chore(release): publish [skip ci]

- @ohif/extension-vtk@1.12.35
 - @ohif/viewer@4.12.41

.circleci/config.yml

@@ -13,11 +13,21 @@ version: 2.1
 ##
 orbs:
   codecov: codecov/codecov@1.0.5
-  cypress: cypress-io/cypress@1.13.0
-
+  cypress: cypress-io/cypress@1.26.0
+executors:
+  # Custom executor to override Cypress config
+  deploy-to-prod-executor:
+    docker:
+      - image: 'cypress/browsers:node14.15.0-chrome86-ff82'
+        environment:
+          CYPRESS_BASE_URL: https://ohif-staging.netlify.com/
+  chrome-and-pacs:
+    docker:
+      # Primary container image where all steps run.
+      - image: 'cypress/browsers:node14.15.0-chrome86-ff82'
 defaults: &defaults
   docker:
-    - image: circleci/node:12.9.1
+    - image: cimg/node:14.19
       environment:
         TERM: xterm # Enable colors in term
         QUICK_BUILD: true
@@ -36,12 +46,12 @@ jobs:
       - checkout:
           post:
             - git fetch --all
-      - 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-
+      # - 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
@@ -95,18 +105,19 @@ jobs:
           post:
             - git fetch --all
 
-      - 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-
+      # - 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:
+          version: 19.03.13
           docker_layer_caching: false
 
       - run:
@@ -131,12 +142,12 @@ jobs:
       - checkout:
           post:
             - git fetch --all
-      - 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-
+      # - 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
@@ -170,7 +181,7 @@ jobs:
 
   DEPLOY_TO_DEV:
     docker:
-      - image: circleci/node:12.9.1
+      - image: circleci/node:14.15.0
         environment:
           TERM: xterm
           NETLIFY_SITE_ID: 32708787-c9b0-4634-b50f-7ca41952da77
@@ -185,7 +196,7 @@ jobs:
 
   DEPLOY_TO_STAGING:
     docker:
-      - image: circleci/node:12.9.1
+      - image: circleci/node:14.15.0
         environment:
           TERM: xterm
           NETLIFY_SITE_ID: c7502ae3-b150-493c-8422-05701e44a969
@@ -200,7 +211,7 @@ jobs:
 
   DEPLOY_TO_PRODUCTION:
     docker:
-      - image: circleci/node:12.9.1
+      - image: circleci/node:14.15.0
         environment:
           TERM: xterm
           NETLIFY_SITE_ID: 79c4a5da-5c95-4dc9-84f7-45fd9dfe21b0
@@ -225,11 +236,11 @@ jobs:
           post:
             - git fetch --all
       # Use increasingly general patterns to restore cache
-      - restore_cache:
-          name: Restore Yarn and Cypress Package Cache
-          keys:
-            - yarn-packages-{{ checksum "yarn.lock" }}
-            - yarn-packages-
+      # - 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
@@ -257,7 +268,12 @@ jobs:
           paths: .
 
   DOCS_PUBLISH:
-    <<: *defaults
+    docker:
+      # Gitbook fails due to graceful-fs updates above this node version :-(
+      - image: circleci/node:12.9.1
+        environment:
+          TERM: xterm # Enable colors in term
+    working_directory: ~/repo
     steps:
       - checkout
       - run:
@@ -278,6 +294,7 @@ jobs:
       - attach_workspace:
           at: ~/repo
       - setup_remote_docker:
+          version: 19.03.13
           docker_layer_caching: false
       - run:
           name: Build and push Docker image
@@ -317,16 +334,21 @@ workflows:
       # E2E: PWA
       - cypress/run:
           name: 'E2E: PWA'
-          executor: cypress/browsers-chrome76
+          executor: chrome-and-pacs
           browser: chrome
           pre-steps:
-            - run: 'rm -rf ~/.yarn && npm i -g yarn && yarn -v && yarn global
-                add wait-on' # Use yarn latest
+            - run: |
+                # Clear yarn cache; update to latest
+                rm -rf ~/.yarn
+                npm i -g yarn
+                yarn -v
           yarn: true
-          record: false
-          store_artifacts: false
+          record: true
+          store_artifacts: true
           working_directory: platform/viewer
-          build: npx cross-env QUICK_BUILD=true yarn run build
+          build:
+            git submodule update --init && npx cross-env QUICK_BUILD=true
+            APP_CONFIG=config/e2e.js yarn run build
           start: yarn run test:e2e:serve
           spec: 'cypress/integration/common/**/*,cypress/integration/pwa/**/*'
           wait-on: 'http://localhost:3000'
@@ -337,21 +359,24 @@ workflows:
                 path: platform/viewer/cypress/screenshots
             - store_artifacts:
                 path: platform/viewer/cypress/videos
+            - store_test_results:
+                path: platform/viewer/cypress/results
           requires:
             - UNIT_TESTS
       # E2E: script-tag
       - cypress/run:
           name: 'E2E: Script Tag'
-          executor: cypress/browsers-chrome76
+          executor: chrome-and-pacs
           browser: chrome
           pre-steps:
-            - run: 'rm -rf ~/.yarn && npm i -g yarn && yarn -v && yarn global
-                add wait-on' # Use yarn latest
+            - run: 'rm -rf ~/.yarn && npm i -g yarn && yarn -v' # Use yarn latest
           yarn: true
-          record: false
-          store_artifacts: false
+          record: true
+          store_artifacts: true
           working_directory: platform/viewer
-          build: npx cross-env QUICK_BUILD=true yarn run build:package
+          build:
+            git submodule update --init && npx cross-env QUICK_BUILD=true
+            APP_CONFIG=config/e2e.js yarn run build:package
           start: yarn run test:e2e:serve
           spec: 'cypress/integration/common/**/*,cypress/integration/script-tag/**/*'
           wait-on: 'http://localhost:3000'
@@ -362,6 +387,8 @@ workflows:
                 path: platform/viewer/cypress/screenshots
             - store_artifacts:
                 path: platform/viewer/cypress/videos
+            - store_test_results:
+                path: platform/viewer/cypress/results
           requires:
             - UNIT_TESTS
 
@@ -372,7 +399,7 @@ workflows:
       # Update hub.docker.org
       - cypress/run:
           name: 'Generate Percy Snapshots'
-          executor: cypress/browsers-chrome76
+          executor: chrome-and-pacs
           browser: chrome
           pre-steps:
             - run: 'rm -rf ~/.yarn && npm i -g yarn && yarn -v && yarn global
@@ -380,7 +407,9 @@ workflows:
           yarn: true
           store_artifacts: false
           working_directory: platform/viewer
-          build: npx cross-env QUICK_BUILD=true yarn run build
+          build:
+            git submodule update --init && 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" }}'
@@ -449,7 +478,7 @@ workflows:
       # and record a Cypress dashboard test run
       - cypress/run:
           name: 'Generate Percy Snapshots'
-          executor: cypress/browsers-chrome76
+          executor: chrome-and-pacs
           browser: chrome
           pre-steps:
             - run: 'rm -rf ~/.yarn && npm i -g yarn && yarn -v && yarn global
@@ -457,7 +486,9 @@ workflows:
           yarn: true
           store_artifacts: false
           working_directory: platform/viewer
-          build: npx cross-env QUICK_BUILD=true yarn run build
+          build:
+            git submodule update --init && 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" }}'

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

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

.github/FUNDING.yml

@@ -0,0 +1 @@
+custom: https://giving.massgeneral.org/ohif

.github/ISSUE_TEMPLATE/---support-question.md

@@ -1,18 +0,0 @@
----
-name: "\U0001F917 Support Question"
-about: "I have a question \U0001F4AC"
-title: ''
-labels: 'Community: Question :question:, Triage :white_flag:'
-assignees: ''
----
-
-> :hand: We are a small team with limited resources. Your question is much more
-> likely to be answered if it is
-> [a good question](https://stackoverflow.com/help/how-to-ask)
-
-**Description**
-
-Questions can often be answered by our documentation. Unable to find an answer
-in our docs? We'll try to help. In the meantime, if you answer your own
-question, please respond with the answer here so that others may benefit as
-well. Better yet, open a PR to expand our docs ^\_^

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: 🤗 Support Question
+    url: https://community.ohif.org/
+    about: Please use our forum if you have questions or need help.

.github/stale.yml

@@ -2,9 +2,9 @@
 # https://github.com/apps/stale
 #
 # Number of days of inactivity before an issue becomes stale
-daysUntilStale: 21
+daysUntilStale: 180
 # Number of days of inactivity before a stale issue is closed
-daysUntilClose: 7
+daysUntilClose: 9000
 # Issues with these labels will never be considered stale
 exemptLabels:
   - 'Story :raised_hands:'

.gitignore

@@ -8,7 +8,10 @@ docs/_book
 src/version.js
 junit.xml
 coverage/
-.docz/
+*.js.map
+.yarn
+platform/docs/.docusaurus
+platform/ui/storybook-static
 
 # YALC (for Erik)
 .yalc

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "testdata"]
+	path = testdata
+	url = https://github.com/OHIF/viewer-testdata-dicomweb.git

.netlify/build-deploy-preview.sh

@@ -11,6 +11,7 @@ node -v
 
 # Install build deps and all monorepo package dependencies. Yarn Workspaces
 # should also symlink all projects appropriately
+yarn run lerna:restore
 yarn install --no-ignore-optional --pure-lockfile
 
 # Build && Move PWA Output
@@ -21,6 +22,9 @@ mv platform/viewer/dist/* .netlify/www/pwa -v
 # Build && Move script output
 # yarn run build:package
 
+# Cache all of the node_module dependencies in
+# extensions, modules, and platform packages
+yarn run lerna:cache
 echo 'Nothing left to see here. Go home, folks.'
 
 # Build using react-scripts

.node-version

@@ -0,0 +1 @@
+14.18.0

.vscode/launch.json

@@ -0,0 +1,15 @@
+{
+  // Use IntelliSense to learn about possible attributes.
+  // Hover to view descriptions of existing attributes.
+  // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+  "version": "0.2.0",
+  "configurations": [
+    {
+      "type": "pwa-chrome",
+      "request": "launch",
+      "name": "Launch Chrome against localhost",
+      "url": "http://localhost:3000",
+      "webRoot": "${workspaceFolder}"
+    }
+  ]
+}

.webpack/webpack.base.js

@@ -3,7 +3,6 @@ const dotenv = require('dotenv');
 //
 const path = require('path');
 const webpack = require('webpack');
-const PACKAGE = require('../platform/viewer/package.json');
 // ~~ RULES
 const loadShadersRule = require('./rules/loadShaders.js');
 const loadWebWorkersRule = require('./rules/loadWebWorkers.js');
@@ -29,7 +28,7 @@ module.exports = (env, argv, { SRC_DIR, DIST_DIR }) => {
 
   const config = {
     mode: isProdBuild ? 'production' : 'development',
-    devtool: isProdBuild ? 'source-map' : 'cheap-module-eval-source-map',
+    devtool: isProdBuild ? 'source-map' : 'eval-cheap-module-source-map',
     entry: {
       app: `${SRC_DIR}/index.js`,
     },
@@ -77,7 +76,10 @@ module.exports = (env, argv, { SRC_DIR, DIST_DIR }) => {
         '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.VERSION_NUMBER': JSON.stringify(PACKAGE.version || ''),
+        'process.env.VERSION_NUMBER': webpack.DefinePlugin.runtimeValue(() => {
+          const package = require('../platform/viewer/package.json');
+          return JSON.stringify(package.version || '');
+        }, ['../platform/viewer/package.json']),
         'process.env.BUILD_NUM': JSON.stringify(BUILD_NUM),
         /* i18n */
         'process.env.USE_LOCIZE': JSON.stringify(process.env.USE_LOCIZE || ''),

CITATION.cff

@@ -0,0 +1,24 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Ziegler"
+  given-names: "Erik"
+  orcid: "https://orcid.org/0000-0003-1857-8129"
+- family-names: "Urban"
+  given-names: "Trinity"
+- family-names: "Brown"
+  given-names: "Danny"
+- family-names: "Petts"
+  given-names: "James"
+- family-names: "Pieper"
+  given-names: "Steve D"
+- family-names: "Lewis"
+  given-names: "Rob"
+- family-names: "Hafey"
+  given-names: "Chris"
+- family-names: "Harris"
+  given-names: "Gordon J"
+title: "Open Health Imaging Foundation Viewer: An Extensible Open-Source Framework for Building Web-Based Imaging Applications to Support Cancer Research"
+doi: 10.1200/CCI.19.00131
+version: 1.0.0
+url: "https://github.com/OHIF/Viewers"

Dockerfile

@@ -21,7 +21,7 @@
 
 # Stage 1: Build the application
 # docker build -t ohif/viewer:latest .
-FROM node:10.16.3-slim as builder
+FROM node:14-slim as builder
 
 RUN mkdir /usr/src/app
 WORKDIR /usr/src/app
@@ -39,9 +39,10 @@ COPY package.json /usr/src/app/package.json
 COPY postcss.config.js /usr/src/app/postcss.config.js
 COPY yarn.lock /usr/src/app/yarn.lock
 
+RUN apt-get update && apt-get install -y python make g++
 # Run the install before copying the rest of the files
 RUN yarn config set workspaces-experimental true
-RUN yarn install
+RUN yarn install --verbose
 
 ENV PATH /usr/src/app/node_modules/.bin:$PATH
 ENV QUICK_BUILD true
@@ -52,7 +53,7 @@ RUN yarn run build
 
 # Stage 2: Bundle the built application into a Docker container
 # which runs Nginx using Alpine Linux
-FROM nginx:1.15.5-alpine
+FROM nginx:1.21.1-alpine
 RUN apk add --no-cache bash
 RUN rm -rf /etc/nginx/conf.d
 COPY .docker/Viewer-v2.x /etc/nginx/conf.d

README.md

@@ -121,8 +121,7 @@ window.config = {
 };
 ```
 
-- Install the viewer:
-  `window.OHIFStandaloneViewer.installViewer(window.config);`
+- Install the viewer: `window.OHIFViewer.installViewer(window.config);`
 
 This exact setup is demonstrated in this
 [CodeSandbox](https://codesandbox.io/s/viewer-script-tag-tprch) and in our
@@ -259,6 +258,33 @@ Cancer Institute, Informatics Technology for Cancer Research (ITCR) program,
 under a
 [grant to Dr. Gordon Harris at Massachusetts General Hospital (U24 CA199460)](https://projectreporter.nih.gov/project_info_description.cfm?aid=8971104).
 
+## Projects that contributed to OHIF Viewer
+
+The following is a (partial) list of projects that contributed resources towards
+development of OHIF Viewer:
+
+- [NCI Imaging Data Commons (IDC) project](https://imaging.datacommons.cancer.gov/)
+  supported development of new features and bug fixes marked with
+  ["IDC:priority"](https://github.com/OHIF/Viewers/issues?q=is%3Aissue+is%3Aopen+label%3AIDC%3Apriority),
+  ["IDC:candidate"](https://github.com/OHIF/Viewers/issues?q=is%3Aissue+is%3Aopen+label%3AIDC%3Acandidate)
+  or
+  ["IDC:collaboration"](https://github.com/OHIF/Viewers/issues?q=is%3Aissue+is%3Aopen+label%3AIDC%3Acollaboration).
+  NCI Imaging Data Commons is supported by the contract number 19X037Q from
+  Leidos Biomedical Research under Task Order HHSN26100071 from NCI.
+  [IDC Viewer](https://learn.canceridc.dev/portal/visualization) is a customized
+  version of the OHIF Viewer.
+  
+### Research notice
+Please note that this repository is participating in a study into sustainability
+ of open source projects. Data will be gathered about this repository for
+ approximately the next 12 months, starting from June 2021.
+
+Data collected will include number of contributors, number of PRs, time taken to
+ close/merge these PRs, and issues closed.
+
+For more information, please visit
+[our informational page](https://sustainable-open-science-and-software.github.io/) or download our [participant information sheet](https://sustainable-open-science-and-software.github.io/assets/PIS_sustainable_software.pdf).
+
 ## License
 
 MIT © [OHIF](https://github.com/OHIF)

docs/latest/book.json

@@ -8,7 +8,6 @@
     "-fontsettings",
     "github",
     "ga",
-    "sitemap",
     "anchors",
     "versions"
   ],
@@ -24,7 +23,8 @@
       "token": "UA-110573590-2"
     },
     "sitemap": {
-      "hostname": "https://docs.ohif.org"
+      "hostname": "https://docs.ohif.org",
+      "todo": "sitemap plugin removed; causing build errors"
     },
     "versions": {
       "gitbookConfigURL": "https://raw.githubusercontent.com/OHIF/Viewers/master/docs/book.json",

docs/latest/deployment/recipes/nginx--image-archive.md

@@ -8,7 +8,9 @@ OHIF Viewer and its medical imaging data. This post covers one of many potential
 setups that accomplish that. Please note, noticably absent is user account
 control.
 
-Do not use this recipe to host sensitive medical data on the open web. Depending
+> **Do not use this recipe to host sensitive medical data on the open web!** 
+
+Depending
 on your company's policies, this may be an appropriate setup on an internal
 network when protected with a server's basic authentication. For a more robust
 setup, check out our [user account control recipe](./user-account-control.md)
@@ -23,7 +25,7 @@ Our two biggest hurdles when hosting our image archive and web client are:
 
 ### Handling Web Requests
 
-We mittigate our first issue by allowing [Nginx][nginx] to handle incoming web
+We mitigate our first issue by allowing [Nginx][nginx] to handle incoming web
 requests. Nginx is open source software for web serving, reverse proxying,
 caching, and more. It's designed for maximum performance and stability --
 allowing us to more reliably serve content than Orthanc's built-in server can.
@@ -38,7 +40,7 @@ resources from our image archive (Orthanc), and when accessing its web admin.
 
 ### CORS Issues
 
-Cross-Origin Resource Sharing (CORS) is a mechanism that uses HTTP headers to
+[Cross-Origin Resource Sharing][understanding-cors] (CORS) is a mechanism that uses HTTP headers to
 tell a browser which web applications have permission to access selected
 resources from a server at a different origin (domain, protocol, port). IE. By
 default, a Web App located at `http://my-website.com` can't access resources
@@ -51,9 +53,6 @@ We can solve this one of two ways:
 
 **This solution uses the first approach.**
 
-You can read more about CORS in this Medium article: [Understanding
-CORS][understanding-cors]
-
 ### Diagram
 
 This setup allows us to create a setup similar to the one pictured below:
@@ -73,6 +72,8 @@ This setup allows us to create a setup similar to the one pictured below:
 - Docker
   - [Docker for Mac](https://docs.docker.com/docker-for-mac/)
   - [Docker for Windows](https://docs.docker.com/docker-for-windows/)
+- Node 16.x with optional Python and Visual Studio Build Tools ([webpack 4 has an issue](https://github.com/webpack/webpack/issues/14532) with Node 17.x)
+  - [Node.js](https://nodejs.org/en/download/)
 
 _Not sure if you have `docker` installed already? Try running `docker --version`
 in command prompt or terminal_
@@ -81,7 +82,7 @@ in command prompt or terminal_
 
 _Spin Things Up_
 
-- Navigate to `<project-root>/docker/OpenResty-Orthanc` in your shell
+- Navigate to `./platform/viewer/.recipes/OpenResty-Orthanc` in your shell
 - Run `docker-compose up`
 
 _Upload Your First Study_
@@ -94,16 +95,16 @@ _Upload Your First Study_
 
 ### Troubleshooting
 
-_Exit code 137_
+#### Exit code 137
 
 This means Docker ran out of memory. Open Docker Desktop, go to the `advanced`
 tab, and increase the amount of Memory available.
 
-_Cannot create container for service X_
+#### Cannot create container for service X
 
 Use this one with caution: `docker system prune`
 
-_X is already running_
+#### X is already running
 
 Stop running all containers:
 
@@ -120,15 +121,12 @@ likely want to update:
 #### OHIF Viewer
 
 The OHIF Viewer's configuration is imported from a static `.js` file. The
-configuration we use is set to a specific file when we build the viewer, and
+configuration we use is set to [a specific file][config-ohif] when we build the viewer, and
 determined by the env variable: `APP_CONFIG`. You can see where we set its value
 in the `dockerfile` for this solution:
 
 `ENV APP_CONFIG=config/docker_openresty-orthanc.js`
 
-You can find the configuration we're using here:
-`/public/config/docker_openresty-orthanc.js`
-
 To rebuild the `webapp` image created by our `dockerfile` after updating the
 Viewer's configuration, you can run:
 
@@ -137,7 +135,7 @@ Viewer's configuration, you can run:
 
 #### Other
 
-All other files are found in: `/docker/OpenResty-Orthanc/`
+All other files in this directory include
 
 | Service           | Configuration                     | Docs                                        |
 | ----------------- | --------------------------------- | ------------------------------------------- |
@@ -236,6 +234,8 @@ members put together:
 [orthanc-docs]: http://book.orthanc-server.com/users/configuration.html#configuration
 [lua-resty-openidc-docs]: https://github.com/zmartzone/lua-resty-openidc
 <!-- SRC -->
+
+[config-ohif]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/public/config/docker_openresty-orthanc.js
 [dockerfile]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/.recipes/OpenResty-Orthanc/dockerfile
 [config-nginx]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/.recipes/OpenResty-Orthanc/config/nginx.conf
 [config-orthanc]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/.recipes/OpenResty-Orthanc/config/orthanc.json

docs/latest/viewer/configuration.md

@@ -67,6 +67,33 @@ window.config = {
   extensions: [],
   showStudyList: true,
   filterQueryParam: false,
+  /**
+   * Disable caching of servers configuration.
+   *
+   * There will be no effect if you update the servers property of this config
+   * while your application is running because this property is cached in local storage.
+   */
+  disableServersCache: false,
+  /**
+   * OHIF's study prefetcher configuration.
+   *
+   * @param {boolean} enabled Whether to enable/disable OHIF's study prefetcher
+   * @param {('all'|'closest'|'downward'|'upward'|'topdown')} order Fetching order: all display sets, the closest ones, downward or top down fashion based on the currently selected display set
+   * @param {number} displaySetCount How much display sets should be prefetched at once (note: this attribute is ignored if order was set to 'all')
+   * @param {boolean} preventCache Prevent images to be cached in Cornerstone Tools's request pool manager
+   * @param {number} prefetchDisplaySetsTimeout Prefetch timeout
+   * @param {boolean} displayProgress Whether to display or not the progress bar in the display set
+   * @param {boolean} includeActiveDisplaySet Include or not the active display set while prefetching
+   */
+  studyPrefetcher: {
+    enabled: true,
+    order: 'all',
+    displaySetCount: 1,
+    preventCache: false,
+    prefetchDisplaySetsTimeout: 300,
+    displayProgress: false,
+    includeActiveDisplaySet: true,
+  },
   servers: {
     dicomWeb: [
       {
@@ -81,7 +108,14 @@ window.config = {
       },
     ],
   },
-  // Supported Keys: https://craig.is/killing/mice
+  /**
+   * Hotkey definitions.
+   * Supported Keys: https://craig.is/killing/mice
+   *
+   * @param {string} commandName
+   * @param {string} label
+   * @param {array} keys
+   */
   hotkeys: [
     { commandName: 'rotateViewportCW', label: 'Rotate Right', keys: ['r'] },
     { commandName: 'rotateViewportCCW', label: 'Rotate Left', keys: ['l'] },
@@ -97,14 +131,16 @@ window.config = {
       keys: ['v'],
     },
   ],
-  /* Configuration passed to the bundled cornerstone extension
+  /**
+   * Configuration passed to the bundled cornerstone extension
    *
    * The cornerstone extension is currently tightly coupled to the platform.
    * Until we're able to decouple it, this key will serve as a workaround to
    * pass it configuration.
+   *
+   * @param {boolean} hideHandles Whether to show/hide annotation "handles"
    */
   cornerstoneExtensionConfig: {
-    /* Whether to show/hide annotation "handles" */
     hideHandles: true,
   },
 };

docs/latest/viewer/studyPrefetcher.md

@@ -0,0 +1,37 @@
+# Viewer: Study Prefetcher & Stack Prefetch
+
+Prefetching the stack of images of the active viewport is enabled by default for
+cornerstone viewports via cornerstone tools's stack prefetch functionality.
+
+In order to have a more customizable alternative for prefetching, OHIF provides
+a built-in study prefetcher functionality which allows the user to set the order
+in which the display sets are prefetched, the granularity, the timeout and
+whether or not display a progress bar in the display set (close to the thumbnail
+image) in the study browser.
+
+You can customize these options via the viewer's configuration:
+
+```js
+window.config = {
+  /**
+   * OHIF's study prefetcher configuration.
+   *
+   * @param {boolean} enabled Whether to enable/disable OHIF's study prefetcher
+   * @param {('all'|'closest'|'downward'|'upward'|'topdown')} order Fetching order: all display sets, the closest ones, downward or top down fashion based on the currently selected display set
+   * @param {number} displaySetCount How much display sets should be prefetched at once (note: this attribute is ignored if order was set to 'all')
+   * @param {boolean} preventCache Prevent images to be cached in Cornerstone Tools's request pool manager
+   * @param {number} prefetchDisplaySetsTimeout Prefetch timeout
+   * @param {boolean} displayProgress Whether to display or not the progress bar in the display set
+   * @param {boolean} includeActiveDisplaySet Include or not the active display set while prefetching
+   */
+  studyPrefetcher: {
+    enabled: true,
+    order: 'all',
+    displaySetCount: 1,
+    preventCache: false,
+    prefetchDisplaySetsTimeout: 300,
+    displayProgress: false,
+    includeActiveDisplaySet: true,
+  },
+};
+```

docs/v1/book.json

@@ -8,7 +8,6 @@
     "-fontsettings",
     "github",
     "ga",
-    "sitemap",
     "anchors",
     "versions"
   ],
@@ -24,7 +23,8 @@
       "token": "UA-110573590-2"
     },
     "sitemap": {
-      "hostname": "https://docs.ohif.org"
+      "hostname": "https://docs.ohif.org",
+      "todo": "sitemap plugin removed; causing build errors"
     },
     "versions": {
       "gitbookConfigURL": "https://raw.githubusercontent.com/OHIF/Viewers/master/docs/book.json",

extensions/cornerstone/CHANGELOG.md

@@ -3,6 +3,370 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [2.12.15](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.14...@ohif/extension-cornerstone@2.12.15) (2022-09-20)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.12.14](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.13...@ohif/extension-cornerstone@2.12.14) (2022-09-01)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.12.13](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.12...@ohif/extension-cornerstone@2.12.13) (2022-06-30)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.12.12](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.11...@ohif/extension-cornerstone@2.12.12) (2022-06-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.12.11](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.10...@ohif/extension-cornerstone@2.12.11) (2022-06-14)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.12.10](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.9...@ohif/extension-cornerstone@2.12.10) (2022-04-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.12.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.8...@ohif/extension-cornerstone@2.12.9) (2022-03-25)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.12.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.7...@ohif/extension-cornerstone@2.12.8) (2022-03-14)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.12.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.6...@ohif/extension-cornerstone@2.12.7) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.12.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.5...@ohif/extension-cornerstone@2.12.6) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.12.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.4...@ohif/extension-cornerstone@2.12.5) (2022-02-02)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.12.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.3...@ohif/extension-cornerstone@2.12.4) (2022-01-20)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.12.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.2...@ohif/extension-cornerstone@2.12.3) (2021-12-02)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.12.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.1...@ohif/extension-cornerstone@2.12.2) (2021-10-26)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.12.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.12.0...@ohif/extension-cornerstone@2.12.1) (2021-09-28)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [2.12.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.11.0...@ohif/extension-cornerstone@2.12.0) (2021-09-23)
+
+
+### Features
+
+* Update to WADO Image Loader 4.0.3 to add dynamically imported WebAssembly codec support 🚀 ([#2537](https://github.com/OHIF/Viewers/issues/2537)) ([489d4b0](https://github.com/OHIF/Viewers/commit/489d4b0584f4657ceda1c5b9b68d5e9733827e47))
+
+
+
+
+
+# [2.11.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.10.10...@ohif/extension-cornerstone@2.11.0) (2021-09-09)
+
+
+### Features
+
+* OHIF-1000: Study prefetcher ([#2466](https://github.com/OHIF/Viewers/issues/2466)) ([8f26045](https://github.com/OHIF/Viewers/commit/8f2604509d24092b721f1333289d838820d68cac))
+
+
+
+
+
+## [2.10.10](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.10.9...@ohif/extension-cornerstone@2.10.10) (2021-07-26)
+
+
+### Bug Fixes
+
+* changed new image handler conditional for 0 edge case ([#2338](https://github.com/OHIF/Viewers/issues/2338)) ([b8ae92c](https://github.com/OHIF/Viewers/commit/b8ae92c2d4f733b3ca89826118029685650b396a))
+
+
+
+
+
+## [2.10.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.10.8...@ohif/extension-cornerstone@2.10.9) (2021-06-02)
+
+
+### Bug Fixes
+
+* **dicom-html:** Add parsed dicom meta info section ([#2419](https://github.com/OHIF/Viewers/issues/2419)) ([403688b](https://github.com/OHIF/Viewers/commit/403688b18c52468fc1101166ec0c1734fb710039))
+
+
+
+
+
+## [2.10.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.10.7...@ohif/extension-cornerstone@2.10.8) (2021-05-17)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.10.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.10.6...@ohif/extension-cornerstone@2.10.7) (2021-04-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.10.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.10.5...@ohif/extension-cornerstone@2.10.6) (2021-03-26)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.10.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.10.4...@ohif/extension-cornerstone@2.10.5) (2021-03-15)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.10.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.10.3...@ohif/extension-cornerstone@2.10.4) (2021-03-09)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.10.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.10.2...@ohif/extension-cornerstone@2.10.3) (2021-03-03)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.10.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.10.1...@ohif/extension-cornerstone@2.10.2) (2021-02-25)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.10.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.10.0...@ohif/extension-cornerstone@2.10.1) (2021-02-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+# [2.10.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.9.6...@ohif/extension-cornerstone@2.10.0) (2020-12-10)
+
+
+### Features
+
+* visualize overlapping segments in cornerstone ([#2185](https://github.com/OHIF/Viewers/issues/2185)) ([29fceac](https://github.com/OHIF/Viewers/commit/29fceacee97d51f1952a0f6b574c66596d32c201))
+
+
+
+
+
+## [2.9.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.9.5...@ohif/extension-cornerstone@2.9.6) (2020-10-07)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.9.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.9.4...@ohif/extension-cornerstone@2.9.5) (2020-09-29)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.9.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.9.3...@ohif/extension-cornerstone@2.9.4) (2020-09-03)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.9.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.9.2...@ohif/extension-cornerstone@2.9.3) (2020-09-02)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.9.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.9.1...@ohif/extension-cornerstone@2.9.2) (2020-08-20)
+
+
+### Bug Fixes
+
+* Updated react-cornerstone-viewport to version 4.0.2 ([#2001](https://github.com/OHIF/Viewers/issues/2001)) ([59ab68b](https://github.com/OHIF/Viewers/commit/59ab68b4edbfec010170c4429c300a53f688bf94))
+
+
+
+
+
+## [2.9.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.9.0...@ohif/extension-cornerstone@2.9.1) (2020-08-20)
+
+
+### Performance Improvements
+
+* **stackPrefetch:** Added stackPrefetch config with 20 max concurrent requests ([#2000](https://github.com/OHIF/Viewers/issues/2000)) ([3b02a06](https://github.com/OHIF/Viewers/commit/3b02a06f5e250660edde4862ce44147db3dc3ab9))
+
+
+
+
+
+# [2.9.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.8.5...@ohif/extension-cornerstone@2.9.0) (2020-08-18)
+
+
+### Features
+
+* 🎸 Update react-vtkjs-viewport usage to use requestPool ([#1984](https://github.com/OHIF/Viewers/issues/1984)) ([bb5f30c](https://github.com/OHIF/Viewers/commit/bb5f30ce2a0192d2e021beaaadfff22fd38e17b9))
+
+
+
+
+
+## [2.8.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.8.4...@ohif/extension-cornerstone@2.8.5) (2020-08-05)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.8.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.8.3...@ohif/extension-cornerstone@2.8.4) (2020-07-13)
+
+
+### Bug Fixes
+
+* 🐛 - Put guards in all places that a cornerstone re-render ([#1899](https://github.com/OHIF/Viewers/issues/1899)) ([451f7ea](https://github.com/OHIF/Viewers/commit/451f7eab9258e7a193eb362e0926b13aedc4b3c9))
+
+
+
+
+
+## [2.8.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.8.2...@ohif/extension-cornerstone@2.8.3) (2020-07-13)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.8.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.8.1...@ohif/extension-cornerstone@2.8.2) (2020-06-15)
+
+
+### Bug Fixes
+
+* 🐛 Disable seg panel when data for seg unavailable ([#1732](https://github.com/OHIF/Viewers/issues/1732)) ([698e900](https://github.com/OHIF/Viewers/commit/698e900b85121d3c2a46747c443ef69fb7a8c95b)), closes [#1728](https://github.com/OHIF/Viewers/issues/1728)
+
+
+
+
+
+## [2.8.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.8.0...@ohif/extension-cornerstone@2.8.1) (2020-06-04)
+
+
+### Bug Fixes
+
+* 🐛 Infinite frame index change when quickly jumping between ([#1734](https://github.com/OHIF/Viewers/issues/1734)) ([a830577](https://github.com/OHIF/Viewers/commit/a8305772d0fbec506549ad7ea08504a8bc3a4f39)), closes [#1733](https://github.com/OHIF/Viewers/issues/1733)
+
+
+
+
+
+# [2.8.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.7.3...@ohif/extension-cornerstone@2.8.0) (2020-06-04)
+
+
+### Features
+
+* 🎸 1729 - error boundary wrapper ([#1764](https://github.com/OHIF/Viewers/issues/1764)) ([c02b232](https://github.com/OHIF/Viewers/commit/c02b232b0cc24f38af5d5e3831d987d048e60ada))
+
+
+
+
+
 ## [2.7.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.7.2...@ohif/extension-cornerstone@2.7.3) (2020-05-12)
 
 

extensions/cornerstone/README.md

@@ -85,12 +85,32 @@ Tools can be configured through extension configuration using the tools key:
   ...
 ```
 
