chore(release): publish [skip ci]

- @ohif/extension-cornerstone@2.12.7
 - @ohif/extension-dicom-html@1.3.18
 - @ohif/extension-dicom-rt@0.7.8
 - @ohif/extension-dicom-segmentation@0.7.8
 - @ohif/extension-dicom-tag-browser@0.2.19
 - @ohif/extension-vtk@1.12.15
 - @ohif/core@2.16.11
 - @ohif/viewer@4.12.17

.circleci/config.yml

@@ -25,11 +25,9 @@ executors:
     docker:
       # Primary container image where all steps run.
       - image: 'cypress/browsers:node14.15.0-chrome86-ff82'
-      - image: 'ohif/viewer-testdata:0.1-test'
-
 defaults: &defaults
   docker:
-    - image: circleci/node:14.15.0
+    - image: cimg/node:14.18
       environment:
         TERM: xterm # Enable colors in term
         QUICK_BUILD: true
@@ -119,6 +117,7 @@ jobs:
           command: yarn install --frozen-lockfile
 
       - setup_remote_docker:
+          version: 19.03.13
           docker_layer_caching: false
 
       - run:
@@ -295,6 +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
@@ -347,7 +347,8 @@ workflows:
           store_artifacts: true
           working_directory: platform/viewer
           build:
-            npx cross-env QUICK_BUILD=true APP_CONFIG=config/dicomweb-server.js
+            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/**/*'
@@ -375,7 +376,8 @@ workflows:
           store_artifacts: true
           working_directory: platform/viewer
           build:
-            npx cross-env QUICK_BUILD=true APP_CONFIG=config/dicomweb-server.js
+            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/**/*'
@@ -408,7 +410,8 @@ workflows:
           store_artifacts: false
           working_directory: platform/viewer
           build:
-            npx cross-env QUICK_BUILD=true APP_CONFIG=config/dicomweb-server.js
+            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
@@ -487,7 +490,8 @@ workflows:
           store_artifacts: false
           working_directory: platform/viewer
           build:
-            npx cross-env QUICK_BUILD=true APP_CONFIG=config/dicomweb-server.js
+            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

.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.

.gitignore

@@ -9,6 +9,10 @@ src/version.js
 junit.xml
 coverage/
 .docz/
+*.js.map
+.yarn
+platform/docs/.docusaurus
+platform/ui/storybook-static
 
 # YALC (for Erik)
 .yalc
@@ -34,3 +38,4 @@ screenshots/
 
 # Locize settings
 .locize
+

.gitmodules

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

.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

@@ -28,7 +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`,
     },

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

@@ -53,7 +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

@@ -273,6 +273,17 @@ development of OHIF Viewer:
   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
 

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)
@@ -23,13 +25,13 @@ 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.
 
 More specifically, we accomplish this by using a
-[`reverse proxy`](https://en.wikipedia.org/wiki/Reverse_proxy) to retrieve
+[`reverse proxy`](https://en.wikipedia.org/wiki/Reverse_proxy) to retrieve 
 resources from our image archive (Orthanc), and when accessing its web admin.
 
 > A reverse proxy is a type of proxy server that retrieves resources on behalf
@@ -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,
+  },
+};
+```

extensions/cornerstone/CHANGELOG.md

@@ -3,6 +3,95 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [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)
 
 

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": "2.10.9",
+  "version": "2.12.7",
   "description": "OHIF extension for Cornerstone",
   "author": "OHIF",
   "license": "MIT",
@@ -32,12 +32,12 @@
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
     "@ohif/ui": "^0.50.0",
-    "cornerstone-core": "^2.2.8",
+    "cornerstone-core": "^2.6.1",
-    "cornerstone-math": "^0.1.8",
+    "cornerstone-math": "^0.1.9",
-    "cornerstone-tools": "^4.20.1",
+    "cornerstone-tools": "^6.0.6",
-    "cornerstone-wado-image-loader": "^3.1.0",
+    "cornerstone-wado-image-loader": "^4.1.0",
-    "dcmjs": "0.18.8",
+    "dcmjs": "0.19.4",
-    "dicom-parser": "^1.8.3",
+    "dicom-parser": "^1.8.11",
     "hammerjs": "^2.0.8",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
@@ -51,6 +51,6 @@
     "classnames": "^2.2.6",
     "lodash.merge": "^4.6.2",
     "lodash.throttle": "^4.1.1",
-    "react-cornerstone-viewport": "4.0.5"
+    "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 OHIFCornerstoneViewportOverlay from './components/OHIFCornerstoneViewportOverlay';
 import ConnectedCornerstoneViewport from './ConnectedCornerstoneViewport';
 import OHIF from '@ohif/core';
 import PropTypes from 'prop-types';
 import cornerstone from 'cornerstone-core';
+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();
     }
   }
@@ -221,7 +227,7 @@ class OHIFCornerstoneViewport extends Component {
       const { displaySet } = this.props.viewportData;
       const { StudyInstanceUID } = displaySet;
 
-      if (currentImageIdIndex > 0) {
+      if (currentImageIdIndex >= 0) {
         this.props.onNewImage({
           StudyInstanceUID,
           SOPInstanceUID: sopInstanceUid,
@@ -232,7 +238,12 @@ class OHIFCornerstoneViewport extends Component {
     };
 
     const warningsOverlay = props => {
-      return <OHIFCornerstoneViewportOverlay {...props} inconsistencyWarnings={inconsistencyWarnings} />
+      return (
+        <OHIFCornerstoneViewportOverlay
+          {...props}
+          inconsistencyWarnings={inconsistencyWarnings}
+        />
+      );
     };
 
     return (
@@ -244,10 +255,11 @@ class OHIFCornerstoneViewport extends Component {
           onNewImageDebounced={newImageHandler}
           onNewImageDebounceTime={300}
           viewportOverlayComponent={warningsOverlay}
+          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/index.js

@@ -36,7 +36,7 @@ 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
@@ -48,8 +48,17 @@ export default {
         jumpData.refreshViewports = false;
         commandsManager.runCommand('jumpToImage', jumpData);
       };
+
+      const { studyPrefetcher } = appConfig;
+      const isStackPrefetchEnabled =
+        studyPrefetcher && !studyPrefetcher.enabled;
+
       return (
-        <OHIFCornerstoneViewport {...props} onNewImage={onNewImageHandler} />
+        <OHIFCornerstoneViewport
+          {...props}
+          onNewImage={onNewImageHandler}
+          isStackPrefetchEnabled={isStackPrefetchEnabled}
+        />
       );
     };
 

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

@@ -37,8 +37,8 @@ export default function(configuration = {}) {
 
   // Configure stack prefetch
   cornerstoneTools.stackPrefetch.setConfiguration({
-    maxImagesToPrefetch: Infinity,
+    maxImagesToPrefetch: configuration.maxImagesToPrefetch,
-    preserveExistingPool: false,
+    preserveExistingPool: configuration.preserveExistingPool,
-    maxSimultaneousRequests: 20,
+    maxSimultaneousRequests: configuration.maxSimultaneousRequests,
   });
 }

extensions/cornerstone/src/tools/DICOMSRDisplayTool.js

@@ -0,0 +1,414 @@
+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.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;
+      }
+
+      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.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 > maxX) {
+      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 +1,8 @@
+export default {
+  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/debugging/CHANGELOG.md

@@ -3,6 +3,25 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [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

extensions/debugging/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-debugging",
-  "version": "0.2.2",
+  "version": "0.3.1",
   "description": "OHIF extension for debugging.",
   "author": "OHIF",
   "license": "MIT",
@@ -28,12 +28,12 @@
   },
   "peerDependencies": {
     "@ohif/core": "^2.6.0",
-    "dicom-parser": "^1.8.3"
+    "dicom-parser": "^1.8.11"
   },
   "dependencies": {
     "@babel/runtime": "^7.5.5",
     "detect-browser": "5.1.1",
-    "dicomweb-client": "^0.8.1",
+    "dicomweb-client": "^0.8.3",
     "file-saver": "^2.0.2",
     "jszip": "^3.2.2"
   }

extensions/dicom-html/CHANGELOG.md

@@ -3,6 +3,70 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [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)
 
 

extensions/dicom-html/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-html",
-  "version": "1.3.10",
+  "version": "1.3.18",
   "description": "OHIF extension for rendering structured reports to HTML",
   "author": "OHIF",
   "license": "MIT",
@@ -29,7 +29,7 @@
   },
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
-    "dcmjs": "0.18.8",
+    "dcmjs": "0.19.4",
     "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>);
   }
@@ -170,7 +170,7 @@ const getContentSequence = (data, level = 1) => {
 
     if (key === '_meta') {
       const HeaderDynamicLevel = `h3`;
-      root.push(<hr />);
+      root.push(<hr key={root.length} />);
       root.push(
         <HeaderDynamicLevel key="Metadata">
           DICOM File Meta Information
@@ -217,7 +217,7 @@ class DicomHtmlViewport extends Component {
   };
 
   componentDidMount() {
-    const dataSet = this.setContentFromByteArray(this.props.byteArray);
+    this.setContentFromByteArray(this.props.byteArray);
   }
 
   setContentFromByteArray(byteArray) {

extensions/dicom-html/src/OHIFDicomHtmlSopClassHandler.js

@@ -5,11 +5,12 @@ 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',
+  ACQUISITION_CONTEXT_SR_STORAGE: '1.2.840.10008.5.1.4.1.1.88.71'
 };
 
 const sopClassUIDs = Object.values(SOP_CLASS_UIDS);
@@ -46,6 +47,8 @@ const OHIFDicomHtmlSopClassHandler = {
       SeriesTime,
       SeriesNumber,
       authorizationHeaders,
+      sopClassUids: sopClassUIDs,
+      images: series._instances,
     };
   },
 };

extensions/dicom-pdf/CHANGELOG.md

@@ -3,6 +3,33 @@
 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

extensions/dicom-pdf/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-pdf",
-  "version": "1.0.6",
+  "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/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-rt/CHANGELOG.md

