation(
-      viewport.displaySetInstanceUIDs,
-      rtDisplaySet.displaySetInstanceUID
-    );
-
-    if (shouldDisplaySeg) {
-      updatedViewports.push({
-        viewportId: viewport.viewportId,
-        displaySetInstanceUIDs: viewport.displaySetInstanceUIDs,
-        viewportOptions: {
-          // Note: This is a hack to get the grid to re-render the OHIFCornerstoneViewport component
-          // Used for segmentation hydration right now, since the logic to decide whether
-          // a viewport needs to render a segmentation lives inside the CornerstoneViewportService
-          // so we need to re-render (force update via change of the needsRerendering) so that React
-          // does the diffing and decides we should render this again (although the id and element has not changed)
-          // so that the CornerstoneViewportService can decide whether to render the segmentation or not.
-          needsRerendering: true,
-          initialImageOptions: {
-            preset: 'middle',
-          },
-        },
-      });
-    }
-  });
-
-  // Do the entire update at once
-  viewportGridService.setDisplaySetsForViewports(updatedViewports);
-  return true;
-}
-
-export default _hydrateRTDisplaySet;

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

@@ -1,7 +1,7 @@
 function createRTToolGroupAndAddTools(ToolGroupService, customizationService, toolGroupId) {
   const { tools } = customizationService.get('cornerstone.overlayViewportTools') ?? {};
 
-  return ToolGroupService.createToolGroupAndAddTools(toolGroupId, tools, {});
+  return ToolGroupService.createToolGroupAndAddTools(toolGroupId, tools);
 }
 
 export default createRTToolGroupAndAddTools;

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

@@ -1,5 +1,4 @@
 import { ButtonEnums } from '@ohif/ui';
-import hydrateRTDisplaySet from './_hydrateRT';
 
 const RESPONSE = {
   NO_NEVER: -1,
@@ -11,13 +10,16 @@ function promptHydrateRT({
   servicesManager,
   rtDisplaySet,
   viewportId,
-  toolGroupId = 'default',
   preHydrateCallbacks,
-}) {
+  hydrateRTDisplaySet,
+}: withAppTypes) {
   const { uiViewportDialogService } = servicesManager.services;
-
+  const extensionManager = servicesManager._extensionManager;
+  const appConfig = extensionManager._appConfig;
   return new Promise(async function (resolve, reject) {
-    const promptResult = await _askHydrate(uiViewportDialogService, viewportId);
+    const promptResult = appConfig?.disableConfirmationPrompts
+      ? RESPONSE.HYDRATE_SEG
+      : await _askHydrate(uiViewportDialogService, viewportId);
 
     if (promptResult === RESPONSE.HYDRATE_SEG) {
       preHydrateCallbacks?.forEach(callback => {
@@ -27,7 +29,6 @@ function promptHydrateRT({
       const isHydrated = await hydrateRTDisplaySet({
         rtDisplaySet,
         viewportId,
-        toolGroupId,
         servicesManager,
       });
 
@@ -36,16 +37,18 @@ function promptHydrateRT({
   });
 }
 
-function _askHydrate(uiViewportDialogService, viewportId) {
+function _askHydrate(uiViewportDialogService: AppTypes.UIViewportDialogService, viewportId) {
   return new Promise(function (resolve, reject) {
     const message = 'Do you want to open this Segmentation?';
     const actions = [
       {
+        id: 'no-hydrate',
         type: ButtonEnums.type.secondary,
         text: 'No',
         value: RESPONSE.CANCEL,
       },
       {
+        id: 'yes-hydrate',
         type: ButtonEnums.type.primary,
         text: 'Yes',
         value: RESPONSE.HYDRATE_SEG,
@@ -57,6 +60,7 @@ function _askHydrate(uiViewportDialogService, viewportId) {
     };
 
     uiViewportDialogService.show({
+      id: 'promptHydrateRT',
       viewportId,
       type: 'info',
       message,
@@ -66,6 +70,11 @@ function _askHydrate(uiViewportDialogService, viewportId) {
         uiViewportDialogService.hide();
         resolve(RESPONSE.CANCEL);
       },
+      onKeyPress: event => {
+        if (event.key === 'Enter') {
+          onSubmit(RESPONSE.HYDRATE_SEG);
+        }
+      },
     });
   });
 }

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

@@ -1,23 +1,20 @@
 import React, { useCallback, useEffect, useRef, useState } from 'react';
 import PropTypes from 'prop-types';
-import OHIF, { utils } from '@ohif/core';
-import { ViewportActionBar, useViewportGrid, LoadingIndicatorTotalPercent } from '@ohif/ui';
+import { useViewportGrid, LoadingIndicatorTotalPercent, ViewportActionArrows } from '@ohif/ui';
 
-import _hydrateRTdisplaySet from '../utils/_hydrateRT';
 import promptHydrateRT from '../utils/promptHydrateRT';
 import _getStatusComponent from './_getStatusComponent';
-import createRTToolGroupAndAddTools from '../utils/initRTToolGroup';
-import _hydrateRTDisplaySet from '../utils/_hydrateRT';
 
-const { formatDate } = utils;
+import createRTToolGroupAndAddTools from '../utils/initRTToolGroup';
+import { usePositionPresentationStore } from '@ohif/extension-cornerstone';
+
 const RT_TOOLGROUP_BASE_NAME = 'RTToolGroup';
 
-function OHIFCornerstoneRTViewport(props) {
+function OHIFCornerstoneRTViewport(props: withAppTypes) {
   const {
     children,
     displaySets,
     viewportOptions,
-    viewportLabel,
     servicesManager,
     extensionManager,
     commandsManager,
@@ -29,6 +26,7 @@ function OHIFCornerstoneRTViewport(props) {
     segmentationService,
     uiNotificationService,
     customizationService,
+    viewportActionCornersService,
   } = servicesManager.services;
 
   const viewportId = viewportOptions.viewportId;
@@ -45,8 +43,8 @@ function OHIFCornerstoneRTViewport(props) {
   const [viewportGrid, viewportGridService] = useViewportGrid();
 
   // States
-  const [isToolGroupCreated, setToolGroupCreated] = useState(false);
   const [selectedSegment, setSelectedSegment] = useState(1);
+  const { setPositionPresentation } = usePositionPresentationStore();
 
   // Hydration means that the RT is opened and segments are loaded into the
   // segmentation panel, and RT is also rendered on any viewport that is in the
@@ -66,7 +64,10 @@ function OHIFCornerstoneRTViewport(props) {
 
   const { viewports, activeViewportId } = viewportGrid;
 
-  const referencedDisplaySet = rtDisplaySet.getReferenceDisplaySet();
+  const referencedDisplaySetInstanceUID = rtDisplaySet.referencedDisplaySetInstanceUID;
+  const referencedDisplaySet = displaySetService.getDisplaySetByUID(
+    referencedDisplaySetInstanceUID
+  );
   const referencedDisplaySetMetadata = _getReferencedDisplaySetMetadata(referencedDisplaySet);
 
   referencedDisplaySetRef.current = {
@@ -95,6 +96,16 @@ function OHIFCornerstoneRTViewport(props) {
     });
   }, [viewportGrid]);
 
+  const hydrateRTDisplaySet = useCallback(
+    ({ rtDisplaySet, viewportId }) => {
+      commandsManager.runCommand('hydrateRTSDisplaySet', {
+        displaySet: rtDisplaySet,
+        viewportId,
+      });
+    },
+    [commandsManager]
+  );
+
   const getCornerstoneViewport = useCallback(() => {
     const { component: Component } = extensionManager.getModuleEntry(
       '@ohif/extension-cornerstone.viewportModule.cornerstone'
@@ -108,12 +119,16 @@ function OHIFCornerstoneRTViewport(props) {
         {...props}
         displaySets={[referencedDisplaySet, rtDisplaySet]}
         viewportOptions={{
-          viewportType: 'volume',
+          viewportType: 'stack',
           toolGroupId: toolGroupId,
           orientation: viewportOptions.orientation,
           viewportId: viewportOptions.viewportId,
+          presentationIds: viewportOptions.presentationIds,
+        }}
+        onElementEnabled={evt => {
+          props.onElementEnabled?.(evt);
+          onElementEnabled(evt);
         }}
-        onElementEnabled={onElementEnabled}
         onElementDisabled={onElementDisabled}
       ></Component>
     );
@@ -121,7 +136,6 @@ function OHIFCornerstoneRTViewport(props) {
 
   const onSegmentChange = useCallback(
     direction => {
-      direction = direction === 'left' ? -1 : 1;
       const segmentationId = rtDisplaySet.displaySetInstanceUID;
       const segmentation = segmentationService.getSegmentation(segmentationId);
 
@@ -138,10 +152,10 @@ function OHIFCornerstoneRTViewport(props) {
         newSelectedSegmentIndex = numberOfSegments - 1;
       }
 
-      segmentationService.jumpToSegmentCenter(segmentationId, newSelectedSegmentIndex, toolGroupId);
+      segmentationService.jumpToSegmentCenter(segmentationId, newSelectedSegmentIndex, viewportId);
       setSelectedSegment(newSelectedSegmentIndex);
     },
-    [selectedSegment]
+    [selectedSegment, segmentationService]
   );
 
   useEffect(() => {
@@ -154,6 +168,7 @@ function OHIFCornerstoneRTViewport(props) {
       viewportId,
       rtDisplaySet,
       preHydrateCallbacks: [storePresentationState],
+      hydrateRTDisplaySet,
     }).then(isHydrated => {
       if (isHydrated) {
         setIsHydrated(true);
@@ -162,6 +177,8 @@ function OHIFCornerstoneRTViewport(props) {
   }, [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 => {
@@ -169,6 +186,19 @@ function OHIFCornerstoneRTViewport(props) {
           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',
@@ -231,11 +261,9 @@ function OHIFCornerstoneRTViewport(props) {
 
     toolGroup = createRTToolGroupAndAddTools(toolGroupService, customizationService, toolGroupId);
 
-    setToolGroupCreated(true);
-
     return () => {
       // remove the segmentation representations if seg displayset changed
-      segmentationService.removeSegmentationRepresentationFromToolGroup(toolGroupId);
+      segmentationService.removeSegmentationRepresentations(viewportId);
 
       toolGroupService.destroyToolGroup(toolGroupId);
     };
@@ -246,11 +274,27 @@ function OHIFCornerstoneRTViewport(props) {
 
     return () => {
       // remove the segmentation representations if seg displayset changed
-      segmentationService.removeSegmentationRepresentationFromToolGroup(toolGroupId);
+      segmentationService.removeSegmentationRepresentations(viewportId);
       referencedDisplaySetRef.current = null;
     };
   }, [rtDisplaySet]);
 
+  const onStatusClick = useCallback(async () => {
+    // Before hydrating a RT and make it added to all viewports in the grid
+    // that share the same frameOfReferenceUID, we need to store the viewport grid
+    // presentation state, so that we can restore it after hydrating the RT. This is
+    // required if the user has changed the viewport (other viewport than RT viewport)
+    // presentation state (w/l and invert) and then opens the RT. If we don't store
+    // the presentation state, the viewport will be reset to the default presentation
+    storePresentationState();
+    const isHydrated = await hydrateRTDisplaySet({
+      rtDisplaySet,
+      viewportId,
+    });
+
+    setIsHydrated(isHydrated);
+  }, [hydrateRTDisplaySet, rtDisplaySet, storePresentationState, viewportId]);
+
   // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   let childrenWithProps = null;
 
@@ -274,69 +318,45 @@ function OHIFCornerstoneRTViewport(props) {
     });
   }
 
-  const {
-    PatientID,
-    PatientName,
-    PatientSex,
-    PatientAge,
-    SliceThickness,
-    ManufacturerModelName,
-    StudyDate,
-    SeriesDescription,
-    SpacingBetweenSlices,
-    SeriesNumber,
-  } = referencedDisplaySetRef.current.metadata;
-
-  const onStatusClick = async () => {
-    // Before hydrating a RT and make it added to all viewports in the grid
-    // that share the same frameOfReferenceUID, we need to store the viewport grid
-    // presentation state, so that we can restore it after hydrating the RT. This is
-    // required if the user has changed the viewport (other viewport than RT viewport)
-    // presentation state (w/l and invert) and then opens the RT. If we don't store
-    // the presentation state, the viewport will be reset to the default presentation
-    storePresentationState();
-    const isHydrated = await _hydrateRTDisplaySet({
-      rtDisplaySet,
-      viewportId,
-      servicesManager,
-    });
-
-    setIsHydrated(isHydrated);
-  };
+  useEffect(() => {
+    viewportActionCornersService.addComponents([
+      {
+        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/pane:visible'
+            }
+          ></ViewportActionArrows>
+        ),
+        indexPriority: 0,
+        location: viewportActionCornersService.LOCATIONS.topRight,
+      },
+    ]);
+  }, [
+    activeViewportId,
+    isHydrated,
+    onSegmentChange,
+    onStatusClick,
+    viewportActionCornersService,
+    viewportId,
+  ]);
 
   return (
     <>
-      <ViewportActionBar
-        onDoubleClick={evt => {
-          evt.stopPropagation();
-          evt.preventDefault();
-        }}
-        onArrowsClick={onSegmentChange}
-        getStatusComponent={() => {
-          return _getStatusComponent({
-            isHydrated,
-            onStatusClick,
-          });
-        }}
-        studyData={{
-          label: viewportLabel,
-          useAltStyling: true,
-          studyDate: formatDate(StudyDate),
-          currentSeries: SeriesNumber,
-          seriesDescription: `RT Viewport ${SeriesDescription}`,
-          patientInformation: {
-            patientName: PatientName ? OHIF.utils.formatPN(PatientName.Alphabetic) : '',
-            patientSex: PatientSex || '',
-            patientAge: PatientAge || '',
-            MRN: PatientID || '',
-            thickness: SliceThickness ? `${SliceThickness.toFixed(2)}mm` : '',
-            spacing:
-              SpacingBetweenSlices !== undefined ? `${SpacingBetweenSlices.toFixed(2)}mm` : '',
-            scanner: ManufacturerModelName || '',
-          },
-        }}
-      />
-
       <div className="relative flex h-full w-full flex-row overflow-hidden">
         {rtIsLoading && (
           <LoadingIndicatorTotalPercent
@@ -358,11 +378,6 @@ 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

@@ -1,23 +1,21 @@
 import React from 'react';
 import { useTranslation } from 'react-i18next';
-import { Icon, Tooltip } from '@ohif/ui';
+import { Icon, Tooltip, ViewportActionButton } from '@ohif/ui';
+import { Icons } from '@ohif/ui-next';
 
 export default function _getStatusComponent({ isHydrated, onStatusClick }) {
   let ToolTipMessage = null;
   let StatusIcon = null;
 
-  const { t } = useTranslation('Common');
-  const loadStr = t('LOAD');
-
   switch (isHydrated) {
     case true:
-      StatusIcon = () => <Icon name="status-alert" />;
+      StatusIcon = () => <Icons.ByName name="status-alert" />;
 
       ToolTipMessage = () => <div>This Segmentation is loaded in the segmentation panel</div>;
       break;
     case false:
       StatusIcon = () => (
-        <Icon
+        <Icons.ByName
           className="text-aqua-pale"
           name="status-untracked"
         />
@@ -26,23 +24,22 @@ export default function _getStatusComponent({ isHydrated, onStatusClick }) {
       ToolTipMessage = () => <div>Click LOAD to load RTSTRUCT.</div>;
   }
 
-  const StatusArea = () => (
-    <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}
+  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>
-      )}
-    </div>
-  );
+        {!isHydrated && (
+          <ViewportActionButton onInteraction={onStatusClick}>{loadStr}</ViewportActionButton>
+        )}
+      </div>
+    );
+  };
 
   return (
     <>

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

@@ -45,10 +45,10 @@ module.exports = (env, argv) => {
       new webpack.optimize.LimitChunkCountPlugin({
         maxChunks: 1,
       }),
-      // new MiniCssExtractPlugin({
-      //   filename: `./dist/${outputName}.css`,
-      //   chunkFilename: `./dist/${outputName}.css`,
-      // }),
+      new MiniCssExtractPlugin({
+        filename: `./dist/${outputName}.css`,
+        chunkFilename: `./dist/${outputName}.css`,
+      }),
     ],
   });
 };