+## Stack prefetch configuration
+
+Stack prefetch can be configured through extension configuration using the
+stackPrefetch key:
+
+```js
+  ...
+  cornerstoneExtensionConfig: {
+    stackPrefetch: {
+      enabled: true,
+      maxImagesToPrefetch: Infinity,
+      preserveExistingPool: false,
+      maxSimultaneousRequests: 20,
+    },
+  },
+  ...
+```
+
 ## Annotate Tools Configuration
 
-*We currently support one property for annotation tools.*
+_We currently support one property for annotation tools._
 
 ### Hide handles
-This extension configuration allows you to toggle on/off handle rendering for all annotate tools:
+
+This extension configuration allows you to toggle on/off handle rendering for
+all annotate tools:
 
 ```js
   ...
@@ -119,3 +139,4 @@ This extension configuration allows you to toggle on/off handle rendering for al
 [cornerstone-tools]: https://github.com/cornerstonejs/cornerstoneTools
 [cornerstone]: https://github.com/cornerstonejs/cornerstone
 <!-- prettier-ignore-end -->
+```

extensions/cornerstone/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone",
-  "version": "2.7.3",
+  "version": "2.12.15",
   "description": "OHIF extension for Cornerstone",
   "author": "OHIF",
   "license": "MIT",
@@ -32,25 +32,26 @@
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
     "@ohif/ui": "^0.50.0",
-    "cornerstone-core": "^2.2.8",
-    "cornerstone-math": "^0.1.8",
-    "cornerstone-tools": "4.15.1",
-    "cornerstone-wado-image-loader": "^3.1.0",
-    "dcmjs": "^0.12.3",
-    "dicom-parser": "^1.8.3",
+    "cornerstone-core": "^2.6.1",
+    "cornerstone-math": "^0.1.9",
+    "cornerstone-tools": "^6.0.6",
+    "cornerstone-wado-image-loader": "^4.2.1",
+    "dcmjs": "0.24.10",
+    "dicom-parser": "^1.8.11",
     "hammerjs": "^2.0.8",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6",
     "react-redux": "^6.0.0",
     "react-resize-detector": "^3.4.0",
-    "redux": "^4.0.1"
+    "redux": "^4.0.1",
+    "styled-components": "^5.3.5"
   },
   "dependencies": {
     "@babel/runtime": "^7.5.5",
     "classnames": "^2.2.6",
     "lodash.merge": "^4.6.2",
     "lodash.throttle": "^4.1.1",
-    "react-cornerstone-viewport": "2.3.8"
+    "react-cornerstone-viewport": "4.1.1"
   }
 }

extensions/cornerstone/src/ConnectedCornerstoneViewport.js

@@ -3,6 +3,7 @@ import OHIF from '@ohif/core';
 import { connect } from 'react-redux';
 import throttle from 'lodash.throttle';
 import { setEnabledElement } from './state';
+import initSRTools from './tools/initSRTools';
 
 const { setViewportActive, setViewportSpecificData } = OHIF.redux.actions;
 const {
@@ -53,7 +54,11 @@ const mapStateToProps = (state, ownProps) => {
     // Currently justing using escape hatch + commands
     // activeTool: activeButton && activeButton.command,
     ...dataFromStore,
-    isStackPrefetchEnabled: isActive,
+    isStackPrefetchEnabled: ownProps.hasOwnProperty('isStackPrefetchEnabled')
+      ? ownProps.isStackPrefetchEnabled
+      : ownProps.stackPrefetch
+      ? ownProps.stackPrefetch.enabled
+      : isActive,
     isPlaying,
     frameRate,
     //stack: viewportSpecificData.stack,
@@ -88,6 +93,7 @@ const mapDispatchToProps = (dispatch, ownProps) => {
           plugin: 'cornerstone',
         })
       );
+      initSRTools(enabledElement);
     },
 
     onMeasurementsChanged: (event, action) => {

extensions/cornerstone/src/OHIFCornerstoneViewport.js

@@ -1,10 +1,11 @@
 import React, { Component } from 'react';
 
+import OHIFCornerstoneViewportOverlay from './components/OHIFCornerstoneViewportOverlay';
 import ConnectedCornerstoneViewport from './ConnectedCornerstoneViewport';
 import OHIF from '@ohif/core';
 import PropTypes from 'prop-types';
 import cornerstone from 'cornerstone-core';
-import debounce from 'lodash.debounce';
+import checkForSRAnnotations from './tools/checkForSRAnnotations';
 
 const { StackManager } = OHIF.utils;
 
@@ -15,6 +16,7 @@ class OHIFCornerstoneViewport extends Component {
 
   static defaultProps = {
     customProps: {},
+    isStackPrefetchEnabled: true,
   };
 
   static propTypes = {
@@ -23,6 +25,8 @@ class OHIFCornerstoneViewport extends Component {
     viewportIndex: PropTypes.number,
     children: PropTypes.node,
     customProps: PropTypes.object,
+    stackPrefetch: PropTypes.object,
+    isStackPrefetchEnabled: PropTypes.bool,
   };
 
   static id = 'OHIFCornerstoneViewport';
@@ -184,6 +188,8 @@ class OHIFCornerstoneViewport extends Component {
       displaySet.SOPInstanceUID !== prevDisplaySet.SOPInstanceUID ||
       displaySet.frameIndex !== prevDisplaySet.frameIndex
     ) {
+      const { viewportIndex } = this.props;
+      checkForSRAnnotations({ displaySet, viewportIndex });
       this.setStateFromProps();
     }
   }
@@ -195,6 +201,7 @@ class OHIFCornerstoneViewport extends Component {
       return null;
     }
     const { viewportIndex } = this.props;
+    const { inconsistencyWarnings } = this.props.viewportData.displaySet;
     const {
       imageIds,
       currentImageIdIndex,
@@ -216,10 +223,11 @@ class OHIFCornerstoneViewport extends Component {
       });
     }
 
-    const debouncedNewImageHandler = debounce(({ currentImageIdIndex, sopInstanceUid }) => {
+    const newImageHandler = ({ currentImageIdIndex, sopInstanceUid }) => {
       const { displaySet } = this.props.viewportData;
       const { StudyInstanceUID } = displaySet;
-      if (currentImageIdIndex > 0) {
+
+      if (currentImageIdIndex >= 0) {
         this.props.onNewImage({
           StudyInstanceUID,
           SOPInstanceUID: sopInstanceUid,
@@ -227,7 +235,26 @@ class OHIFCornerstoneViewport extends Component {
           activeViewportIndex: viewportIndex,
         });
       }
-    }, 700);
+    };
+
+    const overlay = props => {
+      const displaySet = this.props.viewportData.displaySet;
+      let filteredSRLabels;
+      if (displaySet.SRLabels && displaySet.SRLabels.length !== 0) {
+        filteredSRLabels = displaySet.SRLabels.filter(
+          SRLabel =>
+            SRLabel.ReferencedSOPInstanceUID === displaySet.SOPInstanceUID
+        );
+      }
+
+      return (
+        <OHIFCornerstoneViewportOverlay
+          {...props}
+          inconsistencyWarnings={inconsistencyWarnings}
+          SRLabels={filteredSRLabels}
+        />
+      );
+    };
 
     return (
       <>
@@ -235,11 +262,14 @@ class OHIFCornerstoneViewport extends Component {
           viewportIndex={viewportIndex}
           imageIds={imageIds}
           imageIdIndex={currentImageIdIndex}
-          onNewImage={debouncedNewImageHandler}
+          onNewImageDebounced={newImageHandler}
+          onNewImageDebounceTime={300}
+          viewportOverlayComponent={overlay}
+          stackPrefetch={this.props.stackPrefetch}
+          isStackPrefetchEnabled={this.props.isStackPrefetchEnabled}
           // ~~ Connected (From REDUX)
           // frameRate={frameRate}
           // isPlaying={false}
-          // isStackPrefetchEnabled={true}
           // onElementEnabled={() => {}}
           // setViewportActive{() => {}}
           {...this.props.customProps}

extensions/cornerstone/src/commandsModule.js

@@ -10,6 +10,14 @@ const scroll = cornerstoneTools.import('util/scroll');
 const { studyMetadataManager } = OHIF.utils;
 const { setViewportSpecificData } = OHIF.redux.actions;
 
+const refreshCornerstoneViewports = () => {
+  cornerstone.getEnabledElements().forEach(enabledElement => {
+    if (enabledElement.image) {
+      cornerstone.updateImage(enabledElement.element);
+    }
+  });
+};
+
 const commandsModule = ({ servicesManager }) => {
   const actions = {
     rotateViewport: ({ viewports, rotation }) => {
@@ -180,10 +188,7 @@ const commandsModule = ({ servicesManager }) => {
 
       measurementApi.syncMeasurementsAndToolData();
 
-      // Update images in all active viewports
-      cornerstone.getEnabledElements().forEach(enabledElement => {
-        cornerstone.updateImage(enabledElement.element);
-      });
+      refreshCornerstoneViewports();
     },
     getNearbyToolData({ element, canvasCoordinates, availableToolTypes }) {
       const nearbyTool = {};
@@ -262,23 +267,33 @@ const commandsModule = ({ servicesManager }) => {
       StudyInstanceUID,
       SOPInstanceUID,
       frameIndex,
-      activeViewportIndex
+      activeViewportIndex,
+      refreshViewports = true,
     }) => {
       const study = studyMetadataManager.get(StudyInstanceUID);
 
       const displaySet = study.findDisplaySet(ds => {
-        return ds.images && ds.images.find(i => i.getSOPInstanceUID() === SOPInstanceUID)
+        return (
+          ds.images &&
+          ds.images.find(i => i.getSOPInstanceUID() === SOPInstanceUID)
+        );
       });
 
+      if (!displaySet) {
+        return;
+      }
+
       displaySet.SOPInstanceUID = SOPInstanceUID;
       displaySet.frameIndex = frameIndex;
 
-      window.store.dispatch(setViewportSpecificData(activeViewportIndex, displaySet));
+      window.store.dispatch(
+        setViewportSpecificData(activeViewportIndex, displaySet)
+      );
 
-      cornerstone.getEnabledElements().forEach(enabledElement => {
-        cornerstone.updateImage(enabledElement.element);
-      });
+      if (refreshViewports) {
+        refreshCornerstoneViewports();
       }
+    },
   };
 
   const definitions = {

extensions/cornerstone/src/components/OHIFCornerstoneViewportOverlay.css

@@ -0,0 +1,73 @@
+.imageViewerViewport.empty ~ .OHIFCornerstoneViewportOverlay {
+  display: none;
+}
+.OHIFCornerstoneViewportOverlay {
+  color: #9ccef9;
+}
+.OHIFCornerstoneViewportOverlay .overlay-element {
+  position: absolute;
+  font-weight: 400;
+  text-shadow: 1px 1px #000;
+  pointer-events: none;
+}
+.OHIFCornerstoneViewportOverlay .top-left {
+  top: 20px;
+  left: 20px;
+}
+.OHIFCornerstoneViewportOverlay .top-center {
+  top: 20px;
+  padding-top: 20px;
+  width: 100%;
+  text-align: center;
+}
+.OHIFCornerstoneViewportOverlay .top-right {
+  top: 20px;
+  right: 20px;
+  text-align: right;
+}
+.OHIFCornerstoneViewportOverlay .bottom-left {
+  bottom: 20px;
+  left: 20px;
+}
+.OHIFCornerstoneViewportOverlay .bottom-left2 {
+  bottom: 140px;
+  left: 20px;
+}
+.OHIFCornerstoneViewportOverlay .bottom-left3 {
+  bottom: 110px;
+  left: -20px;
+}
+.OHIFCornerstoneViewportOverlay .bottom-right {
+  bottom: 20px;
+  right: 20px;
+  text-align: right;
+}
+.OHIFCornerstoneViewportOverlay.controlsVisible .topright,
+.OHIFCornerstoneViewportOverlay.controlsVisible .bottomright {
+  right: calc(20px + 19px);
+}
+.OHIFCornerstoneViewportOverlay .warning {
+  position: absolute;
+  font-weight: 400;
+  text-shadow: 1px 1px #000;
+  pointer-events: inherit;
+}
+
+.OHIFCornerstoneViewportOverlay .warning svg {
+  opacity: 1;
+  color: #e29e4a;
+  fill: #e29e4a;
+  stroke: #e29e4a;
+  width: 32px;
+  height: 28px;
+}
+
+.OHIFCornerstoneViewportOverlay svg {
+  color: #9ccef9;
+  fill: #9ccef9;
+  stroke: #9ccef9;
+  background-color: transparent;
+  margin: 2px;
+  width: 18px;
+  height: 18px;
+}

extensions/cornerstone/src/components/OHIFCornerstoneViewportOverlay.js

@@ -0,0 +1,267 @@
+import { PureComponent } from 'react';
+import React from 'react';
+import styled from 'styled-components';
+import PropTypes from 'prop-types';
+import cornerstone from 'cornerstone-core';
+import './OHIFCornerstoneViewportOverlay.css';
+import {
+  isValidNumber,
+  formatNumberPrecision,
+  formatDICOMDate,
+  formatDICOMTime,
+  formatPN,
+  getCompression,
+} from '../utils/formatStudy';
+import classNames from 'classnames';
+import { Icon } from '@ohif/ui/src/elements/Icon';
+import { Tooltip } from '@ohif/ui/src/components/tooltip';
+import { OverlayTrigger } from '@ohif/ui/src/components/overlayTrigger';
+
+const Button = styled.button`
+  color: white;
+  padding: 2px 7px;
+  border-radius: 10px;
+  outline: 0;
+  text-transform: none;
+  margin: 2px 2px;
+  cursor: pointer;
+  &:disabled {
+    cursor: default;
+    opacity: 0.9;
+  }
+`;
+
+class OHIFCornerstoneViewportOverlay extends PureComponent {
+  static propTypes = {
+    scale: PropTypes.number.isRequired,
+    windowWidth: PropTypes.oneOfType([
+      PropTypes.number.isRequired,
+      PropTypes.string.isRequired,
+    ]),
+    windowCenter: PropTypes.oneOfType([
+      PropTypes.number.isRequired,
+      PropTypes.string.isRequired,
+    ]),
+    imageId: PropTypes.string.isRequired,
+    imageIndex: PropTypes.number.isRequired,
+    stackSize: PropTypes.number.isRequired,
+    inconsistencyWarnings: PropTypes.array,
+    SRLabels: PropTypes.array,
+  };
+
+  render() {
+    const {
+      imageId,
+      scale,
+      windowWidth,
+      windowCenter,
+      inconsistencyWarnings,
+      SRLabels,
+    } = this.props;
+
+    if (!imageId) {
+      return null;
+    }
+
+    const zoomPercentage = formatNumberPrecision(scale * 100, 0);
+    const seriesMetadata =
+      cornerstone.metaData.get('generalSeriesModule', imageId) || {};
+    const imagePlaneModule =
+      cornerstone.metaData.get('imagePlaneModule', imageId) || {};
+    const { rows, columns, sliceThickness, sliceLocation } = imagePlaneModule;
+    const { seriesNumber, seriesDescription } = seriesMetadata;
+
+    const generalStudyModule =
+      cornerstone.metaData.get('generalStudyModule', imageId) || {};
+    const { studyDate, studyTime, studyDescription } = generalStudyModule;
+
+    const patientModule =
+      cornerstone.metaData.get('patientModule', imageId) || {};
+    const { patientId, patientName } = patientModule;
+
+    const generalImageModule =
+      cornerstone.metaData.get('generalImageModule', imageId) || {};
+    const { instanceNumber } = generalImageModule;
+
+    const cineModule = cornerstone.metaData.get('cineModule', imageId) || {};
+    const { frameTime } = cineModule;
+
+    const frameRate = formatNumberPrecision(1000 / frameTime, 1);
+    const compression = getCompression(imageId);
+    const wwwc = `W: ${
+      windowWidth.toFixed ? windowWidth.toFixed(0) : windowWidth
+    } L: ${windowWidth.toFixed ? windowCenter.toFixed(0) : windowCenter}`;
+    const imageDimensions = `${columns} x ${rows}`;
+
+    const { imageIndex, stackSize } = this.props;
+
+    const inconsistencyWarningsOn =
+      inconsistencyWarnings && inconsistencyWarnings.length !== 0
+        ? true
+        : false;
+    const getWarningContent = warningList => {
+      if (Array.isArray(warningList)) {
+        const listedWarnings = warningList.map((warn, index) => {
+          return <li key={index}>{warn}</li>;
+        });
+
+        return <ol>{listedWarnings}</ol>;
+      } else {
+        return <React.Fragment>{warningList}</React.Fragment>;
+      }
+    };
+
+    const getWarningInfo = (seriesNumber, inconsistencyWarnings) => {
+      return (
+        <React.Fragment>
+          {inconsistencyWarnings.length != 0 ? (
+            <OverlayTrigger
+              key={seriesNumber}
+              placement="left"
+              overlay={
+                <Tooltip
+                  placement="left"
+                  className="in tooltip-warning"
+                  id="tooltip-left"
+                >
+                  <div className="warningTitle">Series Inconsistencies</div>
+                  <div className="warningContent">
+                    {getWarningContent(inconsistencyWarnings)}
+                  </div>
+                </Tooltip>
+              }
+            >
+              <div className={classNames('warning')}>
+                <span className="warning-icon">
+                  <Icon name="exclamation-triangle" />
+                </span>
+              </div>
+            </OverlayTrigger>
+          ) : (
+            <React.Fragment></React.Fragment>
+          )}
+        </React.Fragment>
+      );
+    };
+
+    const SRLabelsOn = SRLabels && SRLabels.length !== 0 ? true : false;
+
+    /**/
+
+    const getSRLabelsContent = SRLabels => {
+      if (Array.isArray(SRLabels)) {
+        const listedSRLabels = SRLabels.map((SRLabel, index) => {
+          const color = SRLabel.labels.color;
+          return (
+            SRLabel.labels.visible && (
+              <OverlayTrigger
+                key={index}
+                placement="top"
+                overlay={
+                  <Tooltip
+                    placement="top"
+                    className="in tooltip-warning"
+                    id="tooltip-top"
+                  >
+                    <div className="warningTitle">
+                      {' '}
+                      Coding scheme designators{' '}
+                    </div>
+                    <div className="warningContent">
+                      {SRLabel.labels.labelCodingSchemeDesignator +
+                        ' : ' +
+                        SRLabel.labels.valueCodingSchemeDesignator}
+                    </div>
+                  </Tooltip>
+                }
+              >
+                <div style={{ display: 'inline-block' }}>
+                  <Button
+                    style={{
+                      backgroundColor: color,
+                    }}
+                    disabled={true}
+                    key={index}
+                  >
+                    {SRLabel.labels.label + ' : ' + SRLabel.labels.value}
+                  </Button>
+                </div>
+              </OverlayTrigger>
+            )
+          );
+        });
+
+        return <ol>{listedSRLabels}</ol>;
+      } else {
+        return <React.Fragment></React.Fragment>;
+      }
+    };
+
+    const getSRLabelsInfo = SRLabels => {
+      return (
+        <React.Fragment>
+          {SRLabels.length != 0 ? (
+            getSRLabelsContent(SRLabels)
+          ) : (
+            <React.Fragment></React.Fragment>
+          )}
+        </React.Fragment>
+      );
+    };
+
+    const normal = (
+      <React.Fragment>
+        <div className="top-left overlay-element">
+          <div>{formatPN(patientName)}</div>
+          <div>{patientId}</div>
+        </div>
+        <div className="top-right overlay-element">
+          <div>{studyDescription}</div>
+          <div>
+            {formatDICOMDate(studyDate)} {formatDICOMTime(studyTime)}
+          </div>
+        </div>
+        <div className="bottom-right overlay-element">
+          <div>Zoom: {zoomPercentage}%</div>
+          <div>{wwwc}</div>
+          <div className="compressionIndicator">{compression}</div>
+        </div>
+        <div className="bottom-left2 warning">
+          <div>
+            {inconsistencyWarningsOn
+              ? getWarningInfo(seriesNumber, inconsistencyWarnings)
+              : ''}
+          </div>
+        </div>
+        <div className="bottom-left3 warning">
+          <div>{SRLabelsOn ? getSRLabelsInfo(SRLabels) : ''}</div>
+        </div>
+        <div className="bottom-left overlay-element">
+          <div>{seriesNumber >= 0 ? `Ser: ${seriesNumber}` : ''}</div>
+          <div>
+            {stackSize > 1
+              ? `Img: ${instanceNumber} ${imageIndex}/${stackSize}`
+              : ''}
+          </div>
+          <div>
+            {frameRate >= 0 ? `${formatNumberPrecision(frameRate, 2)} FPS` : ''}
+            <div>{imageDimensions}</div>
+            <div>
+              {isValidNumber(sliceLocation)
+                ? `Loc: ${formatNumberPrecision(sliceLocation, 2)} mm `
+                : ''}
+              {sliceThickness
+                ? `Thick: ${formatNumberPrecision(sliceThickness, 2)} mm`
+                : ''}
+            </div>
+            <div>{seriesDescription}</div>
+          </div>
+        </div>
+      </React.Fragment>
+    );
+
+    return <div className="OHIFCornerstoneViewportOverlay">{normal}</div>;
+  }
+}
+
+export default OHIFCornerstoneViewportOverlay;

extensions/cornerstone/src/index.js

@@ -3,6 +3,7 @@ import init from './init.js';
 import commandsModule from './commandsModule.js';
 import toolbarModule from './toolbarModule.js';
 import CornerstoneViewportDownloadForm from './CornerstoneViewportDownloadForm';
+import { version } from '../package.json';
 
 const Component = React.lazy(() => {
   return import('./OHIFCornerstoneViewport');
@@ -24,6 +25,7 @@ export default {
    * Only required property. Should be a unique value across all extensions.
    */
   id: 'cornerstone',
+  version,
 
   /**
    *
@@ -34,12 +36,30 @@ export default {
   preRegistration({ servicesManager, configuration = {} }) {
     init({ servicesManager, configuration });
   },
-  getViewportModule({ commandsManager }) {
+  getViewportModule({ commandsManager, appConfig }) {
     const ExtendedOHIFCornerstoneViewport = props => {
+      /**
+       * TODO: This appears to be used to set the redux parameters for
+       * the viewport when new images are loaded. It's very ugly
+       * and we should remove it.
+       */
       const onNewImageHandler = jumpData => {
+        /** Do not trigger all viewports to render unnecessarily */
+        jumpData.refreshViewports = false;
         commandsManager.runCommand('jumpToImage', jumpData);
       };
-      return <OHIFCornerstoneViewport {...props} onNewImage={onNewImageHandler} />;
+
+      const { studyPrefetcher } = appConfig;
+      const isStackPrefetchEnabled =
+        studyPrefetcher && !studyPrefetcher.enabled;
+
+      return (
+        <OHIFCornerstoneViewport
+          {...props}
+          onNewImage={onNewImageHandler}
+          isStackPrefetchEnabled={isStackPrefetchEnabled}
+        />
+      );
     };
 
     return ExtendedOHIFCornerstoneViewport;

extensions/cornerstone/src/init.js

@@ -5,6 +5,8 @@ import csTools from 'cornerstone-tools';
 import merge from 'lodash.merge';
 import initCornerstoneTools from './initCornerstoneTools.js';
 import measurementServiceMappingsFactory from './utils/measurementServiceMappings/measurementServiceMappingsFactory';
+import dicomSRModule from './tools/modules/dicomSRModule';
+import srModuleId from './tools/id';
 
 /**
  *
@@ -15,6 +17,8 @@ import measurementServiceMappingsFactory from './utils/measurementServiceMapping
 export default function init({ servicesManager, configuration }) {
   const { UIDialogService, MeasurementService } = servicesManager.services;
 
+  csTools.register('module', srModuleId, dicomSRModule);
+
   const callInputDialog = (data, event, callback) => {
     if (UIDialogService) {
       let dialogId = UIDialogService.create({
@@ -37,7 +41,14 @@ export default function init({ servicesManager, configuration }) {
     }
   };
 
-  const { csToolsConfig } = configuration;
+  const {
+    csToolsConfig,
+    stackPrefetch = {
+      maxImagesToPrefetch: Infinity,
+      preserveExistingPool: false,
+      maxSimultaneousRequests: 20,
+    },
+  } = configuration;
   const metadataProvider = OHIF.cornerstone.metadataProvider;
 
   cornerstone.metaData.addProvider(
@@ -52,7 +63,7 @@ export default function init({ servicesManager, configuration }) {
     autoResizeViewports: false,
   };
 
-  initCornerstoneTools(defaultCsToolsConfig);
+  initCornerstoneTools({ ...defaultCsToolsConfig, ...stackPrefetch });
 
   const toolsGroupedByType = {
     touch: [csTools.PanMultiTouchTool, csTools.ZoomTouchPinchTool],

extensions/cornerstone/src/initCornerstoneTools.js

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

extensions/cornerstone/src/tools/DICOMSRDisplayTool.js

@@ -0,0 +1,419 @@
+import csTools, {
+  importInternal,
+  getToolState,
+  toolColors,
+} from 'cornerstone-tools';
+
+import cornerstone from 'cornerstone-core';
+
+/** Internal imports */
+import TOOL_NAMES from './constants/toolNames';
+import SCOORD_TYPES from './constants/scoordTypes';
+import id from './id';
+
+/** Cornerstone 3rd party dev kit imports */
+const draw = importInternal('drawing/draw');
+const drawJoinedLines = importInternal('drawing/drawJoinedLines');