@@ -3,6 +3,89 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [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)
 
 

extensions/dicom-rt/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-rt",
-  "version": "0.6.13",
+  "version": "0.7.8",
   "description": "OHIF extension for rendering DICOM RTSTRUCTs on top of cornerstone images.",
   "author": "OHIF",
   "license": "MIT",
@@ -29,9 +29,9 @@
   },
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
-    "cornerstone-core": "^2.2.8",
+    "cornerstone-core": "^2.6.1",
-    "cornerstone-tools": "^4.20.1",
+    "cornerstone-tools": "^6.0.6",
-    "dcmjs": "0.18.8",
+    "dcmjs": "0.19.4",
     "gl-matrix": "^3.3.0",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",

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

@@ -81,13 +81,10 @@ const RTPanel = ({
   useEffect(() => {
     updateStructureSets();
 
-    document.addEventListener('extensiondicomrtrtloaded', updateStructureSets);
+    document.addEventListener('rt-panel-tab-updated', updateStructureSets);
 
     return () => {
-      document.removeEventListener(
+      document.removeEventListener('rt-panel-tab-updated', updateStructureSets);
-        'extensiondicomrtrtloaded',
-        updateStructureSets
-      );
     };
   }, []);
 

extensions/dicom-rt/src/index.js

@@ -1,11 +1,12 @@
 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';
 
-import { utils } from '@ohif/core';
 const { studyMetadataManager } = utils;
 
 export default {
@@ -42,29 +43,60 @@ export default {
       );
     };
 
+    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',
+          stateEvent: RTPanelTabChangedEvent,
           isDisabled: (studies, activeViewport) => {
             if (!studies) {
               return true;
             }
 
             if (activeViewport) {
-              const study = studies.find(
-                s => s.StudyInstanceUID === activeViewport.StudyInstanceUID
-              );
-              const ds = study.displaySets.find(
-                ds =>
-                  ds.displaySetInstanceUID ===
-                  activeViewport.displaySetInstanceUID
-              );
               const studyMetadata = studyMetadataManager.get(
                 activeViewport.StudyInstanceUID
               );
+              if (!studyMetadata) {
+                return;
+              }
               const referencedDisplaySets = studyMetadata.getDerivedDatasets({
                 referencedSeriesInstanceUID: activeViewport.SeriesInstanceUID,
                 Modality: 'RTSTRUCT',
@@ -75,6 +107,10 @@ export default {
                   ['RTSTRUCT'].includes(ds.Modality)
                 )
               ) {
+                triggerRTPanelUpdatedEvent({
+                  badgeNumber: referencedDisplaySets.length,
+                  target: 'rt-panel',
+                });
                 return false;
               }
             }

extensions/dicom-rt/src/loadRTStruct.js

@@ -90,11 +90,11 @@ export default async function loadRTStruct(
       const sopInstanceUID = ContourImageSequence
         ? ContourImageSequence.ReferencedSOPInstanceUID
         : _getClosestSOPInstanceUID(
-          ContourData,
+            ContourData,
-          ContourGeometricType,
+            ContourGeometricType,
-          NumberOfContourPoints,
+            NumberOfContourPoints,
-          imageIdSopInstanceUidPairs
+            imageIdSopInstanceUidPairs
-        );
+          );
       const imageId = _getImageId(imageIdSopInstanceUidPairs, sopInstanceUID);
 
       if (!imageId) {
@@ -171,7 +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);
 }
 
@@ -299,7 +305,9 @@ const _getImageId = (imageIdSopInstanceUidPairs, sopInstanceUID) => {
       imageIdSopInstanceUidPairsEntry.sopInstanceUID === sopInstanceUID
   );
 
-  return imageIdSopInstanceUidPairsEntry ? imageIdSopInstanceUidPairsEntry.imageId : null;
+  return imageIdSopInstanceUidPairsEntry
+    ? imageIdSopInstanceUidPairsEntry.imageId
+    : null;
 };
 
 function _getImageIdSopInstanceUidPairsForDisplaySet(

extensions/dicom-segmentation/CHANGELOG.md

@@ -3,6 +3,89 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [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)
 
 

extensions/dicom-segmentation/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-segmentation",
-  "version": "0.6.10",
+  "version": "0.7.8",
   "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-core": "^2.6.1",
-    "cornerstone-tools": "^4.20.1",
+    "cornerstone-tools": "^6.0.6",
-    "dcmjs": "0.18.8",
+    "dcmjs": "0.19.4",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6"

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

@@ -24,6 +24,7 @@ const SegmentItem = ({
   onClick,
   itemClass,
   color,
+  labelmap3D,
   visible,
   onVisibilityChange,
 }) => {
@@ -39,7 +40,7 @@ const SegmentItem = ({
     event.stopPropagation();
     const newVisibility = !isVisible;
     setIsVisible(newVisibility);
-    onVisibilityChange(newVisibility, index);
+    onVisibilityChange(newVisibility, index, labelmap3D);
   };
 
   return (

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

@@ -224,16 +224,20 @@ const SegmentationPanel = ({
         )
       );
     };
-  }, [activeIndex, viewports]);
+  }, [
+    activeIndex,
+    updateSegmentationComboBox,
+    viewports,
+  ]);
 
-  const updateSegmentationComboBox = (e) => {
+  const updateSegmentationComboBox = e => {
     const index = e.detail.activatedLabelmapIndex;
     if (index !== -1) {
       setState(state => ({ ...state, selectedSegmentation: index }));
     } else {
       cleanSegmentationComboBox();
     }
-  }
+  };
 
   const cleanSegmentationComboBox = () => {
     setState(state => ({
@@ -245,7 +249,7 @@ const SegmentationPanel = ({
       isDisabled: true,
       selectedSegmentation: -1,
     }));
-  }
+  };
 
   const refreshSegmentations = () => {
     const activeViewport = getActiveViewport();
@@ -309,7 +313,8 @@ const SegmentationPanel = ({
     );
 
     const filteredReferencedSegDisplaysets = referencedSegDisplaysets.filter(
-      (segDisplay => segDisplay.loadError !== true));
+      segDisplay => segDisplay.loadError !== true
+    );
 
     return filteredReferencedSegDisplaysets.map((displaySet, index) => {
       const {
@@ -426,23 +431,43 @@ const SegmentationPanel = ({
     return enabledElements[activeIndex].element;
   };
 
-  const onSegmentVisibilityChangeHandler = (isVisible, segmentNumber) => {
+  const onSegmentVisibilityChangeHandler = (
-    /** Get all labelmaps with this segmentNumber (overlapping segments) */
+    isVisible,
-    const { labelmaps3D } = getBrushStackState();
+    segmentNumber,
-    const possibleLabelMaps3D = labelmaps3D.filter(({ labelmaps2D }) => {
+    labelmap3D
-      return labelmaps2D.some(({ segmentsOnLabelmap }) =>
+  ) => {
-        segmentsOnLabelmap.includes(segmentNumber)
-      );
-    });
-
     let segmentsHidden = [];
-    possibleLabelMaps3D.forEach(labelmap3D => {
+    if (labelmap3D.metadata.hasOverlapping) {
-      labelmap3D.segmentsHidden[segmentNumber] = !isVisible;
+      /** Get all labelmaps with this segmentNumber and that
+       * are from the same series (overlapping segments) */
+      const { labelmaps3D } = getBrushStackState();
 
-      segmentsHidden = [
+      const sameSeriesLabelMaps3D = labelmaps3D.filter(({ metadata }) => {
-        ...new Set([...segmentsHidden, ...labelmap3D.segmentsHidden]),
+        return (
-      ];
+          labelmap3D.metadata.segmentationSeriesInstanceUID ===
-    });
+          metadata.segmentationSeriesInstanceUID
+        );
+      });
+
+      const possibleLabelMaps3D = sameSeriesLabelMaps3D.filter(
+        ({ labelmaps2D }) => {
+          return labelmaps2D.some(({ segmentsOnLabelmap }) =>
+            segmentsOnLabelmap.includes(segmentNumber)
+          );
+        }
+      );
+
+      possibleLabelMaps3D.forEach(labelmap3D => {
+        labelmap3D.segmentsHidden[segmentNumber] = !isVisible;
+
+        segmentsHidden = [
+          ...new Set([...segmentsHidden, ...labelmap3D.segmentsHidden]),
+        ];
+      });
+    } else {
+      labelmap3D.segmentsHidden[segmentNumber] = !isVisible;
+      segmentsHidden = [...labelmap3D.segmentsHidden];
+    }
 
     setState(state => ({ ...state, segmentsHidden }));
 