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

@@ -1,5 +1,5 @@
 module.exports = {
-  plugins: ['inline-react-svg', '@babel/plugin-proposal-class-properties'],
+  plugins: ['@babel/plugin-proposal-class-properties'],
   env: {
     test: {
       presets: [
@@ -37,7 +37,7 @@ module.exports = {
         '@babel/preset-react',
         '@babel/preset-typescript',
       ],
-      plugins: ['react-hot-loader/babel'],
+      plugins: ['react-refresh/babel'],
       ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
     },
   },

extensions/cornerstone-dicom-seg/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone-dicom-seg",
-  "version": "3.7.0-beta.64",
+  "version": "3.10.0-beta.39",
   "description": "DICOM SEG read workflow",
   "author": "OHIF",
   "license": "MIT",
@@ -24,6 +24,8 @@
     "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-seg": "yarn run dev",
     "build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
@@ -31,19 +33,22 @@
     "start": "yarn run dev"
   },
   "peerDependencies": {
-    "@ohif/core": "3.7.0-beta.64",
-    "@ohif/extension-cornerstone": "3.7.0-beta.64",
-    "@ohif/extension-default": "3.7.0-beta.64",
-    "@ohif/i18n": "3.7.0-beta.64",
+    "@ohif/core": "3.10.0-beta.39",
+    "@ohif/extension-cornerstone": "3.10.0-beta.39",
+    "@ohif/extension-default": "3.10.0-beta.39",
+    "@ohif/i18n": "3.10.0-beta.39",
     "prop-types": "^15.6.2",
-    "react": "^17.0.2",
-    "react-dom": "^17.0.2",
+    "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"
+    "react-router": "^6.23.1",
+    "react-router-dom": "^6.23.1"
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
+    "@cornerstonejs/adapters": "^2.14.7",
+    "@cornerstonejs/core": "^2.14.7",
+    "@kitware/vtk.js": "32.1.1",
     "react-color": "^2.19.3"
   }
 }

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

@@ -0,0 +1,379 @@
+import dcmjs from 'dcmjs';
+import { createReportDialogPrompt } from '@ohif/extension-default';
+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 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';
+
+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 },
+  },
+} = adaptersSEG;
+
+const {
+  Cornerstone3D: {
+    RTSS: { generateRTSSFromSegmentations },
+  },
+} = adaptersRT;
+
+const { downloadDICOMData } = helpers;
+
+const commandsModule = ({
+  servicesManager,
+  extensionManager,
+}: Types.Extensions.ExtensionParams): Types.Extensions.CommandsModule => {
+  const {
+    segmentationService,
+    uiDialogService,
+    displaySetService,
+    viewportGridService,
+    toolGroupService,
+  } = servicesManager.services as AppTypes.Services;
+
+  const actions = {
+    /**
+     * Loads segmentations for a specified viewport.
+     * The function prepares the viewport for rendering, then loads the segmentation details.
+     * Additionally, if the segmentation has scalar data, it is set for the corresponding label map volume.
+     *
+     * @param {Object} params - Parameters for the function.
+     * @param params.segmentations - Array of segmentations to be loaded.
+     * @param params.viewportId - the target viewport ID.
+     *
+     */
+    loadSegmentationsForViewport: async ({ segmentations, viewportId }) => {
+      // Todo: handle adding more than one segmentation
+      const viewport = getTargetViewport({ viewportId, viewportGridService });
+      const displaySetInstanceUID = viewport.displaySetInstanceUIDs[0];
+
+      const segmentation = segmentations[0];
+      const segmentationId = segmentation.segmentationId;
+      const label = segmentation.config.label;
+      const segments = segmentation.config.segments;
+
+      const displaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
+
+      await segmentationService.createLabelmapForDisplaySet(displaySet, {
+        segmentationId,
+        segments,
+        label,
+      });
+
+      segmentationService.addOrUpdateSegmentation(segmentation);
+
+      await segmentationService.addSegmentationRepresentation(viewport.viewportId, {
+        segmentationId,
+      });
+
+      return segmentationId;
+    },
+    /**
+     * Generates a segmentation from a given segmentation ID.
+     * This function retrieves the associated segmentation and
+     * its referenced volume, extracts label maps from the
+     * segmentation volume, and produces segmentation data
+     * alongside associated metadata.
+     *
+     * @param {Object} params - Parameters for the function.
+     * @param params.segmentationId - ID of the segmentation to be generated.
+     * @param params.options - Optional configuration for the generation process.
+     *
+     * @returns Returns the generated segmentation data.
+     */
+    generateSegmentation: ({ segmentationId, options = {} }) => {
+      const segmentation = cornerstoneToolsSegmentation.state.getSegmentation(segmentationId);
+
+      const { imageIds } = segmentation.representationData.Labelmap;
+
+      const segImages = imageIds.map(imageId => cache.getImage(imageId));
+      const referencedImages = segImages.map(image => cache.getImage(image.referencedImageId));
+
+      const labelmaps2D = [];
+
+      let z = 0;
+
+      for (const segImage of segImages) {
+        const segmentsOnLabelmap = new Set();
+        const pixelData = segImage.getPixelData();
+        const { rows, columns } = segImage;
+
+        // Use a single pass through the pixel data
+        for (let i = 0; i < pixelData.length; i++) {
+          const segment = pixelData[i];
+          if (segment !== 0) {
+            segmentsOnLabelmap.add(segment);
+          }
+        }
+
+        labelmaps2D[z++] = {
+          segmentsOnLabelmap: Array.from(segmentsOnLabelmap),
+          pixelData,
+          rows,
+          columns,
+        };
+      }
+
+      const allSegmentsOnLabelmap = labelmaps2D.map(labelmap => labelmap.segmentsOnLabelmap);
+
+      const labelmap3D = {
+        segmentsOnLabelmap: Array.from(new Set(allSegmentsOnLabelmap.flat())),
+        metadata: [],
+        labelmaps2D,
+      };
+
+      const segmentationInOHIF = segmentationService.getSegmentation(segmentationId);
+      const representations = segmentationService.getRepresentationsForSegmentation(segmentationId);
+
+      Object.entries(segmentationInOHIF.segments).forEach(([segmentIndex, segment]) => {
+        // segmentation service already has a color for each segment
+        if (!segment) {
+          return;
+        }
+
+        const { label } = segment;
+
+        const firstRepresentation = representations[0];
+        const color = segmentationService.getSegmentColor(
+          firstRepresentation.viewportId,
+          segmentationId,
+          segment.segmentIndex
+        );
+
+        const RecommendedDisplayCIELabValue = dcmjs.data.Colors.rgb2DICOMLAB(
+          color.slice(0, 3).map(value => value / 255)
+        ).map(value => Math.round(value));
+
+        const segmentMetadata = {
+          SegmentNumber: segmentIndex.toString(),
+          SegmentLabel: label,
+          SegmentAlgorithmType: segment?.algorithmType || 'MANUAL',
+          SegmentAlgorithmName: segment?.algorithmName || 'OHIF Brush',
+          RecommendedDisplayCIELabValue,
+          SegmentedPropertyCategoryCodeSequence: {
+            CodeValue: 'T-D0050',
+            CodingSchemeDesignator: 'SRT',
+            CodeMeaning: 'Tissue',
+          },
+          SegmentedPropertyTypeCodeSequence: {
+            CodeValue: 'T-D0050',
+            CodingSchemeDesignator: 'SRT',
+            CodeMeaning: 'Tissue',
+          },
+        };
+        labelmap3D.metadata[segmentIndex] = segmentMetadata;
+      });
+
+      const generatedSegmentation = generateSegmentation(
+        referencedImages,
+        labelmap3D,
+        metaData,
+        options
+      );
+
+      return generatedSegmentation;
+    },
+    /**
+     * Downloads a segmentation based on the provided segmentation ID.
+     * This function retrieves the associated segmentation and
+     * uses it to generate the corresponding DICOM dataset, which
+     * is then downloaded with an appropriate filename.
+     *
+     * @param {Object} params - Parameters for the function.
+     * @param params.segmentationId - ID of the segmentation to be downloaded.
+     *
+     */
+    downloadSegmentation: ({ segmentationId }) => {
+      const segmentationInOHIF = segmentationService.getSegmentation(segmentationId);
+      const generatedSegmentation = actions.generateSegmentation({
+        segmentationId,
+      });
+
+      downloadDICOMData(generatedSegmentation.dataset, `${segmentationInOHIF.label}`);
+    },
+    /**
+     * Stores a segmentation based on the provided segmentationId into a specified data source.
+     * The SeriesDescription is derived from user input or defaults to the segmentation label,
+     * and in its absence, defaults to 'Research Derived Series'.
+     *
+     * @param {Object} params - Parameters for the function.
+     * @param params.segmentationId - ID of the segmentation to be stored.
+     * @param params.dataSource - Data source where the generated segmentation will be stored.
+     *
+     * @returns {Object|void} Returns the naturalized report if successfully stored,
+     * 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) {
+        throw new Error('No segmentation found');
+      }
+
+      const { label } = segmentation;
+      const SeriesDescription = promptResult.value || label || 'Research Derived Series';
+
+      const generatedData = actions.generateSegmentation({
+        segmentationId,
+        options: {
+          SeriesDescription,
+        },
+      });
+
+      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.
+     * This sample function retrieves all segentations and passes to
+     * cornerstone tool adapter to convert to DICOM RTSS format. It then
+     * converts dataset to downloadable blob.
+     *
+     */
+    downloadRTSS: ({ segmentationId }) => {
+      const segmentations = segmentationService.getSegmentation(segmentationId);
+      const vtkUtils = {
+        vtkImageMarchingSquares,
+        vtkDataArray,
+        vtkImageData,
+      };
+
+      const RTSS = generateRTSSFromSegmentations(
+        segmentations,
+        classes.MetadataProvider,
+        DicomMetadataStore,
+        cache,
+        cornerstoneToolsEnums,
+        vtkUtils
+      );
+
+      try {
+        const reportBlob = datasetToBlob(RTSS);
+
+        //Create a URL for the binary.
+        const objectUrl = URL.createObjectURL(reportBlob);
+        window.location.assign(objectUrl);
+      } catch (e) {
+        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 = {
+    /**
+     * Obsolete?
+     */
+    loadSegmentationDisplaySetsForViewport: {
+      commandFn: actions.loadSegmentationDisplaySetsForViewport,
+    },
+    /**
+     * Obsolete?
+     */
+    loadSegmentationsForViewport: {
+      commandFn: actions.loadSegmentationsForViewport,
+    },
+
+    generateSegmentation: {
+      commandFn: actions.generateSegmentation,
+    },
+    downloadSegmentation: {
+      commandFn: actions.downloadSegmentation,
+    },
+    storeSegmentation: {
+      commandFn: actions.storeSegmentation,
+    },
+    downloadRTSS: {
+      commandFn: actions.downloadRTSS,
+    },
+    setBrushSize: {
+      commandFn: actions.setBrushSize,
+    },
+    setThresholdRange: {
+      commandFn: actions.setThresholdRange,
+    },
+  };
+
+  return {
+    actions,
+    definitions,
+    defaultContext: 'SEGMENTATION',
+  };
+};
+
+export default commandsModule;

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

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

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

@@ -1,5 +1,6 @@
 import { utils } from '@ohif/core';
-import { metaData, cache, triggerEvent, eventTarget } from '@cornerstonejs/core';
+import { metaData, triggerEvent, eventTarget } from '@cornerstonejs/core';
+import { CONSTANTS, segmentation as cstSegmentation } from '@cornerstonejs/tools';
 import { adaptersSEG, Enums } from '@cornerstonejs/adapters';
 
 import { SOPClassHandlerId } from './id';
@@ -7,9 +8,13 @@ import { dicomlabToRGB } from './utils/dicomlabToRGB';
 
 const sopClassUids = ['1.2.840.10008.5.1.4.1.1.66.4'];
 
-let loadPromises = {};
+const loadPromises = {};
 
-function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager) {
+function _getDisplaySetsFromSeries(
+  instances,
+  servicesManager: AppTypes.ServicesManager,
+  extensionManager
+) {
   const instance = instances[0];
 
   const {
@@ -57,35 +62,40 @@ function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager)
   const referencedSeriesSequence = instance.ReferencedSeriesSequence;
 
   if (!referencedSeriesSequence) {
-    throw new Error('ReferencedSeriesSequence is missing for the SEG');
+    console.error('ReferencedSeriesSequence is missing for the SEG');
+    return;
   }
 
-  const referencedSeries = referencedSeriesSequence[0];
+  const referencedSeries = referencedSeriesSequence[0] || referencedSeriesSequence;
 
   displaySet.referencedImages = instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
   displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID;
+  const { displaySetService } = servicesManager.services;
+  const referencedDisplaySets = displaySetService.getDisplaySetsForSeries(
+    displaySet.referencedSeriesInstanceUID
+  );
 
-  displaySet.getReferenceDisplaySet = () => {
-    const { displaySetService } = servicesManager.services;
-    const referencedDisplaySets = displaySetService.getDisplaySetsForSeries(
-      displaySet.referencedSeriesInstanceUID
+  const referencedDisplaySet = referencedDisplaySets[0];
+
+  if (!referencedDisplaySet) {
+    // subscribe to display sets added which means at some point it will be available
+    const { unsubscribe } = displaySetService.subscribe(
+      displaySetService.EVENTS.DISPLAY_SETS_ADDED,
+      ({ displaySetsAdded }) => {
+        // here we can also do a little bit of search, since sometimes DICOM SEG
+        // does not contain the referenced display set uid , and we can just
+        // see which of the display sets added is more similar and assign it
+        // to the referencedDisplaySet
+        const addedDisplaySet = displaySetsAdded[0];
+        if (addedDisplaySet.SeriesInstanceUID === displaySet.referencedSeriesInstanceUID) {
+          displaySet.referencedDisplaySetInstanceUID = addedDisplaySet.displaySetInstanceUID;
+          unsubscribe();
+        }
+      }
     );
-
-    if (!referencedDisplaySets || referencedDisplaySets.length === 0) {
-      throw new Error('Referenced DisplaySet is missing for the SEG');
-    }
-
-    const referencedDisplaySet = referencedDisplaySets[0];
-
+  } else {
     displaySet.referencedDisplaySetInstanceUID = referencedDisplaySet.displaySetInstanceUID;
-
-    // Todo: this needs to be able to work with other reference volumes (other than streaming) such as nifti, etc.
-    displaySet.referencedVolumeURI = referencedDisplaySet.displaySetInstanceUID;
-    const referencedVolumeId = `cornerstoneStreamingImageVolume:${displaySet.referencedVolumeURI}`;
-    displaySet.referencedVolumeId = referencedVolumeId;
-
-    return referencedDisplaySet;
-  };
+  }
 
   displaySet.load = async ({ headers }) =>
     await _load(displaySet, servicesManager, extensionManager, headers);
@@ -93,14 +103,19 @@ function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager)
   return [displaySet];
 }
 