+const drawCircle = importInternal('drawing/drawCircle');
+const drawEllipse = importInternal('drawing/drawEllipse');
+const drawHandles = importInternal('drawing/drawHandles');
+const drawArrow = importInternal('drawing/drawArrow');
+const getNewContext = importInternal('drawing/getNewContext');
+const BaseTool = importInternal('base/BaseTool');
+const drawLinkedTextBox = importInternal('drawing/drawLinkedTextBox');
+
+/**
+ * @class DICOMSRDisplayTool - Renders DICOMSR data in a read only manner (i.e. as an overlay).
+ *
+ * This is a generic render tool.
+ *
+ * A single tool that, given some schema, can render
+ * POINT, MULTIPOINT, POLYLINE, CIRCLE, and ELLIPSE
+ * value types for a given imageId.
+ *
+ *
+ * @extends cornerstoneTools.BaseTool
+ */
+export default class DICOMSRDisplayTool extends BaseTool {
+  constructor(props = {}) {
+    const defaultProps = {
+      mixins: ['enabledOrDisabledBinaryTool'],
+      name: TOOL_NAMES.DICOM_SR_DISPLAY_TOOL,
+    };
+
+    const initialProps = Object.assign(defaultProps, props);
+
+    super(initialProps);
+
+    this._module = csTools.getModule(id);
+  }
+
+  renderToolData(evt) {
+    const eventData = evt.detail;
+    const { element } = eventData;
+    const module = this._module;
+
+    const toolState = getToolState(element, this.name);
+
+    if (!toolState) {
+      return;
+    }
+
+    const trackingUniqueIdentifiersForElement = module.getters.trackingUniqueIdentifiersForElement(
+      element
+    );
+
+    const {
+      activeIndex,
+      trackingUniqueIdentifiers,
+    } = trackingUniqueIdentifiersForElement;
+
+    const activeTrackingUniqueIdentifier =
+      trackingUniqueIdentifiers[activeIndex];
+
+    // Filter toolData to only render the data for the active SR.
+    const filteredToolData = toolState.data.filter(td =>
+      trackingUniqueIdentifiers.includes(td.TrackingUniqueIdentifier)
+    );
+
+    let shouldRepositionTextBoxes = false;
+
+    for (let i = 0; i < filteredToolData.length; i++) {
+      const data = filteredToolData[i];
+      const { renderableData, labels } = data;
+
+      const color =
+        data.TrackingUniqueIdentifier === activeTrackingUniqueIdentifier
+          ? toolColors.getActiveColor()
+          : toolColors.getToolColor();
+      const lineWidth = 2;
+      const options = {
+        color,
+        lineWidth,
+        handleRadius: 6,
+      };
+
+      Object.keys(renderableData).forEach(GraphicType => {
+        const renderableDataForGraphicType = renderableData[GraphicType];
+
+        switch (GraphicType) {
+          case SCOORD_TYPES.TEXT:
+            break;
+          case SCOORD_TYPES.POINT:
+            this.renderPoint(renderableDataForGraphicType, eventData, options);
+            break;
+          case SCOORD_TYPES.MULTIPOINT:
+            this.renderMultipoint(
+              renderableDataForGraphicType,
+              eventData,
+              options
+            );
+            break;
+          case SCOORD_TYPES.POLYGON:
+          case SCOORD_TYPES.POLYLINE:
+            this.renderPolyLine(
+              renderableDataForGraphicType,
+              eventData,
+              options
+            );
+            break;
+          case SCOORD_TYPES.CIRCLE:
+            this.renderCircle(renderableDataForGraphicType, eventData, options);
+            break;
+          case SCOORD_TYPES.ELLIPSE:
+            this.renderEllipse(
+              renderableDataForGraphicType,
+              eventData,
+              options
+            );
+            break;
+        }
+      });
+
+      const { element } = eventData;
+      const context = getNewContext(eventData.canvasContext.canvas);
+
+      if (!data.handles || !data.handles.textBox) {
+        const textBox = {
+          active: false,
+          hasMoved: true,
+          movesIndependently: false,
+          drawnIndependently: true,
+          allowedOutsideImage: true,
+          hasBoundingBox: true,
+        };
+
+        const anchorPoints = _getTextBoxAnchorPointsForRenderableData(
+          renderableData,
+          eventData
+        );
+        textBox.anchorPoints = anchorPoints;
+
+        const bottomRight = {
+          x: Math.max(...anchorPoints.map(point => point.x)),
+          y: Math.max(...anchorPoints.map(point => point.y)),
+        };
+
+        textBox.x = bottomRight.x;
+        textBox.y = bottomRight.y;
+
+        data.handles = {};
+        data.handles.textBox = textBox;
+
+        shouldRepositionTextBoxes = true;
+      }
+
+      const text = _getTextBoxLinesFromLabels(labels);
+
+      function textBoxAnchorPoints() {
+        return data.handles.textBox.anchorPoints;
+      }
+
+      if (data.handles.textBox.anchorPoints.length !== 0) {
+        draw(context, context => {
+          drawLinkedTextBox(
+            context,
+            element,
+            data.handles.textBox,
+            text,
+            data.handles,
+            textBoxAnchorPoints,
+            color,
+            lineWidth,
+            0,
+            true
+          );
+        });
+      }
+    }
+
+    // TOOD -> text boxes may overlap with other annotations at the moment.
+    // To be fixed after we get requirements.
+    // if (shouldRepositionTextBoxes) {
+    //   this.repositionTextBox(filteredToolData, eventData);
+    // }
+  }
+
+  // repositionTextBox(toolData, eventData) {
+  //   const toolBoundingBoxes = [];
+
+  //   for (let i = 0; i < toolData.length; i++) {
+  //     const toolDataI = toolData[i];
+
+  //     const { textBox } = toolDataI.handles;
+  //     const { anchorPoints } = textBox;
+
+  //     const boundingBox = _getBoundingBoxFromAnchorPoints(anchorPoints);
+  //     // Get the textbox bounding locations.
+  //     // Get the tool extents.
+  //   }
+  // }
+
+  renderPolyLine(renderableData, eventData, options) {
+    const { element } = eventData;
+    const context = getNewContext(eventData.canvasContext.canvas);
+    renderableData.forEach(points => {
+      draw(context, context => {
+        drawJoinedLines(context, element, points[0], points, options);
+      });
+    });
+  }
+
+  renderMultipoint(renderableData, eventData, options) {
+    const context = getNewContext(eventData.canvasContext.canvas);
+
+    renderableData.forEach(points => {
+      draw(context, context => {
+        drawHandles(context, eventData, points, options);
+      });
+    });
+  }
+
+  renderPoint(renderableData, eventData, options) {
+    // Render single point as an arrow.
+    const { element, image } = eventData;
+    const { rows, columns } = image;
+    const context = getNewContext(eventData.canvasContext.canvas);
+    const { color, lineWidth } = options;
+
+    // Find a suitable length for the image size.
+
+    const xOffset = columns / 10;
+    const yOffset = rows / 10;
+
+    renderableData.forEach(points => {
+      const point = points[0]; // The SCOORD type is POINT so the array length is 1.
+      draw(context, context => {
+        // Draw the arrow
+        const handleStartCanvas = cornerstone.pixelToCanvas(element, point);
+        const handleEndCanvas = cornerstone.pixelToCanvas(element, {
+          x: point.x + xOffset,
+          y: point.y + yOffset,
+        });
+
+        drawArrow(
+          context,
+          handleEndCanvas,
+          handleStartCanvas,
+          color,
+          lineWidth,
+          false
+        );
+      });
+    });
+  }
+
+  renderCircle(renderableData, eventData, options) {
+    const { element } = eventData;
+
+    const context = getNewContext(eventData.canvasContext.canvas);
+
+    renderableData.forEach(circle => {
+      const { center, radius } = circle;
+
+      drawCircle(context, element, center, radius, options);
+    });
+  }
+
+  renderEllipse(renderableData, eventData, options) {
+    const { element } = eventData;
+
+    const context = getNewContext(eventData.canvasContext.canvas);
+
+    renderableData.forEach(ellipse => {
+      const { corner1, corner2 } = ellipse;
+
+      drawEllipse(
+        context,
+        element,
+        corner1,
+        corner2,
+        options,
+        'pixel',
+        0 // TODO -> Work our the initial rotation and add it here so we render appropriately rotated ellipses.
+      );
+    });
+  }
+}
+
+function _getTextBoxLinesFromLabels(labels) {
+  // TODO -> max 3 for now (label + shortAxis + longAxis), need a generic solution for this!
+
+  const labelLength = Math.min(labels.length, 3);
+  const lines = [];
+
+  for (let i = 0; i < labelLength; i++) {
+    const labelEntry = labels[i];
+    lines.push(`${_labelToShorthand(labelEntry.label)}${labelEntry.value}`);
+  }
+
+  return lines;
+}
+
+const SHORT_HAND_MAP = {
+  'Short Axis': 'W ',
+  'Long Axis': 'L ',
+  AREA: 'Area ',
+  Length: '',
+  CORNERSTONEFREETEXT: '',
+};
+
+function _labelToShorthand(label) {
+  const shortHand = SHORT_HAND_MAP[label];
+
+  if (shortHand !== undefined) {
+    return shortHand;
+  }
+
+  return label;
+}
+
+function _getTextBoxAnchorPointsForRenderableData(renderableData, eventData) {
+  let anchorPoints = [];
+
+  Object.keys(renderableData).forEach(GraphicType => {
+    const renderableDataForGraphicType = renderableData[GraphicType];
+
+    switch (GraphicType) {
+      case SCOORD_TYPES.TEXT:
+        break;
+      case SCOORD_TYPES.POINT:
+        renderableDataForGraphicType.forEach(points => {
+          anchorPoints = [...anchorPoints, ...points];
+
+          // Add other arrow point based on image size.
+          const { image } = eventData;
+          const { rows, columns } = image;
+
+          const xOffset = columns / 10;
+          const yOffset = rows / 10;
+          const point = points[0];
+
+          anchorPoints.push({ x: point.x + xOffset, y: point.y + yOffset });
+        });
+
+        break;
+      case SCOORD_TYPES.MULTIPOINT:
+      case SCOORD_TYPES.POLYLINE:
+      case SCOORD_TYPES.POLYGON:
+        renderableDataForGraphicType.forEach(points => {
+          anchorPoints = [...anchorPoints, ...points];
+        });
+        break;
+      case SCOORD_TYPES.CIRCLE:
+        renderableDataForGraphicType.forEach(circle => {
+          const { center, radius } = circle;
+
+          anchorPoints.push({ x: center.x + radius, y: center.y });
+          anchorPoints.push({ x: center.x - radius, y: center.y });
+          anchorPoints.push({ x: center.x, y: center.y + radius });
+          anchorPoints.push({ x: center.x, y: center.y - radius });
+        });
+
+        break;
+      case SCOORD_TYPES.ELLIPSE:
+        renderableDataForGraphicType.forEach(ellipse => {
+          const { corner1, corner2 } = ellipse;
+
+          const halfWidth = Math.abs(corner1.x - corner2.x) / 2;
+          const halfHeight = Math.abs(corner1.y - corner2.y) / 2;
+
+          const center = {
+            x: (corner1.x + corner2.x) / 2,
+            y: (corner1.y + corner2.y) / 2,
+          };
+
+          anchorPoints.push({ x: center.x + halfWidth, y: center.y });
+          anchorPoints.push({ x: center.x - halfWidth, y: center.y });
+          anchorPoints.push({ x: center.x, y: center.y + halfHeight });
+          anchorPoints.push({ x: center.x, y: center.y - halfHeight });
+        });
+        break;
+    }
+  });
+
+  return anchorPoints;
+}
+
+function _getBoundingBoxFromAnchorPoints(anchorPoints) {
+  let minX = Infinity;
+  let maxX = -Infinity;
+  let minY = Infinity;
+  let maxY = -Infinity;
+
+  anchorPoints.forEach(point => {
+    const { x, y } = point;
+
+    if (x > maxX) {
+      maxX = x;
+    } else if (x < minX) {
+      minX = x;
+    }
+
+    if (y > maxY) {
+      maxY = y;
+    } else if (y < minY) {
+      minY = y;
+    }
+  });
+}

extensions/cornerstone/src/tools/checkForSRAnnotations.js

@@ -0,0 +1,57 @@
+import csTools from 'cornerstone-tools';
+import cs from 'cornerstone-core';
+import OHIF from '@ohif/core';
+
+import { getEnabledElement } from '../state';
+import id from './id';
+
+const { studyMetadataManager } = OHIF.utils;
+
+const checkForSRAnnotations = ({ viewportIndex, displaySet }) => {
+  const srModule = csTools.getModule(id);
+
+  const element = getEnabledElement(viewportIndex);
+  if (!element) {
+    return;
+  }
+
+  const { StudyInstanceUID } = displaySet;
+  const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
+  if (!studyMetadata) {
+    return;
+  }
+
+  const srDisplaySets = studyMetadata
+    .getDisplaySets()
+    .filter(ds => ds.Modality === 'SR');
+  if (srDisplaySets.length === 0) {
+    return;
+  }
+
+  const { measurements: _measurements } = srDisplaySets[0];
+  if (!_measurements || _measurements.length < 1) {
+    return;
+  }
+
+  const measurements = _measurements.filter(m => m.loaded === true);
+  const measurement = measurements[0];
+  if (!measurement) {
+    return;
+  }
+
+  srModule.setters.trackingUniqueIdentifiersForElement(
+    element,
+    measurements.map(measurement => measurement.TrackingUniqueIdentifier),
+    measurement
+  );
+
+  const { TrackingUniqueIdentifier } = measurement;
+  srModule.setters.activeTrackingUniqueIdentifierForElement(
+    element,
+    TrackingUniqueIdentifier
+  );
+
+  cs.updateImage(element);
+};
+
+export default checkForSRAnnotations;

extensions/cornerstone/src/tools/constants/scoordTypes.js

@@ -0,0 +1,9 @@
+export default {
+  TEXT: 'TEXT',
+  POINT: 'POINT',
+  MULTIPOINT: 'MULTIPOINT',
+  POLYLINE: 'POLYLINE',
+  CIRCLE: 'CIRCLE',
+  ELLIPSE: 'ELLIPSE',
+  POLYGON: 'POLYGON',
+};

extensions/cornerstone/src/tools/constants/toolNames.js

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

extensions/cornerstone/src/tools/id.js

@@ -0,0 +1,7 @@
+const id = 'org.ohif.dicom-sr';
+
+export default id;
+
+const SOPClassHandlerName = 'dicom-sr';
+const SOPClassHandlerId = `${id}.sopClassHandlerModule.${SOPClassHandlerName}`;
+export { SOPClassHandlerName, SOPClassHandlerId };

extensions/cornerstone/src/tools/initSRTools.js

@@ -0,0 +1,108 @@
+import cornerstoneTools from 'cornerstone-tools';
+import DICOMSRDisplayTool from './DICOMSRDisplayTool';
+import TOOL_NAMES from './constants/toolNames';
+import getToolAlias from './utils/getToolAlias';
+
+/**
+ * Initialize SR cornerstone tools.
+ *
+ * @param {*} targetElement
+ */
+const initSRTools = targetElement => {
+  const primaryToolId = 'Wwwc';
+  const toolAlias = getToolAlias(primaryToolId); // These are 1:1 for built-in only
+
+  // ~~ MAGIC
+  cornerstoneTools.addToolForElement(targetElement, DICOMSRDisplayTool);
+  cornerstoneTools.setToolEnabledForElement(
+    targetElement,
+    TOOL_NAMES.DICOM_SR_DISPLAY_TOOL
+  );
+
+  // ~~ Variants
+  cornerstoneTools.addToolForElement(
+    targetElement,
+    cornerstoneTools.LengthTool,
+    {
+      name: 'SRLength',
+      configuration: {
+        renderDashed: true,
+      },
+    }
+  );
+  cornerstoneTools.addToolForElement(
+    targetElement,
+    cornerstoneTools.ArrowAnnotateTool,
+    {
+      name: 'SRArrowAnnotate',
+      configuration: {
+        renderDashed: true,
+      },
+    }
+  );
+  cornerstoneTools.addToolForElement(
+    targetElement,
+    cornerstoneTools.BidirectionalTool,
+    {
+      name: 'SRBidirectional',
+      configuration: {
+        renderDashed: true,
+      },
+    }
+  );
+  cornerstoneTools.addToolForElement(
+    targetElement,
+    cornerstoneTools.EllipticalRoiTool,
+    {
+      name: 'SREllipticalRoi',
+      configuration: {
+        renderDashed: true,
+      },
+    }
+  );
+  cornerstoneTools.addToolForElement(
+    targetElement,
+    cornerstoneTools.RectangleRoiTool,
+    {
+      name: 'SRRectangleRoi',
+      configuration: {
+        renderDashed: true,
+      },
+    }
+  );
+  cornerstoneTools.addToolForElement(
+    targetElement,
+    cornerstoneTools.FreehandRoiTool,
+    {
+      name: 'SRFreehandRoi',
+      configuration: {
+        renderDashed: true,
+      },
+    }
+  );
+
+  // ~~ Business as usual
+  cornerstoneTools.setToolActiveForElement(targetElement, 'PanMultiTouch', {
+    pointers: 2,
+  });
+  cornerstoneTools.setToolActiveForElement(targetElement, 'ZoomTouchPinch', {});
+
+  // TODO: Add always dashed tool alternative aliases
+  // TODO: or same name... alternative config?
+  cornerstoneTools.setToolActiveForElement(targetElement, toolAlias, {
+    mouseButtonMask: 1,
+  });
+  cornerstoneTools.setToolActiveForElement(targetElement, 'Pan', {
+    mouseButtonMask: 4,
+  });
+  cornerstoneTools.setToolActiveForElement(targetElement, 'Zoom', {
+    mouseButtonMask: 2,
+  });
+  cornerstoneTools.setToolActiveForElement(
+    targetElement,
+    'StackScrollMouseWheel',
+    {}
+  );
+};
+
+export default initSRTools;

extensions/cornerstone/src/tools/modules/dicomSRModule.js

@@ -0,0 +1,61 @@
+import cornerstone from 'cornerstone-core';
+
+const state = {
+  TrackingUniqueIdentifier: null,
+  trackingIdentifiersByEnabledElementUUID: {},
+};
+
+function setTrackingUniqueIdentifiersForElement(
+  element,
+  trackingUniqueIdentifiers,
+  activeIndex = 0
+) {
+  const enabledElement = cornerstone.getEnabledElement(element);
+  const { uuid } = enabledElement;
+
+  state.trackingIdentifiersByEnabledElementUUID[uuid] = {
+    trackingUniqueIdentifiers,
+    activeIndex,
+  };
+}
+
+function setActiveTrackingUniqueIdentifierForElement(
+  element,
+  TrackingUniqueIdentifier
+) {
+  const enabledElement = cornerstone.getEnabledElement(element);
+  const { uuid } = enabledElement;
+
+  const trackingIdentifiersForElement =
+    state.trackingIdentifiersByEnabledElementUUID[uuid];
+
+  if (trackingIdentifiersForElement) {
+    const activeIndex = trackingIdentifiersForElement.trackingUniqueIdentifiers.findIndex(
+      tuid => tuid === TrackingUniqueIdentifier
+    );
+
+    trackingIdentifiersForElement.activeIndex = activeIndex;
+  }
+}
+
+function getTrackingUniqueIdentifiersForElement(element) {
+  const enabledElement = cornerstone.getEnabledElement(element);
+  const { uuid } = enabledElement;
+
+  if (state.trackingIdentifiersByEnabledElementUUID[uuid]) {
+    return state.trackingIdentifiersByEnabledElementUUID[uuid];
+  }
+
+  return { trackingUniqueIdentifiers: [] };
+}
+
+export default {
+  state,
+  getters: {
+    trackingUniqueIdentifiersForElement: getTrackingUniqueIdentifiersForElement,
+  },
+  setters: {
+    trackingUniqueIdentifiersForElement: setTrackingUniqueIdentifiersForElement,
+    activeTrackingUniqueIdentifierForElement: setActiveTrackingUniqueIdentifierForElement,
+  },
+};

extensions/cornerstone/src/tools/utils/getToolAlias.js

@@ -0,0 +1,32 @@
+/**
+ * Get cornerstone tool alias.
+ *
+ * @param {string} toolName
+ * @returns tool alias
+ */
+export default function getToolAlias(toolName) {
+  let toolAlias = toolName;
+
+  switch (toolName) {
+    case 'Length':
+      toolAlias = 'SRLength';
+      break;
+    case 'Bidirectional':
+      toolAlias = 'SRBidirectional';
+      break;
+    case 'ArrowAnnotate':
+      toolAlias = 'SRArrowAnnotate';
+      break;
+    case 'EllipticalRoi':
+      toolAlias = 'SREllipticalRoi';
+      break;
+    case 'FreehandRoi':
+      toolAlias = 'SRFreehandRoi';
+      break;
+    case 'RectangleRoi':
+      toolAlias = 'SRRectangleRoi';
+      break;
+  }
+
+  return toolAlias;
+}

extensions/cornerstone/src/utils/formatStudy.js

@@ -0,0 +1,109 @@
+import moment from 'moment';
+
+/**
+ * Checks if value is valid.
+ *
+ * @param {number} value
+ * @returns {boolean} is valid.
+ */
+function isValidNumber(value) {
+  return typeof value === 'number' && !isNaN(value);
+}
+
+/**
+ * Formats number precision.
+ *
+ * @param {number} number
+ * @param {number} precision
+ * @returns {number} formatted number.
+ */
+function formatNumberPrecision(number, precision) {
+  if (number !== null) {
+    return parseFloat(number).toFixed(precision);
+  }
+}
+
+/**
+ * Formats DICOM date.
+ *
+ * @param {string} date
+ * @param {string} strFormat
+ * @returns {string} formatted date.
+ */
+function formatDICOMDate(date, strFormat = 'MMM D, YYYY') {
+  return moment(date, 'YYYYMMDD').format(strFormat);
+}
+
+/**
+ *    DICOM Time is stored as HHmmss.SSS, where:
+ *      HH 24 hour time:
+ *        m mm        0..59   Minutes
+ *        s ss        0..59   Seconds
+ *        S SS SSS    0..999  Fractional seconds
+ *
+ *        Goal: '24:12:12'
+ *
+ * @param {*} time
+ * @param {string} strFormat
+ * @returns {string} formatted name.
+ */
+function formatDICOMTime(time, strFormat = 'HH:mm:ss') {
+  return moment(time, 'HH:mm:ss').format(strFormat);
+}
+
+/**
+ * Formats a patient name for display purposes
+ *
+ * @param {string} name
+ * @returns {string} formatted name.
+ */
+function formatPN(name) {
+  if (!name) {
+    return;
+  }
+
+  // Convert the first ^ to a ', '. String.replace() only affects
+  // the first appearance of the character.
+  const commaBetweenFirstAndLast = name.replace('^', ', ');
+
+  // Replace any remaining '^' characters with spaces
+  const cleaned = commaBetweenFirstAndLast.replace(/\^/g, ' ');
+
+  // Trim any extraneous whitespace
+  return cleaned.trim();
+}
+
+/**
+ * Gets compression type
+ *
+ * @param {number} imageId
+ * @returns {string} comrpession type.
+ */
+function getCompression(imageId) {
+  const generalImageModule =
+    cornerstone.metaData.get('generalImageModule', imageId) || {};
+  const {
+    lossyImageCompression,
+    lossyImageCompressionRatio,
+    lossyImageCompressionMethod,
+  } = generalImageModule;
+
+  if (lossyImageCompression === '01' && lossyImageCompressionRatio !== '') {
+    const compressionMethod = lossyImageCompressionMethod || 'Lossy: ';
+    const compressionRatio = formatNumberPrecision(
+      lossyImageCompressionRatio,
+      2
+    );
+    return compressionMethod + compressionRatio + ' : 1';
+  }
+
+  return 'Lossless / Uncompressed';
+}
+
+export { isValidNumber,
+  formatNumberPrecision,
+  formatDICOMDate,
+  formatDICOMTime,
+  formatPN,
+  getCompression
+};

extensions/debugging/CHANGELOG.md

@@ -0,0 +1,138 @@
+# Change Log
+
+All notable changes to this project will be documented in this file.
+See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+## [0.3.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-debugging@0.3.2...@ohif/extension-debugging@0.3.3) (2022-06-30)
+
+**Note:** Version bump only for package @ohif/extension-debugging
+
+
+
+
+
+## [0.3.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-debugging@0.3.1...@ohif/extension-debugging@0.3.2) (2022-03-10)
+
+**Note:** Version bump only for package @ohif/extension-debugging
+
+
+
+
+
+## [0.3.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-debugging@0.3.0...@ohif/extension-debugging@0.3.1) (2021-12-02)
+
+**Note:** Version bump only for package @ohif/extension-debugging
+
+
+
+
+
+# [0.3.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-debugging@0.2.2...@ohif/extension-debugging@0.3.0) (2021-09-23)
+
+
+### Features
+
+* Update to WADO Image Loader 4.0.3 to add dynamically imported WebAssembly codec support 🚀 ([#2537](https://github.com/OHIF/Viewers/issues/2537)) ([489d4b0](https://github.com/OHIF/Viewers/commit/489d4b0584f4657ceda1c5b9b68d5e9733827e47))
+
+
+
+
+
+## [0.2.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-debugging@0.2.1...@ohif/extension-debugging@0.2.2) (2021-06-03)
+
+**Note:** Version bump only for package @ohif/extension-debugging
+
+
+
+
+
+## [0.2.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-debugging@0.2.0...@ohif/extension-debugging@0.2.1) (2021-03-19)
+
+**Note:** Version bump only for package @ohif/extension-debugging
+
+
+
+
+
+# [0.2.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-debugging@0.1.6...@ohif/extension-debugging@0.2.0) (2021-03-04)
+
+
+### Features
+
+* **log:** add new log service ([14d6454](https://github.com/OHIF/Viewers/commit/14d6454eafaa2ccb50e133c2945c9558052ea27e))
+
+
+
+
+
+## [0.1.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-debugging@0.1.5...@ohif/extension-debugging@0.1.6) (2020-10-06)