@@ -509,6 +534,7 @@ const SegmentationPanel = ({
           label={segmentLabel}
           index={segmentNumber}
           color={color}
+          labelmap3D={labelmap3D}
           visible={!labelmap3D.segmentsHidden[segmentIndex]}
           onVisibilityChange={onSegmentVisibilityChangeHandler}
         />

extensions/dicom-segmentation/src/getOHIFDicomSegSopClassHandler.js

@@ -64,8 +64,17 @@ export default function getSopClassHandlerModule({ servicesManager }) {
         metadata,
       };
 
-      segDisplaySet.getSourceDisplaySet = function(studies, activateLabelMap = true, onDisplaySetLoadFailureHandler) {
+      segDisplaySet.getSourceDisplaySet = function(
-        return getSourceDisplaySet(studies, segDisplaySet, activateLabelMap, onDisplaySetLoadFailureHandler);
+        studies,
+        activateLabelMap = true,
+        onDisplaySetLoadFailureHandler
+      ) {
+        return getSourceDisplaySet(
+          studies,
+          segDisplaySet,
+          activateLabelMap,
+          onDisplaySetLoadFailureHandler
+        );
       };
 
       segDisplaySet.load = async function(referencedDisplaySet, studies) {
@@ -98,6 +107,9 @@ export default function getSopClassHandlerModule({ servicesManager }) {
         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,
@@ -118,6 +130,9 @@ export default function getSopClassHandlerModule({ servicesManager }) {
           labelmapIndex = labelmapIndexes[0];
           console.warn('Overlapping segments!');
         } else {
+          segMetadata.segmentationSeriesInstanceUID =
+            segDisplaySet.SeriesInstanceUID;
+          segMetadata.hasOverlapping = false;
           labelmapIndex = await loadSegmentation(
             imageIds,
             segDisplaySet,
@@ -135,10 +150,16 @@ export default function getSopClassHandlerModule({ servicesManager }) {
 }
 
 function _parseSeg(arrayBuffer, imageIds) {
+  const skipOverlapping = false;
+  const tolerance = 1e-2;
+  const cornerstoneToolsVersion = 4;
   return dcmjs.adapters.Cornerstone.Segmentation.generateToolState(
     imageIds,
     arrayBuffer,
-    cornerstone.metaData
+    cornerstone.metaData,
+    skipOverlapping,
+    tolerance,
+    cornerstoneToolsVersion
   );
 }
 

extensions/dicom-segmentation/src/index.js

@@ -1,9 +1,12 @@
 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 {
   /**
@@ -79,13 +82,51 @@ export default {
       );
     };
 
+    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;
             }
@@ -98,6 +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/loadSegmentation.js

@@ -59,7 +59,16 @@ 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);
 
   return labelmapIndex;

extensions/dicom-tag-browser/CHANGELOG.md

@@ -3,6 +3,70 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [0.2.19](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.18...@ohif/extension-dicom-tag-browser@0.2.19) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
+## [0.2.18](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.17...@ohif/extension-dicom-tag-browser@0.2.18) (2022-02-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
+## [0.2.17](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.16...@ohif/extension-dicom-tag-browser@0.2.17) (2022-01-20)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
+## [0.2.16](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.15...@ohif/extension-dicom-tag-browser@0.2.16) (2021-12-10)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
+## [0.2.15](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.14...@ohif/extension-dicom-tag-browser@0.2.15) (2021-12-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
+## [0.2.14](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.13...@ohif/extension-dicom-tag-browser@0.2.14) (2021-11-30)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
+## [0.2.13](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.12...@ohif/extension-dicom-tag-browser@0.2.13) (2021-10-26)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
+## [0.2.12](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.11...@ohif/extension-dicom-tag-browser@0.2.12) (2021-09-28)
+
+**Note:** Version bump only for package @ohif/extension-dicom-tag-browser
+
+
+
+
+
 ## [0.2.11](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-tag-browser@0.2.10...@ohif/extension-dicom-tag-browser@0.2.11) (2021-06-03)
 
 **Note:** Version bump only for package @ohif/extension-dicom-tag-browser

extensions/dicom-tag-browser/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-tag-browser",
-  "version": "0.2.11",
+  "version": "0.2.19",
   "description": "OHIF extension for checking DICOM headers.",
   "author": "OHIF",
   "license": "MIT",
@@ -28,12 +28,12 @@
   },
   "peerDependencies": {
     "@ohif/core": "^2.6.0",
-    "dcmjs": "0.18.8",
+    "dcmjs": "0.19.4",
     "react": "^16.8.6"
   },
   "dependencies": {
     "@babel/runtime": "^7.5.5",
-    "dicomweb-client": "^0.8.1",
+    "dicomweb-client": "^0.8.3",
     "moment": "2.24.0",
     "react-select": "^3.0.8"
   }

extensions/dicom-tag-browser/src/components/DicomTagBrowser.js

@@ -18,7 +18,7 @@ const DicomTagBrowser = ({ displaySets, displaySetInstanceUID }) => {
     activeDisplaySetInstanceUID,
     setActiveDisplaySetInstanceUID,
   ] = useState(displaySetInstanceUID);
-  const [activeInstance, setActiveInstance] = useState(0);
+  const [activeInstance, setActiveInstance] = useState(1);
   const [tags, setTags] = useState([]);
   const [meta, setMeta] = useState('');
   const [instanceList, setInstanceList] = useState([]);
@@ -51,20 +51,21 @@ const DicomTagBrowser = ({ displaySets, displaySetInstanceUID }) => {
         description: displayDate,
         onClick: () => {
           setActiveDisplaySetInstanceUID(displaySetInstanceUID);
-          setActiveInstance(0);
+          setActiveInstance(1);
         },
       };
     });
 
     let metadata;
-    const isImageStack = activeDisplaySet instanceof ImageSet;
+    const isImageStack =
+      activeDisplaySet instanceof ImageSet &&
+      activeDisplaySet.isModalitySupported === true;
 
-    let selectedInstanceValue;
     let instanceList;
 
     if (isImageStack) {
       const { images } = activeDisplaySet;
-      const image = images[activeInstance];
+      const image = images[activeInstance - 1];
 
       instanceList = images.map((image, index) => {
         const metadata = image.getData().metadata;
@@ -91,7 +92,7 @@ const DicomTagBrowser = ({ displaySets, displaySetInstanceUID }) => {
     setInstanceList(instanceList);
     setDisplaySetList(newDisplaySetList);
     setIsImageStack(isImageStack);
-  }, [activeDisplaySetInstanceUID, activeInstance]);
+  }, [activeDisplaySetInstanceUID, activeInstance, displaySets]);
 
   const selectedDisplaySetValue = displaySetList.find(
     ds => ds.value === activeDisplaySetInstanceUID
@@ -106,7 +107,7 @@ const DicomTagBrowser = ({ displaySets, displaySetInstanceUID }) => {
           showValue
           step={1}
           min={1}
-          max={instanceList.length - 1}
+          max={instanceList.length}
           value={activeInstance}
           valueRenderer={value => <p>Instance Number: {value}</p>}
           onChange={({ target }) => {

extensions/vtk/CHANGELOG.md

@@ -3,6 +3,172 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [1.12.15](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.14...@ohif/extension-vtk@1.12.15) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.14](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.13...@ohif/extension-vtk@1.12.14) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.13](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.12...@ohif/extension-vtk@1.12.13) (2022-02-02)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.12](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.11...@ohif/extension-vtk@1.12.12) (2022-01-29)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.11](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.10...@ohif/extension-vtk@1.12.11) (2022-01-20)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.10](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.9...@ohif/extension-vtk@1.12.10) (2022-01-13)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.8...@ohif/extension-vtk@1.12.9) (2021-12-23)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.7...@ohif/extension-vtk@1.12.8) (2021-12-23)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.6...@ohif/extension-vtk@1.12.7) (2021-12-02)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.5...@ohif/extension-vtk@1.12.6) (2021-11-30)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.4...@ohif/extension-vtk@1.12.5) (2021-10-26)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.3...@ohif/extension-vtk@1.12.4) (2021-10-15)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.2...@ohif/extension-vtk@1.12.3) (2021-10-04)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.1...@ohif/extension-vtk@1.12.2) (2021-09-28)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.12.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.12.0...@ohif/extension-vtk@1.12.1) (2021-09-24)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+# [1.12.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.11.18...@ohif/extension-vtk@1.12.0) (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))
+
+
+
+
+
+## [1.11.18](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.11.17...@ohif/extension-vtk@1.11.18) (2021-09-13)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.11.17](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.11.16...@ohif/extension-vtk@1.11.17) (2021-09-09)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.11.16](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.11.15...@ohif/extension-vtk@1.11.16) (2021-09-03)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.11.15](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.11.14...@ohif/extension-vtk@1.11.15) (2021-08-30)
+
+
+### Bug Fixes
+
+* MPR metadata parsing for spacings ([#2517](https://github.com/OHIF/Viewers/issues/2517)) ([715dfc5](https://github.com/OHIF/Viewers/commit/715dfc556a3883de31d74012dcc99e431d91f57d))
+
+
+
+
+
 ## [1.11.14](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.11.13...@ohif/extension-vtk@1.11.14) (2021-06-03)
 