-function _load(segDisplaySet, servicesManager, extensionManager, headers) {
+function _load(
+  segDisplaySet,
+  servicesManager: AppTypes.ServicesManager,
+  extensionManager,
+  headers
+) {
   const { SOPInstanceUID } = segDisplaySet;
   const { segmentationService } = servicesManager.services;
 
   if (
     (segDisplaySet.loading || segDisplaySet.isLoaded) &&
     loadPromises[SOPInstanceUID] &&
-    _segmentationExists(segDisplaySet, segmentationService)
+    _segmentationExists(segDisplaySet)
   ) {
     return loadPromises[SOPInstanceUID];
   }
@@ -111,17 +126,21 @@ function _load(segDisplaySet, servicesManager, extensionManager, headers) {
   // and also return the same promise to any other callers.
   loadPromises[SOPInstanceUID] = new Promise(async (resolve, reject) => {
     if (!segDisplaySet.segments || Object.keys(segDisplaySet.segments).length === 0) {
-      await _loadSegments({
-        extensionManager,
-        servicesManager,
-        segDisplaySet,
-        headers,
-      });
+      try {
+        await _loadSegments({
+          extensionManager,
+          servicesManager,
+          segDisplaySet,
+          headers,
+        });
+      } catch (e) {
+        segDisplaySet.loading = false;
+        return reject(e);
+      }
     }
 
-    const suppressEvents = true;
     segmentationService
-      .createSegmentationForSEGDisplaySet(segDisplaySet, null, suppressEvents)
+      .createSegmentationForSEGDisplaySet(segDisplaySet)
       .then(() => {
         segDisplaySet.loading = false;
         resolve();
@@ -135,30 +154,35 @@ function _load(segDisplaySet, servicesManager, extensionManager, headers) {
   return loadPromises[SOPInstanceUID];
 }
 
-async function _loadSegments({ extensionManager, servicesManager, segDisplaySet, headers }) {
+async function _loadSegments({
+  extensionManager,
+  servicesManager,
+  segDisplaySet,
+  headers,
+}: withAppTypes) {
   const utilityModule = extensionManager.getModuleEntry(
     '@ohif/extension-cornerstone.utilityModule.common'
   );
 
-  const { segmentationService } = servicesManager.services;
+  const { segmentationService, uiNotificationService } = servicesManager.services;
 
   const { dicomLoaderService } = utilityModule.exports;
   const arrayBuffer = await dicomLoaderService.findDicomDataPromise(segDisplaySet, null, headers);
 
-  const cachedReferencedVolume = cache.getVolume(segDisplaySet.referencedVolumeId);
+  const referencedDisplaySet = servicesManager.services.displaySetService.getDisplaySetByUID(
+    segDisplaySet.referencedDisplaySetInstanceUID
+  );
 
-  if (!cachedReferencedVolume) {
-    throw new Error(
-      'Referenced Volume is missing for the SEG, and stack viewport SEG is not supported yet'
-    );
+  if (!referencedDisplaySet) {
+    throw new Error('referencedDisplaySet is missing for SEG');
   }
 
-  const { imageIds } = cachedReferencedVolume;
+  const { instances: images } = referencedDisplaySet;
+  const imageIds = images.map(({ imageId }) => imageId);
 
   // Todo: what should be defaults here
   const tolerance = 0.001;
   const skipOverlapping = true;
-
   eventTarget.addEventListener(Enums.Events.SEGMENTATION_LOAD_PROGRESS, evt => {
     const { percentComplete } = evt.detail;
     segmentationService._broadcastEvent(segmentationService.EVENTS.SEGMENT_LOADING_COMPLETE, {
@@ -173,18 +197,45 @@ async function _loadSegments({ extensionManager, servicesManager, segDisplaySet,
     { skipOverlapping, tolerance, eventTarget, triggerEvent }
   );
 
+  let usedRecommendedDisplayCIELabValue = true;
   results.segMetadata.data.forEach((data, i) => {
     if (i > 0) {
-      data.rgba = dicomlabToRGB(data.RecommendedDisplayCIELabValue);
+      data.rgba = data.RecommendedDisplayCIELabValue;
+
+      if (data.rgba) {
+        data.rgba = dicomlabToRGB(data.rgba);
+      } else {
+        usedRecommendedDisplayCIELabValue = false;
+        data.rgba = CONSTANTS.COLOR_LUT[i % CONSTANTS.COLOR_LUT.length];
+      }
     }
   });
 
+  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({
+      title: 'DICOM SEG import',
+      message:
+        'RecommendedDisplayCIELabValue not found for one or more segments. The default color was used instead.',
+      type: 'warning',
+      duration: 5000,
+    });
+  }
+
   Object.assign(segDisplaySet, results);
 }
 
-function _segmentationExists(segDisplaySet, segmentationService) {
-  // This should be abstracted with the CornerstoneCacheService
-  return segmentationService.getSegmentation(segDisplaySet.displaySetInstanceUID);
+function _segmentationExists(segDisplaySet) {
+  return cstSegmentation.state.getSegmentation(segDisplaySet.displaySetInstanceUID);
 }
 
 function getSopClassHandlerModule({ servicesManager, extensionManager }) {

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

@@ -0,0 +1,57 @@
+export function getToolbarModule({ servicesManager }: withAppTypes) {
+  const { segmentationService, toolbarService, toolGroupService } = servicesManager.services;
+  return [
+    {
+      name: 'evaluate.cornerstone.segmentation',
+      evaluate: ({ viewportId, button, toolNames, disabledText }) => {
+        // Todo: we need to pass in the button section Id since we are kind of
+        // 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);
+        if (!segmentations?.length) {
+          return {
+            disabled: true,
+            className: '!text-common-bright !bg-black opacity-50',
+            disabledText: disabledText ?? 'No segmentations available',
+          };
+        }
+
+        const toolGroup = toolGroupService.getToolGroupForViewport(viewportId);
+
+        if (!toolGroup) {
+          return {
+            disabled: true,
+            className: '!text-common-bright ohif-disabled',
+            disabledText: disabledText ?? 'Not available on the current viewport',
+          };
+        }
+
+        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',
+          };
+        }
+
+        const isPrimaryActive = toolNames
+          ? toolNames.includes(toolGroup.getActivePrimaryMouseButtonTool())
+          : toolGroup.getActivePrimaryMouseButtonTool() === toolName;
+
+        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

@@ -1,12 +1,10 @@
 import { id } from './id';
 import React from 'react';
 
-import { Types } from '@ohif/core';
-
 import getSopClassHandlerModule from './getSopClassHandlerModule';
-import PanelSegmentation from './panels/PanelSegmentation';
 import getHangingProtocolModule from './getHangingProtocolModule';
-import hydrateSEGDisplaySet from './utils/_hydrateSEG';
+import getCommandsModule from './commandsModule';
+import { getToolbarModule } from './getToolbarModule';
 
 const Component = React.lazy(() => {
   return import(/* webpackPrefetch: true */ './viewports/OHIFCornerstoneSEGViewport');
@@ -29,36 +27,9 @@ 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: ({ servicesManager, commandsManager, extensionManager }): Types.Panel[] => {
-    const wrappedPanelSegmentation = () => {
-      return (
-        <PanelSegmentation
-          commandsManager={commandsManager}
-          servicesManager={servicesManager}
-          extensionManager={extensionManager}
-        />
-      );
-    };
-
-    return [
-      {
-        name: 'panelSegmentation',
-        iconName: 'tab-segmentation',
-        iconLabel: 'Segmentation',
-        label: 'Segmentation',
-        component: wrappedPanelSegmentation,
-      },
-    ];
-  },
-
-  getViewportModule({ servicesManager, extensionManager }) {
+  getCommandsModule,
+  getToolbarModule,
+  getViewportModule({ servicesManager, extensionManager, commandsManager }) {
     const ExtendedOHIFCornerstoneSEGViewport = props => {
       return (
         <OHIFCornerstoneSEGViewport
@@ -83,4 +54,3 @@ const extension = {
 };
 
 export default extension;
-export { hydrateSEGDisplaySet };

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

@@ -1,240 +0,0 @@
-import React, { useEffect, useState, useCallback } from 'react';
-import PropTypes from 'prop-types';
-import { SegmentationGroupTable } from '@ohif/ui';
-import callInputDialog from './callInputDialog';
-import { useAppConfig } from '@state';
-import { useTranslation } from 'react-i18next';
-
-export default function PanelSegmentation({ servicesManager, commandsManager }) {
-  const { segmentationService, uiDialogService } = servicesManager.services;
-  const [appConfig] = useAppConfig();
-  const disableEditing = appConfig?.disableEditing;
-
-  const { t } = useTranslation('PanelSegmentation');
-  const [selectedSegmentationId, setSelectedSegmentationId] = useState(null);
-  const [segmentationConfiguration, setSegmentationConfiguration] = useState(
-    segmentationService.getConfiguration()
-  );
-
-  const [segmentations, setSegmentations] = useState(() => segmentationService.getSegmentations());
-
-  const [isMinimized, setIsMinimized] = useState({});
-
-  const onToggleMinimizeSegmentation = useCallback(
-    id => {
-      setIsMinimized(prevState => ({
-        ...prevState,
-        [id]: !prevState[id],
-      }));
-    },
-    [setIsMinimized]
-  );
-
-  // Only expand the last segmentation added to the list and collapse the rest
-  useEffect(() => {
-    const lastSegmentationId = segmentations[segmentations.length - 1]?.id;
-    if (lastSegmentationId) {
-      setIsMinimized(prevState => ({
-        ...prevState,
-        [lastSegmentationId]: false,
-      }));
-    }
-  }, [segmentations, setIsMinimized]);
-
-  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();
-      });
-    };
-  }, []);
-
-  const onSegmentationClick = (segmentationId: string) => {
-    segmentationService.setActiveSegmentationForToolGroup(segmentationId);
-  };
-
-  const onSegmentationDelete = (segmentationId: string) => {
-    segmentationService.remove(segmentationId);
-  };
-
-  const getToolGroupIds = segmentationId => {
-    const toolGroupIds = segmentationService.getToolGroupIdsWithSegmentation(segmentationId);
-
-    return toolGroupIds;
-  };
-
-  const onSegmentClick = (segmentationId, segmentIndex) => {
-    segmentationService.setActiveSegmentForSegmentation(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.setSegmentLabelForSegmentation(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) => {
-    // Todo: Implement color picker later
-    return;
-  };
-
-  const onSegmentDelete = (segmentationId, segmentIndex) => {
-    // segmentationService.removeSegmentFromSegmentation(
-    //   segmentationId,
-    //   segmentIndex
-    // );
-    console.warn('not implemented yet');
-  };
-
-  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 onToggleSegmentationVisibility = segmentationId => {
-    segmentationService.toggleSegmentationVisibility(segmentationId);
-  };
-
-  const _setSegmentationConfiguration = useCallback(
-    (segmentationId, key, value) => {
-      segmentationService.setConfiguration({
-        segmentationId,
-        [key]: value,
-      });
-    },
-    [segmentationService]
-  );
-
-  return (
-    <div className="mt-1 flex min-h-0 flex-auto flex-col justify-between">
-      {/* show segmentation table */}
-      {segmentations?.length ? (
-        <SegmentationGroupTable
-          title={t('Segmentations')}
-          showAddSegmentation={false}
-          segmentations={segmentations}
-          isMinimized={isMinimized}
-          activeSegmentationId={selectedSegmentationId || ''}
-          onSegmentationClick={onSegmentationClick}
-          onSegmentationDelete={onSegmentationDelete}
-          onSegmentationEdit={onSegmentationEdit}
-          onSegmentClick={onSegmentClick}
-          onSegmentEdit={onSegmentEdit}
-          disableEditing={disableEditing}
-          onSegmentColorClick={onSegmentColorClick}
-          onSegmentDelete={onSegmentDelete}
-          onToggleSegmentVisibility={onToggleSegmentVisibility}
-          onToggleSegmentationVisibility={onToggleSegmentationVisibility}
-          onToggleMinimizeSegmentation={onToggleMinimizeSegmentation}
-          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)
-          }
-        />
-      ) : null}
-    </div>
-  );
-}
-
-PanelSegmentation.propTypes = {
-  commandsManager: PropTypes.shape({
-    runCommand: PropTypes.func.isRequired,
-  }),
-  servicesManager: PropTypes.shape({
-    services: PropTypes.shape({
-      segmentationService: PropTypes.shape({
-        getSegmentation: PropTypes.func.isRequired,
-        getSegmentations: PropTypes.func.isRequired,
-        toggleSegmentationVisibility: PropTypes.func.isRequired,
-        subscribe: PropTypes.func.isRequired,
-        EVENTS: PropTypes.object.isRequired,
-      }).isRequired,
-    }).isRequired,
-  }).isRequired,
-};

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

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

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

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

extensions/cornerstone-dicom-seg/src/types/segmentation.tsx

@@ -0,0 +1,4 @@
+export enum SegmentationPanelMode {
+  Expanded = 'expanded',
+  Dropdown = 'dropdown',
+}

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

@@ -1,73 +0,0 @@
-async function _hydrateSEGDisplaySet({
-  segDisplaySet,
-  viewportId: targetViewportId,
-  servicesManager,
-}) {
-  const { segmentationService, hangingProtocolService, viewportGridService } =
-    servicesManager.services;
-
-  const displaySetInstanceUID = segDisplaySet.referencedDisplaySetInstanceUID;
-
-  let segmentationId = null;
-
-  // We need the hydration to notify panels about the new segmentation added
-  const suppressEvents = false;
-
-  segmentationId = await segmentationService.createSegmentationForSEGDisplaySet(
-    segDisplaySet,
-    segmentationId,
-    suppressEvents
-  );
-
-  segmentationService.hydrateSegmentation(segDisplaySet.displaySetInstanceUID);
-
-  const { viewports } = viewportGridService.getState();
-
-  const updatedViewports = hangingProtocolService.getViewportsRequireUpdate(
-    targetViewportId,
-    displaySetInstanceUID
-  );
-
-  // Todo: fix this after we have a better way for stack viewport segmentations
-
-  // check every viewport in the viewports to see if the displaySetInstanceUID
-  // is being displayed, if so we need to update the viewport to use volume viewport
-  // (if already is not using it) since Cornerstone3D currently only supports
-  // volume viewport for segmentation
-  viewports.forEach((viewport, viewportId) => {
-    if (targetViewportId === viewportId) {
-      return;
-    }
-
-    const shouldDisplaySeg = segmentationService.shouldRenderSegmentation(
-      viewport.displaySetInstanceUIDs,
-      segDisplaySet.displaySetInstanceUID
-    );
-
-    if (shouldDisplaySeg) {
-      updatedViewports.push({
-        viewportId,
-        displaySetInstanceUIDs: viewport.displaySetInstanceUIDs,
-        viewportOptions: {
-          // Note: This is a hack to get the grid to re-render the OHIFCornerstoneViewport component
-          // Used for segmentation hydration right now, since the logic to decide whether
-          // a viewport needs to render a segmentation lives inside the CornerstoneViewportService
-          // so we need to re-render (force update via change of the needsRerendering) so that React
-          // does the diffing and decides we should render this again (although the id and element has not changed)
-          // so that the CornerstoneViewportService can decide whether to render the segmentation or not.
-          needsRerendering: true,
-          initialImageOptions: {
-            preset: 'middle',
-          },
-        },
-      });
-    }
-  });
-
-  // Do the entire update at once
-  viewportGridService.setDisplaySetsForViewports(updatedViewports);
-
-  return true;
-}
-
-export default _hydrateSEGDisplaySet;

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

@@ -1,7 +1,7 @@
 function createSEGToolGroupAndAddTools(ToolGroupService, customizationService, toolGroupId) {
   const { tools } = customizationService.get('cornerstone.overlayViewportTools') ?? {};
 
-  return ToolGroupService.createToolGroupAndAddTools(toolGroupId, tools, {});
+  return ToolGroupService.createToolGroupAndAddTools(toolGroupId, tools);
 }
 
 export default createSEGToolGroupAndAddTools;

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

@@ -1,5 +1,4 @@
 import { ButtonEnums } from '@ohif/ui';
-import hydrateSEGDisplaySet from './_hydrateSEG';
 
 const RESPONSE = {
   NO_NEVER: -1,
@@ -7,24 +6,35 @@ const RESPONSE = {
   HYDRATE_SEG: 5,
 };
 