+
+**Note:** Version bump only for package @ohif/extension-debugging
+
+
+
+
+
+## [0.1.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-debugging@0.1.4...@ohif/extension-debugging@0.1.5) (2020-09-17)
+
+**Note:** Version bump only for package @ohif/extension-debugging
+
+
+
+
+
+## [0.1.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-debugging@0.1.3...@ohif/extension-debugging@0.1.4) (2020-09-10)
+
+**Note:** Version bump only for package @ohif/extension-debugging
+
+
+
+
+
+## 0.1.3 (2020-09-03)
+
+**Note:** Version bump only for package @ohif/extension-debugging
+
+
+
+
+
+## [0.1.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-p10-downloader@0.1.1...@ohif/extension-dicom-p10-downloader@0.1.2) (2020-06-18)
+
+**Note:** Version bump only for package @ohif/extension-dicom-p10-downloader
+
+
+
+
+
+## [0.1.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-p10-downloader@0.1.0...@ohif/extension-dicom-p10-downloader@0.1.1) (2020-06-04)
+
+**Note:** Version bump only for package @ohif/extension-dicom-p10-downloader
+
+
+
+
+
+# [0.1.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-p10-downloader@0.0.2...@ohif/extension-dicom-p10-downloader@0.1.0) (2020-04-23)
+
+
+### Features
+
+* configuration to hook into XHR Error handling ([e96205d](https://github.com/OHIF/Viewers/commit/e96205de35e5bec14dc8a9a8509db3dd4e6ecdb6))
+
+
+
+
+
+## 0.0.2 (2020-04-15)
+
+**Note:** Version bump only for package @ohif/extension-dicom-p10-downloader
+
+
+
+
+
+# Change Log
+
+All notable changes to this project will be documented in this file. See
+[Conventional Commits](https://conventionalcommits.org) for commit guidelines.

extensions/debugging/package.json

@@ -1,7 +1,7 @@
 {
-  "name": "@ohif/extension-dicom-p10-downloader",
-  "version": "0.1.0",
-  "description": "OHIF extension for downloading DICOM P10 files",
+  "name": "@ohif/extension-debugging",
+  "version": "0.3.3",
+  "description": "OHIF extension for debugging.",
   "author": "OHIF",
   "license": "MIT",
   "repository": "OHIF/Viewers",
@@ -28,12 +28,12 @@
   },
   "peerDependencies": {
     "@ohif/core": "^2.6.0",
-    "dicom-parser": "^1.8.3",
-    "dicomweb-client": "^0.5.2"
+    "dicom-parser": "^1.8.11"
   },
   "dependencies": {
     "@babel/runtime": "^7.5.5",
-    "dicomweb-client": "^0.6.0",
+    "detect-browser": "5.1.1",
+    "dicomweb-client": "^0.8.3",
     "file-saver": "^2.0.2",
     "jszip": "^3.2.2"
   }

extensions/debugging/src/DebugReportModal.css

@@ -0,0 +1,44 @@
+.debugReportModalHeader {
+  padding: 10px 0 10px;
+  color: var(--active-color);
+}
+
+.debug-report-modal-container {
+  display: flex;
+  flex-direction: column;
+}
+
+.debug-report-modal-buttons-container {
+  display: flex;
+  flex-direction: row;
+}
+
+.debug-report-modal-container .errors {
+  margin-top: 10px;
+}
+
+.debug-report-modal-container .errors-container {
+  border: 1px solid var(--active-color);
+  border-radius: 5px;
+  padding: 10px;
+  overflow: scroll;
+  max-height: 300px;
+}
+
+.debug-overflowText {
+  margin: 0 auto;
+  max-width: 300px;
+  overflow-wrap: break-word;
+  word-wrap: break-word;
+  hyphens: auto;
+}
+
+.debug-overflowText-border {
+  margin: 0 auto;
+  max-width: 300px;
+  border: solid 2px #ccc;
+  padding: 12px;
+  overflow-wrap: break-word;
+  word-wrap: break-word;
+  hyphens: auto;
+}

extensions/debugging/src/DebugReportModal.js

@@ -0,0 +1,439 @@
+import React from 'react';
+import { detect } from 'detect-browser';
+import './DebugReportModal.css';
+import { ToolbarButton } from '@ohif/ui';
+import { utils } from '@ohif/core';
+const { studyMetadataManager } = utils;
+
+const DubugReportModal = ({
+  viewports,
+  studies,
+  servers,
+  extensionManager,
+  mailTo,
+  debugModalMessage,
+  errors = [],
+}) => {
+  const copyDebugDataToClipboard = () => {
+    const body = getEmailBody();
+
+    const textArea = document.createElement('textarea');
+
+    textArea.value = body;
+    document.body.appendChild(textArea);
+    textArea.select();
+    document.execCommand('copy');
+    document.body.removeChild(textArea);
+  };
+
+  const getEmailBody = () => {
+    let body = `Enter the description of your problem here: \n\n\n`;
+
+    body += `============= SESSION INFO =============\n\n`;
+
+    // App version
+
+    body += '== App ==\n';
+    body += `version\t${window.version}\n\n`;
+
+    // Extensions Versions
+
+    body += '== Extensions Versions ==\n';
+
+    const { registeredExtensionVesions } = extensionManager;
+
+    Object.keys(registeredExtensionVesions).forEach(extensionId => {
+      const version = registeredExtensionVesions[extensionId];
+
+      body += `${extensionId}\t${version}\n`;
+    });
+
+    body += '\n';
+
+    // Browser Info
+
+    const browser = detect();
+
+    const { name, os, type, version } = browser;
+
+    body += '== Browser Info ==\n';
+    body += `name\t ${name}\n`;
+    body += `os\t ${os}\n`;
+    body += `type\t ${type}\n`;
+    body += `version\t ${version}\n\n`;
+
+    // Study URL
+    body += '== URL ==\n';
+    body += `URL\t ${window.location.href}\n\n`;
+
+    // Layout
+    const { numRows, numColumns, viewportSpecificData } = viewports;
+
+    body += '== Viewport Layout ==\n';
+    body += `Rows\t${numRows}\n`;
+    body += `Columns\t${numColumns}\n\n`;
+    body += '== SeriesInstanceUIDs ==\n';
+
+    Object.keys(viewportSpecificData).forEach(viewportIndex => {
+      const vsd = viewportSpecificData[viewportIndex];
+
+      const [row, column] = _viewportIndexToViewportPosition(
+        viewportIndex,
+        numColumns
+      );
+
+      body += `[${row},${column}]\t${vsd.SeriesInstanceUID}\n`;
+    });
+
+    body += '== ReferencedSEGSeriesInstanceUIDs ==\n';
+
+    Object.keys(viewportSpecificData).forEach(viewportIndex => {
+      const displaySet = viewportSpecificData[viewportIndex];
+      const [referencedDisplaySetsRef] = _getReferencedSeriesInstanceUIDsString(
+        displaySet,
+        'SEG'
+      );
+
+      const [row, column] = _viewportIndexToViewportPosition(
+        viewportIndex,
+        numColumns
+      );
+
+      body += `[${row},${column}]\t${referencedDisplaySetsRef}\n`;
+    });
+
+    body += '== ReferencedRTSTRUCTSeriesInstanceUIDs ==\n';
+
+    Object.keys(viewportSpecificData).forEach(viewportIndex => {
+      const displaySet = viewportSpecificData[viewportIndex];
+      const [referencedDisplaySetsRef] = _getReferencedSeriesInstanceUIDsString(
+        displaySet,
+        'RTSTRUCT'
+      );
+
+      const [row, column] = _viewportIndexToViewportPosition(
+        viewportIndex,
+        numColumns
+      );
+
+      body += `[${row},${column}]\t${referencedDisplaySetsRef}\n`;
+    });
+
+    body += '== ReferencedSRSeriesInstanceUIDs ==\n';
+
+    Object.keys(viewportSpecificData).forEach(viewportIndex => {
+      const displaySet = viewportSpecificData[viewportIndex];
+      const [referencedDisplaySetsRef] = _getReferencedSeriesInstanceUIDsString(
+        displaySet,
+        'SR'
+      );
+
+      const [row, column] = _viewportIndexToViewportPosition(
+        viewportIndex,
+        numColumns
+      );
+
+      body += `[${row},${column}]\t${referencedDisplaySetsRef}\n`;
+    });
+
+    return body;
+  };
+
+  const mailToFunction = () => {
+    const StudyInstanceUID = Object.keys(studies.studyData)[0];
+
+    const subject = encodeURI(`Issue with Study: ${StudyInstanceUID}`);
+
+    let body = getEmailBody();
+
+    // TODO Text dump of rest of stuff.
+
+    body = encodeURI(body);
+
+    window.location.href = `mailto:${mailTo}?subject=${subject}&body=${body}`;
+  };
+
+  return (
+    <div className="debug-report-modal-container">
+      {debugModalMessage ? <p>{debugModalMessage}</p> : null}
+      <div className="debug-report-modal-buttons-container">
+        {mailTo ? (
+          <div>
+            <ToolbarButton
+              label={'Send Bug Report'}
+              onClick={mailToFunction}
+              icon={'envelope-square'}
+              isActive={false}
+            />
+          </div>
+        ) : null}
+        <div>
+          <ToolbarButton
+            label={'Copy To Clipboard'}
+            onClick={copyDebugDataToClipboard}
+            icon={'clipboard'}
+            isActive={false}
+          />
+        </div>
+      </div>
+      <div>
+        <table>
+          {getAppVersion()}
+          {getExtensionVersions(extensionManager)}
+          {getBrowserInfo()}
+          {getCurrentStudyUrl()}
+          {getLayout(viewports)}
+        </table>
+      </div>
+      <div className="errors">
+        <h3>Errors ({errors.length})</h3>
+        <div className="errors-container">
+          {errors.map(error => {
+            return (
+              <div>
+                <pre>Message: {error.message}</pre>
+                {error.error && <pre>Stack: {error.error.stack}</pre>}
+              </div>
+            );
+          })}
+        </div>
+      </div>
+    </div>
+  );
+};
+
+const getAppVersion = () => {
+  return (
+    <React.Fragment>
+      <tr>
+        <th className="debugReportModalHeader">App</th>
+      </tr>
+      <tr>
+        <td>Version</td>
+        <td>{window.version}</td>
+      </tr>
+    </React.Fragment>
+  );
+};
+
+const getCurrentStudyUrl = () => {
+  return (
+    <React.Fragment>
+      <tr>
+        <th className="debugReportModalHeader">URL</th>
+      </tr>
+      <tr>
+        <td>URL</td>
+        <td className="debug-overflowText">{window.location.href}</td>
+      </tr>
+    </React.Fragment>
+  );
+};
+
+const getExtensionVersions = extensionManager => {
+  const { registeredExtensionVesions } = extensionManager;
+
+  const lineItems = Object.keys(registeredExtensionVesions).map(extensionId => {
+    const version = registeredExtensionVesions[extensionId];
+
+    return (
+      <tr>
+        <td>{extensionId}</td>
+        <td>{version}</td>
+      </tr>
+    );
+  });
+
+  return (
+    <React.Fragment>
+      <th className="debugReportModalHeader">Extensions</th>
+      {lineItems}
+    </React.Fragment>
+  );
+};
+
+const getLayout = viewports => {
+  const { numRows, numColumns } = viewports;
+
+  return (
+    <React.Fragment>
+      <tr>
+        <th className="debugReportModalHeader">Viewports</th>
+      </tr>
+      <tr>
+        <th>Layout</th>
+      </tr>
+      <tr>
+        <td>Rows</td>
+        <td>{numRows}</td>
+      </tr>
+      <tr>
+        <td>Columns</td>
+        <td>{numColumns}</td>
+      </tr>
+      <tr>
+        <th>SeriesInstanceUIDs</th>
+      </tr>
+      {getSeriesInstanceUIDsPerRow(viewports)}
+      <tr>
+        <th>ReferencedSEGSeriesInstanceUIDs</th>
+      </tr>
+      {getReferencedSeriesInstanceUIDsPerRow(viewports, 'SEG')}
+      <tr>
+        <th>ReferencedRTSTRUCTSeriesInstanceUIDs</th>
+      </tr>
+      {getReferencedSeriesInstanceUIDsPerRow(viewports, 'RTSTRUCT')}
+      <tr>
+        <th>ReferencedSRSeriesInstanceUIDs</th>
+      </tr>
+      {getReferencedSeriesInstanceUIDsPerRow(viewports, 'SR')}
+    </React.Fragment>
+  );
+};
+
+const getBrowserInfo = () => {
+  const browser = detect();
+
+  const { name, os, type, version } = browser;
+
+  return (
+    <React.Fragment>
+      <tr>
+        <th className="debugReportModalHeader">Platform</th>
+      </tr>
+      <tr>
+        <td>name</td>
+        <td>{name}</td>
+      </tr>
+      <tr>
+        <td>os</td>
+        <td>{os}</td>
+      </tr>
+      <tr>
+        <td>type</td>
+        <td>{type}</td>
+      </tr>
+      <tr>
+        <td>version</td>
+        <td>{version}</td>
+      </tr>
+    </React.Fragment>
+  );
+};
+
+/**
+ * Returns DisplaySets that reference the target series, sorted by dateTime
+ *
+ * @param {string} StudyInstanceUID
+ * @param {string} SeriesInstanceUID
+ * @returns Array
+ */
+const _getReferencedDisplaysets = (
+  StudyInstanceUID,
+  SeriesInstanceUID,
+  Modality
+) => {
+  /* Referenced DisplaySets */
+  const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
+  const referencedDisplaysets = studyMetadata.getDerivedDatasets({
+    referencedSeriesInstanceUID: SeriesInstanceUID,
+    Modality,
+  });
+
+  /* Sort */
+  referencedDisplaysets.sort((a, b) => {
+    const aNumber = Number(`${a.SeriesDate}${a.SeriesTime}`);
+    const bNumber = Number(`${b.SeriesDate}${b.SeriesTime}`);
+    return bNumber - aNumber;
+  });
+
+  return referencedDisplaysets;
+};
+
+const _getReferencedSeriesInstanceUIDsString = (displaySet, Modality) => {
+  const referencedDisplaySets = _getReferencedDisplaysets(
+    displaySet.StudyInstanceUID,
+    displaySet.SeriesInstanceUID,
+    Modality
+  );
+
+  let referencedDisplaySetsRef = 'None';
+  const referencedDisplaySetsCount = referencedDisplaySets.length;
+  if (referencedDisplaySetsCount !== 0) {
+    referencedDisplaySetsRef = '';
+    for (let i = 0; i < referencedDisplaySetsCount - 1; i++) {
+      referencedDisplaySetsRef +=
+        referencedDisplaySets[i].SeriesInstanceUID + ', ';
+    }
+    referencedDisplaySetsRef +=
+      referencedDisplaySets[referencedDisplaySetsCount - 1].SeriesInstanceUID;
+  }
+
+  return [referencedDisplaySetsRef, referencedDisplaySetsCount];
+};
+
+const getReferencedSeriesInstanceUIDsPerRow = (viewports, Modality) => {
+  const { viewportSpecificData, numColumns } = viewports;
+
+  // NOTE viewportSpecificData is actually an object with numerical keys.
+  return Object.keys(viewportSpecificData).map(viewportIndex => {
+    const displaySet = viewportSpecificData[viewportIndex];
+    const [
+      referencedDisplaySetsRef,
+      referencedDisplaySetsCount,
+    ] = _getReferencedSeriesInstanceUIDsString(displaySet, Modality);
+
+    const [row, column] = _viewportIndexToViewportPosition(
+      viewportIndex,
+      numColumns
+    );
+
+    if (referencedDisplaySetsCount > 1) {
+      return (
+        <tr>
+          <td>{`[${row},${column}]`}</td>
+          <td className="debug-overflowText-border">
+            {referencedDisplaySetsRef}
+          </td>
+        </tr>
+      );
+    } else {
+      return (
+        <tr>
+          <td>{`[${row},${column}]`}</td>
+          <td className="debug-overflowText">{referencedDisplaySetsRef}</td>
+        </tr>
+      );
+    }
+  });
+};
+
+const getSeriesInstanceUIDsPerRow = viewports => {
+  const { viewportSpecificData, numColumns } = viewports;
+
+  // NOTE viewportSpecificData is actually an object with numerical keys.
+  return Object.keys(viewportSpecificData).map(viewportIndex => {
+    const vsd = viewportSpecificData[viewportIndex];
+
+    const [row, column] = _viewportIndexToViewportPosition(
+      viewportIndex,
+      numColumns
+    );
+
+    return (
+      <tr>
+        <td>{`[${row},${column}]`}</td>
+        <td>{vsd.SeriesInstanceUID}</td>
+      </tr>
+    );
+  });
+};
+
+const _viewportIndexToViewportPosition = (viewportIndex, numColumns) => {
+  const row = Math.floor(viewportIndex / numColumns);
+  const column = viewportIndex % numColumns;
+
+  return [row, column];
+};
+
+export default DubugReportModal;

extensions/debugging/src/commandsModule.js

@@ -1,19 +1,25 @@
 import OHIF from '@ohif/core';
+import { useLogger } from '@ohif/ui';
+
 import {
   save,
+  upload,
   getDicomWebClientFromContext,
+  getStudyInstanceUIDFromStudies,
   getSOPInstanceReferenceFromActiveViewport,
   getSOPInstanceReferencesFromViewports,
 } from './utils';
-import _downloadAndZip from './downloadAndZip';
+import _downloadAndZip, { downloadInstances } from './downloadAndZip';
+import DebugReportModal from './DebugReportModal';
+import React from 'react';
+
+import state from './state';
 
 const {
-  utils: {
-    Queue,
-  },
+  utils: { Queue },
 } = OHIF;
 
-export function getCommands(context) {
+export function getCommands(context, servicesManager, extensionManager) {
   const queue = new Queue(1);
   const actions = {
     /**
@@ -41,6 +47,14 @@ export function getCommands(context) {
         listOfUIDs
       );
     },
+    downloadAndZipStudy({ servers, studies, progress }) {
+      const dicomWebClient = getDicomWebClientFromContext(context, servers);
+      const listOfUIDs = getStudyInstanceUIDFromStudies(studies);
+      return save(
+        _downloadAndZip(dicomWebClient, listOfUIDs, { progress }),
+        listOfUIDs
+      );
+    },
     downloadAndZipSeriesOnViewports({ servers, viewports, progress }) {
       const dicomWebClient = getDicomWebClientFromContext(context, servers);
       const listOfUIDs = getSOPInstanceReferencesFromViewports(viewports);
@@ -57,13 +71,67 @@ export function getCommands(context) {
         listOfUIDs
       );
     },
+    downloadAndUploadStudy({ servers, studies, progress, serverConfig }) {
+      const dicomWebClient = getDicomWebClientFromContext(context, servers);
+      const listOfUIDs = getStudyInstanceUIDFromStudies(studies);
+      return upload(
+        downloadInstances(dicomWebClient, listOfUIDs, { progress }),
+        /**
+         * serverConfig is an object with the values used to create a new
+         * instance of DICOMwebClient.
+         *
+         * Basic Structure:
+         *
+         * const config = {
+         *    url,
+         *    headers,
+         *    errorInterceptor
+         * }
+         *
+         * const dicomWeb = new api.DICOMwebClient(config);
+         */
+        serverConfig
+      );
+    },
+    openDebugInfoModal({ viewports, studies, servers }) {
+      const { UIModalService } = servicesManager.services;
+
+      const WrappedDebugReportModal = function() {
+        const { state: loggerState } = useLogger();
+        return (
+          <DebugReportModal
+            viewports={viewports}
+            studies={studies}
+            servers={servers}
+            extensionManager={extensionManager}
+            mailTo={state.mailTo}
+            debugModalMessage={state.debugModalMessage}
+            errors={loggerState.errors}
+          />
+        );
+      };
+
+      UIModalService.show({
+        content: WrappedDebugReportModal,
+        title: `Debugging Information`,
+      });
+    },
   };
 
   const definitions = {
+    openDebugInfoModal: {
+      commandFn: actions.openDebugInfoModal,
+      storeContexts: ['viewports', 'servers', 'studies'],
+    },
     downloadAndZip: {
       commandFn: queue.bindSafe(actions.downloadAndZip, error),
       storeContexts: ['servers'],
     },
+    downloadAndZipStudy: {
+      commandFn: queue.bindSafe(actions.downloadAndZipStudy, error),
+      storeContexts: ['servers', 'studies'],
+      options: { progress },
+    },
     downloadAndZipSeriesOnViewports: {
       commandFn: queue.bindSafe(actions.downloadAndZipSeriesOnViewports, error),
       storeContexts: ['servers', 'viewports'],
@@ -77,6 +145,11 @@ export function getCommands(context) {
       storeContexts: ['servers', 'viewports'],
       options: { progress },
     },
+    downloadAndUploadStudy: {
+      commandFn: queue.bindSafe(actions.downloadAndUploadStudy, error),
+      storeContexts: ['servers', 'studies'],
+      options: { progress },
+    },
   };
 
   return {

extensions/debugging/src/downloadAndZip.js

@@ -78,6 +78,25 @@ const {
 async function downloadAndZip(dicomWebClient, listOfUIDs, options) {
   if (dicomWebClient instanceof api.DICOMwebClient) {
     const settings = buildSettings(listOfUIDs, options);
+    const { compression } = settings.tasks;
+    const buffers = await downloadBuffers(settings, dicomWebClient);
+    compression.deferred.resolve(zipAll(buffers, settings));
+    const url = await compression.deferred.promise;
+    return url;
+  }
+  throw new Error('A valid DICOM Web Client instance is expected');
+}
+
+async function downloadInstances(dicomWebClient, listOfUIDs, options) {
+  if (dicomWebClient instanceof api.DICOMwebClient) {
+    const settings = buildSettings(listOfUIDs, options);
+    const buffers = await downloadBuffers(settings, dicomWebClient);
+    return buffers;
+  }
+  throw new Error('A valid DICOM Web Client instance is expected');
+}
+
+async function downloadBuffers(settings, dicomWebClient) {
   const { compression } = settings.tasks;
   // Register user-provided progress handler as a task list observer
   progressUtils.addObserver(settings.taskList, settings.options.progress);
@@ -86,11 +105,7 @@ async function downloadAndZip(dicomWebClient, listOfUIDs, options) {
     compression.deferred.reject(error);
     throw error;
   });
-    compression.deferred.resolve(zipAll(buffers, settings));
-    const url = await compression.deferred.promise;
-    return url;
-  }
-  throw new Error('A valid DICOM Web Client instance is expected');
+  return buffers;
 }
 
 /**
@@ -241,4 +256,4 @@ async function download(
  * Exports
  */
 
-export { downloadAndZip as default, downloadAndZip };
+export { downloadAndZip as default, downloadAndZip, downloadInstances };

extensions/debugging/src/index.js

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

extensions/debugging/src/state.js

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

extensions/debugging/src/toolbarModule.js

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

extensions/debugging/src/utils.js

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

extensions/dicom-html/CHANGELOG.md

@@ -3,6 +3,263 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [1.3.23](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.22...@ohif/extension-dicom-html@1.3.23) (2022-09-01)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.22](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.21...@ohif/extension-dicom-html@1.3.22) (2022-06-30)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.21](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.20...@ohif/extension-dicom-html@1.3.21) (2022-04-05)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.20](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.19...@ohif/extension-dicom-html@1.3.20) (2022-03-25)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.19](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.18...@ohif/extension-dicom-html@1.3.19) (2022-03-14)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.18](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.17...@ohif/extension-dicom-html@1.3.18) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.17](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.16...@ohif/extension-dicom-html@1.3.17) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.16](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.15...@ohif/extension-dicom-html@1.3.16) (2022-02-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.15](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.14...@ohif/extension-dicom-html@1.3.15) (2022-01-20)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.14](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.13...@ohif/extension-dicom-html@1.3.14) (2021-12-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.13](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.12...@ohif/extension-dicom-html@1.3.13) (2021-10-26)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.12](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.11...@ohif/extension-dicom-html@1.3.12) (2021-10-25)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.11](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.10...@ohif/extension-dicom-html@1.3.11) (2021-09-28)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.10](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.9...@ohif/extension-dicom-html@1.3.10) (2021-06-02)
+
+
+### Bug Fixes
+
+* **dicom-html:** Add parsed dicom meta info section ([#2419](https://github.com/OHIF/Viewers/issues/2419)) ([403688b](https://github.com/OHIF/Viewers/commit/403688b18c52468fc1101166ec0c1734fb710039))
+
+
+
+
+