 **Note:** Version bump only for package @ohif/extension-vtk

extensions/vtk/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-vtk",
-  "version": "1.11.14",
+  "version": "1.12.15",
   "description": "OHIF extension for VTK.js",
   "author": "OHIF",
   "license": "MIT",
@@ -32,11 +32,11 @@
     "@ohif/core": "^0.50.0",
     "@ohif/i18n": "^0.50.0",
     "@ohif/ui": "^0.50.0",
-    "cornerstone-core": "^2.2.8",
+    "cornerstone-core": "^2.6.1",
-    "cornerstone-tools": "^4.20.1",
+    "cornerstone-tools": "^6.0.6",
-    "cornerstone-wado-image-loader": "^3.1.0",
+    "cornerstone-wado-image-loader": "^4.1.0",
-    "dcmjs": "0.18.8",
+    "dcmjs": "0.19.4",
-    "dicom-parser": "^1.8.3",
+    "dicom-parser": "^1.8.11",
     "i18next": "^17.0.3",
     "i18next-browser-languagedetector": "^3.0.1",
     "prop-types": "^15.7.2",
@@ -50,14 +50,14 @@
   "dependencies": {
     "@babel/runtime": "^7.5.5",
     "lodash.throttle": "^4.1.1",
-    "react-vtkjs-viewport": "^0.14.2"
+    "react-vtkjs-viewport": "^0.14.4"
   },
   "devDependencies": {
-    "@ohif/core": "^2.13.13",
+    "@ohif/core": "^2.16.11",
-    "@ohif/ui": "^1.9.2",
+    "@ohif/ui": "^1.10.6",
-    "cornerstone-tools": "^4.20.1",
+    "cornerstone-tools": "^6.0.6",
-    "cornerstone-wado-image-loader": "^3.1.0",
+    "cornerstone-wado-image-loader": "^4.1.0",
-    "dicom-parser": "^1.8.3",
+    "dicom-parser": "^1.8.11",
     "gh-pages": "^2.0.1",
     "i18next": "^17.0.3",
     "i18next-browser-languagedetector": "^3.0.1",

extensions/vtk/src/OHIFVTKViewport.js

@@ -72,7 +72,7 @@ class OHIFVTKViewport extends Component {
   };
 
   static defaultProps = {
-    onScroll: () => {},
+    onScroll: () => { },
   };
 
   static id = 'OHIFVTKViewport';
@@ -271,7 +271,7 @@ class OHIFVTKViewport extends Component {
 
     volumeMapper.setSampleDistance(sampleDistance);
 
-    // Be generous to surpress warnings, as the logging really hurts performance.
+    // Be generous to suppress warnings, as the logging really hurts performance.
     // TODO: maybe we should auto adjust samples to 1000.
     volumeMapper.setMaximumSamplesPerRay(4000);
 
@@ -398,7 +398,7 @@ class OHIFVTKViewport extends Component {
 
     if (
       displaySet.displaySetInstanceUID !==
-        prevDisplaySet.displaySetInstanceUID ||
+      prevDisplaySet.displaySetInstanceUID ||
       displaySet.SOPInstanceUID !== prevDisplaySet.SOPInstanceUID ||
       displaySet.frameIndex !== prevDisplaySet.frameIndex
     ) {

lerna-debug.log

@@ -0,0 +1,23 @@
+0 silly argv {
+0 silly argv   _: [ 'run' ],
+0 silly argv   stream: true,
+0 silly argv   lernaVersion: '3.18.3',
+0 silly argv   '$0': 'node_modules/.bin/lerna',
+0 silly argv   script: 'dev:viewer'
+0 silly argv }
+1 notice cli v3.18.3
+2 verbose rootPath /home/davide/Development/OIHF/Viewers
+3 info versioning independent
+4 info Executing command in 1 package: "yarn run dev:viewer"
+5 silly npmRunScript.stream [ 'dev:viewer', [], '@ohif/viewer' ]
+6 silly getExecOpts /home/davide/Development/OIHF/Viewers/platform/viewer undefined
+7 error MaxBufferError: stderr maxBuffer exceeded
+7 error     at PassThrough.<anonymous> (/home/davide/Development/OIHF/Viewers/node_modules/get-stream/index.js:41:19)
+7 error     at PassThrough.emit (events.js:412:35)
+7 error     at addChunk (internal/streams/readable.js:290:12)
+7 error     at readableAddChunk (internal/streams/readable.js:261:11)
+7 error     at PassThrough.Readable.push (internal/streams/readable.js:204:10)
+7 error     at PassThrough.Transform.push (internal/streams/transform.js:166:32)
+7 error     at PassThrough.afterTransform (internal/streams/transform.js:101:10)
+7 error     at PassThrough._transform (internal/streams/passthrough.js:46:3)
+7 error     at PassThrough.Transform._read (internal/streams/transform.js:205:10)

package.json

@@ -56,6 +56,7 @@
     "@babel/preset-env": "^7.5.0",
     "@babel/preset-react": "^7.0.0",
     "@percy/cypress": "^2.2.0",
+    "@webpack-cli/serve": "^1.6.1",
     "babel-eslint": "9.x",
     "babel-loader": "^8.0.6",
     "babel-plugin-inline-react-svg": "1.1.0",
@@ -104,8 +105,8 @@
     "stylus-loader": "^3.0.2",
     "terser-webpack-plugin": "^2.1.0",
     "webpack": "^4.35.2",
-    "webpack-cli": "^3.3.5",
+    "webpack-cli": "^4.9.2",
-    "webpack-dev-server": "^3.7.2",
+    "webpack-dev-server": "^4.7.3",
     "webpack-hot-middleware": "^2.25.0",
     "webpack-merge": "^4.2.1",
     "workbox-webpack-plugin": "^5.0.0-beta.1",
@@ -123,6 +124,7 @@
     ]
   },
   "resolutions": {
+    "**/node-gyp": "8.4.1",
     "**/@babel/runtime": "7.5.5"
   }
 }

platform/core/CHANGELOG.md

@@ -3,6 +3,168 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [2.16.11](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.10...@ohif/core@2.16.11) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.16.10](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.9...@ohif/core@2.16.10) (2022-02-03)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.16.9](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.8...@ohif/core@2.16.9) (2022-02-02)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.16.8](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.7...@ohif/core@2.16.8) (2022-01-29)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.16.7](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.6...@ohif/core@2.16.7) (2022-01-20)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.16.6](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.5...@ohif/core@2.16.6) (2022-01-13)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.16.5](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.4...@ohif/core@2.16.5) (2021-12-23)
+
+
+### Bug Fixes
+
+* DICOMFileLoadingListener typo in method name ([#2647](https://github.com/OHIF/Viewers/issues/2647)) ([761d54f](https://github.com/OHIF/Viewers/commit/761d54fbbfb376c20ee15794ef7bb7111f64a06f))
+
+
+
+
+
+## [2.16.4](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.3...@ohif/core@2.16.4) (2021-12-23)
+
+
+### Bug Fixes
+
+* SeriesTime and SeriesDate are only set for the first series and undefined for the remaining ones ([#2476](https://github.com/OHIF/Viewers/issues/2476)) ([6a401c9](https://github.com/OHIF/Viewers/commit/6a401c9e5204cb4f7af6aa33190ad5a8d0879de6))
+
+
+
+
+
+## [2.16.3](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.2...@ohif/core@2.16.3) (2021-12-02)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.16.2](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.1...@ohif/core@2.16.2) (2021-11-30)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.16.1](https://github.com/OHIF/Viewers/compare/@ohif/core@2.16.0...@ohif/core@2.16.1) (2021-10-26)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+# [2.16.0](https://github.com/OHIF/Viewers/compare/@ohif/core@2.15.1...@ohif/core@2.16.0) (2021-10-04)
+
+
+### Features
+
+* Added support for WADO servers built with static hosting (e.g. S3) ([#2566](https://github.com/OHIF/Viewers/issues/2566)) ([a046c6c](https://github.com/OHIF/Viewers/commit/a046c6c9017a84e5ead71d5113b5e892333b4130))
+
+
+
+
+
+## [2.15.1](https://github.com/OHIF/Viewers/compare/@ohif/core@2.15.0...@ohif/core@2.15.1) (2021-09-28)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+# [2.15.0](https://github.com/OHIF/Viewers/compare/@ohif/core@2.14.1...@ohif/core@2.15.0) (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))
+
+
+
+
+
+## [2.14.1](https://github.com/OHIF/Viewers/compare/@ohif/core@2.14.0...@ohif/core@2.14.1) (2021-09-13)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+# [2.14.0](https://github.com/OHIF/Viewers/compare/@ohif/core@2.13.15...@ohif/core@2.14.0) (2021-09-09)
+
+
+### Features
+
+* OHIF-1000: Study prefetcher ([#2466](https://github.com/OHIF/Viewers/issues/2466)) ([8f26045](https://github.com/OHIF/Viewers/commit/8f2604509d24092b721f1333289d838820d68cac))
+
+
+
+
+
+## [2.13.15](https://github.com/OHIF/Viewers/compare/@ohif/core@2.13.14...@ohif/core@2.13.15) (2021-09-03)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.13.14](https://github.com/OHIF/Viewers/compare/@ohif/core@2.13.13...@ohif/core@2.13.14) (2021-08-30)
+
+
+### Bug Fixes
+
+* MPR metadata parsing for spacings ([#2517](https://github.com/OHIF/Viewers/issues/2517)) ([715dfc5](https://github.com/OHIF/Viewers/commit/715dfc556a3883de31d74012dcc99e431d91f57d))
+
+
+
+
+
 ## [2.13.13](https://github.com/OHIF/Viewers/compare/@ohif/core@2.13.12...@ohif/core@2.13.13) (2021-06-03)
 