-function promptHydrateSEG({ servicesManager, segDisplaySet, viewportId, preHydrateCallbacks }) {
+function promptHydrateSEG({
+  servicesManager,
+  segDisplaySet,
+  viewportId,
+  preHydrateCallbacks,
+  hydrateCallback,
+}: withAppTypes) {
   const { uiViewportDialogService } = servicesManager.services;
+  const extensionManager = servicesManager._extensionManager;
+  const appConfig = extensionManager._appConfig;
 
   return new Promise(async function (resolve, reject) {
-    const promptResult = await _askHydrate(uiViewportDialogService, viewportId);
+    const promptResult = appConfig?.disableConfirmationPrompts
+      ? RESPONSE.HYDRATE_SEG
+      : await _askHydrate(uiViewportDialogService, viewportId);
 
     if (promptResult === RESPONSE.HYDRATE_SEG) {
       preHydrateCallbacks?.forEach(callback => {
         callback();
       });
 
-      const isHydrated = await hydrateSEGDisplaySet({
-        segDisplaySet,
-        viewportId,
-        servicesManager,
-      });
+      window.setTimeout(async () => {
+        const isHydrated = await hydrateCallback({
+          segDisplaySet,
+          viewportId,
+        });
 
-      resolve(isHydrated);
+        resolve(isHydrated);
+      }, 0);
     }
   });
 }
@@ -34,11 +44,13 @@ function _askHydrate(uiViewportDialogService, viewportId) {
     const message = 'Do you want to open this Segmentation?';
     const actions = [
       {
+        id: 'no-hydrate',
         type: ButtonEnums.type.secondary,
         text: 'No',
         value: RESPONSE.CANCEL,
       },
       {
+        id: 'yes-hydrate',
         type: ButtonEnums.type.primary,
         text: 'Yes',
         value: RESPONSE.HYDRATE_SEG,
@@ -59,6 +71,11 @@ function _askHydrate(uiViewportDialogService, viewportId) {
         uiViewportDialogService.hide();
         resolve(RESPONSE.CANCEL);
       },
+      onKeyPress: event => {
+        if (event.key === 'Enter') {
+          onSubmit(RESPONSE.HYDRATE_SEG);
+        }
+      },
     });
   });
 }

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

@@ -1,22 +1,19 @@
-import PropTypes from 'prop-types';
 import React, { useCallback, useEffect, useRef, useState } from 'react';
 import { useTranslation } from 'react-i18next';
-import OHIF, { utils } from '@ohif/core';
-import { LoadingIndicatorTotalPercent, useViewportGrid, ViewportActionBar } from '@ohif/ui';
+import { LoadingIndicatorTotalPercent, useViewportGrid, ViewportActionArrows } from '@ohif/ui';
 import createSEGToolGroupAndAddTools from '../utils/initSEGToolGroup';
 import promptHydrateSEG from '../utils/promptHydrateSEG';
-import hydrateSEGDisplaySet from '../utils/_hydrateSEG';
 import _getStatusComponent from './_getStatusComponent';
+import { usePositionPresentationStore } from '@ohif/extension-cornerstone';
+import { SegmentationRepresentations } from '@cornerstonejs/tools/enums';
 
-const { formatDate } = utils;
 const SEG_TOOLGROUP_BASE_NAME = 'SEGToolGroup';
 
-function OHIFCornerstoneSEGViewport(props) {
+function OHIFCornerstoneSEGViewport(props: withAppTypes) {
   const {
     children,
     displaySets,
     viewportOptions,
-    viewportLabel,
     servicesManager,
     extensionManager,
     commandsManager,
@@ -29,8 +26,8 @@ function OHIFCornerstoneSEGViewport(props) {
     displaySetService,
     toolGroupService,
     segmentationService,
-    uiNotificationService,
     customizationService,
+    viewportActionCornersService,
   } = servicesManager.services;
 
   const toolGroupId = `${SEG_TOOLGROUP_BASE_NAME}-${viewportId}`;
@@ -41,11 +38,11 @@ function OHIFCornerstoneSEGViewport(props) {
   }
 
   const segDisplaySet = displaySets[0];
-
   const [viewportGrid, viewportGridService] = useViewportGrid();
 
   // States
   const [selectedSegment, setSelectedSegment] = useState(1);
+  const { setPositionPresentation } = usePositionPresentationStore();
 
   // Hydration means that the SEG is opened and segments are loaded into the
   // segmentation panel, and SEG is also rendered on any viewport that is in the
@@ -65,7 +62,11 @@ function OHIFCornerstoneSEGViewport(props) {
 
   const { viewports, activeViewportId } = viewportGrid;
 
-  const referencedDisplaySet = segDisplaySet.getReferenceDisplaySet();
+  const referencedDisplaySetInstanceUID = segDisplaySet.referencedDisplaySetInstanceUID;
+  const referencedDisplaySet = displaySetService.getDisplaySetByUID(
+    referencedDisplaySetInstanceUID
+  );
+
   const referencedDisplaySetMetadata = _getReferencedDisplaySetMetadata(
     referencedDisplaySet,
     segDisplaySet
@@ -102,29 +103,29 @@ function OHIFCornerstoneSEGViewport(props) {
       '@ohif/extension-cornerstone.viewportModule.cornerstone'
     );
 
-    const { displaySet: referencedDisplaySet } = referencedDisplaySetRef.current;
-
     // Todo: jump to the center of the first segment
     return (
       <Component
         {...props}
-        displaySets={[referencedDisplaySet, segDisplaySet]}
+        displaySets={[segDisplaySet]}
         viewportOptions={{
-          viewportType: 'volume',
+          viewportType: viewportOptions.viewportType,
           toolGroupId: toolGroupId,
           orientation: viewportOptions.orientation,
           viewportId: viewportOptions.viewportId,
+          presentationIds: viewportOptions.presentationIds,
+        }}
+        onElementEnabled={evt => {
+          props.onElementEnabled?.(evt);
+          onElementEnabled(evt);
         }}
-        onElementEnabled={onElementEnabled}
         onElementDisabled={onElementDisabled}
-        // initialImageIndex={initialImageIndex}
       ></Component>
     );
   }, [viewportId, segDisplaySet, toolGroupId]);
 
   const onSegmentChange = useCallback(
     direction => {
-      direction = direction === 'left' ? -1 : 1;
       const segmentationId = segDisplaySet.displaySetInstanceUID;
       const segmentation = segmentationService.getSegmentation(segmentationId);
 
@@ -142,12 +143,35 @@ function OHIFCornerstoneSEGViewport(props) {
         newSelectedSegmentIndex = numberOfSegments - 1;
       }
 
-      segmentationService.jumpToSegmentCenter(segmentationId, newSelectedSegmentIndex, toolGroupId);
+      segmentationService.jumpToSegmentCenter(segmentationId, newSelectedSegmentIndex, viewportId);
       setSelectedSegment(newSelectedSegmentIndex);
     },
     [selectedSegment]
   );
 
+  const hydrateSEG = useCallback(() => {
+    // update the previously stored segmentationPresentation with the new viewportId
+    // presentation so that when we put the referencedDisplaySet back in the viewport
+    // it will have the correct segmentation representation hydrated
+    commandsManager.runCommand('updateStoredSegmentationPresentation', {
+      displaySet: segDisplaySet,
+      type: SegmentationRepresentations.Labelmap,
+    });
+
+    // update the previously stored positionPresentation with the new viewportId
+    // presentation so that when we put the referencedDisplaySet back in the viewport
+    // it will be in the correct position zoom and pan
+    commandsManager.runCommand('updateStoredPositionPresentation', {
+      viewportId,
+      displaySetInstanceUID: referencedDisplaySet.displaySetInstanceUID,
+    });
+
+    viewportGridService.setDisplaySetsForViewport({
+      viewportId,
+      displaySetInstanceUIDs: [referencedDisplaySet.displaySetInstanceUID],
+    });
+  }, [commandsManager, viewportId, referencedDisplaySet, segDisplaySet]);
+
   useEffect(() => {
     if (segIsLoading) {
       return;
@@ -158,14 +182,18 @@ function OHIFCornerstoneSEGViewport(props) {
       viewportId,
       segDisplaySet,
       preHydrateCallbacks: [storePresentationState],
+      hydrateCallback: hydrateSEG,
     }).then(isHydrated => {
       if (isHydrated) {
         setIsHydrated(true);
       }
     });
-  }, [servicesManager, viewportId, segDisplaySet, segIsLoading]);
+  }, [servicesManager, viewportId, segDisplaySet, segIsLoading, hydrateSEG]);
 
   useEffect(() => {
+    // on new seg display set, remove all segmentations from all viewports
+    segmentationService.clearSegmentationRepresentations(viewportId);
+
     const { unsubscribe } = segmentationService.subscribe(
       segmentationService.EVENTS.SEGMENTATION_LOADING_COMPLETE,
       evt => {
@@ -173,11 +201,14 @@ function OHIFCornerstoneSEGViewport(props) {
           setSegIsLoading(false);
         }
 
-        if (evt.overlappingSegments) {
-          uiNotificationService.show({
-            title: 'Overlapping Segments',
-            message: 'Overlapping segments detected which is not currently supported',
-            type: 'warning',
+        if (segDisplaySet?.firstSegmentedSliceImageId && viewportOptions?.presentationIds) {
+          const { firstSegmentedSliceImageId } = segDisplaySet;
+          const { presentationIds } = viewportOptions;
+
+          setPositionPresentation(presentationIds.positionPresentationId, {
+            viewReference: {
+              referencedImageId: firstSegmentedSliceImageId,
+            },
           });
         }
       }
@@ -233,28 +264,78 @@ function OHIFCornerstoneSEGViewport(props) {
       return;
     }
 
+    // keep the already stored segmentationPresentation for this viewport in memory
+    // so that we can restore it after hydrating the SEG
+    commandsManager.runCommand('updateStoredSegmentationPresentation', {
+      displaySet: segDisplaySet,
+      type: SegmentationRepresentations.Labelmap,
+    });
+
+    // always start fresh for this viewport since it is special type of viewport
+    // that should only show one segmentation at a time.
+    segmentationService.clearSegmentationRepresentations(viewportId);
+
     // This creates a custom tool group which has the lifetime of this view
     // only, and does NOT interfere with currently displayed segmentations.
     toolGroup = createSEGToolGroupAndAddTools(toolGroupService, customizationService, toolGroupId);
 
     return () => {
       // remove the segmentation representations if seg displayset changed
-      segmentationService.removeSegmentationRepresentationFromToolGroup(toolGroupId);
+      // e.g., another seg displayset is dragged into the viewport
+      segmentationService.clearSegmentationRepresentations(viewportId);
 
       // Only destroy the viewport specific implementation
       toolGroupService.destroyToolGroup(toolGroupId);
     };
   }, []);
 
-  useEffect(() => {
-    setIsHydrated(segDisplaySet.isHydrated);
+  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();
+    hydrateSEG();
+  }, [storePresentationState, hydrateSEG]);
 
-    return () => {
-      // remove the segmentation representations if seg displayset changed
-      segmentationService.removeSegmentationRepresentationFromToolGroup(toolGroupId);
-      referencedDisplaySetRef.current = null;
-    };
-  }, [segDisplaySet]);
+  useEffect(() => {
+    viewportActionCornersService.addComponents([
+      {
+        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/pane:visible'
+            }
+          ></ViewportActionArrows>
+        ),
+        indexPriority: 0,
+        location: viewportActionCornersService.LOCATIONS.topRight,
+      },
+    ]);
+  }, [
+    activeViewportId,
+    isHydrated,
+    onSegmentChange,
+    onStatusClick,
+    viewportActionCornersService,
+    viewportId,
+  ]);
 
   // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   let childrenWithProps = null;
@@ -279,67 +360,8 @@ function OHIFCornerstoneSEGViewport(props) {
     });
   }
 
-  const {
-    PatientID,
-    PatientName,
-    PatientSex,
-    PatientAge,
-    SliceThickness,
-    ManufacturerModelName,
-    StudyDate,
-    SeriesDescription,
-    SpacingBetweenSlices,
-  } = referencedDisplaySetRef.current.metadata;
-
-  const onStatusClick = async () => {
-    // Before hydrating a SEG and make it added to all viewports in the grid
-    // that share the same frameOfReferenceUID, we need to store the viewport grid
-    // presentation state, so that we can restore it after hydrating the SEG. This is
-    // required if the user has changed the viewport (other viewport than SEG viewport)
-    // presentation state (w/l and invert) and then opens the SEG. If we don't store
-    // the presentation state, the viewport will be reset to the default presentation
-    storePresentationState();
-    const isHydrated = await hydrateSEGDisplaySet({
-      segDisplaySet,
-      viewportId,
-      servicesManager,
-    });
-
-    setIsHydrated(isHydrated);
-  };
   return (
     <>
-      <ViewportActionBar
-        onDoubleClick={evt => {
-          evt.stopPropagation();
-          evt.preventDefault();
-        }}
-        onArrowsClick={onSegmentChange}
-        getStatusComponent={() => {
-          return _getStatusComponent({
-            isHydrated,
-            onStatusClick,
-          });
-        }}
-        studyData={{
-          label: viewportLabel,
-          useAltStyling: true,
-          studyDate: formatDate(StudyDate),
-          seriesDescription: `SEG Viewport ${SeriesDescription}`,
-          patientInformation: {
-            patientName: PatientName ? OHIF.utils.formatPN(PatientName.Alphabetic) : '',
-            patientSex: PatientSex || '',
-            patientAge: PatientAge || '',
-            MRN: PatientID || '',
-            thickness: SliceThickness ? utils.roundNumber(SliceThickness, 2) : '',
-            thicknessUnits: SliceThickness !== undefined ? 'mm' : '',
-            spacing:
-              SpacingBetweenSlices !== undefined ? utils.roundNumber(SpacingBetweenSlices, 2) : '',
-            scanner: ManufacturerModelName || '',
-          },
-        }}
-      />
-
       <div className="relative flex h-full w-full flex-row overflow-hidden">
         {segIsLoading && (
           <LoadingIndicatorTotalPercent
@@ -356,25 +378,19 @@ function OHIFCornerstoneSEGViewport(props) {
   );
 }
 
-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: [SharedFunctionalGroup],
-  } = segDisplaySet.instance;
-  const {
-    PixelMeasuresSequence: [PixelMeasures],
-  } = SharedFunctionalGroup;
+  const { SharedFunctionalGroupsSequence } = segDisplaySet.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];

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

@@ -1,23 +1,21 @@
 import React from 'react';
 import { useTranslation } from 'react-i18next';
-import { Icon, Tooltip } from '@ohif/ui';
+import { Tooltip, ViewportActionButton } from '@ohif/ui';
+import { Icons } from '@ohif/ui-next';
 
 export default function _getStatusComponent({ isHydrated, onStatusClick }) {
   let ToolTipMessage = null;
   let StatusIcon = null;
 
-  const { t } = useTranslation('Common');
-  const loadStr = t('LOAD');
-
   switch (isHydrated) {
     case true:
-      StatusIcon = () => <Icon name="status-alert" />;
+      StatusIcon = () => <Icons.ByName name="status-alert" />;
 
       ToolTipMessage = () => <div>This Segmentation is loaded in the segmentation panel</div>;
       break;
     case false:
       StatusIcon = () => (
-        <Icon
+        <Icons.ByName
           className="text-aqua-pale"
           name="status-untracked"
         />
@@ -26,23 +24,22 @@ export default function _getStatusComponent({ isHydrated, onStatusClick }) {
       ToolTipMessage = () => <div>Click LOAD to load segmentation.</div>;
   }
 