+## [1.3.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.8...@ohif/extension-dicom-html@1.3.9) (2021-04-22)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.7...@ohif/extension-dicom-html@1.3.8) (2021-04-22)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.6...@ohif/extension-dicom-html@1.3.7) (2021-04-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.5...@ohif/extension-dicom-html@1.3.6) (2021-04-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.4...@ohif/extension-dicom-html@1.3.5) (2021-04-15)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.3...@ohif/extension-dicom-html@1.3.4) (2021-03-09)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.2...@ohif/extension-dicom-html@1.3.3) (2021-03-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.1...@ohif/extension-dicom-html@1.3.2) (2021-02-25)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.3.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.3.0...@ohif/extension-dicom-html@1.3.1) (2021-02-05)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+# [1.3.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.2.9...@ohif/extension-dicom-html@1.3.0) (2020-12-10)
+
+
+### Features
+
+* visualize overlapping segments in cornerstone ([#2185](https://github.com/OHIF/Viewers/issues/2185)) ([29fceac](https://github.com/OHIF/Viewers/commit/29fceacee97d51f1952a0f6b574c66596d32c201))
+
+
+
+
+
+## [1.2.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.2.8...@ohif/extension-dicom-html@1.2.9) (2020-10-07)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.2.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.2.7...@ohif/extension-dicom-html@1.2.8) (2020-09-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.2.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.2.6...@ohif/extension-dicom-html@1.2.7) (2020-09-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.2.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.2.5...@ohif/extension-dicom-html@1.2.6) (2020-09-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.2.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.2.4...@ohif/extension-dicom-html@1.2.5) (2020-08-28)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.2.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.2.3...@ohif/extension-dicom-html@1.2.4) (2020-07-13)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+## [1.2.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.2.2...@ohif/extension-dicom-html@1.2.3) (2020-06-15)
+
+
+### Bug Fixes
+
+* 🐛 Disable seg panel when data for seg unavailable ([#1732](https://github.com/OHIF/Viewers/issues/1732)) ([698e900](https://github.com/OHIF/Viewers/commit/698e900b85121d3c2a46747c443ef69fb7a8c95b)), closes [#1728](https://github.com/OHIF/Viewers/issues/1728)
+
+
+
+
+
 ## [1.2.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.2.1...@ohif/extension-dicom-html@1.2.2) (2020-05-04)
 
 

extensions/dicom-html/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-html",
-  "version": "1.2.2",
+  "version": "1.3.23",
   "description": "OHIF extension for rendering structured reports to HTML",
   "author": "OHIF",
   "license": "MIT",
@@ -29,7 +29,7 @@
   },
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
-    "dcmjs": "^0.12.3",
+    "dcmjs": "0.24.10",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6"

extensions/dicom-html/src/DicomHtmlViewport.js

@@ -160,7 +160,7 @@ const getContentSequence = (data, level = 1) => {
 
   const root = [];
   if (header) {
-    const HeaderDynamicLevel = `h${level}`;
+    const HeaderDynamicLevel = `h${Math.min(level, 6)}`;
 
     root.push(<HeaderDynamicLevel key={header}>{header}</HeaderDynamicLevel>);
   }
@@ -168,6 +168,16 @@ const getContentSequence = (data, level = 1) => {
   Object.keys(data).forEach(key => {
     const value = data[key];
 
+    if (key === '_meta') {
+      const HeaderDynamicLevel = `h3`;
+      root.push(<hr key={root.length} />);
+      root.push(
+        <HeaderDynamicLevel key="Metadata">
+          DICOM File Meta Information
+        </HeaderDynamicLevel>
+      );
+    }
+
     let content;
     if (value instanceof Object) {
       content = getContentSequence(value, level + 1);
@@ -207,7 +217,7 @@ class DicomHtmlViewport extends Component {
   };
 
   componentDidMount() {
-    const dataSet = this.setContentFromByteArray(this.props.byteArray);
+    this.setContentFromByteArray(this.props.byteArray);
   }
 
   setContentFromByteArray(byteArray) {
@@ -215,6 +225,7 @@ class DicomHtmlViewport extends Component {
     const dicomData = DicomMessage.readFile(arrayBuffer);
     const dataset = DicomMetaDictionary.naturalizeDataset(dicomData.dict);
     dataset._meta = DicomMetaDictionary.namifyDataset(dicomData.meta);
+    dataset._meta = DicomMetaDictionary.naturalizeDataset(dataset._meta);
 
     const mainData = getMainData(dataset);
     const contentSequence = getContentSequence(dataset);

extensions/dicom-html/src/OHIFDicomHtmlSopClassHandler.js

@@ -1,14 +1,16 @@
-import { MODULE_TYPES, utils } from '@ohif/core';
+import { MODULE_TYPES, utils, metadata } from '@ohif/core';
 
 // TODO: Should probably use dcmjs for this
 const SOP_CLASS_UIDS = {
   BASIC_TEXT_SR: '1.2.840.10008.5.1.4.1.1.88.11',
   ENHANCED_SR: '1.2.840.10008.5.1.4.1.1.88.22',
   COMPREHENSIVE_SR: '1.2.840.10008.5.1.4.1.1.88.33',
+  COMPREHENSIVE_3D_SR: '1.2.840.10008.5.1.4.1.1.88.34',
   PROCEDURE_LOG_STORAGE: '1.2.840.10008.5.1.4.1.1.88.40',
   MAMMOGRAPHY_CAD_SR: '1.2.840.10008.5.1.4.1.1.88.50',
   CHEST_CAD_SR: '1.2.840.10008.5.1.4.1.1.88.65',
   X_RAY_RADIATION_DOSE_SR: '1.2.840.10008.5.1.4.1.1.88.67',
+  ACQUISITION_CONTEXT_SR_STORAGE: '1.2.840.10008.5.1.4.1.1.88.71',
 };
 
 const sopClassUIDs = Object.values(SOP_CLASS_UIDS);
@@ -22,7 +24,15 @@ const OHIFDicomHtmlSopClassHandler = {
   getDisplaySetFromSeries(series, study, dicomWebClient, authorizationHeaders) {
     const instance = series.getFirstInstance();
 
-    return {
+    const metadata = instance.getData().metadata;
+    const {
+      SeriesDescription,
+      SeriesNumber,
+      SeriesDate,
+      SeriesTime,
+    } = metadata;
+
+    const srDisplaySet = {
       plugin: 'html',
       Modality: 'SR',
       displaySetInstanceUID: utils.guid(),
@@ -31,8 +41,23 @@ const OHIFDicomHtmlSopClassHandler = {
       SOPInstanceUID: instance.getSOPInstanceUID(),
       SeriesInstanceUID: series.getSeriesInstanceUID(),
       StudyInstanceUID: study.getStudyInstanceUID(),
+      SeriesDescription,
+      metadata,
+      SeriesDate,
+      SeriesTime,
+      SeriesNumber,
       authorizationHeaders,
+      sopClassUids: sopClassUIDs,
+      images: series._instances,
+      isDerived: true,
+      referencedDisplaySets: [],
     };
+
+    srDisplaySet.getSourceDisplaySet = function() {
+      return srDisplaySet.referencedDisplaySets;
+    };
+
+    return srDisplaySet;
   },
 };
 

extensions/dicom-html/src/index.js

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

extensions/dicom-microscopy/CHANGELOG.md

@@ -3,6 +3,60 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+# [0.52.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.51.4...@ohif/extension-dicom-microscopy@0.52.0) (2021-03-04)
+
+
+### Features
+
+* **log:** add new log service ([14d6454](https://github.com/OHIF/Viewers/commit/14d6454eafaa2ccb50e133c2945c9558052ea27e))
+
+
+
+
+
+## [0.51.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.51.3...@ohif/extension-dicom-microscopy@0.51.4) (2021-01-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-microscopy
+
+
+
+
+
+## [0.51.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.51.2...@ohif/extension-dicom-microscopy@0.51.3) (2020-09-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-microscopy
+
+
+
+
+
+## [0.51.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.51.1...@ohif/extension-dicom-microscopy@0.51.2) (2020-09-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-microscopy
+
+
+
+
+
+## [0.51.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.51.0...@ohif/extension-dicom-microscopy@0.51.1) (2020-08-28)
+
+**Note:** Version bump only for package @ohif/extension-dicom-microscopy
+
+
+
+
+
+# [0.51.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.9...@ohif/extension-dicom-microscopy@0.51.0) (2020-06-04)
+
+
+### Features
+
+* 🎸 1729 - error boundary wrapper ([#1764](https://github.com/OHIF/Viewers/issues/1764)) ([c02b232](https://github.com/OHIF/Viewers/commit/c02b232b0cc24f38af5d5e3831d987d048e60ada))
+
+
+
+
+
 ## [0.50.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.8...@ohif/extension-dicom-microscopy@0.50.9) (2020-04-02)
 
 **Note:** Version bump only for package @ohif/extension-dicom-microscopy

extensions/dicom-microscopy/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-microscopy",
-  "version": "0.50.9",
+  "version": "0.52.0",
   "description": "OHIF extension for Dicom Microscopy",
   "author": "OHIF",
   "license": "MIT",

extensions/dicom-microscopy/src/DicomMicroscopySopClassHandler.js

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

extensions/dicom-microscopy/src/DicomMicroscopyViewport.js

@@ -62,11 +62,30 @@ class DicomMicroscopyViewport extends Component {
         );
         const microscopyViewer = api.VLWholeSlideMicroscopyImageViewer;
 
+        try {
           this.viewer = new microscopyViewer({
             client: dicomWebClient,
             metadata,
             retrieveRendered: false,
           });
+        } catch (error) {
+          console.error('[Microscopy Viewer] Failed to load:', error);
+          const {
+            UINotificationService,
+            LoggerService,
+          } = this.props.servicesManager.services;
+          if (UINotificationService) {
+            const message =
+              'Failed to load viewport. Please check that you have hardware acceleration enabled.';
+            LoggerService.error({ error, message });
+            UINotificationService.show({
+              autoClose: false,
+              title: 'Microscopy Viewport',
+              message,
+              type: 'error',
+            });
+          }
+        }
 
         this.viewer.render({ container });
       });

extensions/dicom-microscopy/src/index.js

@@ -1,26 +1,26 @@
 import React from 'react';
 import DicomMicroscopySopClassHandler from './DicomMicroscopySopClassHandler.js';
+import { version } from '../package.json';
 
 const Component = React.lazy(() => {
   return import('./DicomMicroscopyViewport');
 });
 
-const DicomMicroscopyViewport = props => {
-  return (
-    <React.Suspense fallback={<div>Loading...</div>}>
-      <Component {...props} />
-    </React.Suspense>
-  );
-};
-
 export default {
   /**
    * Only required property. Should be a unique value across all extensions.
    */
   id: 'microscopy',
+  version,
 
-  getViewportModule() {
-    return DicomMicroscopyViewport;
+  getViewportModule({ servicesManager }) {
+    return props => {
+      return (
+        <React.Suspense fallback={<div>Loading...</div>}>
+          <Component {...props} servicesManager={servicesManager} />
+        </React.Suspense>
+      );
+    };
   },
   getSopClassHandlerModule() {
     return DicomMicroscopySopClassHandler;

extensions/dicom-p10-downloader/CHANGELOG.md

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

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

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

extensions/dicom-pdf/CHANGELOG.md

@@ -3,6 +3,57 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [1.1.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@1.1.1...@ohif/extension-dicom-pdf@1.1.2) (2022-01-29)
+
+**Note:** Version bump only for package @ohif/extension-dicom-pdf
+
+
+
+
+
+## [1.1.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@1.1.0...@ohif/extension-dicom-pdf@1.1.1) (2021-12-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-pdf
+
+
+
+
+
+# [1.1.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@1.0.6...@ohif/extension-dicom-pdf@1.1.0) (2021-09-23)
+
+
+### Features
+
+* Update to WADO Image Loader 4.0.3 to add dynamically imported WebAssembly codec support 🚀 ([#2537](https://github.com/OHIF/Viewers/issues/2537)) ([489d4b0](https://github.com/OHIF/Viewers/commit/489d4b0584f4657ceda1c5b9b68d5e9733827e47))
+
+
+
+
+
+## [1.0.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@1.0.5...@ohif/extension-dicom-pdf@1.0.6) (2020-09-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-pdf
+
+
+
+
+
+## [1.0.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@1.0.4...@ohif/extension-dicom-pdf@1.0.5) (2020-09-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-pdf
+
+
+
+
+
+## [1.0.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@1.0.3...@ohif/extension-dicom-pdf@1.0.4) (2020-08-28)
+
+**Note:** Version bump only for package @ohif/extension-dicom-pdf
+
+
+
+
+
 ## [1.0.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@1.0.2...@ohif/extension-dicom-pdf@1.0.3) (2020-04-02)
 
 **Note:** Version bump only for package @ohif/extension-dicom-pdf

extensions/dicom-pdf/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-pdf",
-  "version": "1.0.3",
+  "version": "1.1.2",
   "description": "OHIF extension for Dicom PDF",
   "author": "OHIF",
   "license": "MIT",
@@ -29,7 +29,7 @@
   },
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
-    "dicom-parser": "^1.8.3",
+    "dicom-parser": "^1.8.11",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6"

extensions/dicom-pdf/src/DicomPDFViewport.js

@@ -33,6 +33,7 @@ class DicomPDFViewport extends Component {
 
   static propTypes = {
     byteArray: TypedArrayProp.uint8,
+    rawPdf: PropTypes.bool,
     useNative: PropTypes.bool,
     viewportData: PropTypes.object,
     activeViewportIndex: PropTypes.number,
@@ -45,7 +46,8 @@ class DicomPDFViewport extends Component {
   };
 
   async componentDidMount() {
-    const dataSet = this.parseByteArray(this.props.byteArray);
+    const { rawPdf } = this.props
+    const dataSet = !rawPdf && this.parseByteArray(this.props.byteArray);
     const fileURL = this.getPDFFileUrl(dataSet, this.props.byteArray);
 
     this.setState(state => ({ ...state, fileURL }));

extensions/dicom-pdf/src/OHIFDicomPDFSopClassHandler.js

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

extensions/dicom-pdf/src/OHIFDicomPDFViewport.js

@@ -3,6 +3,7 @@ import PropTypes from 'prop-types';
 import OHIF from '@ohif/core';
 import OHIFComponentPlugin from './OHIFComponentPlugin.js';
 import DicomPDFViewport from './DicomPDFViewport';
+import { str2ab } from '@ohif/core';
 
 const { DicomLoaderService } = OHIF.utils;
 
@@ -18,6 +19,7 @@ class OHIFDicomPDFViewport extends Component {
 
   state = {
     byteArray: null,
+    rawPdf: false,
     error: null,
   };
 
@@ -34,6 +36,15 @@ class OHIFDicomPDFViewport extends Component {
   componentDidMount() {
     const { displaySet, studies } = this.props.viewportData;
 
+    if (displaySet.metadata && displaySet.metadata.EncapsulatedDocument) {
+      const { InlineBinary, BulkDataURI } = displaySet.metadata.EncapsulatedDocument;
+      if (InlineBinary) {
+        const inlineBinaryData = atob(InlineBinary);
+        const byteArray = str2ab(inlineBinaryData);
+        this.setState({ byteArray, rawPdf: true });
+        return;
+      }
+    }
     DicomLoaderService.findDicomDataPromise(displaySet, studies).then(
       data => this.setState({ byteArray: new Uint8Array(data) }),
       error => {
@@ -49,15 +60,16 @@ class OHIFDicomPDFViewport extends Component {
       viewportIndex,
       activeViewportIndex,
     } = this.props;
-    const { byteArray, error } = this.state;
+    const { byteArray, error, rawPdf } = this.state;
     const { id, init, destroy } = OHIFDicomPDFViewport;
     const pluginProps = { id, init, destroy };
 
     return (
       <OHIFComponentPlugin {...pluginProps}>
-        {byteArray && (
+        {(byteArray) && (
           <DicomPDFViewport
             byteArray={byteArray}
+            rawPdf={rawPdf}
             setViewportActive={setViewportActive}
             viewportIndex={viewportIndex}
             activeViewportIndex={activeViewportIndex}

extensions/dicom-pdf/src/index.js

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

extensions/dicom-rt/CHANGELOG.md

@@ -3,6 +3,431 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [0.7.13](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.7.12...@ohif/extension-dicom-rt@0.7.13) (2022-09-01)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.7.12](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.7.11...@ohif/extension-dicom-rt@0.7.12) (2022-08-31)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.7.11](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.7.10...@ohif/extension-dicom-rt@0.7.11) (2022-04-05)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.7.10](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.7.9...@ohif/extension-dicom-rt@0.7.10) (2022-03-25)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.7.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.7.8...@ohif/extension-dicom-rt@0.7.9) (2022-03-14)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.7.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.7.7...@ohif/extension-dicom-rt@0.7.8) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.7.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.7.6...@ohif/extension-dicom-rt@0.7.7) (2022-02-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.7.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.7.5...@ohif/extension-dicom-rt@0.7.6) (2022-01-20)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.7.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.7.4...@ohif/extension-dicom-rt@0.7.5) (2022-01-19)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.7.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.7.3...@ohif/extension-dicom-rt@0.7.4) (2021-12-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.7.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.7.2...@ohif/extension-dicom-rt@0.7.3) (2021-10-26)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.7.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.7.1...@ohif/extension-dicom-rt@0.7.2) (2021-10-06)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.7.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.7.0...@ohif/extension-dicom-rt@0.7.1) (2021-09-28)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+# [0.7.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.14...@ohif/extension-dicom-rt@0.7.0) (2021-09-23)
+
+
+### Features
+
+* Update to WADO Image Loader 4.0.3 to add dynamically imported WebAssembly codec support 🚀 ([#2537](https://github.com/OHIF/Viewers/issues/2537)) ([489d4b0](https://github.com/OHIF/Viewers/commit/489d4b0584f4657ceda1c5b9b68d5e9733827e47))
+
+
+
+
+
+## [0.6.14](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.13...@ohif/extension-dicom-rt@0.6.14) (2021-09-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.13](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.12...@ohif/extension-dicom-rt@0.6.13) (2021-06-02)
+
+
+### Bug Fixes
+
+* **dicom-html:** Add parsed dicom meta info section ([#2419](https://github.com/OHIF/Viewers/issues/2419)) ([403688b](https://github.com/OHIF/Viewers/commit/403688b18c52468fc1101166ec0c1734fb710039))
+
+
+
+
+
+## [0.6.12](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.11...@ohif/extension-dicom-rt@0.6.12) (2021-05-17)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.11](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.10...@ohif/extension-dicom-rt@0.6.11) (2021-04-22)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.10](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.9...@ohif/extension-dicom-rt@0.6.10) (2021-04-22)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.8...@ohif/extension-dicom-rt@0.6.9) (2021-04-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.7...@ohif/extension-dicom-rt@0.6.8) (2021-04-15)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.6...@ohif/extension-dicom-rt@0.6.7) (2021-03-09)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.5...@ohif/extension-dicom-rt@0.6.6) (2021-03-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.4...@ohif/extension-dicom-rt@0.6.5) (2021-02-25)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.3...@ohif/extension-dicom-rt@0.6.4) (2021-02-05)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.2...@ohif/extension-dicom-rt@0.6.3) (2021-01-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.1...@ohif/extension-dicom-rt@0.6.2) (2021-01-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.6.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.6.0...@ohif/extension-dicom-rt@0.6.1) (2020-12-10)
+
+
+### Bug Fixes
+
+* panel issues and mpr button (IDC2122-IDC2117) ([32022f5](https://github.com/OHIF/Viewers/commit/32022f51f2d24f53f4c98188980db038a6dfe76c))
+
+
+
+
+
+# [0.6.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.5.0...@ohif/extension-dicom-rt@0.6.0) (2020-12-10)
+
+
+### Features
+
+* visualize overlapping segments in cornerstone ([#2185](https://github.com/OHIF/Viewers/issues/2185)) ([29fceac](https://github.com/OHIF/Viewers/commit/29fceacee97d51f1952a0f6b574c66596d32c201))
+
+
+
+
+
+# [0.5.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.4.9...@ohif/extension-dicom-rt@0.5.0) (2020-12-03)
+
+
+### Features
+
+* Update approach to better handle rtdose instead of disabling panel ([f3cecf1](https://github.com/OHIF/Viewers/commit/f3cecf129b16f8d24d239aa44fdff7f46e6ba683))
+
+
+
+
+
+## [0.4.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.4.8...@ohif/extension-dicom-rt@0.4.9) (2020-10-12)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.4.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.4.7...@ohif/extension-dicom-rt@0.4.8) (2020-10-07)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.4.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.4.6...@ohif/extension-dicom-rt@0.4.7) (2020-10-06)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.4.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.4.5...@ohif/extension-dicom-rt@0.4.6) (2020-09-17)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.4.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.4.4...@ohif/extension-dicom-rt@0.4.5) (2020-09-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.4.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.4.3...@ohif/extension-dicom-rt@0.4.4) (2020-09-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.4.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.4.2...@ohif/extension-dicom-rt@0.4.3) (2020-09-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.4.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.4.1...@ohif/extension-dicom-rt@0.4.2) (2020-09-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.4.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.4.0...@ohif/extension-dicom-rt@0.4.1) (2020-08-28)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+# [0.4.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.3.0...@ohif/extension-dicom-rt@0.4.0) (2020-08-18)
+
+
+### Features
+
+* 🎸 Update react-vtkjs-viewport usage to use requestPool ([#1984](https://github.com/OHIF/Viewers/issues/1984)) ([bb5f30c](https://github.com/OHIF/Viewers/commit/bb5f30ce2a0192d2e021beaaadfff22fd38e17b9))
+
+
+
+
+
+# [0.3.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.2.7...@ohif/extension-dicom-rt@0.3.0) (2020-08-10)
+
+
+### Features
+
+* 🎸 Add support for POINT and OPEN_PLANAR for RT ([0e87ab3](https://github.com/OHIF/Viewers/commit/0e87ab37c29fcf9af74bbcefca854c6e6b8707bc))
+
+
+
+
+
+## [0.2.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.2.6...@ohif/extension-dicom-rt@0.2.7) (2020-08-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.2.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.2.5...@ohif/extension-dicom-rt@0.2.6) (2020-08-05)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.2.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.2.4...@ohif/extension-dicom-rt@0.2.5) (2020-07-13)