 **Note:** Version bump only for package @ohif/core

platform/core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/core",
-  "version": "2.13.13",
+  "version": "2.16.11",
   "description": "Generic business logic for web-based medical imaging applications",
   "author": "OHIF Core Team",
   "license": "MIT",
@@ -31,20 +31,21 @@
     "test:unit:ci": "jest --ci --runInBand --collectCoverage"
   },
   "peerDependencies": {
-    "cornerstone-core": "^2.2.8",
+    "cornerstone-core": "^2.6.1",
-    "cornerstone-tools": "^4.20.1",
+    "cornerstone-tools": "^6.0.6",
-    "cornerstone-wado-image-loader": "^3.1.0",
+    "cornerstone-wado-image-loader": "^4.1.0",
-    "dicom-parser": "^1.8.3"
+    "dicom-parser": "^1.8.11"
   },
   "dependencies": {
     "@babel/runtime": "^7.5.5",
     "ajv": "^6.10.0",
-    "dcmjs": "0.18.8",
+    "dcmjs": "0.19.4",
-    "dicomweb-client": "^0.8.1",
+    "dicomweb-client": "^0.8.3",
     "immer": "6.0.2",
     "isomorphic-base64": "^1.0.2",
     "lodash.clonedeep": "^4.5.0",
     "lodash.merge": "^4.6.1",
+    "mathjs": "^10.1.0",
     "mousetrap": "^1.6.3",
     "retry": "^0.12.0",
     "validate.js": "^0.12.0"

platform/core/src/DICOMSR/SCOORD3D/constants/scoordTypes.js

@@ -0,0 +1,8 @@
+export default {
+  POINT: 'POINT',
+  MULTIPOINT: 'MULTIPOINT',
+  POLYLINE: 'POLYLINE',
+  CIRCLE: 'CIRCLE',
+  ELLIPSE: 'ELLIPSE',
+  POLYGON: 'POLYGON',
+};

platform/core/src/DICOMSR/SCOORD3D/constants/toolNames.js

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

platform/core/src/DICOMSR/SCOORD3D/enums.js

@@ -0,0 +1,29 @@
+export const CodeNameCodeSequenceValues = {
+  ImagingMeasurementReport: '126000',
+  ImageLibrary: '111028',
+  ImagingMeasurements: '126010',
+  MeasurementGroup: '125007',
+  ImageLibraryGroup: '126200',
+  TrackingUniqueIdentifier: '112040',
+  TrackingIdentifier: '112039',
+  Finding: '121071',
+  FindingSite: 'G-C0E3', // SRT
+  CornerstoneFreeText: 'CORNERSTONEFREETEXT', // CST4
+  Score: '246262008',
+};
+
+export const RELATIONSHIP_TYPE = {
+  INFERRED_FROM: 'INFERRED FROM',
+  SELECTED_FROM: 'SELECTED FROM',
+};
+
+export const CodingSchemeDesignators = {
+  SRT: 'SRT',
+  cornerstoneTools4: 'CST4',
+};
+
+export default {
+  CodeNameCodeSequenceValues,
+  RELATIONSHIP_TYPE,
+  CodingSchemeDesignators,
+};

platform/core/src/DICOMSR/SCOORD3D/parseSCOORD3D.js

@@ -0,0 +1,155 @@
+import { ImageSet } from '../../classes';
+import getMeasurements from './utils/getMeasurements';
+import getReferencedImagesList from './utils/getReferencedImagesList';
+import isRehydratable from './utils/isRehydratable';
+import addMeasurement from './utils/addMeasurement';
+
+const parseSCOORD3D = ({ servicesManager, displaySets }) => {
+  const { MeasurementService } = servicesManager.services;
+
+  const srDisplaySets = displaySets.filter(ds => ds.Modality === 'SR');
+
+  srDisplaySets.forEach(srDisplaySet => {
+    const firstInstance = srDisplaySet.metadata;
+    if (!firstInstance) {
+      return;
+    }
+
+    const { ContentSequence } = firstInstance;
+
+    srDisplaySet.referencedImages = getReferencedImagesList(ContentSequence);
+    srDisplaySet.measurements = getMeasurements(ContentSequence, srDisplaySet);
+    const mappings = MeasurementService.getSourceMappings(
+      'CornerstoneTools',
+      '4'
+    );
+
+    srDisplaySet.isHydrated = false;
+    srDisplaySet.isRehydratable = isRehydratable(srDisplaySet, mappings);
+    srDisplaySet.isLoaded = true;
+
+    const imageDisplaySets = displaySets.filter(
+      ds =>
+        ds.Modality !== 'SR' &&
+        ds.Modality !== 'SEG' &&
+        ds.Modality !== 'RTSTRUCT' &&
+        ds.Modality !== 'RTDOSE'
+    );
+    imageDisplaySets.forEach(imageDisplaySet => {
+      // Check currently added displaySets and add measurements if the sources exist.
+      checkIfCanAddMeasurementsToDisplaySet(srDisplaySet, imageDisplaySet);
+    });
+  });
+};
+
+const checkIfCanAddMeasurementsToDisplaySet = (
+  srDisplaySet,
+  imageDisplaySet
+) => {
+  let measurements = srDisplaySet.measurements;
+
+  /**
+   * Look for image sets.
+   * This also filters out _this_ displaySet, as it is not an image set.
+   */
+  if (!(imageDisplaySet instanceof ImageSet)) {
+    return;
+  }
+
+  const { sopClassUIDs, images } = imageDisplaySet;
+
+  /**
+   * Filter measurements that references the correct sop class.
+   */
+  measurements = measurements.filter(measurement => {
+    return measurement.coords.some(coord => {
+      if (coord.ReferencedSOPSequence === undefined) {
+        /** we miss the referenced information. We can compare the annotation SCOORD3D coordinates with
+         * the ImagePatientPosition of the frames. However (WARNING!!!),
+         * if more than a source series is present, this logic can find the wrong frame
+         * (i.e. two source series, with the same frameOfReferenceUID,
+         * that have each a frame with the same ImagePositionPatient of the annotation 3D coordinates)
+         */
+        for (let i = 0; i < images.length; ++i) {
+          const imageMetadata = images[i].getData().metadata;
+          if (
+            imageMetadata.FrameOfReferenceUID !==
+            coord.ReferencedFrameOfReferenceSequence
+          ) {
+            continue;
+          }
+
+          let sliceNormal = [0, 0, 0];
+          const orientation = imageMetadata.ImageOrientationPatient;
+          sliceNormal[0] =
+            orientation[1] * orientation[5] - orientation[2] * orientation[4];
+          sliceNormal[1] =
+            orientation[2] * orientation[3] - orientation[0] * orientation[5];
+          sliceNormal[2] =
+            orientation[0] * orientation[4] - orientation[1] * orientation[3];
+
+          let distanceAlongNormal = 0;
+          for (let j = 0; j < 3; ++j) {
+            distanceAlongNormal +=
+              sliceNormal[j] * imageMetadata.ImagePositionPatient[j];
+          }
+
+          // assuming 1 mm tolerance
+          if (Math.abs(distanceAlongNormal - coord.GraphicData[2]) > 1) {
+            continue;
+          }
+
+          coord.ReferencedSOPSequence = {
+            ReferencedSOPClassUID: imageMetadata.SOPClassUID,
+            ReferencedSOPInstanceUID: imageMetadata.SOPInstanceUID,
+          };
+
+          break;
+        }
+
+        if (coord.ReferencedSOPSequence === undefined) {
+          return false;
+        }
+      }
+
+      return sopClassUIDs.includes(
+        coord.ReferencedSOPSequence.ReferencedSOPClassUID
+      );
+    });
+  });
+
+  /**
+   * New display set doesn't have measurements that references the correct sop class.
+   */
+  if (measurements.length === 0) {
+    return;
+  }
+
+  const imageIds = images.map(i => i.getImageId());
+  const SOPInstanceUIDs = images.map(i => i.SOPInstanceUID);
+  measurements.forEach(measurement => {
+    const { coords } = measurement;
+
+    coords.forEach(coord => {
+      if (coord.ReferencedSOPSequence !== undefined) {
+        const imageIndex = SOPInstanceUIDs.findIndex(
+          SOPInstanceUID =>
+            SOPInstanceUID ===
+            coord.ReferencedSOPSequence.ReferencedSOPInstanceUID
+        );
+        if (imageIndex > -1) {
+          const imageId = imageIds[imageIndex];
+          const imageMetadata = images[imageIndex].getData().metadata;
+          addMeasurement(
+            measurement,
+            imageId,
+            imageMetadata,
+            imageDisplaySet.displaySetInstanceUID
+          );
+        }
+      }
+    });
+  });
+};
+
+export default parseSCOORD3D;