-  const StatusArea = () => (
-    <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}
+  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>
-      )}
-    </div>
-  );
+        {!isHydrated && (
+          <ViewportActionButton onInteraction={onStatusClick}>{loadStr}</ViewportActionButton>
+        )}
+      </div>
+    );
+  };
 
   return (
     <>

extensions/cornerstone-dicom-sr/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone-dicom-sr",
-  "version": "3.7.0-beta.64",
+  "version": "3.10.0-beta.39",
   "description": "OHIF extension for an SR Cornerstone Viewport",
   "author": "OHIF",
   "license": "MIT",
@@ -23,6 +23,8 @@
     "ohif-extension"
   ],
   "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:cornerstone": "yarn run dev",
     "build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
@@ -32,21 +34,21 @@
     "test:unit:ci": "jest --ci --runInBand --collectCoverage --passWithNoTests"
   },
   "peerDependencies": {
-    "@ohif/core": "3.7.0-beta.64",
-    "@ohif/extension-cornerstone": "3.7.0-beta.64",
-    "@ohif/extension-measurement-tracking": "3.7.0-beta.64",
-    "@ohif/ui": "3.7.0-beta.64",
-    "dcmjs": "^0.29.5",
+    "@ohif/core": "3.10.0-beta.39",
+    "@ohif/extension-cornerstone": "3.10.0-beta.39",
+    "@ohif/extension-measurement-tracking": "3.10.0-beta.39",
+    "@ohif/ui": "3.10.0-beta.39",
+    "dcmjs": "*",
     "dicom-parser": "^1.8.9",
     "hammerjs": "^2.0.8",
     "prop-types": "^15.6.2",
-    "react": "^17.0.2"
+    "react": "^18.3.1"
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/adapters": "^1.11.4",
-    "@cornerstonejs/core": "^1.11.4",
-    "@cornerstonejs/tools": "^1.11.4",
+    "@cornerstonejs/adapters": "^2.14.7",
+    "@cornerstonejs/core": "^2.14.7",
+    "@cornerstonejs/tools": "^2.14.7",
     "classnames": "^2.3.2"
   }
 }

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

@@ -5,6 +5,7 @@ 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;
@@ -40,7 +41,9 @@ const _generateReport = (measurementData, additionalFindingTypes, options = {})
   return dataset;
 };
 
-const commandsModule = ({}) => {
+const commandsModule = (props: withAppTypes) => {
+  const { servicesManager, extensionManager, commandsManager } = props;
+  const { customizationService, displaySetService, viewportGridService } = servicesManager.services;
   const actions = {
     /**
      *
@@ -55,7 +58,7 @@ const commandsModule = ({}) => {
       const reportBlob = dcmjs.data.datasetToBlob(srDataset);
 
       //Create a URL for the binary.
-      var objectUrl = URL.createObjectURL(reportBlob);
+      const objectUrl = URL.createObjectURL(reportBlob);
       window.location.assign(objectUrl);
     },
 
@@ -95,7 +98,15 @@ const commandsModule = ({}) => {
           throw new Error('Invalid report, no content');
         }
 
-        await dataSource.store.dicom(naturalizedReport);
+        const onBeforeDicomStore =
+          customizationService.getModeCustomization('onBeforeDicomStore')?.value;
+
+        let dicomDict;
+        if (typeof onBeforeDicomStore === 'function') {
+          dicomDict = onBeforeDicomStore({ measurementData, naturalizedReport });
+        }
+
+        await dataSource.store.dicom(naturalizedReport, null, dicomDict);
 
         if (StudyInstanceUID) {
           dataSource.deleteStudyMetadataPromise(StudyInstanceUID);
@@ -113,18 +124,38 @@ const commandsModule = ({}) => {
         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.
+     */
+    loadSRMeasurements: ({ displaySetInstanceUID }) => {
+      const { SeriesInstanceUIDs } = hydrateStructuredReport(
+        { servicesManager, extensionManager },
+        displaySetInstanceUID
+      );
+
+      const displaySets = displaySetService.getDisplaySetsForSeries(SeriesInstanceUIDs[0]);
+      if (displaySets.length) {
+        viewportGridService.setDisplaySetsForViewports([
+          {
+            viewportId: viewportGridService.getActiveViewportId(),
+            displaySetInstanceUIDs: [displaySets[0].displaySetInstanceUID],
+          },
+        ]);
+      }
+    },
   };
 
   const definitions = {
     downloadReport: {
       commandFn: actions.downloadReport,
-      storeContexts: [],
-      options: {},
     },
     storeMeasurements: {
       commandFn: actions.storeMeasurements,
-      storeContexts: [],
-      options: {},
+    },
+    loadSRMeasurements: {
+      commandFn: actions.loadSRMeasurements,
     },
   };
 

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

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

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

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

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

@@ -1,35 +1,23 @@
 import PropTypes from 'prop-types';
 import React, { useCallback, useContext, useEffect, useState } from 'react';
 import { useTranslation } from 'react-i18next';
-import OHIF, { utils, ServicesManager, ExtensionManager } from '@ohif/core';
+import { ExtensionManager, useToolbar } from '@ohif/core';
 
 import { setTrackingUniqueIdentifiersForElement } from '../tools/modules/dicomSRModule';
 
-import { Icon, Tooltip, useViewportGrid, ViewportActionBar } from '@ohif/ui';
-import hydrateStructuredReport from '../utils/hydrateStructuredReport';
-import { useAppConfig } from '@state';
-
-const { formatDate } = utils;
-
+import { Icon, Tooltip, useViewportGrid, ViewportActionArrows } from '@ohif/ui';
+import createReferencedImageDisplaySet from '../utils/createReferencedImageDisplaySet';
+import { usePositionPresentationStore } from '@ohif/extension-cornerstone';
+import { Icons } from '@ohif/ui-next';
 const MEASUREMENT_TRACKING_EXTENSION_ID = '@ohif/extension-measurement-tracking';
 
 const SR_TOOLGROUP_BASE_NAME = 'SRToolGroup';
 
-function OHIFCornerstoneSRViewport(props) {
-  const {
-    children,
-    dataSource,
-    displaySets,
-    viewportLabel,
-    viewportOptions,
-    servicesManager,
-    extensionManager,
-  } = props;
+function OHIFCornerstoneSRMeasurementViewport(props: withAppTypes) {
+  const { children, dataSource, displaySets, viewportOptions, servicesManager, extensionManager } =
+    props;
 
-  const [appConfig] = useAppConfig();
-
-  const { displaySetService, cornerstoneViewportService, measurementService } =
-    servicesManager.services;
+  const { displaySetService, viewportActionCornersService } = servicesManager.services;
 
   const viewportId = viewportOptions.viewportId;
 
@@ -40,6 +28,8 @@ function OHIFCornerstoneSRViewport(props) {
 
   const srDisplaySet = displaySets[0];
 
+  const { setPositionPresentation } = usePositionPresentationStore();
+
   const [viewportGrid, viewportGridService] = useViewportGrid();
   const [measurementSelected, setMeasurementSelected] = useState(0);
   const [measurementCount, setMeasurementCount] = useState(1);
@@ -48,9 +38,10 @@ function OHIFCornerstoneSRViewport(props) {
   const [element, setElement] = useState(null);
   const { viewports, activeViewportId } = viewportGrid;
 
+  const { t } = useTranslation('Common');
+
   // Optional hook into tracking extension, if present.
   let trackedMeasurements;
-  let sendTrackedMeasurementsEvent;
 
   const hasMeasurementTrackingExtension = extensionManager.registeredExtensionIds.includes(
     MEASUREMENT_TRACKING_EXTENSION_ID
@@ -63,29 +54,13 @@ function OHIFCornerstoneSRViewport(props) {
 
     const tracked = useContext(contextModule.context);
     trackedMeasurements = tracked?.[0];
-    sendTrackedMeasurementsEvent = tracked?.[1];
-  }
-  if (!sendTrackedMeasurementsEvent) {
-    // if no panels from measurement-tracking extension is used, this code will run
-    trackedMeasurements = null;
-    sendTrackedMeasurementsEvent = (eventName, { displaySetInstanceUID }) => {
-      measurementService.clearMeasurements();
-      const { SeriesInstanceUIDs } = hydrateStructuredReport(
-        { servicesManager, extensionManager, appConfig },
-        displaySetInstanceUID
-      );
-      const displaySets = displaySetService.getDisplaySetsForSeries(SeriesInstanceUIDs[0]);
-      if (displaySets.length) {
-        viewportGridService.setDisplaySetsForViewports([
-          {
-            viewportId: activeViewportId,
-            displaySetInstanceUIDs: [displaySets[0].displaySetInstanceUID],
-          },
-        ]);
-      }
-    };
   }
 
+  /**
+   * Todo: what is this, not sure what it does regarding the react aspect,
+   * it is updating a local variable? which is not state.
+   */
+  const [isLocked, setIsLocked] = useState(trackedMeasurements?.context?.trackedSeries?.length > 0);
   /**
    * Store the tracking identifiers per viewport in order to be able to
    * show the SR measurements on the referenced image on the correct viewport,
@@ -128,35 +103,31 @@ function OHIFCornerstoneSRViewport(props) {
         console.warn('More than one SOPClassUID in the same series is not yet supported.');
       }
 
+      // if (!srDisplaySet.measurements || !srDisplaySet.measurements.length) {
+      //   return;
+      // }
+
       _getViewportReferencedDisplaySetData(
         srDisplaySet,
         newMeasurementSelected,
         displaySetService
       ).then(({ referencedDisplaySet, referencedDisplaySetMetadata }) => {
+        if (!referencedDisplaySet || !referencedDisplaySetMetadata) {
+          return;
+        }
+
         setMeasurementSelected(newMeasurementSelected);
+
         setActiveImageDisplaySetData(referencedDisplaySet);
         setReferencedDisplaySetMetadata(referencedDisplaySetMetadata);
 
-        if (
-          referencedDisplaySet.displaySetInstanceUID ===
-          activeImageDisplaySetData?.displaySetInstanceUID
-        ) {
-          const { measurements } = srDisplaySet;
-
-          // it means that we have a new referenced display set, and the
-          // imageIdIndex will handle it by updating the viewport, but if they
-          // are the same we just need to use measurementService to jump to the
-          // new measurement
-          const csViewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
-
-          const imageIds = csViewport.getImageIds();
-
-          const imageIdIndex = imageIds.indexOf(measurements[newMeasurementSelected].imageId);
-
-          if (imageIdIndex !== -1) {
-            csViewport.setImageIdIndex(imageIdIndex);
-          }
-        }
+        const { presentationIds } = viewportOptions;
+        const measurement = srDisplaySet.measurements[newMeasurementSelected];
+        setPositionPresentation(presentationIds.positionPresentationId, {
+          viewReference: {
+            referencedImageId: measurement.imageId,
+          },
+        });
       });
     },
     [dataSource, srDisplaySet, activeImageDisplaySetData, viewportId]
@@ -178,10 +149,6 @@ function OHIFCornerstoneSRViewport(props) {
       return null;
     }
 
-    const initialImageIndex = activeImageDisplaySetData.images.findIndex(
-      image => image.imageId === measurement.imageId
-    );
-
     return (
       <Component
         {...props}
@@ -202,8 +169,10 @@ function OHIFCornerstoneSRViewport(props) {
           // The positionIds for the viewport aren't meaningful for the child display sets
           positionIds: null,
         }}
-        onElementEnabled={onElementEnabled}
-        initialImageIndex={initialImageIndex}
+        onElementEnabled={evt => {
+          props.onElementEnabled?.(evt);
+          onElementEnabled(evt);
+        }}
         isJumpToMeasurementDisabled={true}
       ></Component>
     );
@@ -213,18 +182,11 @@ function OHIFCornerstoneSRViewport(props) {
     direction => {
       let newMeasurementSelected = measurementSelected;
 
-      if (direction === 'right') {
-        newMeasurementSelected++;
-
-        if (newMeasurementSelected >= measurementCount) {
-          newMeasurementSelected = 0;
-        }
-      } else {
-        newMeasurementSelected--;
-
-        if (newMeasurementSelected < 0) {
-          newMeasurementSelected = measurementCount - 1;
-        }
+      newMeasurementSelected += direction;
+      if (newMeasurementSelected >= measurementCount) {
+        newMeasurementSelected = 0;
+      } else if (newMeasurementSelected < 0) {
+        newMeasurementSelected = measurementCount - 1;
       }
 
       setTrackingIdentifiers(newMeasurementSelected);
@@ -240,7 +202,7 @@ function OHIFCornerstoneSRViewport(props) {
     const onDisplaySetsRemovedSubscription = displaySetService.subscribe(
       displaySetService.EVENTS.DISPLAY_SETS_REMOVED,
       ({ displaySetInstanceUIDs }) => {
-        const activeViewport = viewports[activeViewportId];
+        const activeViewport = viewports.get(activeViewportId);
         if (displaySetInstanceUIDs.includes(activeViewport.displaySetInstanceUID)) {
           viewportGridService.setDisplaySetsForViewport({
             viewportId: activeViewportId,
@@ -263,11 +225,15 @@ function OHIFCornerstoneSRViewport(props) {
    * if it is hydrated we don't even use the SR viewport.
    */
   useEffect(() => {
-    if (!srDisplaySet.isLoaded) {
-      srDisplaySet.load();
-    }
-    const numMeasurements = srDisplaySet.measurements.length;
-    setMeasurementCount(numMeasurements);
+    const loadSR = async () => {
+      if (!srDisplaySet.isLoaded) {
+        await srDisplaySet.load();
+      }
+      const numMeasurements = srDisplaySet.measurements.length;
+      setMeasurementCount(numMeasurements);
+      updateViewport(measurementSelected);
+    };
+    loadSR();
   }, [srDisplaySet]);
 
   /**
@@ -275,28 +241,53 @@ function OHIFCornerstoneSRViewport(props) {
    * the element changes
    */
   useEffect(() => {
-    if (!element || !srDisplaySet.isLoaded) {
-      return;
-    }
-    setTrackingIdentifiers(measurementSelected);
+    const updateSR = async () => {
+      if (!srDisplaySet.isLoaded) {
+        await srDisplaySet.load();
+      }
+      if (!element || !srDisplaySet.isLoaded) {
+        return;
+      }
+      setTrackingIdentifiers(measurementSelected);
+    };
+    updateSR();
   }, [measurementSelected, element, setTrackingIdentifiers, srDisplaySet]);
 
-  /**
-   * Todo: what is this, not sure what it does regarding the react aspect,
-   * it is updating a local variable? which is not state.
-   */
-  let isLocked = trackedMeasurements?.context?.trackedSeries?.length > 0;
   useEffect(() => {
-    isLocked = trackedMeasurements?.context?.trackedSeries?.length > 0;
+    setIsLocked(trackedMeasurements?.context?.trackedSeries?.length > 0);
   }, [trackedMeasurements]);
 
-  /**
-   * Data fetching for the SR displaySet, which updates the measurements and
-   * also gets the referenced image displaySet that SR is based on.
-   */
   useEffect(() => {
-    updateViewport(measurementSelected);
-  }, [dataSource, srDisplaySet]);
+    viewportActionCornersService.addComponents([
+      {
+        viewportId,
+        id: 'viewportStatusComponent',
+        component: _getStatusComponent({
+          srDisplaySet,
+          viewportId,
+          isRehydratable: srDisplaySet.isRehydratable,
+          isLocked,
+          t,
+          servicesManager,
+        }),
+        indexPriority: -100,
+        location: viewportActionCornersService.LOCATIONS.topLeft,
+      },
+      {
+        viewportId,
+        id: 'viewportActionArrowsComponent',
+        index: 0,
+        component: (
+          <ViewportActionArrows
+            key="actionArrows"
+            onArrowsClick={onMeasurementChange}
+          ></ViewportActionArrows>
+        ),
+        indexPriority: 0,
+        location: viewportActionCornersService.LOCATIONS.topRight,
+      },
+    ]);
+  }, [isLocked, onMeasurementChange, srDisplaySet, t, viewportActionCornersService, viewportId]);
 
   // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   let childrenWithProps = null;
@@ -317,57 +308,8 @@ function OHIFCornerstoneSRViewport(props) {
     });
   }
 