+
+
+### Bug Fixes
+
+* 🐛 - Put guards in all places that a cornerstone re-render ([#1899](https://github.com/OHIF/Viewers/issues/1899)) ([451f7ea](https://github.com/OHIF/Viewers/commit/451f7eab9258e7a193eb362e0926b13aedc4b3c9))
+
+
+
+
+
+## [0.2.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.2.3...@ohif/extension-dicom-rt@0.2.4) (2020-07-13)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.2.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.2.2...@ohif/extension-dicom-rt@0.2.3) (2020-07-13)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+## [0.2.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.2.1...@ohif/extension-dicom-rt@0.2.2) (2020-07-13)
+
+
+### Bug Fixes
+
+* 🐛 Fix RT Panel hide/show and Fix looping load errors ([#1877](https://github.com/OHIF/Viewers/issues/1877)) ([e7cc735](https://github.com/OHIF/Viewers/commit/e7cc735c03d02eeb0d3af4ba02c15ed4f81bbec2))
+
+
+
+
+
+## [0.2.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.2.0...@ohif/extension-dicom-rt@0.2.1) (2020-06-15)
+
+
+### Bug Fixes
+
+* 🐛 Disable seg panel when data for seg unavailable ([#1732](https://github.com/OHIF/Viewers/issues/1732)) ([698e900](https://github.com/OHIF/Viewers/commit/698e900b85121d3c2a46747c443ef69fb7a8c95b)), closes [#1728](https://github.com/OHIF/Viewers/issues/1728)
+
+
+
+
+
+# [0.2.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.1.4...@ohif/extension-dicom-rt@0.2.0) (2020-06-04)
+
+
+### Features
+
+* 🎸 1729 - error boundary wrapper ([#1764](https://github.com/OHIF/Viewers/issues/1764)) ([c02b232](https://github.com/OHIF/Viewers/commit/c02b232b0cc24f38af5d5e3831d987d048e60ada))
+
+
+
+
+
 ## [0.1.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.1.3...@ohif/extension-dicom-rt@0.1.4) (2020-05-14)
 
 

extensions/dicom-rt/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-rt",
-  "version": "0.1.4",
+  "version": "0.7.13",
   "description": "OHIF extension for rendering DICOM RTSTRUCTs on top of cornerstone images.",
   "author": "OHIF",
   "license": "MIT",
@@ -29,12 +29,14 @@
   },
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
-    "cornerstone-core": "^2.2.8",
-    "cornerstone-tools": "4.15.1",
-    "dcmjs": "^0.12.3",
+    "cornerstone-core": "^2.6.1",
+    "cornerstone-tools": "^6.0.6",
+    "dcmjs": "0.24.10",
+    "gl-matrix": "^3.3.0",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
-    "react-dom": "^16.8.6"
+    "react-dom": "^16.8.6",
+    "react-tooltip": "4.2.10"
   },
   "dependencies": {
     "@babel/runtime": "^7.5.5",

extensions/dicom-rt/src/OHIFDicomRTStructSopClassHandler.js

@@ -1,5 +1,6 @@
 import { MODULE_TYPES, utils, DICOMWeb } from '@ohif/core';
 import loadRTStruct from './loadRTStruct';
+import getSourceDisplaySet from './getSourceDisplaySet';
 
 import id from './id';
 
@@ -26,6 +27,7 @@ const OHIFDicomRTStructSopClassHandler = {
     const {
       SeriesDate,
       SeriesTime,
+      SeriesNumber,
       SeriesDescription,
       FrameOfReferenceUID,
       SOPInstanceUID,
@@ -52,7 +54,9 @@ const OHIFDicomRTStructSopClassHandler = {
       isLoaded: false,
       SeriesDate,
       SeriesTime,
+      SeriesNumber,
       SeriesDescription,
+      metadata,
     };
 
     if (!metadata.ReferencedSeriesSequence) {
@@ -67,6 +71,10 @@ const OHIFDicomRTStructSopClassHandler = {
       }
     }
 
+    rtStructDisplaySet.getSourceDisplaySet = function (studies, activateLabelMap = true) {
+      return getSourceDisplaySet(studies, rtStructDisplaySet, activateLabelMap);
+    };
+
     rtStructDisplaySet.load = function (referencedDisplaySet, studies) {
       return loadRTStruct(
         rtStructDisplaySet,
@@ -74,6 +82,7 @@ const OHIFDicomRTStructSopClassHandler = {
         studies
       ).catch(error => {
         rtStructDisplaySet.isLoaded = false;
+        rtStructDisplaySet.loadError = true;
         throw new Error(error);
       });
     };

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

@@ -39,6 +39,8 @@
   border-radius: 5px;
 }
 
-.icons .angle-double-down, .icons .angle-double-up {
+.icons .angle-double-down,
+.icons .angle-double-up {
   margin-left: 15px;
+  margin-right: -5px;
 }

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

@@ -9,16 +9,21 @@
 
 .dcmrt-panel .dcmrt-panel-header {
   display: flex;
-  flex-direction: row;
+  flex-direction: column;
   justify-content: space-between;
   color: white;
 }
 
+.dcmrt-panel .dcmrt-panel-header h3 {
+  margin-top: 0;
+}
+
 .dcmrt-panel .dcmrt-panel-header .cog-icon {
   align-self: flex-end;
   color: var(--default-color);
   cursor: pointer;
-  margin-bottom: 20px;
+  min-height: 23px;
+  max-height: 23px;
 }
 
 .dcmrt-panel .dcmrt-panel-header .cog-icon:hover {

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

@@ -12,12 +12,17 @@ import StructureSetItem from '../StructureSetItem/StructureSetItem';
 import RTPanelSettings from '../RTSettings/RTSettings';
 import PanelSection from '../PanelSection/PanelSection';
 import LoadingIndicator from '../LoadingIndicator/LoadingIndicator';
+import TOOL_NAMES from '../../utils/toolNames';
+
+const { RTSTRUCT_DISPLAY_TOOL } = TOOL_NAMES;
 
 const { studyMetadataManager } = utils;
 
 const refreshViewport = () => {
   cornerstone.getEnabledElements().forEach(enabledElement => {
+    if (enabledElement.image) {
       cornerstone.updateImage(enabledElement.element);
+    }
   });
 };
 
@@ -26,23 +31,35 @@ const refreshViewport = () => {
  *
  * @param {Object} props
  * @param {Array} props.studies
- * @param {Array} props.viewports - viewportSpecificData
+ * @param {Array} props.getActiveViewport - get active viewport data
  * @param {number} props.activeIndex - activeViewportIndex
  * @param {number} props.isOpen - isOpen
  * @returns component
  */
-const RTPanel = ({ studies, viewports, activeIndex, isOpen, onContourItemClick }) => {
+const RTPanel = ({
+  studies,
+  activeIndex,
+  isOpen,
+  onContourItemClick,
+  activeContexts = [],
+  contexts = {},
+  activeViewport,
+  getActiveViewport,
+}) => {
+  const isVTK = () => activeContexts.includes(contexts.VTK);
+  const isCornerstone = () => activeContexts.includes(contexts.CORNERSTONE);
+
   const [selectedContour, setSelectedContour] = useState();
   const DEFAULT_SET_INDEX = 0;
   const DEFAULT_STATE = {
     referencedDisplaysets: [],
     sets: [],
     selectedSet: null,
+    isLocked: false,
   };
 
   const [state, setState] = useState(DEFAULT_STATE);
   const [showSettings, setShowSettings] = useState(false);
-  const activeViewport = viewports[activeIndex];
 
   /*
    * TODO: Improve the way we notify parts of the app that depends on rts to be loaded.
@@ -62,25 +79,39 @@ const RTPanel = ({ studies, viewports, activeIndex, isOpen, onContourItemClick }
    * without subscribing to external events.
    */
   useEffect(() => {
-    document.addEventListener('extensiondicomrtrtloaded', updateStructureSets);
+    updateStructureSets();
+
+    document.addEventListener('rt-panel-tab-updated', updateStructureSets);
 
     return () => {
-      document.removeEventListener('extensiondicomrtrtloaded', updateStructureSets);
+      document.removeEventListener('rt-panel-tab-updated', updateStructureSets);
     };
   }, []);
 
+  useEffect(() => {
+    const studyMetadata = studyMetadataManager.get(
+      activeViewport.StudyInstanceUID
+    );
+    const referencedDisplaysets = studyMetadata.getDerivedDatasets({
+      referencedSeriesInstanceUID: activeViewport.SeriesInstanceUID,
+      Modality: 'RTSTRUCT',
+    });
+    setState(state => ({ ...state, isLocked: !referencedDisplaysets.length }));
+  }, [activeViewport]);
+
   const updateStructureSets = () => {
+    const viewport = getActiveViewport();
     const module = cornerstoneTools.getModule('rtstruct');
     const StructureSets = module.state.StructureSets;
 
     if (StructureSets && StructureSets.length) {
       const viewportSets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(
-        activeViewport.SeriesInstanceUID
+        viewport.SeriesInstanceUID
       );
 
-      const studyMetadata = studyMetadataManager.get(activeViewport.StudyInstanceUID);
+      const studyMetadata = studyMetadataManager.get(viewport.StudyInstanceUID);
       const referencedDisplaysets = studyMetadata.getDerivedDatasets({
-        referencedSeriesInstanceUID: activeViewport.SeriesInstanceUID,
+        referencedSeriesInstanceUID: viewport.SeriesInstanceUID,
         Modality: 'RTSTRUCT',
       });
 
@@ -89,7 +120,7 @@ const RTPanel = ({ studies, viewports, activeIndex, isOpen, onContourItemClick }
         setState({
           referencedDisplaysets,
           selectedSet: defaultSet,
-          sets: viewportSets
+          sets: viewportSets,
         });
       } else {
         setState(DEFAULT_STATE);
@@ -97,15 +128,14 @@ const RTPanel = ({ studies, viewports, activeIndex, isOpen, onContourItemClick }
     }
   };
 
-  useEffect(() => {
-    updateStructureSets();
-  }, [studies, viewports, activeIndex]);
-
   useEffect(() => {
     setShowSettings(showSettings && !isOpen);
   }, [isOpen]);
 
-  const toContourItem = ({ ROINumber, ROIName, RTROIObservations, colorArray, visible }, loadedSet) => {
+  const toContourItem = (
+    { ROINumber, ROIName, RTROIObservations, colorArray, visible, isSupported },
+    loadedSet
+  ) => {
     let interpretedType = '';
     if (RTROIObservations && RTROIObservations.RTROIInterpretedType) {
       interpretedType = `(${RTROIObservations.RTROIInterpretedType})`;
@@ -116,18 +146,23 @@ const RTPanel = ({ studies, viewports, activeIndex, isOpen, onContourItemClick }
       <StructureSetItem
         key={ROINumber}
         selected={isSameContour}
+        isDisabled={!isSupported}
         onClick={() => {
           setSelectedContour(isSameContour ? null : ROINumber);
 
+          if (isCornerstone()) {
             const enabledElements = cornerstone.getEnabledElements();
             const element = enabledElements[activeIndex].element;
-          const toolState = cornerstoneTools.getToolState(element, 'stack');
+            const stackToolState = cornerstoneTools.getToolState(
+              element,
+              'stack'
+            );
 
-          if (!toolState) {
+            if (!stackToolState) {
               return;
             }
 
-          const imageIds = toolState.data[0].imageIds;
+            const imageIds = stackToolState.data[0].imageIds;
 
             const module = cornerstoneTools.getModule('rtstruct');
             const imageId = module.getters.imageIdOfCenterFrameOfROIContour(
@@ -136,16 +171,35 @@ const RTPanel = ({ studies, viewports, activeIndex, isOpen, onContourItemClick }
               imageIds
             );
 
+            const toolState = cornerstoneTools.globalImageIdSpecificToolStateManager.saveToolState();
+            const imageIdSpecificToolState = toolState[imageId];
+
+            const rtstructData =
+              imageIdSpecificToolState[RTSTRUCT_DISPLAY_TOOL];
+
+            const specificData = rtstructData.data.find(
+              rtData => rtData.ROINumber === ROINumber
+            );
+
+            specificData.highlight = true;
+
             const frameIndex = imageIds.indexOf(imageId);
-          const SOPInstanceUID = cornerstone.metaData.get('SOPInstanceUID', imageId);
-          const StudyInstanceUID = cornerstone.metaData.get('StudyInstanceUID', imageId);
+            const SOPInstanceUID = cornerstone.metaData.get(
+              'SOPInstanceUID',
+              imageId
+            );
+            const StudyInstanceUID = cornerstone.metaData.get(
+              'StudyInstanceUID',
+              imageId
+            );
 
             onContourItemClick({
               StudyInstanceUID,
               SOPInstanceUID,
               frameIndex,
-            activeViewportIndex: activeIndex
+              activeViewportIndex: activeIndex,
             });
+          }
         }}
         label={`${ROIName} ${interpretedType}`}
         index={ROINumber}
@@ -153,7 +207,10 @@ const RTPanel = ({ studies, viewports, activeIndex, isOpen, onContourItemClick }
         visible={visible}
         onVisibilityChange={() => {
           const module = cornerstoneTools.getModule('rtstruct');
-          module.setters.toggleROIContour(state.selectedSet.SeriesInstanceUID, ROINumber);
+          module.setters.toggleROIContour(
+            state.selectedSet.SeriesInstanceUID,
+            ROINumber
+          );
         }}
       />
     );
@@ -180,7 +237,8 @@ const RTPanel = ({ studies, viewports, activeIndex, isOpen, onContourItemClick }
   return (
     <div className="dcmrt-panel">
       <div className="dcmrt-panel-header">
-        <h3>RT Structure Sets</h3>
+        {' '}
+        {!state.isLocked && (
           <Icon
             className="cog-icon"
             name="cog"
@@ -188,45 +246,71 @@ const RTPanel = ({ studies, viewports, activeIndex, isOpen, onContourItemClick }
             height="25px"
             onClick={() => setShowSettings(true)}
           />
+        )}
+        <h3>RT Structure Sets</h3>
       </div>
-      {!state.referencedDisplaysets.length && <LoadingIndicator expand height="70px" width="70px" />}
-      {state.sets && state.referencedDisplaysets.map(displaySet => {
+      {!state.isLocked && !state.referencedDisplaysets.length && (
+        <LoadingIndicator expand height="70px" width="70px" />
+      )}
+      {state.sets &&
+        state.referencedDisplaysets.map(displaySet => {
           const { SeriesInstanceUID, metadata, isLoaded } = displaySet;
 
           const module = cornerstoneTools.getModule('rtstruct');
-        const sets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(viewports[activeIndex].SeriesInstanceUID);
+          const sets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(
+            activeViewport.SeriesInstanceUID
+          );
+
+          const loadedSet = sets.find(
+            set => set.SeriesInstanceUID === SeriesInstanceUID
+          );
+
+          if (!loadedSet) return null;
 
-        const loadedSet = sets.find(set => set.SeriesInstanceUID === SeriesInstanceUID);
           return (
             <PanelSection
               key={SeriesInstanceUID}
               title={metadata.StructureSetLabel}
               loading={!isLoaded || !loadedSet}
-            visible={isLoaded && loadedSet.visible}
+              visible={isLoaded && loadedSet && loadedSet.visible}
               hideVisibleButton={!isLoaded}
-            expanded={isLoaded && loadedSet.SeriesInstanceUID === state.selectedSet.SeriesInstanceUID}
+              expanded={
+                isLoaded &&
+                loadedSet.SeriesInstanceUID ===
+                  state.selectedSet.SeriesInstanceUID
+              }
               onVisibilityChange={newVisibility => {
                 const module = cornerstoneTools.getModule('rtstruct');
-              loadedSet.ROIContours.forEach(({ ROINumber }) => {
-                module.setters.toggleROIContour(loadedSet.SeriesInstanceUID, ROINumber);
-              });
-              const sets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(viewports[activeIndex].SeriesInstanceUID);
+
+                if (newVisibility) {
+                  module.setters.showStructureSet(loadedSet.SeriesInstanceUID);
+                } else {
+                  module.setters.hideStructureSet(loadedSet.SeriesInstanceUID);
+                }
+                const sets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(
+                  activeViewport.SeriesInstanceUID
+                );
                 setState(state => ({ ...state, sets }));
                 refreshViewport();
               }}
               onExpandChange={async () => {
                 if (!isLoaded) {
-                await displaySet.load(viewports[activeIndex], studies);
+                  await displaySet.load(activeViewport, studies);
                   const module = cornerstoneTools.getModule('rtstruct');
-                const sets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(viewports[activeIndex].SeriesInstanceUID);
-                const selectedSet = sets.find(set => set.SeriesInstanceUID === SeriesInstanceUID);
+                  const sets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(
+                    activeViewport.SeriesInstanceUID
+                  );
+                  const selectedSet = sets.find(
+                    set => set.SeriesInstanceUID === SeriesInstanceUID
+                  );
                   setState(state => ({ ...state, selectedSet, sets }));
                 }
               }}
             >
               <ScrollableArea>
                 <TableList headless>
-                {isLoaded && loadedSet.ROIContours.map(c => toContourItem(c, loadedSet))}
+                  {isLoaded &&
+                    loadedSet.ROIContours.map(c => toContourItem(c, loadedSet))}
                 </TableList>
               </ScrollableArea>
             </PanelSection>

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

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

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

@@ -1,6 +1,7 @@
 import React, { useState, useEffect } from 'react';
 import PropTypes from 'prop-types';
-import { TableListItem, Icon } from '@ohif/ui';
+import { TableListItem, Icon, Tooltip, OverlayTrigger } from '@ohif/ui';
+import ReactTooltip from 'react-tooltip';
 
 import './StructureSetItem.css';
 
@@ -20,6 +21,7 @@ ColoredCircle.propTypes = {
 const StructureSetItem = ({
   index,
   label,
+  isDisabled,
   onClick,
   itemClass,
   color,
@@ -31,22 +33,55 @@ const StructureSetItem = ({
 
   useEffect(() => {
     setIsVisible(visible);
-  }, [visible])
+  }, [visible]);
 
-  return (
-    <div className={`dcmrt-structure-set-item ${selected && 'selected'}`}>
+  let dcmrtClassNames = `dcmrt-structure-set-item`;
+
+  if (selected) {
+    dcmrtClassNames += ' selected';
+  }
+
+  if (isDisabled) {
+    dcmrtClassNames += ' isDisabled';
+  }
+
+  const warningIcon = (
+    <span>
+      <Icon name="exclamation-triangle" />
+    </span>
+  );
+
+  const tableListItem = (
     <TableListItem
       key={index}
       itemKey={index}
       itemIndex={index}
       itemClass={itemClass}
-        itemMeta={<ColoredCircle color={color} />}
+      itemMeta={isDisabled ? warningIcon : <ColoredCircle color={color} />}
       itemMetaClass="item-color-section"
-        onItemClick={onClick}
+      onItemClick={() => {
+        if (isDisabled) {
+          return;
+        }
+
+        onClick();
+      }}
     >
       <div>
         <div className="item-label" style={{ marginBottom: 4 }}>
+          <a data-tip data-for={`StructureHover${index}`}>
             <span>{label}</span>
+          </a>
+          <ReactTooltip
+            id={`StructureHover${index}`}
+            delayShow={250}
+            place="right"
+            border={true}
+            type="light"
+          >
+            <span>{label}</span>
+          </ReactTooltip>
+          {!isDisabled && (
             <Icon
               className={`eye-icon ${isVisible && '--visible'}`}
               name={isVisible ? 'eye' : 'eye-closed'}
@@ -54,12 +89,19 @@ const StructureSetItem = ({
               height="20px"
               onClick={event => {
                 event.stopPropagation();
+
+                if (isDisabled) {
+                  return;
+                }
+
                 const newVisibility = !isVisible;
                 setIsVisible(newVisibility);
                 onVisibilityChange(newVisibility);
               }}
             />
+          )}
         </div>
+
         {false && <div className="item-info">{'...'}</div>}
         {false && (
           <div className="item-actions">
@@ -85,6 +127,34 @@ const StructureSetItem = ({
         )}
       </div>
     </TableListItem>
+  );
+
+  return (
+    <div className={dcmrtClassNames}>
+      <React.Fragment>
+        {isDisabled ? (
+          <OverlayTrigger
+            key={index}
+            placement="left"
+            overlay={
+              <Tooltip
+                placement="left"
+                className="in tooltip-warning"
+                id="tooltip-left"
+              >
+                <div className="warningTitle">Unsupported Region</div>
+                <div className="warningContent">
+                  Contour type currently unsupported.
+                </div>
+              </Tooltip>
+            }
+          >
+            <div>{tableListItem}</div>
+          </OverlayTrigger>
+        ) : (
+          <React.Fragment>{tableListItem} </React.Fragment>
+        )}
+      </React.Fragment>
     </div>
   );
 };
@@ -99,7 +169,7 @@ StructureSetItem.propTypes = {
 
 StructureSetItem.defaultProps = {
   itemClass: '',
-  onClick: () => { },
+  onClick: () => {},
 };
 
 export default StructureSetItem;

extensions/dicom-rt/src/getSourceDisplaySet.js

@@ -0,0 +1,14 @@
+import { metadata } from '@ohif/core';
+
+export default function getSourceDisplaySet(studies, rtStructDisplaySet, activateLabelMap = true) {
+  const referencedDisplaySet = metadata.StudyMetadata.getReferencedDisplaySet(
+    rtStructDisplaySet,
+    studies
+  );
+
+  if (activateLabelMap) {
+    rtStructDisplaySet.load(referencedDisplaySet, studies);
+  }
+
+  return referencedDisplaySet;
+}

extensions/dicom-rt/src/index.js

@@ -1,15 +1,20 @@
 import React from 'react';
+import { utils } from '@ohif/core';
 
 import init from './init.js';
 import sopClassHandlerModule from './OHIFDicomRTStructSopClassHandler';
 import id from './id.js';
 import RTPanel from './components/RTPanel/RTPanel';
+import { version } from '../package.json';
+
+const { studyMetadataManager } = utils;
 
 export default {
   /**
    * Only required property. Should be a unique value across all extensions.
    */
   id,
+  version,
 
   /**
    *
@@ -20,43 +25,95 @@ export default {
   preRegistration({ servicesManager, configuration = {} }) {
     init({ servicesManager, configuration });
   },
-  getPanelModule({ commandsManager }) {
+  getPanelModule({ commandsManager, servicesManager, api }) {
     const ExtendedRTPanel = props => {
+      const { activeContexts } = api.hooks.useAppContext();
+
       const contourItemClickHandler = contourData => {
         commandsManager.runCommand('jumpToImage', contourData);
       };
 
       return (
-        <RTPanel {...props} onContourItemClick={contourItemClickHandler} />
+        <RTPanel
+          {...props}
+          onContourItemClick={contourItemClickHandler}
+          activeContexts={activeContexts}
+          contexts={api.contexts}
+        />
       );
     };
 
+    const RTPanelTabChangedEvent = 'rt-panel-tab-updated';
+
+    /**
+     * Trigger's an event to update the state of the panel's RoundedButtonGroup.
+     *
+     * This is required to avoid extension state
+     * coupling with the viewer's ToolbarRow component.
+     *
+     * @param {object} data
+     */
+    const triggerRTPanelUpdatedEvent = data => {
+      const event = new CustomEvent(RTPanelTabChangedEvent, {
+        detail: data,
+      });
+      document.dispatchEvent(event);
+    };
+
+    const onRTStructsLoaded = ({ detail }) => {
+      const { rtStructDisplaySet, referencedDisplaySet } = detail;
+
+      const studyMetadata = studyMetadataManager.get(
+        rtStructDisplaySet.StudyInstanceUID
+      );
+      const referencedDisplaysets = studyMetadata.getDerivedDatasets({
+        referencedSeriesInstanceUID: referencedDisplaySet.SeriesInstanceUID,
+        Modality: 'RTSTRUCT',
+      });
+      triggerRTPanelUpdatedEvent({
+        badgeNumber: referencedDisplaysets.length,
+        target: 'rt-panel',
+      });
+    };
+