platform/core/src/DICOMSR/SCOORD3D/utils/addMeasurement.js

@@ -0,0 +1,102 @@
+import csTools from 'cornerstone-tools';
+import OHIF from '../../../';
+
+/** Internal imports */
+import TOOL_NAMES from '../constants/toolNames';
+import getRenderableData from './getRenderableData';
+
+const globalImageIdSpecificToolStateManager =
+  csTools.globalImageIdSpecificToolStateManager;
+
+/**
+ * Add a measurement to a display set.
+ *
+ * @param {*} measurement
+ * @param {*} imageId
+ * @param {*} displaySetInstanceUID
+ */
+export default function addMeasurement(
+  measurement,
+  imageId,
+  imageMetadata,
+  displaySetInstanceUID
+) {
+  // TODO -> Render rotated ellipse .
+  const toolName = TOOL_NAMES.DICOM_SR_DISPLAY_TOOL;
+
+  const measurementData = {
+    TrackingUniqueIdentifier: measurement.TrackingUniqueIdentifier,
+    renderableData: {},
+    labels: measurement.labels,
+  };
+
+  measurement.coords.forEach(coord => {
+    const { GraphicType, GraphicData, ValueType } = coord;
+
+    if (measurementData.renderableData[GraphicType] === undefined) {
+      measurementData.renderableData[GraphicType] = [];
+    }
+    measurementData.renderableData[GraphicType].push(
+      getRenderableData(GraphicType, GraphicData, ValueType, imageMetadata)
+    );
+  });
+
+  const toolState = globalImageIdSpecificToolStateManager.saveToolState();
+
+  if (toolState[imageId] === undefined) {
+    toolState[imageId] = {};
+  }
+
+  const imageIdToolState = toolState[imageId];
+
+  // If we don't have tool state for this type of tool, add an empty object
+  if (imageIdToolState[toolName] === undefined) {
+    imageIdToolState[toolName] = {
+      data: [],
+    };
+  }
+
+  const toolData = imageIdToolState[toolName];
+
+  measurementData.description = `Read-only annotation`;
+  measurementData.isReadOnly = true;
+  toolData.data.push(measurementData);
+
+  addToMeasurementApi({ measurementData, toolName, imageId });
+
+  measurement.loaded = true;
+  measurement.imageId = imageId;
+  measurement.displaySetInstanceUID = displaySetInstanceUID;
+
+  // Remove the unneeded coord now its processed, but keep the SOPInstanceUID.
+  // NOTE: We assume that each SCOORD in the MeasurementGroup maps onto one frame,
+  // It'd be super werid if it didn't anyway as a SCOORD.
+  measurement.ReferencedSOPInstanceUID =
+    measurement.coords[0].ReferencedSOPSequence.ReferencedSOPInstanceUID;
+
+  return measurement;
+}
+
+const addToMeasurementApi = ({ measurementData, toolName, imageId }) => {
+  const measurementApi = OHIF.measurements.MeasurementApi.Instance;
+
+  const toolType = toolName;
+  const collection = measurementApi.tools[toolType];
+  if (!collection) return;
+  if (!measurementData || measurementData.cancelled) return;
+
+  const imageAttributes = OHIF.measurements.getImageAttributes(null, imageId);
+  const measurement = Object.assign({}, measurementData, imageAttributes, {
+    lesionNamingNumber: measurementData.lesionNamingNumber,
+    userId: OHIF.user.getUserId(),
+    toolType,
+  });
+
+  const addedMeasurement = measurementApi.addMeasurement(toolType, measurement);
+  Object.assign(measurementData, addedMeasurement);
+
+  const measurementLabel = OHIF.measurements.getLabel(measurementData);
+  if (measurementLabel) {
+    measurementData.labels = [measurementLabel];
+  }
+};

platform/core/src/DICOMSR/SCOORD3D/utils/getCoordsFromSCOORDOrSCOORD3D.js

@@ -0,0 +1,31 @@
+const getCoordsFromSCOORDOrSCOORD3D = (graphicItem, displaySet) => {
+  const { ValueType, RelationshipType, GraphicType, GraphicData } = graphicItem;
+
+  // if (RelationshipType !== RELATIONSHIP_TYPE.INFERRED_FROM) {
+  //   console.warn(
+  //     `Relationshiptype === ${RelationshipType}. Cannot deal with NON TID-1400 SCOORD group with RelationshipType !== "INFERRED FROM."`
+  //   );
+  //   return;
+  // }
+
+  const coords = { ValueType, GraphicType, GraphicData };
+
+  // ContentSequence has length of 1 as RelationshipType === 'INFERRED FROM'
+  if (ValueType === 'SCOORD') {
+    const { ReferencedSOPSequence } = graphicItem.ContentSequence;
+    coords.ReferencedSOPSequence = ReferencedSOPSequence;
+  } else if (ValueType === 'SCOORD3D') {
+    if (graphicItem.ReferencedFrameOfReferenceUID) {
+      coords.ReferencedFrameOfReferenceSequence = graphicItem.ReferencedFrameOfReferenceUID;
+    } else if (graphicItem.ContentSequence) {
+      const {
+        ReferencedFrameOfReferenceSequence,
+      } = graphicItem.ContentSequence;
+      coords.ReferencedFrameOfReferenceSequence = ReferencedFrameOfReferenceSequence;
+    }
+  }
+
+  return coords;
+};
+
+export default getCoordsFromSCOORDOrSCOORD3D;

platform/core/src/DICOMSR/SCOORD3D/utils/getLabelFromMeasuredValueSequence.js

@@ -0,0 +1,19 @@
+const getLabelFromMeasuredValueSequence = (
+  ConceptNameCodeSequence,
+  MeasuredValueSequence
+) => {
+  const { CodeMeaning } = ConceptNameCodeSequence;
+  const { NumericValue, MeasurementUnitsCodeSequence } = MeasuredValueSequence;
+  const { CodeValue } = MeasurementUnitsCodeSequence;
+
+  const formatedNumericValue = NumericValue
+    ? Number(NumericValue).toFixed(1)
+    : '';
+
+  return {
+    label: CodeMeaning,
+    value: `${formatedNumericValue} ${CodeValue}`,
+  }; // E.g. Long Axis: 31.0 mm
+};
+
+export default getLabelFromMeasuredValueSequence;

platform/core/src/DICOMSR/SCOORD3D/utils/getMeasurements.js

@@ -0,0 +1,47 @@
+import { CodeNameCodeSequenceValues } from '../enums';
+import getSequenceAsArray from './getSequenceAsArray';
+import getMergedContentSequencesByTrackingUniqueIdentifiers from './getMergedContentSequencesByTrackingUniqueIdentifiers';
+import processMeasurement from './processMeasurement';
+
+const getMeasurements = (
+  ImagingMeasurementReportContentSequence,
+  displaySet
+) => {
+  const ImagingMeasurements = ImagingMeasurementReportContentSequence.find(
+    item =>
+      item.ConceptNameCodeSequence.CodeValue ===
+      CodeNameCodeSequenceValues.ImagingMeasurements
+  );
+
+  const MeasurementGroups = getSequenceAsArray(
+    ImagingMeasurements.ContentSequence
+  ).filter(
+    item =>
+      item.ConceptNameCodeSequence.CodeValue ===
+      CodeNameCodeSequenceValues.MeasurementGroup
+  );
+
+  const mergedContentSequencesByTrackingUniqueIdentifiers = getMergedContentSequencesByTrackingUniqueIdentifiers(
+    MeasurementGroups
+  );
+
+  let measurements = [];
+
+  Object.keys(mergedContentSequencesByTrackingUniqueIdentifiers).forEach(
+    trackingUniqueIdentifier => {
+      const mergedContentSequence =
+        mergedContentSequencesByTrackingUniqueIdentifiers[
+          trackingUniqueIdentifier
+        ];
+
+      const measurement = processMeasurement(mergedContentSequence, displaySet);
+      if (measurement) {
+        measurements.push(measurement);
+      }
+    }
+  );
+
+  return measurements;
+};
+
+export default getMeasurements;

platform/core/src/DICOMSR/SCOORD3D/utils/getMergedContentSequencesByTrackingUniqueIdentifiers.js