-  const {
-    PatientID,
-    PatientName,
-    PatientSex,
-    PatientAge,
-    SliceThickness,
-    ManufacturerModelName,
-    StudyDate,
-    SeriesDescription,
-    SpacingBetweenSlices,
-    SeriesNumber,
-  } = referencedDisplaySetMetadata;
-
-  // TODO -> disabled double click for now: onDoubleClick={_onDoubleClick}
   return (
     <>
-      <ViewportActionBar
-        onDoubleClick={evt => {
-          evt.stopPropagation();
-          evt.preventDefault();
-        }}
-        onArrowsClick={onMeasurementChange}
-        getStatusComponent={() =>
-          _getStatusComponent({
-            srDisplaySet,
-            viewportId,
-            isTracked: false,
-            isRehydratable: srDisplaySet.isRehydratable,
-            isLocked,
-            sendTrackedMeasurementsEvent,
-          })
-        }
-        studyData={{
-          label: viewportLabel,
-          useAltStyling: true,
-          studyDate: formatDate(StudyDate),
-          currentSeries: SeriesNumber,
-          seriesDescription: SeriesDescription || '',
-          patientInformation: {
-            patientName: PatientName ? OHIF.utils.formatPN(PatientName.Alphabetic) : '',
-            patientSex: PatientSex || '',
-            patientAge: PatientAge || '',
-            MRN: PatientID || '',
-            thickness: SliceThickness ? `${SliceThickness.toFixed(2)}mm` : '',
-            spacing:
-              SpacingBetweenSlices !== undefined ? `${SpacingBetweenSlices.toFixed(2)}mm` : '',
-            scanner: ManufacturerModelName || '',
-          },
-        }}
-      />
-
       <div className="relative flex h-full w-full flex-row overflow-hidden">
         {getCornerstoneViewport()}
         {childrenWithProps}
@@ -376,23 +318,17 @@ function OHIFCornerstoneSRViewport(props) {
   );
 }
 
-OHIFCornerstoneSRViewport.propTypes = {
+OHIFCornerstoneSRMeasurementViewport.propTypes = {
   displaySets: PropTypes.arrayOf(PropTypes.object),
   viewportId: PropTypes.string.isRequired,
   dataSource: PropTypes.object,
   children: PropTypes.node,
   viewportLabel: PropTypes.string,
-  customProps: PropTypes.object,
   viewportOptions: PropTypes.object,
-  viewportLabel: PropTypes.string,
-  servicesManager: PropTypes.instanceOf(ServicesManager).isRequired,
+  servicesManager: PropTypes.object.isRequired,
   extensionManager: PropTypes.instanceOf(ExtensionManager).isRequired,
 };
 
-OHIFCornerstoneSRViewport.defaultProps = {
-  customProps: {},
-};
-
 async function _getViewportReferencedDisplaySetData(
   displaySet,
   measurementSelected,
@@ -402,6 +338,17 @@ async function _getViewportReferencedDisplaySetData(
   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);
 
@@ -428,16 +375,9 @@ function _getStatusComponent({
   viewportId,
   isRehydratable,
   isLocked,
-  sendTrackedMeasurementsEvent,
+  t,
+  servicesManager,
 }) {
-  const handleMouseUp = () => {
-    sendTrackedMeasurementsEvent('HYDRATE_SR', {
-      displaySetInstanceUID: srDisplaySet.displaySetInstanceUID,
-      viewportId,
-    });
-  };
-
-  const { t } = useTranslation('Common');
   const loadStr = t('LOAD');
 
   // 1 - Incompatible
@@ -449,7 +389,7 @@ function _getStatusComponent({
 
   switch (state) {
     case 1:
-      StatusIcon = () => <Icon name="status-alert" />;
+      StatusIcon = () => <Icons.ByName name="status-alert" />;
 
       ToolTipMessage = () => (
         <div>
@@ -460,7 +400,7 @@ function _getStatusComponent({
       );
       break;
     case 2:
-      StatusIcon = () => <Icon name="status-locked" />;
+      StatusIcon = () => <Icons.ByName name="status-locked" />;
 
       ToolTipMessage = () => (
         <div>
@@ -474,7 +414,7 @@ function _getStatusComponent({
       break;
     case 3:
       StatusIcon = () => (
-        <Icon
+        <Icons.ByName
           className="text-aqua-pale"
           name="status-untracked"
         />
@@ -483,23 +423,46 @@ function _getStatusComponent({
       ToolTipMessage = () => <div>{`Click ${loadStr} to restore measurements.`}</div>;
   }
 
-  const StatusArea = () => (
-    <div className="flex h-6 cursor-default text-sm leading-6 text-white">
-      <div className="bg-customgray-100 flex min-w-[45px] items-center rounded-l-xl rounded-r p-1">
-        <StatusIcon />
-        <span className="ml-1">SR</span>
-      </div>
-      {state === 3 && (
-        <div
-          className="bg-primary-main hover:bg-primary-light ml-1 cursor-pointer rounded px-1.5 hover:text-black"
-          // Using onMouseUp here because onClick is not working when the viewport is not active and is styled with pointer-events:none
-          onMouseUp={handleMouseUp}
-        >
-          {loadStr}
+  const StatusArea = () => {
+    const { toolbarButtons: loadSRMeasurementsButtons, onInteraction } = useToolbar({
+      servicesManager,
+      buttonSection: 'loadSRMeasurements',
+    });
+
+    const commandOptions = {
+      displaySetInstanceUID: srDisplaySet.displaySetInstanceUID,
+      viewportId,
+    };
+
+    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">SR</span>
         </div>
-      )}
-    </div>
-  );
+        {state === 3 && (
+          <>
+            {loadSRMeasurementsButtons.map(toolDef => {
+              if (!toolDef) {
+                return null;
+              }
+              const { id, Component, componentProps } = toolDef;
+              const tool = (
+                <Component
+                  key={id}
+                  id={id}
+                  onInteraction={args => onInteraction({ ...args, ...commandOptions })}
+                  {...componentProps}
+                />
+              );
+
+              return <div key={id}>{tool}</div>;
+            })}
+          </>
+        )}
+      </div>
+    );
+  };
 
   return (
     <>
@@ -516,4 +479,4 @@ function _getStatusComponent({
   );
 }
 
-export default OHIFCornerstoneSRViewport;
+export default OHIFCornerstoneSRMeasurementViewport;

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

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

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

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

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

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

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

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

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

@@ -1,30 +1,37 @@
-import { SOPClassHandlerName, SOPClassHandlerId } from './id';
 import { utils, classes, DisplaySetService, Types } from '@ohif/core';
-import addMeasurement from './utils/addMeasurement';
-import isRehydratable from './utils/isRehydratable';
+import { Enums as CSExtensionEnums } from '@ohif/extension-cornerstone';
 import { adaptersSR } from '@cornerstonejs/adapters';
 
+import addSRAnnotation from './utils/addSRAnnotation';
+import isRehydratable from './utils/isRehydratable';
+import {
+  SOPClassHandlerName,
+  SOPClassHandlerId,
+  SOPClassHandlerId3D,
+  SOPClassHandlerName3D,
+} from './id';
+import { CodeNameCodeSequenceValues, CodingSchemeDesignators } from './enums';
+
+const { sopClassDictionary } = utils;
+const { CORNERSTONE_3D_TOOLS_SOURCE_NAME, CORNERSTONE_3D_TOOLS_SOURCE_VERSION } = CSExtensionEnums;
+const { ImageSet, MetadataProvider: metadataProvider } = classes;
+const { CodeScheme: Cornerstone3DCodeScheme } = adaptersSR.Cornerstone3D;
+
 type InstanceMetadata = Types.InstanceMetadata;
 
-const { CodeScheme: Cornerstone3DCodeScheme } = adaptersSR.Cornerstone3D;
-
-const { ImageSet, MetadataProvider: metadataProvider } = classes;
-
-// TODO ->
-// Add SR thumbnail
-// Make viewport
-// Get stacks from referenced displayInstanceUID and load into wrapped CornerStone viewport.
+/**
+ * TODO
+ * - [ ] Add SR thumbnail
+ * - [ ] Make viewport
+ * - [ ] Get stacks from referenced displayInstanceUID and load into wrapped CornerStone viewport
+ */
 
 const sopClassUids = [
-  '1.2.840.10008.5.1.4.1.1.88.11', //BASIC_TEXT_SR:
-  '1.2.840.10008.5.1.4.1.1.88.22', //ENHANCED_SR:
-  '1.2.840.10008.5.1.4.1.1.88.33', //COMPREHENSIVE_SR:
-  '1.2.840.10008.5.1.4.1.1.88.34', //COMPREHENSIVE_3D_SR:
+  sopClassDictionary.BasicTextSR,
+  sopClassDictionary.EnhancedSR,
+  sopClassDictionary.ComprehensiveSR,
 ];
 
-const CORNERSTONE_3D_TOOLS_SOURCE_NAME = 'Cornerstone3DTools';
-const CORNERSTONE_3D_TOOLS_SOURCE_VERSION = '0.1';
-
 const validateSameStudyUID = (uid: string, instances): void => {
   instances.forEach(it => {
     if (it.StudyInstanceUID !== uid) {
@@ -34,31 +41,6 @@ const validateSameStudyUID = (uid: string, instances): void => {
   });
 };
 
-const CodeNameCodeSequenceValues = {
-  ImagingMeasurementReport: '126000',
-  ImageLibrary: '111028',
-  ImagingMeasurements: '126010',
-  MeasurementGroup: '125007',
-  ImageLibraryGroup: '126200',
-  TrackingUniqueIdentifier: '112040',
-  TrackingIdentifier: '112039',
-  Finding: '121071',
-  FindingSite: 'G-C0E3', // SRT
-  CornerstoneFreeText: Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT, //
-};
-
-const CodingSchemeDesignators = {
-  SRT: 'SRT',
-  CornerstoneCodeSchemes: [Cornerstone3DCodeScheme.CodingSchemeDesignator, 'CST4'],
-};
-
-const RELATIONSHIP_TYPE = {
-  INFERRED_FROM: 'INFERRED FROM',
-  CONTAINS: 'CONTAINS',
-};
-
-const CORNERSTONE_FREETEXT_CODE_VALUE = 'CORNERSTONEFREETEXT';
-
 /**
  * Adds instances to the DICOM SR series, rather than creating a new
  * series, so that as SR's are saved, they append to the series, and the
@@ -85,7 +67,11 @@ function addInstances(instances: InstanceMetadata[], displaySetService: DisplayS
  * @param servicesManager is the services that can be used for creating
  * @returns The list of display sets created for the given instances object
  */
-function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager) {
+function _getDisplaySetsFromSeries(
+  instances,
+  servicesManager: AppTypes.ServicesManager,
+  extensionManager
+) {
   // If the series has no instances, stop here
   if (!instances || !instances.length) {
     throw new Error('No instances were provided');
@@ -109,22 +95,12 @@ function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager)
   } = instance;
   validateSameStudyUID(instance.StudyInstanceUID, instances);
 
-  if (
-    !ConceptNameCodeSequence ||
-    ConceptNameCodeSequence.CodeValue !== CodeNameCodeSequenceValues.ImagingMeasurementReport
-  ) {
-    servicesManager.services.uiNotificationService.show({
-      title: 'DICOM SR',
-      message:
-        'OHIF only supports TID1500 Imaging Measurement Report Structured Reports. The SR you’re trying to view is not supported.',
-      type: 'warning',
-      duration: 6000,
-    });
-    return [];
-  }
+  const is3DSR = SOPClassUID === sopClassDictionary.Comprehensive3DSR;
+
+  const isImagingMeasurementReport =
+    ConceptNameCodeSequence?.CodeValue === CodeNameCodeSequenceValues.ImagingMeasurementReport;
 
   const displaySet = {
-    //plugin: id,
     Modality: 'SR',
     displaySetInstanceUID: utils.guid(),
     SeriesDescription,
@@ -133,13 +109,14 @@ function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager)
     SOPInstanceUID,
     SeriesInstanceUID,
     StudyInstanceUID,
-    SOPClassHandlerId,
+    SOPClassHandlerId: is3DSR ? SOPClassHandlerId3D : SOPClassHandlerId,
     SOPClassUID,
     instances,
     referencedImages: null,
     measurements: null,
     isDerivedDisplaySet: true,
     isLoaded: false,
+    isImagingMeasurementReport,
     sopClassUids,
     instance,
     addInstances,
@@ -150,115 +127,206 @@ function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager)
   return [displaySet];
 }
 
-function _load(displaySet, servicesManager, extensionManager) {
+/**
+ * Loads the display set with the given services and extension manager.
+ * @param srDisplaySet - The display set to load.
+ * @param servicesManager - The services manager containing displaySetService and measurementService.
+ * @param extensionManager - The extension manager containing data sources.
+ */
+async function _load(
+  srDisplaySet: Types.DisplaySet,
+  servicesManager: AppTypes.ServicesManager,
+  extensionManager: AppTypes.ExtensionManager
+) {
   const { displaySetService, measurementService } = servicesManager.services;
   const dataSources = extensionManager.getDataSources();
   const dataSource = dataSources[0];
+  const { ContentSequence } = srDisplaySet.instance;
 
-  const { ContentSequence } = displaySet.instance;
+  async function retrieveBulkData(obj, parentObj = null, key = null) {
+    for (const prop in obj) {
+      if (typeof obj[prop] === 'object' && obj[prop] !== null) {
+        await retrieveBulkData(obj[prop], obj, prop);
+      } else if (Array.isArray(obj[prop])) {
+        await Promise.all(obj[prop].map(item => retrieveBulkData(item, obj, prop)));
+      } 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,
+        });
+        if (parentObj && key) {
+          parentObj[key] = new Float32Array(value);
+        }
+      }
+    }
+  }
 
-  displaySet.referencedImages = _getReferencedImagesList(ContentSequence);
-  displaySet.measurements = _getMeasurements(ContentSequence);
+  if (srDisplaySet.isLoaded !== true) {
+    await retrieveBulkData(ContentSequence);
+  }
+
+  if (srDisplaySet.isImagingMeasurementReport) {
+    srDisplaySet.referencedImages = _getReferencedImagesList(ContentSequence);
+    srDisplaySet.measurements = _getMeasurements(ContentSequence);
+  } else {
+    srDisplaySet.referencedImages = [];
+    srDisplaySet.measurements = [];
+  }
 
   const mappings = measurementService.getSourceMappings(
     CORNERSTONE_3D_TOOLS_SOURCE_NAME,
     CORNERSTONE_3D_TOOLS_SOURCE_VERSION
   );
 
-  displaySet.isHydrated = false;
-  displaySet.isRehydratable = isRehydratable(displaySet, mappings);
-  displaySet.isLoaded = true;
+  srDisplaySet.isHydrated = false;
+  srDisplaySet.isRehydratable = isRehydratable(srDisplaySet, mappings);
+  srDisplaySet.isLoaded = true;
 
-  // Check currently added displaySets and add measurements if the sources exist.
+  /** Check currently added displaySets and add measurements if the sources exist */
   displaySetService.activeDisplaySets.forEach(activeDisplaySet => {
-    _checkIfCanAddMeasurementsToDisplaySet(displaySet, activeDisplaySet, dataSource);
+    _checkIfCanAddMeasurementsToDisplaySet(
+      srDisplaySet,
+      activeDisplaySet,
+      dataSource,
+      servicesManager
+    );
   });
 
-  // Subscribe to new displaySets as the source may come in after.
+  /** Subscribe to new displaySets as the source may come in after */
   displaySetService.subscribe(displaySetService.EVENTS.DISPLAY_SETS_ADDED, data => {
     const { displaySetsAdded } = data;
-    // If there are still some measurements that have not yet been loaded into cornerstone,
-    // See if we can load them onto any of the new displaySets.
+    /**
+     * If there are still some measurements that have not yet been loaded into cornerstone,
+     * See if we can load them onto any of the new displaySets.
+     */
     displaySetsAdded.forEach(newDisplaySet => {
-      _checkIfCanAddMeasurementsToDisplaySet(displaySet, newDisplaySet, dataSource);
+      _checkIfCanAddMeasurementsToDisplaySet(
+        srDisplaySet,
+        newDisplaySet,
+        dataSource,
+        servicesManager
+      );
     });
   });
 }
 