+    document.addEventListener('extensiondicomrtrtloaded', onRTStructsLoaded);
+
     return {
       menuOptions: [
         {
           icon: 'list',
           label: 'RTSTRUCT',
           target: 'rt-panel',
-          isDisabled: studies => {
+          stateEvent: RTPanelTabChangedEvent,
+          isDisabled: (studies, activeViewport) => {
             if (!studies) {
               return true;
             }
 
-            for (let i = 0; i < studies.length; i++) {
-              const study = studies[i];
-
-              if (study && study.series) {
-                for (let j = 0; j < study.series.length; j++) {
-                  const series = study.series[j];
+            if (activeViewport) {
+              const studyMetadata = studyMetadataManager.get(
+                activeViewport.StudyInstanceUID
+              );
+              if (!studyMetadata) {
+                return;
+              }
+              const referencedDisplaySets = studyMetadata.getDerivedDatasets({
+                referencedSeriesInstanceUID: activeViewport.SeriesInstanceUID,
+                Modality: 'RTSTRUCT',
+              });
               if (
-                    /* Could be expanded to contain RTPLAN and RTDOSE information in the future */
-                    ['RTSTRUCT'].includes(series.Modality)
+                referencedDisplaySets &&
+                referencedDisplaySets.some(ds =>
+                  ['RTSTRUCT'].includes(ds.Modality)
+                )
               ) {
+                triggerRTPanelUpdatedEvent({
+                  badgeNumber: referencedDisplaySets.length,
+                  target: 'rt-panel',
+                });
                 return false;
               }
             }
-              }
-            }
 
             return true;
           },

extensions/dicom-rt/src/loadRTStruct.js

@@ -4,6 +4,7 @@ import cornerstone from 'cornerstone-core';
 import cornerstoneTools from 'cornerstone-tools';
 import transformPointsToImagePlane from './utils/transformPointsToImagePlane';
 import TOOL_NAMES from './utils/toolNames';
+import { vec3 } from 'gl-matrix';
 
 const dicomlab2RGB = dcmjs.data.Colors.dicomlab2RGB;
 const globalImageIdSpecificToolStateManager =
@@ -16,7 +17,6 @@ export default async function loadRTStruct(
   studies
 ) {
   const rtStructModule = cornerstoneTools.getModule('rtstruct');
-
   // Set here is loading is asynchronous.
   // If this function throws its set back to false.
   rtStructDisplaySet.isLoaded = true;
@@ -68,7 +68,6 @@ export default async function loadRTStruct(
   const rtStructDisplayToolName = TOOL_NAMES.RTSTRUCT_DISPLAY_TOOL;
 
   for (let i = 0; i < ROIContourSequence.length; i++) {
-
     const ROIContour = ROIContourSequence[i];
     const { ReferencedROINumber, ContourSequence } = ROIContour;
 
@@ -76,29 +75,32 @@ export default async function loadRTStruct(
       continue;
     }
 
-    _setROIContourMetadata(
-      structureSet,
-      StructureSetROISequence,
-      RTROIObservationsSequence,
-      ROIContour
-    );
+    const isSupported = false;
 
-    for (let c = 0; c < ContourSequence.length; c++) {
+    const ContourSequenceArray = _toArray(ContourSequence);
+
+    for (let c = 0; c < ContourSequenceArray.length; c++) {
       const {
         ContourImageSequence,
         ContourData,
         NumberOfContourPoints,
         ContourGeometricType,
-      } = ContourSequence[c];
+      } = ContourSequenceArray[c];
 
-      if (ContourGeometricType !== 'CLOSED_PLANAR') {
-        // TODO: Do we want to visualise types other than closed planar?
-        // We could easily do open planar.
+      const sopInstanceUID = ContourImageSequence
+        ? ContourImageSequence.ReferencedSOPInstanceUID
+        : _getClosestSOPInstanceUID(
+            ContourData,
+            ContourGeometricType,
+            NumberOfContourPoints,
+            imageIdSopInstanceUidPairs
+          );
+      const imageId = _getImageId(imageIdSopInstanceUidPairs, sopInstanceUID);
+
+      if (!imageId) {
         continue;
       }
 
-      const sopInstanceUID = ContourImageSequence.ReferencedSOPInstanceUID;
-      const imageId = _getImageId(imageIdSopInstanceUidPairs, sopInstanceUID);
       const imageIdSpecificToolData = _getOrCreateImageIdSpecificToolData(
         toolState,
         imageId,
@@ -107,6 +109,13 @@ export default async function loadRTStruct(
 
       const imagePlane = cornerstone.metaData.get('imagePlaneModule', imageId);
       const points = [];
+      let measurementData;
+
+      switch (ContourGeometricType) {
+        case 'CLOSED_PLANAR':
+        case 'OPEN_PLANAR':
+        case 'POINT':
+          isSupported = true;
 
           for (let p = 0; p < NumberOfContourPoints * 3; p += 3) {
             points.push({
@@ -118,18 +127,31 @@ export default async function loadRTStruct(
 
           transformPointsToImagePlane(points, imagePlane);
 
-      const measurementData = {
+          measurementData = {
             handles: {
               points,
             },
+            type: ContourGeometricType,
             structureSetSeriesInstanceUid: rtStructDataset.SeriesInstanceUID,
             ROINumber: ReferencedROINumber,
           };
 
           imageIdSpecificToolData.push(measurementData);
+          break;
+        default:
+          continue;
       }
     }
 
+    _setROIContourMetadata(
+      structureSet,
+      StructureSetROISequence,
+      RTROIObservationsSequence,
+      ROIContour,
+      isSupported
+    );
+  }
+
   _setToolEnabledIfNotEnabled(rtStructDisplayToolName);
 
   /*
@@ -149,7 +171,13 @@ export default async function loadRTStruct(
    * allows us to easily watch the module or the rtstruct loading process in any other component
    * without subscribing to external events.
    */
-  const event = new CustomEvent('extensiondicomrtrtloaded');
+  const event = new CustomEvent('extensiondicomrtrtloaded', {
+    detail: {
+      rtStructDisplaySet,
+      referencedDisplaySet,
+      studies,
+    },
+  });
   document.dispatchEvent(event);
 }
 
@@ -157,7 +185,8 @@ function _setROIContourMetadata(
   structureSet,
   StructureSetROISequence,
   RTROIObservationsSequence,
-  ROIContour
+  ROIContour,
+  isSupported
 ) {
   const StructureSetROI = StructureSetROISequence.find(
     structureSetROI =>
@@ -169,6 +198,7 @@ function _setROIContourMetadata(
     ROIName: StructureSetROI.ROIName,
     ROIGenerationAlgorithm: StructureSetROI.ROIGenerationAlgorithm,
     ROIDescription: StructureSetROI.ROIDescription,
+    isSupported,
     visible: true,
   };
 
@@ -238,7 +268,7 @@ function _setROIContourRTROIObservations(
 
 function _setToolEnabledIfNotEnabled(toolName) {
   cornerstone.getEnabledElements().forEach(enabledElement => {
-    const { element } = enabledElement;
+    const { element, image } = enabledElement;
     const tool = cornerstoneTools.getToolForElement(element, toolName);
 
     if (tool.mode !== 'enabled') {
@@ -246,7 +276,9 @@ function _setToolEnabledIfNotEnabled(toolName) {
       cornerstoneTools.setToolEnabled(toolName);
     }
 
+    if (image) {
       cornerstone.updateImage(element);
+    }
   });
 }
 
@@ -273,7 +305,9 @@ const _getImageId = (imageIdSopInstanceUidPairs, sopInstanceUID) => {
       imageIdSopInstanceUidPairsEntry.sopInstanceUID === sopInstanceUID
   );
 
-  return imageIdSopInstanceUidPairsEntry.imageId;
+  return imageIdSopInstanceUidPairsEntry
+    ? imageIdSopInstanceUidPairsEntry.imageId
+    : null;
 };
 
 function _getImageIdSopInstanceUidPairsForDisplaySet(
@@ -307,3 +341,82 @@ function _getImageIdSopInstanceUidPairsForDisplaySet(
     };
   });
 }
+
+function _toArray(objOrArray) {
+  return Array.isArray(objOrArray) ? objOrArray : [objOrArray];
+}
+
+function _getClosestSOPInstanceUID(
+  ContourData,
+  ContourGeometricType,
+  NumberOfContourPoints,
+  imageIdSopInstanceUidPairs
+) {
+  const closest = {
+    distance: Infinity,
+    sopInstanceUID: null,
+  };
+
+  let point;
+
+  switch (ContourGeometricType) {
+    case 'POINT':
+      point = ContourData;
+      break;
+    case 'CLOSED_PLANAR':
+    case 'OPEN_PLANAR':
+      // These are defined as planar, so get the of the region to get the
+      // Best mapping to a plane even if its potentially off center.
+
+      point = [0, 0, 0];
+      for (let p = 0; p < NumberOfContourPoints * 3; p += 3) {
+        point[0] += ContourData[p];
+        point[1] += ContourData[p + 1];
+        point[2] += ContourData[p + 2];
+      }
+
+      point[0] /= NumberOfContourPoints;
+      point[1] /= NumberOfContourPoints;
+      point[2] /= NumberOfContourPoints;
+  }
+
+  imageIdSopInstanceUidPairs.forEach(pair => {
+    const { imageId } = pair;
+
+    const imagePlaneModule = cornerstone.metaData.get(
+      'imagePlaneModule',
+      imageId
+    );
+
+    const distance = distanceFromPointToPlane(point, imagePlaneModule);
+
+    if (distance < closest.distance) {
+      closest.distance = distance;
+      closest.sopInstanceUID = pair.sopInstanceUID;
+    }
+  });
+
+  return closest.sopInstanceUID;
+}
+
+/**
+ *
+ * @param {number[3]} P - The point
+ * @param {object} imagePlaneModule The cornerstone metadata object for the imagePlane
+ */
+function distanceFromPointToPlane(P, imagePlaneModule) {
+  const {
+    rowCosines,
+    columnCosines,
+    imagePositionPatient: Q,
+  } = imagePlaneModule;
+
+  let N = [];
+  vec3.cross(N, rowCosines, columnCosines);
+
+  const [A, B, C] = N;
+
+  const D = -A * Q[0] - B * Q[1] - C * Q[2];
+
+  return Math.abs(A * P[0] + B * P[1] + C * P[2] + D); // Denominator is sqrt(A**2 + B**2 + C**2) which is 1 as its a normal vector
+}

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

@@ -1,9 +1,10 @@
 import { importInternal, getToolState, toolColors } from 'cornerstone-tools';
-
 import TOOL_NAMES from '../utils/toolNames';
+import drawCanvasCrosshairs from '../utils/drawCanvasCrosshairs';
 
 // Cornerstone 3rd party dev kit imports
 const draw = importInternal('drawing/draw');
+const drawCircle = importInternal('drawing/drawCircle');
 const drawJoinedLines = importInternal('drawing/drawJoinedLines');
 const getNewContext = importInternal('drawing/getNewContext');
 const BaseTool = importInternal('base/BaseTool');
@@ -36,11 +37,17 @@ export default class RTStructDisplayTool extends BaseTool {
       return;
     }
 
-    const { lineWidth, opacity } = rtstructModule.configuration;
+    const {
+      lineWidth,
+      opacity,
+      highlightOpacity,
+    } = rtstructModule.configuration;
 
     // We have tool data for this element - iterate over each one and draw it
     const context = getNewContext(eventData.canvasContext.canvas);
 
+    let crossHairCenter;
+
     for (let i = 0; i < toolState.data.length; i++) {
       const data = toolState.data[i];
 
@@ -74,20 +81,74 @@ export default class RTStructDisplayTool extends BaseTool {
         colorArray[2]
       },${opacity})`;
 
-      lineWidth;
+      let highlight = data.highlight;
+      const options = { color, lineWidth };
 
-      draw(context, context => {
-        drawJoinedLines(
-          context,
-          eventData.element,
-          points[points.length - 1],
-          points,
-          {
-            color,
-            lineWidth,
+      if (highlight) {
+        crossHairCenter = { x: 0, y: 0 };
+
+        points.forEach(point => {
+          crossHairCenter.x += point.x;
+          crossHairCenter.y += point.y;
+        });
+
+        crossHairCenter.x /= points.length;
+        crossHairCenter.y /= points.length;
+
+        // TODO: Disabling hightlight for now, it'd be good to bring it back
+        // when we have a good way of doing this for SEG.
+
+        // options.fillStyle = color = `rgba(${colorArray[0]},${colorArray[1]},${
+        //   colorArray[2]
+        // },${highlightOpacity})`;
+
+        // Draw highlight lines.
+
+        delete data.highlight; // Don't highlight on next render.
       }
-        );
+
+      switch (data.type) {
+        case 'CLOSED_PLANAR':
+          this._renderClosedPlanar(context, eventData.element, points, options);
+          break;
+        case 'POINT':
+          this._renderPoint(context, eventData.element, points, options);
+          break;
+        case 'OPEN_PLANAR':
+          this._renderOpenPlanar(context, eventData.element, points, options);
+          break;
+      }
+    }
+
+    if (crossHairCenter) {
+      drawCanvasCrosshairs(eventData, crossHairCenter, {
+        color: toolColors.getActiveColor(),
+        lineWidth: 1,
       });
     }
   }
+
+  _renderClosedPlanar(context, element, points, options) {
+    draw(context, context => {
+      drawJoinedLines(
+        context,
+        element,
+        points[points.length - 1],
+        points,
+        options
+      );
+    });
+  }
+
+  _renderPoint(context, element, points, options) {
+    draw(context, context => {
+      drawCircle(context, element, points[0], 3, options);
+    });
+  }
+
+  _renderOpenPlanar(context, element, points, options) {
+    draw(context, context => {
+      drawJoinedLines(context, element, points[0], points, options);
+    });
+  }
 }

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

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

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

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

extensions/dicom-segmentation/CHANGELOG.md

@@ -3,6 +3,398 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [0.7.15](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.14...@ohif/extension-dicom-segmentation@0.7.15) (2022-09-19)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.7.14](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.13...@ohif/extension-dicom-segmentation@0.7.14) (2022-09-12)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.7.13](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.12...@ohif/extension-dicom-segmentation@0.7.13) (2022-09-01)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.7.12](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.11...@ohif/extension-dicom-segmentation@0.7.12) (2022-08-31)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.7.11](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.10...@ohif/extension-dicom-segmentation@0.7.11) (2022-04-05)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.7.10](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.9...@ohif/extension-dicom-segmentation@0.7.10) (2022-03-25)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.7.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.8...@ohif/extension-dicom-segmentation@0.7.9) (2022-03-14)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.7.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.7...@ohif/extension-dicom-segmentation@0.7.8) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.7.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.6...@ohif/extension-dicom-segmentation@0.7.7) (2022-02-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.7.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.5...@ohif/extension-dicom-segmentation@0.7.6) (2022-01-20)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.7.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.4...@ohif/extension-dicom-segmentation@0.7.5) (2021-12-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.7.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.3...@ohif/extension-dicom-segmentation@0.7.4) (2021-10-27)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.7.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.2...@ohif/extension-dicom-segmentation@0.7.3) (2021-10-26)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.7.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.1...@ohif/extension-dicom-segmentation@0.7.2) (2021-10-06)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.7.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.0...@ohif/extension-dicom-segmentation@0.7.1) (2021-09-28)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+# [0.7.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.11...@ohif/extension-dicom-segmentation@0.7.0) (2021-09-23)
+
+
+### Features
+
+* Update to WADO Image Loader 4.0.3 to add dynamically imported WebAssembly codec support 🚀 ([#2537](https://github.com/OHIF/Viewers/issues/2537)) ([489d4b0](https://github.com/OHIF/Viewers/commit/489d4b0584f4657ceda1c5b9b68d5e9733827e47))
+
+
+
+
+
+## [0.6.11](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.10...@ohif/extension-dicom-segmentation@0.6.11) (2021-09-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.6.10](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.9...@ohif/extension-dicom-segmentation@0.6.10) (2021-06-02)
+
+
+### Bug Fixes
+
+* **dicom-html:** Add parsed dicom meta info section ([#2419](https://github.com/OHIF/Viewers/issues/2419)) ([403688b](https://github.com/OHIF/Viewers/commit/403688b18c52468fc1101166ec0c1734fb710039))
+
+
+
+
+
+## [0.6.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.8...@ohif/extension-dicom-segmentation@0.6.9) (2021-05-17)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.6.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.7...@ohif/extension-dicom-segmentation@0.6.8) (2021-04-22)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.6.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.6...@ohif/extension-dicom-segmentation@0.6.7) (2021-04-22)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.6.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.5...@ohif/extension-dicom-segmentation@0.6.6) (2021-04-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.6.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.4...@ohif/extension-dicom-segmentation@0.6.5) (2021-04-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.6.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.3...@ohif/extension-dicom-segmentation@0.6.4) (2021-04-16)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.6.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.2...@ohif/extension-dicom-segmentation@0.6.3) (2021-04-15)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.6.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.1...@ohif/extension-dicom-segmentation@0.6.2) (2021-03-31)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.6.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.6.0...@ohif/extension-dicom-segmentation@0.6.1) (2021-03-09)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+# [0.6.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.5.4...@ohif/extension-dicom-segmentation@0.6.0) (2021-03-04)
+
+
+### Features
+
+* **log:** add new log service ([14d6454](https://github.com/OHIF/Viewers/commit/14d6454eafaa2ccb50e133c2945c9558052ea27e))
+
+
+
+
+
+## [0.5.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.5.3...@ohif/extension-dicom-segmentation@0.5.4) (2021-03-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.5.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.5.2...@ohif/extension-dicom-segmentation@0.5.3) (2021-02-25)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.5.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.5.1...@ohif/extension-dicom-segmentation@0.5.2) (2021-02-05)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.5.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.5.0...@ohif/extension-dicom-segmentation@0.5.1) (2021-01-21)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+# [0.5.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.4.7...@ohif/extension-dicom-segmentation@0.5.0) (2020-12-10)
+
+
+### Features
+
+* visualize overlapping segments in cornerstone ([#2185](https://github.com/OHIF/Viewers/issues/2185)) ([29fceac](https://github.com/OHIF/Viewers/commit/29fceacee97d51f1952a0f6b574c66596d32c201))
+
+
+
+
+
+## [0.4.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.4.6...@ohif/extension-dicom-segmentation@0.4.7) (2020-10-07)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.4.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.4.5...@ohif/extension-dicom-segmentation@0.4.6) (2020-09-17)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.4.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.4.4...@ohif/extension-dicom-segmentation@0.4.5) (2020-09-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.4.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.4.3...@ohif/extension-dicom-segmentation@0.4.4) (2020-09-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.4.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.4.2...@ohif/extension-dicom-segmentation@0.4.3) (2020-09-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.4.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.4.1...@ohif/extension-dicom-segmentation@0.4.2) (2020-09-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.4.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.4.0...@ohif/extension-dicom-segmentation@0.4.1) (2020-08-28)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+# [0.4.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.3.4...@ohif/extension-dicom-segmentation@0.4.0) (2020-08-18)
+
+
+### Features
+
+* 🎸 Update react-vtkjs-viewport usage to use requestPool ([#1984](https://github.com/OHIF/Viewers/issues/1984)) ([bb5f30c](https://github.com/OHIF/Viewers/commit/bb5f30ce2a0192d2e021beaaadfff22fd38e17b9))
+
+
+
+
+
+## [0.3.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.3.3...@ohif/extension-dicom-segmentation@0.3.4) (2020-08-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.3.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.3.2...@ohif/extension-dicom-segmentation@0.3.3) (2020-07-13)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.3.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.3.1...@ohif/extension-dicom-segmentation@0.3.2) (2020-07-13)
+
+
+### Bug Fixes
+
+* 🐛 Fix RT Panel hide/show and Fix looping load errors ([#1877](https://github.com/OHIF/Viewers/issues/1877)) ([e7cc735](https://github.com/OHIF/Viewers/commit/e7cc735c03d02eeb0d3af4ba02c15ed4f81bbec2))
+
+
+
+
+
+## [0.3.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.3.0...@ohif/extension-dicom-segmentation@0.3.1) (2020-06-15)
+
+
+### Bug Fixes
+
+* 🐛 Disable seg panel when data for seg unavailable ([#1732](https://github.com/OHIF/Viewers/issues/1732)) ([698e900](https://github.com/OHIF/Viewers/commit/698e900b85121d3c2a46747c443ef69fb7a8c95b)), closes [#1728](https://github.com/OHIF/Viewers/issues/1728)
+
+
+
+
+
+# [0.3.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.2.6...@ohif/extension-dicom-segmentation@0.3.0) (2020-06-04)
+
+
+### Features
+
+* 🎸 1729 - error boundary wrapper ([#1764](https://github.com/OHIF/Viewers/issues/1764)) ([c02b232](https://github.com/OHIF/Viewers/commit/c02b232b0cc24f38af5d5e3831d987d048e60ada))
+
+
+
+
+
 ## [0.2.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.2.5...@ohif/extension-dicom-segmentation@0.2.6) (2020-05-12)
 
 

extensions/dicom-segmentation/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-segmentation",
-  "version": "0.2.6",
+  "version": "0.7.15",
   "description": "OHIF extension for viewing segmentations in the 2D MPR view",
   "author": "OHIF",
   "license": "MIT",
@@ -29,9 +29,9 @@
   },
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
-    "cornerstone-core": "^2.2.8",
-    "cornerstone-tools": "4.15.1",
-    "dcmjs": "^0.12.2",
+    "cornerstone-core": "^2.6.1",
+    "cornerstone-tools": "^6.0.6",
+    "dcmjs": "0.24.10",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6"
@@ -39,6 +39,7 @@
   "dependencies": {
     "@babel/runtime": "^7.5.5",
     "gl-matrix": "^3.3.0",
-    "react-select": "^3.0.8"
+    "react-select": "^3.0.8",
+    "react-tooltip": "4.2.10"
   }
 }

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

@@ -1,6 +1,7 @@
 import React, { useState, useEffect } from 'react';
 import PropTypes from 'prop-types';
 import { TableListItem, Icon } from '@ohif/ui';