@@ -0,0 +1,54 @@
+import getSequenceAsArray from './getSequenceAsArray';
+import { CodeNameCodeSequenceValues } from '../enums';
+
+const getMergedContentSequencesByTrackingUniqueIdentifiers = MeasurementGroups => {
+  const mergedContentSequencesByTrackingUniqueIdentifiers = {};
+
+  MeasurementGroups.forEach(MeasurementGroup => {
+    const ContentSequence = getSequenceAsArray(
+      MeasurementGroup.ContentSequence
+    );
+
+    const TrackingUniqueIdentifierItem = ContentSequence.find(
+      item =>
+        item.ConceptNameCodeSequence.CodeValue ===
+        CodeNameCodeSequenceValues.TrackingUniqueIdentifier
+    );
+
+    if (!TrackingUniqueIdentifierItem) {
+      console.warn(
+        'No Tracking Unique Identifier, skipping ambiguous measurement.'
+      );
+    }
+
+    const trackingUniqueIdentifier = TrackingUniqueIdentifierItem.UID;
+
+    if (
+      mergedContentSequencesByTrackingUniqueIdentifiers[
+        trackingUniqueIdentifier
+      ] === undefined
+    ) {
+      // Add the full ContentSequence
+      mergedContentSequencesByTrackingUniqueIdentifiers[
+        trackingUniqueIdentifier
+      ] = [...ContentSequence];
+    } else {
+      // Add the ContentSequence minus the tracking identifier, as we have this
+      // Information in the merged ContentSequence anyway.
+      ContentSequence.forEach(item => {
+        if (
+          item.ConceptNameCodeSequence.CodeValue !==
+          CodeNameCodeSequenceValues.TrackingUniqueIdentifier
+        ) {
+          mergedContentSequencesByTrackingUniqueIdentifiers[
+            trackingUniqueIdentifier
+          ].push(item);
+        }
+      });
+    }
+  });
+
+  return mergedContentSequencesByTrackingUniqueIdentifiers;
+};
+
+export default getMergedContentSequencesByTrackingUniqueIdentifiers;

platform/core/src/DICOMSR/SCOORD3D/utils/getReferencedImagesList.js

@@ -0,0 +1,43 @@
+import getSequenceAsArray from './getSequenceAsArray';
+import { CodeNameCodeSequenceValues } from '../enums';
+
+const getReferencedImagesList = ImagingMeasurementReportContentSequence => {
+  const referencedImages = [];
+
+  const ImageLibrary = ImagingMeasurementReportContentSequence.find(
+    item =>
+      item.ConceptNameCodeSequence.CodeValue ===
+      CodeNameCodeSequenceValues.ImageLibrary
+  );
+
+  if (!ImageLibrary.ContentSequence) {
+    return referencedImages;
+  }
+
+  const ImageLibraryGroup = getSequenceAsArray(
+    ImageLibrary.ContentSequence
+  ).find(
+    item =>
+      item.ConceptNameCodeSequence.CodeValue ===
+      CodeNameCodeSequenceValues.ImageLibraryGroup
+  );
+
+  getSequenceAsArray(ImageLibraryGroup.ContentSequence).forEach(item => {
+    const { ReferencedSOPSequence } = item;
+    if (ReferencedSOPSequence) {
+      const {
+        ReferencedSOPClassUID,
+        ReferencedSOPInstanceUID,
+      } = ReferencedSOPSequence;
+
+      referencedImages.push({
+        ReferencedSOPClassUID,
+        ReferencedSOPInstanceUID,
+      });
+    }
+  });
+
+  return referencedImages;
+};
+
+export default getReferencedImagesList;

platform/core/src/DICOMSR/SCOORD3D/utils/getRenderableData.js

@@ -0,0 +1,192 @@
+import csMath from 'cornerstone-math';
+import SCOORD_TYPES from '../constants/scoordTypes';
+import { inv } from 'mathjs';
+
+const getRenderableData = (
+  GraphicType,
+  GraphicData,
+  ValueType,
+  imageMetadata
+) => {
+  let renderableData;
+
+  const orientation = imageMetadata.ImageOrientationPatient;
+  const position = imageMetadata.ImagePositionPatient;
+  const pixelSpacing = imageMetadata.PixelSpacing;
+  const sliceSpacing = imageMetadata.SliceThickness
+    ? imageMetadata.SliceThickness
+    : 1;
+  //  https://nipy.org/nibabel/dicom/dicom_orientation.html
+  const M = [
+    [
+      orientation[0] * pixelSpacing[0],
+      orientation[3] * pixelSpacing[1],
+      sliceSpacing,
+      position[0],
+    ],
+    [
+      orientation[1] * pixelSpacing[0],
+      orientation[4] * pixelSpacing[1],
+      sliceSpacing,
+      position[1],
+    ],
+    [
+      orientation[2] * pixelSpacing[0],
+      orientation[5] * pixelSpacing[1],
+      sliceSpacing,
+      position[2],
+    ],
+    [0, 0, 0, 1],
+  ];
+
+  // we need to go from 3D to pixel (cornerstone2D works in pixel coordinates),
+  // we take the inverse.
+  const M1 = inv(M);
+
+  const worldToIJK = (point, M1) => {
+    const worldPoint = {
+      x:
+        M1[0][0] * point.x + M1[0][1] * point.y + M1[0][2] * point.z + M1[0][3],
+      y:
+        M1[1][0] * point.x + M1[1][1] * point.y + M1[1][2] * point.z + M1[1][3],
+      z:
+        M1[2][0] * point.x + M1[2][1] * point.y + M1[2][2] * point.z + M1[2][3],
+    };
+    return worldPoint;
+  };
+
+  // https://dicom.innolitics.com/ciods/procedure-log/sr-document-content/00700023
+  switch (GraphicType) {
+    case SCOORD_TYPES.POINT:
+      renderableData = [];
+
+      if (ValueType === 'SCOORD3D') {
+        for (let i = 0; i < GraphicData.length; i += 3) {
+          const point = {
+            x: GraphicData[i],
+            y: GraphicData[i + 1],
+            z: GraphicData[i + 2],
+          };
+
+          renderableData.push(worldToIJK(point, M1));
+        }
+      } else {
+        for (let i = 0; i < GraphicData.length; i += 2) {
+          renderableData.push({ x: GraphicData[i], y: GraphicData[i + 1] });
+        }
+      }
+
+      break;
+    case SCOORD_TYPES.MULTIPOINT:
+      renderableData = [];
+
+      if (ValueType === 'SCOORD3D') {
+        for (let i = 0; i < GraphicData.length; i += 3) {
+          const point = {
+            x: GraphicData[i],
+            y: GraphicData[i + 1],
+            z: GraphicData[i + 2],
+          };
+
+          renderableData.push(worldToIJK(point, M1));
+        }
+      } else {
+        for (let i = 0; i < GraphicData.length; i += 2) {
+          renderableData.push({ x: GraphicData[i], y: GraphicData[i + 1] });
+        }
+      }
+
+      break;
+    case SCOORD_TYPES.POLYLINE:
+      renderableData = [];
+
+      if (ValueType === 'SCOORD3D') {
+        for (let i = 0; i < GraphicData.length; i += 3) {
+          const point = {
+            x: GraphicData[i],
+            y: GraphicData[i + 1],
+            z: GraphicData[i + 2],
+          };
+
+          renderableData.push(worldToIJK(point, M1));
+        }
+      } else {
+        for (let i = 0; i < GraphicData.length; i += 2) {
+          renderableData.push({ x: GraphicData[i], y: GraphicData[i + 1] });
+        }
+      }
+
+      break;
+    case SCOORD_TYPES.POLYGON:
+      // this is only scoord3d
+      renderableData = [];
+      for (let i = 0; i < GraphicData.length; i += 3) {
+        const point = {
+          x: GraphicData[i],
+          y: GraphicData[i + 1],
+          z: GraphicData[i + 2],
+        };
+
+        renderableData.push(worldToIJK(point, M1));
+      }
+      break;
+    case SCOORD_TYPES.CIRCLE: {
+      // this is only scoord
+      const center = { x: GraphicData[0], y: GraphicData[1] };
+      const onPerimeter = { x: GraphicData[2], y: GraphicData[3] };
+
+      const radius = csMath.point.distance(center, onPerimeter);
+
+      renderableData = {
+        center,
+        radius,
+      };
+      break;
+    }
+    case SCOORD_TYPES.ELLIPSE: {
+      console.warn('ROTATED ELLIPSE NOT YET SUPPORTED!');
+      // To Do: scoord3d ellips, need data for testing
+      const majorAxis = [
+        { x: GraphicData[0], y: GraphicData[1] },
+        { x: GraphicData[2], y: GraphicData[3] },
+      ];
+      const minorAxis = [
+        { x: GraphicData[4], y: GraphicData[5] },
+        { x: GraphicData[6], y: GraphicData[7] },
+      ];
+
+      // Calculate two opposite corners of box defined by two axes.
+
+      const minorAxisLength = csMath.point.distance(minorAxis[0], minorAxis[1]);
+
+      const minorAxisDirection = {
+        x: (minorAxis[1].x - minorAxis[0].x) / minorAxisLength,
+        y: (minorAxis[1].y - minorAxis[0].y) / minorAxisLength,
+      };
+
+      const halfMinorAxisLength = minorAxisLength / 2;
+
+      // First end point of major axis + half minor axis vector
+      const corner1 = {
+        x: majorAxis[0].x + minorAxisDirection.x * halfMinorAxisLength,
+        y: majorAxis[0].y + minorAxisDirection.y * halfMinorAxisLength,
+      };
+
+      // Second end point of major axis - half of minor axis vector
+      const corner2 = {
+        x: majorAxis[1].x - minorAxisDirection.x * halfMinorAxisLength,
+        y: majorAxis[1].y - minorAxisDirection.y * halfMinorAxisLength,
+      };
+
+      renderableData = {
+        corner1,
+        corner2,
+      };
+      break;
+    }
+  }
+
+  return renderableData;
+};
+
+export default getRenderableData;

platform/core/src/DICOMSR/SCOORD3D/utils/getSequenceAsArray.js

@@ -0,0 +1,4 @@
+const getSequenceAsArray = sequence =>
+  Array.isArray(sequence) ? sequence : [sequence];
+
+export default getSequenceAsArray;