-function _checkIfCanAddMeasurementsToDisplaySet(srDisplaySet, newDisplaySet, dataSource) {
-  let unloadedMeasurements = srDisplaySet.measurements.filter(
+/**
+ * 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,
+  dataSource,
+  servicesManager: AppTypes.ServicesManager
+) {
+  const { customizationService } = servicesManager.services;
+
+  const unloadedMeasurements = srDisplaySet.measurements.filter(
     measurement => measurement.loaded === false
   );
 
-  if (unloadedMeasurements.length === 0) {
-    // All already loaded!
+  if (
+    unloadedMeasurements.length === 0 ||
+    !(newDisplaySet instanceof ImageSet) ||
+    newDisplaySet.unsupported
+  ) {
     return;
   }
 
-  if (!newDisplaySet instanceof ImageSet) {
-    // This also filters out _this_ displaySet, as it is not an ImageSet.
+  // const { sopClassUids } = newDisplaySet;
+  // Create a Set for faster lookups
+  // const sopClassUidSet = new Set(sopClassUids);
+
+  // Create a Map to efficiently look up ImageIds by SOPInstanceUID and frame number
+  const imageIdMap = new Map<string, string>();
+  const imageIds = dataSource.getImageIdsForDisplaySet(newDisplaySet);
+
+  for (const imageId of imageIds) {
+    const { SOPInstanceUID, frameNumber } = metadataProvider.getUIDsFromImageID(imageId);
+    const key = `${SOPInstanceUID}:${frameNumber || 1}`;
+    imageIdMap.set(key, imageId);
+  }
+
+  if (!unloadedMeasurements?.length) {
     return;
   }
 
-  const { sopClassUids, images } = newDisplaySet;
+  const is3DSR = srDisplaySet.SOPClassUID === sopClassDictionary.Comprehensive3DSR;
 
-  // Check if any have the newDisplaySet is the correct SOPClass.
-  unloadedMeasurements = unloadedMeasurements.filter(measurement =>
-    measurement.coords.some(coord =>
-      sopClassUids.includes(coord.ReferencedSOPSequence.ReferencedSOPClassUID)
-    )
-  );
+  for (let j = unloadedMeasurements.length - 1; j >= 0; j--) {
+    let measurement = unloadedMeasurements[j];
 
-  if (unloadedMeasurements.length === 0) {
-    // New displaySet isn't the correct SOPClass, so can't contain the referenced images.
-    return;
-  }
+    const onBeforeSRAddMeasurement = customizationService.getModeCustomization(
+      'onBeforeSRAddMeasurement'
+    )?.value;
 
-  const SOPInstanceUIDs = [];
-
-  unloadedMeasurements.forEach(measurement => {
-    const { coords } = measurement;
-
-    coords.forEach(coord => {
-      const SOPInstanceUID = coord.ReferencedSOPSequence.ReferencedSOPInstanceUID;
-
-      if (!SOPInstanceUIDs.includes(SOPInstanceUID)) {
-        SOPInstanceUIDs.push(SOPInstanceUID);
-      }
-    });
-  });
-
-  const imageIdsForDisplaySet = dataSource.getImageIdsForDisplaySet(newDisplaySet);
-
-  for (const imageId of imageIdsForDisplaySet) {
-    if (!unloadedMeasurements.length) {
-      // All measurements loaded.
-      return;
+    if (typeof onBeforeSRAddMeasurement === 'function') {
+      measurement = onBeforeSRAddMeasurement({
+        measurement,
+        StudyInstanceUID: srDisplaySet.StudyInstanceUID,
+        SeriesInstanceUID: srDisplaySet.SeriesInstanceUID,
+      });
     }
 
-    const { SOPInstanceUID, frameNumber } = metadataProvider.getUIDsFromImageID(imageId);
+    // if it is 3d SR we can just add the SR annotation
+    if (is3DSR) {
+      addSRAnnotation(measurement, null, null);
+      measurement.loaded = true;
+      continue;
+    }
 
-    if (SOPInstanceUIDs.includes(SOPInstanceUID)) {
-      for (let j = unloadedMeasurements.length - 1; j >= 0; j--) {
-        const measurement = unloadedMeasurements[j];
-        if (_measurementReferencesSOPInstanceUID(measurement, SOPInstanceUID, frameNumber)) {
-          addMeasurement(measurement, imageId, newDisplaySet.displaySetInstanceUID);
+    const referencedSOPSequence = measurement.coords[0].ReferencedSOPSequence;
+    if (!referencedSOPSequence) {
+      continue;
+    }
 
-          unloadedMeasurements.splice(j, 1);
-        }
-      }
+    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);
     }
   }
 }
 
+/**
+ * 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[0]?.ReferencedFrameNumber) ||
+      measurement.coords[0].ReferencedSOPSequence?.ReferencedFrameNumber) ||
     1;
 
   if (frameNumber && Number(frameNumber) !== Number(ReferencedFrameNumber)) {
@@ -268,40 +336,62 @@ function _measurementReferencesSOPInstanceUID(measurement, SOPInstanceUID, frame
   for (let j = 0; j < coords.length; j++) {
     const coord = coords[j];
     const { ReferencedSOPInstanceUID } = coord.ReferencedSOPSequence;
-
     if (ReferencedSOPInstanceUID === SOPInstanceUID) {
       return true;
     }
   }
+
+  return false;
 }
 
+/**
+ * Retrieves the SOP class handler module.
+ *
+ * @param {Object} options - The options for retrieving the SOP class handler module.
+ * @param {Object} options.servicesManager - The services manager.
+ * @param {Object} options.extensionManager - The extension manager.
+ * @returns {Array} An array containing the SOP class handler module.
+ */
 function getSopClassHandlerModule({ servicesManager, extensionManager }) {
   const getDisplaySetsFromSeries = instances => {
     return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
   };
-
   return [
     {
       name: SOPClassHandlerName,
       sopClassUids,
       getDisplaySetsFromSeries,
     },
+    {
+      name: SOPClassHandlerName3D,
+      sopClassUids: [sopClassDictionary.Comprehensive3DSR],
+      getDisplaySetsFromSeries,
+    },
   ];
 }
 
+/**
+ * Retrieves the measurements from the ImagingMeasurementReportContentSequence.
+ *
+ * @param {Array} ImagingMeasurementReportContentSequence - The ImagingMeasurementReportContentSequence array.
+ * @returns {Array} - The array of measurements.
+ */
 function _getMeasurements(ImagingMeasurementReportContentSequence) {
   const ImagingMeasurements = ImagingMeasurementReportContentSequence.find(
     item =>
       item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.ImagingMeasurements
   );
 
+  if (!ImagingMeasurements) {
+    return [];
+  }
+
   const MeasurementGroups = _getSequenceAsArray(ImagingMeasurements.ContentSequence).filter(
     item => item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.MeasurementGroup
   );
 
   const mergedContentSequencesByTrackingUniqueIdentifiers =
     _getMergedContentSequencesByTrackingUniqueIdentifiers(MeasurementGroups);
-
   const measurements = [];
 
   Object.keys(mergedContentSequencesByTrackingUniqueIdentifiers).forEach(
@@ -310,7 +400,6 @@ function _getMeasurements(ImagingMeasurementReportContentSequence) {
         mergedContentSequencesByTrackingUniqueIdentifiers[trackingUniqueIdentifier];
 
       const measurement = _processMeasurement(mergedContentSequence);
-
       if (measurement) {
         measurements.push(measurement);
       }
@@ -320,6 +409,12 @@ function _getMeasurements(ImagingMeasurementReportContentSequence) {
   return measurements;
 }
 
+/**
+ * Retrieves merged content sequences by tracking unique identifiers.
+ *
+ * @param {Array} MeasurementGroups - The measurement groups.
+ * @returns {Object} - The merged content sequences by tracking unique identifiers.
+ */
 function _getMergedContentSequencesByTrackingUniqueIdentifiers(MeasurementGroups) {
   const mergedContentSequencesByTrackingUniqueIdentifiers = {};
 
@@ -331,7 +426,6 @@ function _getMergedContentSequencesByTrackingUniqueIdentifiers(MeasurementGroups
         item.ConceptNameCodeSequence.CodeValue ===
         CodeNameCodeSequenceValues.TrackingUniqueIdentifier
     );
-
     if (!TrackingUniqueIdentifierItem) {
       console.warn('No Tracking Unique Identifier, skipping ambiguous measurement.');
     }
@@ -360,6 +454,15 @@ function _getMergedContentSequencesByTrackingUniqueIdentifiers(MeasurementGroups
   return mergedContentSequencesByTrackingUniqueIdentifiers;
 }
 
+/**
+ * Processes the measurement based on the merged content sequence.
+ * If the merged content sequence contains SCOORD or SCOORD3D value types,
+ * it calls the _processTID1410Measurement function.
+ * Otherwise, it calls the _processNonGeometricallyDefinedMeasurement function.
+ *
+ * @param {Array<Object>} mergedContentSequence - The merged content sequence to process.
+ * @returns {any} - The processed measurement result.
+ */
 function _processMeasurement(mergedContentSequence) {
   if (
     mergedContentSequence.some(
@@ -372,11 +475,21 @@ function _processMeasurement(mergedContentSequence) {
   return _processNonGeometricallyDefinedMeasurement(mergedContentSequence);
 }
 
+/**
+ * Processes TID 1410 style measurements from the mergedContentSequence.
+ * TID 1410 style measurements have a SCOORD or SCOORD3D at the top level,
+ * and non-geometric representations where each NUM has "INFERRED FROM" SCOORD/SCOORD3D.
+ *
+ * @param mergedContentSequence - The merged content sequence containing the measurements.
+ * @returns The measurement object containing the loaded status, labels, coordinates, tracking unique identifier, and tracking identifier.
+ */
 function _processTID1410Measurement(mergedContentSequence) {
   // Need to deal with TID 1410 style measurements, which will have a SCOORD or SCOORD3D at the top level,
   // And non-geometric representations where each NUM has "INFERRED FROM" SCOORD/SCOORD3D
 
-  const graphicItem = mergedContentSequence.find(group => group.ValueType === 'SCOORD');
+  const graphicItem = mergedContentSequence.find(
+    group => group.ValueType === 'SCOORD' || group.ValueType === 'SCOORD3D'
+  );
 
   const UIDREFContentItem = mergedContentSequence.find(group => group.ValueType === 'UIDREF');
 
@@ -403,7 +516,6 @@ function _processTID1410Measurement(mergedContentSequence) {
 
   NUMContentItems.forEach(item => {
     const { ConceptNameCodeSequence, MeasuredValueSequence } = item;
-
     if (MeasuredValueSequence) {
       measurement.labels.push(
         _getLabelFromMeasuredValueSequence(ConceptNameCodeSequence, MeasuredValueSequence)
@@ -411,12 +523,29 @@ function _processTID1410Measurement(mergedContentSequence) {
     }
   });
 
+  const findingSites = mergedContentSequence.filter(
+    item =>
+      item.ConceptNameCodeSequence.CodingSchemeDesignator === CodingSchemeDesignators.SCT &&
+      item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.FindingSiteSCT
+  );
+  if (findingSites.length) {
+    measurement.labels.push({
+      label: CodeNameCodeSequenceValues.FindingSiteSCT,
+      value: findingSites[0].ConceptCodeSequence.CodeMeaning,
+    });
+  }
+
   return measurement;
 }
 
+/**
+ * Processes the non-geometrically defined measurement from the merged content sequence.
+ *
+ * @param mergedContentSequence The merged content sequence containing the measurement data.
+ * @returns The processed measurement object.
+ */
 function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
   const NUMContentItems = mergedContentSequence.filter(group => group.ValueType === 'NUM');
-
   const UIDREFContentItem = mergedContentSequence.find(group => group.ValueType === 'UIDREF');
 
   const TrackingIdentifierContentItem = mergedContentSequence.find(
@@ -446,10 +575,10 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
     CodingSchemeDesignators.CornerstoneCodeSchemes.includes(
       finding.ConceptCodeSequence.CodingSchemeDesignator
     ) &&
-    finding.ConceptCodeSequence.CodeValue === CodeNameCodeSequenceValues.CornerstoneFreeText
+    finding.ConceptCodeSequence.CodeValue === Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT
   ) {
     measurement.labels.push({
-      label: CORNERSTONE_FREETEXT_CODE_VALUE,
+      label: Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT,
       value: finding.ConceptCodeSequence.CodeMeaning,
     });
   }
@@ -461,12 +590,13 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
         CodingSchemeDesignators.CornerstoneCodeSchemes.includes(
           FindingSite.ConceptCodeSequence.CodingSchemeDesignator
         ) &&
-        FindingSite.ConceptCodeSequence.CodeValue === CodeNameCodeSequenceValues.CornerstoneFreeText
+        FindingSite.ConceptCodeSequence.CodeValue ===
+          Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT
     );
 
     if (cornerstoneFreeTextFindingSite) {
       measurement.labels.push({
-        label: CORNERSTONE_FREETEXT_CODE_VALUE,
+        label: Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT,
         value: cornerstoneFreeTextFindingSite.ConceptCodeSequence.CodeMeaning,
       });
     }
@@ -476,15 +606,12 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
     const { ConceptNameCodeSequence, ContentSequence, MeasuredValueSequence } = item;
 
     const { ValueType } = ContentSequence;
-
     if (!ValueType === 'SCOORD') {
       console.warn(`Graphic ${ValueType} not currently supported, skipping annotation.`);
-
       return;
     }
 
     const coords = _getCoordsFromSCOORDOrSCOORD3D(ContentSequence);
-
     if (coords) {
       measurement.coords.push(coords);
     }
@@ -499,59 +626,62 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
   return measurement;
 }
 
-function _getCoordsFromSCOORDOrSCOORD3D(item) {
-  const { ValueType, RelationshipType, GraphicType, GraphicData } = item;
-
-  if (
-    !(
-      RelationshipType == RELATIONSHIP_TYPE.INFERRED_FROM ||
-      RelationshipType == RELATIONSHIP_TYPE.CONTAINS
-    )
-  ) {
-    console.warn(
-      `Relationshiptype === ${RelationshipType}. Cannot deal with NON TID-1400 SCOORD group with RelationshipType !== "INFERRED FROM" or "CONTAINS"`
-    );
-
-    return;
-  }
-
+/**
+ * Extracts coordinates from a graphic item of type SCOORD or SCOORD3D.
+ * @param {object} graphicItem - The graphic item containing the coordinates.
+ * @returns {object} - The extracted coordinates.
+ */
+const _getCoordsFromSCOORDOrSCOORD3D = graphicItem => {
+  const { ValueType, GraphicType, GraphicData } = graphicItem;
   const coords = { ValueType, GraphicType, GraphicData };
-
-  // ContentSequence has length of 1 as RelationshipType === 'INFERRED FROM'
-  if (ValueType === 'SCOORD') {
-    const { ReferencedSOPSequence } = item.ContentSequence;
-
-    coords.ReferencedSOPSequence = ReferencedSOPSequence;
-  } else if (ValueType === 'SCOORD3D') {
-    const { ReferencedFrameOfReferenceSequence } = item.ContentSequence;
-
-    coords.ReferencedFrameOfReferenceSequence = ReferencedFrameOfReferenceSequence;
-  }
-
+  coords.ReferencedSOPSequence = graphicItem.ContentSequence?.ReferencedSOPSequence;
+  coords.ReferencedFrameOfReferenceSequence =
+    graphicItem.ReferencedFrameOfReferenceUID ||
+    graphicItem.ContentSequence?.ReferencedFrameOfReferenceSequence;
   return coords;
-}
+};
 