+import ReactTooltip from 'react-tooltip';
 
 import './SegmentItem.css';
 
@@ -17,13 +18,31 @@ ColoredCircle.propTypes = {
   color: PropTypes.array.isRequired,
 };
 
-const SegmentItem = ({ index, label, onClick, itemClass, color, visible = true, onVisibilityChange }) => {
+const SegmentItem = ({
+  index,
+  label,
+  onClick,
+  itemClass,
+  color,
+  labelmap3D,
+  visible,
+  onVisibilityChange,
+}) => {
   const [isVisible, setIsVisible] = useState(visible);
 
   useEffect(() => {
     setIsVisible(visible);
   }, [visible]);
 
+  const onClickHandler = () => onClick(index);
+
+  const onVisibilityChangeHandler = event => {
+    event.stopPropagation();
+    const newVisibility = !isVisible;
+    setIsVisible(newVisibility);
+    onVisibilityChange(newVisibility, index, labelmap3D);
+  };
+
   return (
     <div className="dcmseg-segment-item">
       <TableListItem
@@ -33,22 +52,28 @@ const SegmentItem = ({ index, label, onClick, itemClass, color, visible = true,
         itemClass={itemClass}
         itemMeta={<ColoredCircle color={color} />}
         itemMetaClass="segment-color-section"
-        onItemClick={onClick}
+        onItemClick={onClickHandler}
       >
         <div>
           <div className="segment-label" style={{ marginBottom: 4 }}>
+            <a data-tip data-for={`SegmentHover${index}`}>
               <span>{label}</span>
+            </a>
+            <ReactTooltip
+              id={`SegmentHover${index}`}
+              delayShow={250}
+              place="right"
+              border={true}
+              type="light"
+            >
+              <span>{label}</span>
+            </ReactTooltip>
             <Icon
               className={`eye-icon ${isVisible && '--visible'}`}
               name={isVisible ? 'eye' : 'eye-closed'}
               width="20px"
               height="20px"
-              onClick={event => {
-                event.stopPropagation();
-                const newVisibility = !isVisible;
-                setIsVisible(newVisibility);
-                onVisibilityChange(newVisibility);
-              }}
+              onClick={onVisibilityChangeHandler}
             />
           </div>
           {false && <div className="segment-info">{'...'}</div>}
@@ -90,7 +115,7 @@ SegmentItem.propTypes = {
 
 SegmentItem.defaultProps = {
   itemClass: '',
-  onClick: () => { }
+  onClick: () => {},
 };
 
 export default SegmentItem;

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

@@ -6,22 +6,28 @@
   width: 100%;
   display: flex;
   flex-direction: column;
+  padding: 20px;
+}
+
+.dcmseg-segmentation-panel.disabled {
+  opacity: 0.6;
+  pointer-events: none;
 }
 
 .dcmseg-segmentation-panel h3 {
-  padding-left: 20px;
   margin-top: 0;
 }
 
 .dcmseg-segmentation-panel .segmentations {
-  padding: 0 20px 20px 20px;
+  padding-bottom: 10px;
 }
 
 .dcmseg-segmentation-panel .cog-icon {
-  margin: 20px 20px 0 0;
   align-self: flex-end;
   color: var(--default-color);
   cursor: pointer;
+  min-height: 23px;
+  max-height: 23px;
 }
 
 .dcmseg-segmentation-panel .cog-icon:hover {
@@ -43,11 +49,11 @@
   height: 150px;
 }
 
-.dcmseg-segmentation-panel .selector-form>div {
+.dcmseg-segmentation-panel .selector-form > div {
   width: 100%;
 }
 
-.dcmseg-segmentation-panel .selector-form>div:first-of-type {
+.dcmseg-segmentation-panel .selector-form > div:first-of-type {
   display: flex;
   flex-direction: row;
   justify-content: center;
@@ -59,3 +65,61 @@
   flex: unset;
   margin-right: 16px;
 }
+
+.SegmentsSection {
+  display: flex;
+  flex-direction: column;
+  color: var(--text-primary-color);
+  font-size: 12px;
+  margin-bottom: 0px;
+  height: 100%;
+}
+
+.SegmentsSection .header {
+  display: flex;
+  flex-direction: row;
+  align-items: center;
+  justify-content: space-between;
+  background-color: var(--ui-gray-dark);
+  border-radius: 5px;
+  font-weight: bold;
+  padding: 10px 15px;
+}
+
+.SegmentsSection .count {
+  font-size: 15px;
+  color: var(--active-color);
+  margin-left: 15px;
+  border-radius: 5px;
+  background-color: var(--ui-gray-darker);
+  text-align: center;
+  min-width: 25px;
+}
+
+.SegmentsSection .header .eye-icon,
+.SegmentsSection .header .angle-double-down,
+.SegmentsSection .header .angle-double-up {
+  cursor: pointer;
+  color: var(--active-color);
+}
+
+.SegmentsSection .header .eye-icon:hover,
+.SegmentsSection .header .angle-double-down:hover,
+.SegmentsSection .header .angle-double-up:hover {
+  color: var(--hover-color);
+}
+
+.SegmentsSection .header .eye-icon.expanded {
+  color: var(--default-color);
+}
+
+.SegmentsSection .header .icons {
+  display: flex;
+  align-items: center;
+  border-radius: 5px;
+}
+
+.SegmentsSection .header .icons .angle-double-down,
+.SegmentsSection .header .icons .angle-double-up {
+  margin-left: 15px;
+}

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

@@ -3,7 +3,7 @@ import Select from 'react-select';
 
 const SegmentationSelect = ({ value, formatOptionLabel, options }) => (
   <Select
-    value={value}
+    value={value === undefined ? null : value}
     formatOptionLabel={formatOptionLabel}
     styles={segmentationSelectStyles}
     options={options}

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

@@ -4,7 +4,7 @@ import { Range } from '@ohif/ui';
 
 import './SegmentationSettings.css';
 
-const SegmentationSettings = ({ configuration, onBack, onChange, disabledFields = [] }) => {
+const SegmentationSettings = ({ configuration, onBack, onChange, servicesManager, disabledFields = [] }) => {
   const [state, setState] = useState({
     renderFill: configuration.renderFill,
     renderOutline: configuration.renderOutline,
@@ -13,7 +13,8 @@ const SegmentationSettings = ({ configuration, onBack, onChange, disabledFields
     outlineAlpha: configuration.outlineAlpha,
     outlineWidth: configuration.outlineWidth,
     fillAlphaInactive: configuration.fillAlphaInactive,
-    outlineAlphaInactive: configuration.outlineAlphaInactive
+    outlineAlphaInactive: configuration.outlineAlphaInactive,
+    segsTolerance: configuration.segsTolerance,
   });
 
   useEffect(() => {
@@ -133,6 +134,40 @@ const SegmentationSettings = ({ configuration, onBack, onChange, disabledFields
           )}
         </div>
       )}
+      <div className="settings-group" style={{ marginBottom: 15 }}>
+        <label style={{ margin: '0 15px' }}>
+          Tolerance:
+          <input
+            style={{ margin: '0 15px' }}
+            label="Tolerance"
+            onKeyPress={event => {
+              const validate = string => {
+                let rgx = /[^-.e0-9]+/g;
+                return string.match(rgx);
+              };
+
+              if (validate(event.key)) {
+                event.preventDefault();
+              }
+            }}
+            onChange={event => {
+              save('segsTolerance', event.target.value);
+
+              const { UINotificationService, LoggerService } = servicesManager.services;
+              const error = new Error('Segmentation loader tolerance changed. This operation can potentially generate errors in the Segmentation parsing.');
+              LoggerService.error({ error, message: error.message });
+              UINotificationService.show({
+                title: 'Segmentation panel',
+                message: error.message,
+                type: 'warning',
+                autoClose: true,
+              });
+              }
+            }
+            value={state.segsTolerance}
+          />
+        </label>
+      </div>
     </div>
   );
 };
@@ -169,11 +204,12 @@ SegmentationSettings.propTypes = {
     renderFill: PropTypes.bool.isRequired,
     renderOutline: PropTypes.bool.isRequired,
     shouldRenderInactiveLabelmaps: PropTypes.bool.isRequired,
-    fillAlpha: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired, /* TODO: why fillAlpha is string? */
-    outlineAlpha: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired, /* TODO: why fillAlpha is string? */
+    fillAlpha: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired,
+    outlineAlpha: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired,
     outlineWidth: PropTypes.number.isRequired,
-    fillAlphaInactive: PropTypes.number.isRequired,
-    outlineAlphaInactive: PropTypes.number.isRequired,
+    fillAlphaInactive: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired,
+    outlineAlphaInactive: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired,
+    segsTolerance: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired,
   }).isRequired,
   onBack: PropTypes.func.isRequired,
   onChange: PropTypes.func.isRequired,

extensions/dicom-segmentation/src/getOHIFDicomSegSopClassHandler.js

@@ -1,5 +1,11 @@
 import { MODULE_TYPES, utils } from '@ohif/core';
 import loadSegmentation from './loadSegmentation';
+import getSourceDisplaySet from './getSourceDisplaySet';
+import OHIF from '@ohif/core';
+import dcmjs from 'dcmjs';
+
+const { DicomLoaderService } = OHIF.utils;
+const { DicomMessage, DicomMetaDictionary } = dcmjs.data;
 
 // TODO: Should probably use dcmjs for this
 const SOP_CLASS_UIDS = {
@@ -32,6 +38,7 @@ export default function getSopClassHandlerModule({ servicesManager }) {
         SOPInstanceUID,
         SeriesInstanceUID,
         StudyInstanceUID,
+        SeriesNumber,
       } = metadata;
 
       const segDisplaySet = {
@@ -44,21 +51,145 @@ export default function getSopClassHandlerModule({ servicesManager }) {
         StudyInstanceUID,
         FrameOfReferenceUID,
         authorizationHeaders,
-        metadata,
         isDerived: true,
         referencedDisplaySetUID: null, // Assigned when loaded.
         labelmapIndex: null, // Assigned when loaded.
         isLoaded: false,
+        loadError: false,
+        hasOverlapping: false,
         SeriesDate,
         SeriesTime,
+        SeriesNumber,
         SeriesDescription,
+        metadata,
+        tolerance: 1e-2,
       };
 
-      segDisplaySet.load = function(referencedDisplaySet, studies) {
-        return loadSegmentation(segDisplaySet, referencedDisplaySet, studies);
+      segDisplaySet.getSourceDisplaySet = function(
+        studies,
+        activateLabelMap = true,
+        onDisplaySetLoadFailureHandler
+      ) {
+        return getSourceDisplaySet(
+          studies,
+          segDisplaySet,
+          activateLabelMap,
+          onDisplaySetLoadFailureHandler
+        );
+      };
+
+      segDisplaySet.load = async function(referencedDisplaySet, studies) {
+        segDisplaySet.isLoaded = true;
+        const { StudyInstanceUID } = referencedDisplaySet;
+        const segArrayBuffer = await DicomLoaderService.findDicomDataPromise(
+          segDisplaySet,
+          studies
+        );
+        const dicomData = DicomMessage.readFile(segArrayBuffer);
+        const dataset = DicomMetaDictionary.naturalizeDataset(dicomData.dict);
+        dataset._meta = DicomMetaDictionary.namifyDataset(dicomData.meta);
+        const imageIds = _getImageIdsForDisplaySet(
+          studies,
+          StudyInstanceUID,
+          referencedDisplaySet.SeriesInstanceUID
+        );
+
+        const results = await _parseSeg(segArrayBuffer, imageIds, segDisplaySet.tolerance);
+        if (results === undefined) {
+          return;
+        }
+        const {
+          labelmapBufferArray,
+          segMetadata,
+          segmentsOnFrame,
+          segmentsOnFrameArray,
+        } = results;
+        let labelmapIndex;
+        if (labelmapBufferArray.length > 1) {
+          let labelmapIndexes = [];
+          for (let i = 0; i < labelmapBufferArray.length; ++i) {
+            segMetadata.segmentationSeriesInstanceUID =
+              segDisplaySet.SeriesInstanceUID;
+            segMetadata.hasOverlapping = true;
+            labelmapIndexes.push(
+              await loadSegmentation(
+                imageIds,
+                segDisplaySet,
+                labelmapBufferArray[i],
+                segMetadata,
+                segmentsOnFrame,
+                segmentsOnFrameArray[i]
+              )
+            );
+          }
+          /**
+           * Since overlapping segments have virtual labelmaps,
+           * originLabelMapIndex is used in the panel to select the correct dropdown value.
+           */
+          segDisplaySet.hasOverlapping = true;
+          segDisplaySet.originLabelMapIndex = labelmapIndexes[0];
+          labelmapIndex = labelmapIndexes[0];
+          console.warn('Overlapping segments!');
+        } else {
+          segMetadata.segmentationSeriesInstanceUID =
+            segDisplaySet.SeriesInstanceUID;
+          segMetadata.hasOverlapping = false;
+          labelmapIndex = await loadSegmentation(
+            imageIds,
+            segDisplaySet,
+            labelmapBufferArray[0],
+            segMetadata,
+            segmentsOnFrame,
+            []
+          );
+        }
       };
 
       return segDisplaySet;
     },
   };
 }
+
+function _parseSeg(
+  arrayBuffer,
+  imageIds,
+  tolerance = 1e-2,
+  skipOverlapping = false,
+  cornerstoneToolsVersion = 4
+) {
+  return dcmjs.adapters.Cornerstone.Segmentation.generateToolState(
+    imageIds,
+    arrayBuffer,
+    cornerstone.metaData,
+    skipOverlapping,
+    tolerance,
+    cornerstoneToolsVersion
+  );
+}
+
+function _getImageIdsForDisplaySet(
+  studies,
+  StudyInstanceUID,
+  SeriesInstanceUID
+) {
+  const study = studies.find(
+    study => study.StudyInstanceUID === StudyInstanceUID
+  );
+
+  const displaySets = study.displaySets.filter(displaySet => {
+    return displaySet.SeriesInstanceUID === SeriesInstanceUID;
+  });
+
+  if (displaySets.length > 1) {
+    console.warn(
+      'More than one display set with the same SeriesInstanceUID. This is not supported yet...'
+    );
+    // TODO -> We could make check the instance list and see if any match?
+    // Do we split the segmentation into two cornerstoneTools segmentations if there are images in both series?
+    // ^ Will that even happen?
+  }
+
+  const referencedDisplaySet = displaySets[0];
+
+  return referencedDisplaySet.images.map(image => image.getImageId());
+}

extensions/dicom-segmentation/src/getSourceDisplaySet.js

@@ -0,0 +1,16 @@
+import setActiveLabelmap from './utils/setActiveLabelMap';
+import { metadata } from '@ohif/core';
+
+export default function getSourceDisplaySet(studies, segDisplaySet, activateLabelMap = true, onDisplaySetLoadFailureHandler) {
+  const referencedDisplaySet = metadata.StudyMetadata.getReferencedDisplaySet(segDisplaySet, studies);
+
+  let activatedLabelmapPromise;
+  if (activateLabelMap) {
+    activatedLabelmapPromise = setActiveLabelmap(referencedDisplaySet, studies, segDisplaySet, undefined, onDisplaySetLoadFailureHandler);
+  }
+
+  return {
+    referencedDisplaySet : referencedDisplaySet,
+    activatedLabelmapPromise : activatedLabelmapPromise
+  }
+}

extensions/dicom-segmentation/src/index.js

@@ -1,15 +1,19 @@
 import React from 'react';
+import OHIF from '@ohif/core';
 
 import init from './init.js';
 import toolbarModule from './toolbarModule.js';
 import getSopClassHandlerModule from './getOHIFDicomSegSopClassHandler.js';
 import SegmentationPanel from './components/SegmentationPanel/SegmentationPanel.js';
+import { version } from '../package.json';
+const { studyMetadataManager } = OHIF.utils;
 
 export default {
   /**
    * Only required property. Should be a unique value across all extensions.
    */
   id: 'com.ohif.dicom-segmentation',
+  version,
 
   /**
    *
@@ -24,12 +28,12 @@ export default {
     return toolbarModule;
   },
   getPanelModule({ commandsManager, api, servicesManager }) {
-    const { UINotificationService } = servicesManager;
+    const { UINotificationService, LoggerService } = servicesManager.services;
 
     const ExtendedSegmentationPanel = props => {
       const { activeContexts } = api.hooks.useAppContext();
-
       const onDisplaySetLoadFailureHandler = error => {
+        LoggerService.error({ error, message: error.message });
         UINotificationService.show({
           title: 'DICOM Segmentation Loader',
           message: error.message,
@@ -46,7 +50,7 @@ export default {
       const onSegmentVisibilityChangeHandler = (segmentNumber, visible) => {
         commandsManager.runCommand('setSegmentConfiguration', {
           segmentNumber,
-          visible
+          visible,
         });
       };
 
@@ -55,7 +59,7 @@ export default {
           globalOpacity: configuration.fillAlpha,
           outlineThickness: configuration.outlineWidth,
           renderOutline: configuration.renderOutline,
-          visible: configuration.renderFill
+          visible: configuration.renderFill,
         });
       };
 
@@ -73,17 +77,56 @@ export default {
           onConfigurationChange={onConfigurationChangeHandler}
           onSelectedSegmentationChange={onSelectedSegmentationChangeHandler}
           onDisplaySetLoadFailure={onDisplaySetLoadFailureHandler}
+          servicesManager={servicesManager}
         />
       );
     };
 
+    const SegmentationPanelTabUpdatedEvent = 'segmentation-panel-tab-updated';
+
+    /**
+     * Trigger's an event to update the state of the panel's RoundedButtonGroup.
+     *
+     * This is required to avoid extension state
+     * coupling with the viewer's ToolbarRow component.
+     *
+     * @param {object} data
+     */
+    const triggerSegmentationPanelTabUpdatedEvent = data => {
+      const event = new CustomEvent(SegmentationPanelTabUpdatedEvent, {
+        detail: data,
+      });
+      document.dispatchEvent(event);
+    };
+
+    const onSegmentationsLoaded = ({ detail }) => {
+      const { segDisplaySet, segMetadata } = detail;
+      const studyMetadata = studyMetadataManager.get(
+        segDisplaySet.StudyInstanceUID
+      );
+      const referencedDisplaysets = studyMetadata.getDerivedDatasets({
+        referencedSeriesInstanceUID: segMetadata.seriesInstanceUid,
+        Modality: 'SEG',
+      });
+      triggerSegmentationPanelTabUpdatedEvent({
+        badgeNumber: referencedDisplaysets.length,
+        target: 'segmentation-panel',
+      });
+    };
+
+    document.addEventListener(
+      'extensiondicomsegmentationsegloaded',
+      onSegmentationsLoaded
+    );
+
     return {
       menuOptions: [
         {
           icon: 'list',
           label: 'Segmentations',
           target: 'segmentation-panel',
-          isDisabled: studies => {
+          stateEvent: SegmentationPanelTabUpdatedEvent,
+          isDisabled: (studies, activeViewport) => {
             if (!studies) {
               return true;
             }
@@ -96,6 +139,23 @@ export default {
                   const series = study.series[j];
 
                   if (series.Modality === 'SEG') {
+                    if (activeViewport) {
+                      const studyMetadata = studyMetadataManager.get(
+                        activeViewport.StudyInstanceUID
+                      );
+                      if (!studyMetadata) {
+                        return;
+                      }
+                      const referencedDS = studyMetadata.getDerivedDatasets({
+                        referencedSeriesInstanceUID:
+                          activeViewport.SeriesInstanceUID,
+                        Modality: 'SEG',
+                      });
+                      triggerSegmentationPanelTabUpdatedEvent({
+                        badgeNumber: referencedDS.length,
+                        target: 'segmentation-panel',
+                      });
+                    }
                     return false;
                   }
                 }

extensions/dicom-segmentation/src/init.js

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

extensions/dicom-segmentation/src/loadSegmentation.js

@@ -1,50 +1,15 @@
-import OHIF from '@ohif/core';
 import dcmjs from 'dcmjs';
 import cornerstone from 'cornerstone-core';
 import cornerstoneTools from 'cornerstone-tools';
 
-const { DicomLoaderService } = OHIF.utils;
-
 export default async function loadSegmentation(
+  imageIds,
   segDisplaySet,
-  referencedDisplaySet,
-  studies
+  labelmapBuffer,
+  segMetadata,
+  segmentsOnFrame,
+  labelmapSegments
 ) {
-  const { StudyInstanceUID } = referencedDisplaySet;
-
-  // Set here is loading is asynchronous.
-  // If this function throws its set back to false.
-  segDisplaySet.isLoaded = true;
-
-  const segArrayBuffer = await DicomLoaderService.findDicomDataPromise(
-    segDisplaySet,
-    studies
-  );
-
-  const dicomData = dcmjs.data.DicomMessage.readFile(segArrayBuffer);
-  const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
-    dicomData.dict
-  );
-
-  dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(dicomData.meta);
-
-  const imageIds = _getImageIdsForDisplaySet(
-    studies,
-    StudyInstanceUID,
-    referencedDisplaySet.SeriesInstanceUID
-  );
-
-  return new Promise((resolve, reject) => {
-    let results;
-
-    try {
-      results = _parseSeg(segArrayBuffer, imageIds);
-    } catch (error) {
-      segDisplaySet.isLoaded = false;
-      reject(error);
-    }
-
-    const { labelmapBuffer, segMetadata, segmentsOnFrame } = results;
   const { setters } = cornerstoneTools.getModule('segmentation');
 
   // TODO: Could define a color LUT based on colors in the SEG.
@@ -61,6 +26,19 @@ export default async function loadSegmentation(
     colorLUTIndex
   );
 
+  if (!segDisplaySet.labelmapSegments) {
+    segDisplaySet.labelmapSegments = {};
+  }
+
+  /**
+   * Cache each labelmap segments.
+   * This data is used to determine the active label map when a given segment is activated/clicked.
+   */
+  segDisplaySet.labelmapSegments[labelmapIndex] = labelmapSegments.length
+    ? Array.from(
+        new Set(labelmapSegments.filter(a => !!a).reduce((a, b) => a.concat(b)))
+      )
+    : [];
   segDisplaySet.labelmapIndex = labelmapIndex;
 
   /*
@@ -81,11 +59,19 @@ export default async function loadSegmentation(
    * without subscribing to external events.
    */
   console.log('Segmentation loaded.');
-    const event = new CustomEvent('extensiondicomsegmentationsegloaded');
+  const event = new CustomEvent('extensiondicomsegmentationsegloaded', {
+    detail: {
+      imageIds,
+      segDisplaySet,
+      labelmapBuffer,
+      segMetadata,
+      segmentsOnFrame,
+      labelmapSegments,
+    },
+  });
   document.dispatchEvent(event);
 
-    resolve(labelmapIndex);
-  });
+  return labelmapIndex;
 }
 
 function _getNextLabelmapIndex(firstImageId) {
@@ -171,38 +157,3 @@ function _getNextColorLUTIndex() {
 
   return colorLUTIndex;
 }
-
-function _parseSeg(arrayBuffer, imageIds) {
-  return dcmjs.adapters.Cornerstone.Segmentation.generateToolState(
-    imageIds,
-    arrayBuffer,
-    cornerstone.metaData
-  );
-}
-
-function _getImageIdsForDisplaySet(
-  studies,
-  StudyInstanceUID,
-  SeriesInstanceUID
-) {
-  const study = studies.find(
-    study => study.StudyInstanceUID === StudyInstanceUID
-  );
-
-  const displaySets = study.displaySets.filter(displaySet => {
-    return displaySet.SeriesInstanceUID === SeriesInstanceUID;
-  });
-
-  if (displaySets.length > 1) {
-    console.warn(
-      'More than one display set with the same SeriesInstanceUID. This is not supported yet...'
-    );
-    // TODO -> We could make check the instance list and see if any match?
-    // Do we split the segmentation into two cornerstoneTools segmentations if there are images in both series?
-    // ^ Will that even happen?
-  }
-
-  const referencedDisplaySet = displaySets[0];
-
-  return referencedDisplaySet.images.map(image => image.getImageId());
-}

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

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

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

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