+/**
+ * Retrieves the label and value from the provided ConceptNameCodeSequence and MeasuredValueSequence.
+ * @param {Object} ConceptNameCodeSequence - The ConceptNameCodeSequence object.
+ * @param {Object} MeasuredValueSequence - The MeasuredValueSequence object.
+ * @returns {Object} - An object containing the label and value.
+ *                    The label represents the CodeMeaning from the ConceptNameCodeSequence.
+ *                    The value represents the formatted NumericValue and CodeValue from the MeasuredValueSequence.
+ *                    Example: { label: 'Long Axis', value: '31.00 mm' }
+ */
 function _getLabelFromMeasuredValueSequence(ConceptNameCodeSequence, MeasuredValueSequence) {
   const { CodeMeaning } = ConceptNameCodeSequence;
   const { NumericValue, MeasurementUnitsCodeSequence } = MeasuredValueSequence;
   const { CodeValue } = MeasurementUnitsCodeSequence;
-
   const formatedNumericValue = NumericValue ? Number(NumericValue).toFixed(2) : '';
-
   return {
     label: CodeMeaning,
     value: `${formatedNumericValue} ${CodeValue}`,
   }; // E.g. Long Axis: 31.0 mm
 }
 
+/**
+ * Retrieves a list of referenced images from the Imaging Measurement Report Content Sequence.
+ *
+ * @param {Array} ImagingMeasurementReportContentSequence - The Imaging Measurement Report Content Sequence.
+ * @returns {Array} - The list of referenced images.
+ */
 function _getReferencedImagesList(ImagingMeasurementReportContentSequence) {
   const ImageLibrary = ImagingMeasurementReportContentSequence.find(
     item => item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.ImageLibrary
   );
 
+  if (!ImageLibrary) {
+    return [];
+  }
+
   const ImageLibraryGroup = _getSequenceAsArray(ImageLibrary.ContentSequence).find(
     item => item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.ImageLibraryGroup
   );
+  if (!ImageLibraryGroup) {
+    return [];
+  }
 
   const referencedImages = [];
 
@@ -575,6 +705,15 @@ function _getReferencedImagesList(ImagingMeasurementReportContentSequence) {
   return referencedImages;
 }
 
+/**
+ * Converts a DICOM sequence to an array.
+ * If the sequence is null or undefined, an empty array is returned.
+ * If the sequence is already an array, it is returned as is.
+ * Otherwise, the sequence is wrapped in an array and returned.
+ *
+ * @param {any} sequence - The DICOM sequence to convert.
+ * @returns {any[]} - The converted array.
+ */
 function _getSequenceAsArray(sequence) {
   if (!sequence) {
     return [];

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

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

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

@@ -1,6 +1,6 @@
 import React from 'react';
 import getSopClassHandlerModule from './getSopClassHandlerModule';
-import getHangingProtocolModule, { srProtocol } from './getHangingProtocolModule';
+import { srProtocol } from './getHangingProtocolModule';
 import onModeEnter from './onModeEnter';
 import getCommandsModule from './commandsModule';
 import preRegistration from './init';
@@ -8,9 +8,10 @@ import { id } from './id.js';
 import toolNames from './tools/toolNames';
 import hydrateStructuredReport from './utils/hydrateStructuredReport';
 import createReferencedImageDisplaySet from './utils/createReferencedImageDisplaySet';
+import Enums from './enums';
 
 const Component = React.lazy(() => {
-  return import(/* webpackPrefetch: true */ './viewports/OHIFCornerstoneSRViewport');
+  return import(/* webpackPrefetch: true */ './components/OHIFCornerstoneSRViewport');
 });
 
 const OHIFCornerstoneSRViewport = props => {
@@ -29,6 +30,7 @@ const dicomSRExtension = {
    * Only required property. Should be a unique value across all extensions.
    */
   id,
+
   onModeEnter,
 
   preRegistration,
@@ -54,7 +56,7 @@ const dicomSRExtension = {
   },
   getCommandsModule,
   getSopClassHandlerModule,
-  // Include dynmically computed values such as toolNames not known till instantiation
+  // Include dynamically computed values such as toolNames not known till instantiation
   getUtilityModule({ servicesManager }) {
     return [
       {
@@ -70,4 +72,4 @@ const dicomSRExtension = {
 export default dicomSRExtension;
 
 // Put static exports here so they can be type checked
-export { hydrateStructuredReport, createReferencedImageDisplaySet, srProtocol };
+export { hydrateStructuredReport, createReferencedImageDisplaySet, srProtocol, Enums, toolNames };

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

@@ -1,5 +1,4 @@
 import {
-  addTool,
   AngleTool,
   annotation,
   ArrowAnnotateTool,
@@ -9,34 +8,64 @@ import {
   CircleROITool,
   LengthTool,
   PlanarFreehandROITool,
+  RectangleROITool,
+  utilities as csToolsUtils,
 } from '@cornerstonejs/tools';
+import { Types, MeasurementService } from '@ohif/core';
+import { StackViewport, utilities as csUtils } from '@cornerstonejs/core';
+import { Enums as CSExtensionEnums } from '@ohif/extension-cornerstone';
 import DICOMSRDisplayTool from './tools/DICOMSRDisplayTool';
+import SCOORD3DPointTool from './tools/SCOORD3DPointTool';
+import SRSCOOR3DProbeMapper from './utils/SRSCOOR3DProbeMapper';
 import addToolInstance from './utils/addToolInstance';
-import { Types } from '@ohif/core';
 import toolNames from './tools/toolNames';
 
+const { CORNERSTONE_3D_TOOLS_SOURCE_NAME, CORNERSTONE_3D_TOOLS_SOURCE_VERSION } = CSExtensionEnums;
+
 /**
  * @param {object} configuration
  */
-export default function init({ configuration = {} }: Types.Extensions.ExtensionParams): void {
-  addTool(DICOMSRDisplayTool);
-  addToolInstance(toolNames.SRLength, LengthTool, {});
+export default function init({
+  configuration = {},
+  servicesManager,
+}: Types.Extensions.ExtensionParams): void {
+  const { measurementService, cornerstoneViewportService } = servicesManager.services;
+
+  addToolInstance(toolNames.DICOMSRDisplay, DICOMSRDisplayTool);
+  addToolInstance(toolNames.SRLength, LengthTool);
   addToolInstance(toolNames.SRBidirectional, BidirectionalTool);
   addToolInstance(toolNames.SREllipticalROI, EllipticalROITool);
   addToolInstance(toolNames.SRCircleROI, CircleROITool);
   addToolInstance(toolNames.SRArrowAnnotate, ArrowAnnotateTool);
   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);
-  // TODO - fix the rehydration of Freehand, as it throws an exception
-  // on a missing polyline. The fix is probably in CS3D
-  addToolInstance(toolNames.SRPlanarFreehandROI, PlanarFreehandROITool);
+
+  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',
   };
   annotation.config.style.setToolGroupToolStyles('SRToolGroup', {
+    [toolNames.DICOMSRDisplay]: dashedLine,
     SRLength: dashedLine,
     SRBidirectional: dashedLine,
     SREllipticalROI: dashedLine,
@@ -45,6 +74,31 @@ export default function init({ configuration = {} }: Types.Extensions.ExtensionP
     SRCobbAngle: dashedLine,
     SRAngle: dashedLine,
     SRPlanarFreehandROI: dashedLine,
+    SRRectangleROI: dashedLine,
     global: {},
   });
+
+  measurementService.subscribe(
+    MeasurementService.EVENTS.JUMP_TO_MEASUREMENT_LAYOUT,
+    ({ viewportId, measurement, isConsumed }) => {
+      if (isConsumed) {
+        return;
+      }
+      try {
+        const currentViewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
+        const { viewPlaneNormal } = currentViewport.getCamera();
+        const referencedImageId = csToolsUtils.getClosestImageIdForStackViewport(
+          currentViewport as StackViewport,
+          measurement.points[0],
+          viewPlaneNormal
+        );
+        const imageIndex = (currentViewport as StackViewport)
+          .getImageIds()
+          .indexOf(referencedImageId);
+        csUtils.jumpToSlice(currentViewport.element, { imageIndex });
+      } catch (error) {
+        console.warn('Unable to jump to image based on measurement coordinate', error);
+      }
+    }
+  );
 }

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

@@ -1,15 +0,0 @@
-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

@@ -0,0 +1,39 @@
+import React from 'react';
+
+import { SOPClassHandlerId, SOPClassHandlerId3D } from './id';
+import { ViewportActionButton } from '@ohif/ui';
+import i18n from '@ohif/i18n';
+
+export default function onModeEnter({ servicesManager }) {
+  const { displaySetService, toolbarService } = 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;
+  });
+
+  toolbarService.addButtons([
+    {
+      // A base/default button for loading measurements. It is added to the toolbar below.
+      // Customizations to this button can be made in the mode or by another extension.
+      // For example, the button label can be changed and/or the command to clear
+      // the measurements can be dropped.
+      id: 'loadSRMeasurements',
+      component: props => (
+        <ViewportActionButton {...props}>{i18n.t('Common:LOAD')}</ViewportActionButton>
+      ),
+      props: {
+        commands: ['clearMeasurements', 'loadSRMeasurements'],
+      },
+    },
+  ]);
+
+  // The toolbar used in the viewport's status bar. Modes and extensions can further customize
+  // it to optionally add other buttons.
+  toolbarService.createButtonSection('loadSRMeasurements', ['loadSRMeasurements']);
+}

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

@@ -7,10 +7,11 @@ import {
   Types as cs3DToolsTypes,
 } from '@cornerstonejs/tools';
 import { getTrackingUniqueIdentifiersForElement } from './modules/dicomSRModule';
-import SCOORD_TYPES from '../constants/scoordTypes';
+import { SCOORDTypes } from '../enums';
+import toolNames from './toolNames';
 
 export default class DICOMSRDisplayTool extends AnnotationTool {
-  static toolName = 'DICOMSRDisplay';
+  static toolName = toolNames.DICOMSRDisplay;
 
   constructor(
     toolProps = {},
@@ -22,14 +23,14 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
   }
 
   _getTextBoxLinesFromLabels(labels) {
-    // TODO -> max 3 for now (label + shortAxis + longAxis), need a generic solution for this!
+    // TODO -> max 5 for now (label + shortAxis + longAxis), need a generic solution for this!
 
-    const labelLength = Math.min(labels.length, 3);
+    const labelLength = Math.min(labels.length, 5);
     const lines = [];
 
     for (let i = 0; i < labelLength; i++) {
       const labelEntry = labels[i];
-      lines.push(`${_labelToShorthand(labelEntry.label)}${labelEntry.value}`);
+      lines.push(`${_labelToShorthand(labelEntry.label)}: ${labelEntry.value}`);
     }
 
     return lines;
@@ -65,7 +66,7 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
 
     // Filter toolData to only render the data for the active SR.
     const filteredAnnotations = annotations.filter(annotation =>
-      trackingUniqueIdentifiers.includes(annotation.data?.cachedStats?.TrackingUniqueIdentifier)
+      trackingUniqueIdentifiers.includes(annotation.data?.TrackingUniqueIdentifier)
     );
 
     if (!viewport._actors?.size) {
@@ -77,20 +78,24 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
       toolName: this.getToolName(),
       viewportId: enabledElement.viewport.id,
     };
+    const { style: annotationStyle } = annotation.config;
 
     for (let i = 0; i < filteredAnnotations.length; i++) {
       const annotation = filteredAnnotations[i];
       const annotationUID = annotation.annotationUID;
-      const { renderableData } = annotation.data.cachedStats;
-      const { cachedStats } = annotation.data;
+      const { renderableData, TrackingUniqueIdentifier } = annotation.data;
       const { referencedImageId } = annotation.metadata;
 
       styleSpecifier.annotationUID = annotationUID;
 
+      const groupStyle = annotationStyle.getToolGroupToolStyles(this.toolGroupId)[
+        this.getToolName()
+      ];
+
       const lineWidth = this.getStyle('lineWidth', styleSpecifier, annotation);
       const lineDash = this.getStyle('lineDash', styleSpecifier, annotation);
       const color =
-        cachedStats.TrackingUniqueIdentifier === activeTrackingUniqueIdentifier
+        TrackingUniqueIdentifier === activeTrackingUniqueIdentifier
           ? 'rgb(0, 255, 0)'
           : this.getStyle('color', styleSpecifier, annotation);
 
@@ -98,6 +103,7 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
         color,
         lineDash,
         lineWidth,
+        ...groupStyle,
       };
 
       Object.keys(renderableData).forEach(GraphicType => {
@@ -107,19 +113,19 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
         let canvasCoordinatesAdapter;
 
         switch (GraphicType) {
-          case SCOORD_TYPES.POINT:
+          case SCOORDTypes.POINT:
             renderMethod = this.renderPoint;
             break;
-          case SCOORD_TYPES.MULTIPOINT:
+          case SCOORDTypes.MULTIPOINT:
             renderMethod = this.renderMultipoint;
             break;
-          case SCOORD_TYPES.POLYLINE:
+          case SCOORDTypes.POLYLINE:
             renderMethod = this.renderPolyLine;
             break;
-          case SCOORD_TYPES.CIRCLE:
+          case SCOORDTypes.CIRCLE:
             renderMethod = this.renderEllipse;
             break;
-          case SCOORD_TYPES.ELLIPSE:
+          case SCOORDTypes.ELLIPSE:
             renderMethod = this.renderEllipse;
             canvasCoordinatesAdapter = utilities.math.ellipse.getCanvasEllipseCorners;
             break;
@@ -160,6 +166,7 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
     const drawingOptions = {
       color: options.color,
       width: options.lineWidth,
+      lineDash: options.lineDash,
     };
     let allCanvasCoordinates = [];
     renderableData.map((data, index) => {
@@ -223,7 +230,11 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
       // This gives us one point for arrow
       canvasCoordinates.push(viewport.worldToCanvas(point));
 
-      // We get the other point for the arrow by using the image size
+      if (data[1] !== undefined) {
+        canvasCoordinates.push(viewport.worldToCanvas(data[1]));
+      }
+      else{
+         // We get the other point for the arrow by using the image size
       const imagePixelModule = metaData.get('imagePixelModule', referencedImageId);
 
       let xOffset = 10;
@@ -242,6 +253,9 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
       ]);
 
       canvasCoordinates.push(viewport.worldToCanvas(arrowEnd));
+        
+      }
+     
 
       const arrowUID = `${index}`;
 
@@ -307,6 +321,7 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
         {
           color: options.color,
           width: options.lineWidth,
+          lineDash: options.lineDash,
         }
       );
     });
@@ -328,7 +343,7 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
     }
 
     const { annotationUID, data = {} } = annotation;
-    const { label } = data;
+    const { labels } = data;
     const { color } = options;
 
     let adaptedCanvasCoordinates = canvasCoordinates;
@@ -336,10 +351,12 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
     if (typeof canvasCoordinatesAdapter === 'function') {
       adaptedCanvasCoordinates = canvasCoordinatesAdapter(canvasCoordinates);
     }
-    const textLines = this._getTextBoxLinesFromLabels(label);
+    const textLines = this._getTextBoxLinesFromLabels(labels);
     const canvasTextBoxCoords = utilities.drawing.getTextBoxCoordsCanvas(adaptedCanvasCoordinates);
 
-    annotation.data.handles.textBox.worldPosition = viewport.canvasToWorld(canvasTextBoxCoords);
+    if (!annotation.data?.handles?.textBox?.worldPosition) {
+      annotation.data.handles.textBox.worldPosition = viewport.canvasToWorld(canvasTextBoxCoords);
+    }
 
     const textBoxPosition = viewport.worldToCanvas(annotation.data.handles.textBox.worldPosition);
 

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

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

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

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

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

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

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

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

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

@@ -1,8 +1,14 @@
 import { addTool } from '@cornerstonejs/tools';
 
-export default function addToolInstance(name: string, toolClass, configuration?): void {
+export default function addToolInstance(name: string, toolClass, configuration = {}): void {
   class InstanceClass extends toolClass {
     static toolName = name;
+    constructor(toolProps, defaultToolProps) {
+      toolProps.configuration = toolProps.configuration
+        ? { ...toolProps.configuration, ...configuration }
+        : configuration;
+      super(toolProps, defaultToolProps);
+    }
   }
   addTool(InstanceClass);
 }