platform/core/src/DICOMSR/SCOORD3D/utils/isRehydratable.js

@@ -0,0 +1,48 @@
+import { adapters } from 'dcmjs';
+
+const cornerstoneAdapters = adapters.Cornerstone;
+
+/**
+ * Checks if the given `displaySet`can be rehydrated into the `MeasurementService`.
+ *
+ * @param {object} displaySet The SR `displaySet` to check.
+ * @param {object[]} mappings The CornerstoneTools 4 mappings to the `MeasurementService`.
+ * @returns {boolean} True if the SR can be rehydrated into the `MeasurementService`.
+ */
+export default function isRehydratable(displaySet, mappings) {
+  if (!mappings || !mappings.length) {
+    return false;
+  }
+
+  const mappingDefinitions = mappings.map(m => m.definition);
+  const { measurements } = displaySet;
+
+  const adapterKeys = Object.keys(cornerstoneAdapters).filter(
+    adapterKey =>
+      typeof cornerstoneAdapters[adapterKey]
+        .isValidCornerstoneTrackingIdentifier === 'function'
+  );
+
+  const adapters = [];
+
+  adapterKeys.forEach(key => {
+    if (mappingDefinitions.includes(key)) {
+      // Must have both a dcmjs adapter and a MeasurementService
+      // Definition in order to be a candidate for import.
+      adapters.push(cornerstoneAdapters[key]);
+    }
+  });
+
+  for (let i = 0; i < measurements.length; i++) {
+    const TrackingIdentifier = measurements[i].TrackingIdentifier;
+    const hydratable = adapters.some(adapter =>
+      adapter.isValidCornerstoneTrackingIdentifier(TrackingIdentifier)
+    );
+
+    if (hydratable) {
+      return true;
+    }
+  }
+
+  return false;
+}

platform/core/src/DICOMSR/SCOORD3D/utils/processMeasurement.js

@@ -0,0 +1,16 @@
+import processTID1410Measurement from './processTID1410Measurement';
+import processNonGeometricallyDefinedMeasurement from './processNonGeometricallyDefinedMeasurement';
+
+const processMeasurement = (mergedContentSequence, displaySet) => {
+  if (
+    mergedContentSequence.some(
+      group => group.ValueType === 'SCOORD' || group.ValueType === 'SCOORD3D'
+    )
+  ) {
+    return processTID1410Measurement(mergedContentSequence, displaySet);
+  }
+
+  return processNonGeometricallyDefinedMeasurement(mergedContentSequence);
+};
+
+export default processMeasurement;

platform/core/src/DICOMSR/SCOORD3D/utils/processNonGeometricallyDefinedMeasurement.js

@@ -0,0 +1,117 @@
+import getLabelFromMeasuredValueSequence from './getLabelFromMeasuredValueSequence';
+import getCoordsFromSCOORDOrSCOORD3D from './getCoordsFromSCOORDOrSCOORD3D';
+import { CodeNameCodeSequenceValues, CodingSchemeDesignators } from '../enums';
+
+const CORNERSTONE_FREETEXT_CODE_VALUE = 'CORNERSTONEFREETEXT';
+
+const processNonGeometricallyDefinedMeasurement = mergedContentSequence => {
+  const NUMContentItems = mergedContentSequence.filter(
+    group => group.ValueType === 'NUM'
+  );
+
+  const UIDREFContentItem = mergedContentSequence.find(
+    group => group.ValueType === 'UIDREF'
+  );
+
+  const TrackingIdentifierContentItem = mergedContentSequence.find(
+    item =>
+      item.ConceptNameCodeSequence.CodeValue ===
+      CodeNameCodeSequenceValues.TrackingIdentifier
+  );
+
+  const Finding = mergedContentSequence.find(
+    item =>
+      item.ConceptNameCodeSequence.CodeValue ===
+      CodeNameCodeSequenceValues.Finding
+  );
+
+  const FindingSites = mergedContentSequence.filter(
+    item =>
+      item.ConceptNameCodeSequence.CodingSchemeDesignator ===
+        CodingSchemeDesignators.SRT &&
+      item.ConceptNameCodeSequence.CodeValue ===
+        CodeNameCodeSequenceValues.FindingSite
+  );
+
+  const measurement = {
+    loaded: false,
+    labels: [],
+    coords: [],
+    TrackingUniqueIdentifier: UIDREFContentItem.UID,
+    TrackingIdentifier: TrackingIdentifierContentItem.TextValue,
+  };
+
+  if (
+    Finding &&
+    Finding.ConceptCodeSequence.CodingSchemeDesignator ===
+      CodingSchemeDesignators.cornerstoneTools4 &&
+    Finding.ConceptCodeSequence.CodeValue ===
+      CodeNameCodeSequenceValues.CornerstoneFreeText
+  ) {
+    measurement.labels.push({
+      label: CORNERSTONE_FREETEXT_CODE_VALUE,
+      value: Finding.ConceptCodeSequence.CodeMeaning,
+    });
+  }
+
+  // TODO -> Eventually hopefully support SNOMED or some proper code library, just free text for now.
+  if (FindingSites.length) {
+    const cornerstoneFreeTextFindingSite = FindingSites.find(
+      FindingSite =>
+        FindingSite.ConceptCodeSequence.CodingSchemeDesignator ===
+          CodingSchemeDesignators.cornerstoneTools4 &&
+        FindingSite.ConceptCodeSequence.CodeValue ===
+          CodeNameCodeSequenceValues.CornerstoneFreeText
+    );
+
+    if (cornerstoneFreeTextFindingSite) {
+      measurement.labels.push({
+        label: CORNERSTONE_FREETEXT_CODE_VALUE,
+        value: cornerstoneFreeTextFindingSite.ConceptCodeSequence.CodeMeaning,
+      });
+    }
+  }
+
+  NUMContentItems.forEach(item => {
+    const {
+      ConceptNameCodeSequence,
+      ContentSequence,
+      MeasuredValueSequence,
+    } = item;
+
+    if (!ContentSequence) {
+      console.warn(`Graphic ${ContentSequence} missing, skipping annotation.`);
+
+      return;
+    }
+
+    const { ValueType } = ContentSequence;
+
+    if (!ValueType === 'SCOORD' && !ValueType === 'SCOORD3D') {
+      console.warn(
+        `Graphic ${ValueType} not currently supported, skipping annotation.`
+      );
+
+      return;
+    }
+
+    const coords = getCoordsFromSCOORDOrSCOORD3D(ContentSequence);
+
+    if (coords) {
+      measurement.coords.push(coords);
+    }
+
+    if (MeasuredValueSequence) {
+      measurement.labels.push(
+        getLabelFromMeasuredValueSequence(
+          ConceptNameCodeSequence,
+          MeasuredValueSequence
+        )
+      );
+    }
+  });
+
+  return measurement;
+};
+
+export default processNonGeometricallyDefinedMeasurement;

platform/core/src/DICOMSR/SCOORD3D/utils/processTID1410Measurement.js

@@ -0,0 +1,88 @@
+import getLabelFromMeasuredValueSequence from './getLabelFromMeasuredValueSequence';
+import getCoordsFromSCOORDOrSCOORD3D from './getCoordsFromSCOORDOrSCOORD3D';
+import { RELATIONSHIP_TYPE, CodeNameCodeSequenceValues } from '../enums';
+
+/**
+ * TID 1410 Planar ROI Measurements and Qualitative Evaluations.
+ *
+ * @param {*} mergedContentSequence
+ * @returns
+ */
+const processTID1410Measurement = (mergedContentSequence, displaySet) => {
+  // Need to deal with TID 1410 style measurements, which will have a SCOORD or SCOORD3D at the top level,
+  // And non-geometric representations where each NUM has "INFERRED FROM" SCOORD/SCOORD3D
+
+  const graphicItem = mergedContentSequence.find(
+    group => group.ValueType === 'SCOORD' || group.ValueType === 'SCOORD3D'
+  );
+
+  if (!graphicItem) {
+    console.warn(
+      `graphic ValueType ${graphicItem.ValueType} not currently supported, skipping annotation.`
+    );
+    return;
+  }
+
+  const UIDREFContentItem = mergedContentSequence.find(
+    group => group.ValueType === 'UIDREF'
+  );
+
+  const TrackingIdentifierContentItem = mergedContentSequence.find(
+    item =>
+      item.ConceptNameCodeSequence.CodeValue ===
+      CodeNameCodeSequenceValues.TrackingIdentifier
+  );
+
+  const NUMContentItems = mergedContentSequence.filter(
+    group => group.ValueType === 'NUM'
+  );
+
+  const measurement = {
+    loaded: false,
+    labels: [],
+    coords: [getCoordsFromSCOORDOrSCOORD3D(graphicItem, displaySet)],
+    TrackingUniqueIdentifier: UIDREFContentItem.UID,
+    TrackingIdentifier: TrackingIdentifierContentItem.TextValue,
+  };
+
+  NUMContentItems.forEach(item => {
+    const {
+      ConceptNameCodeSequence,
+      ContentSequence,
+      MeasuredValueSequence,
+    } = item;
+
+    if (
+      item.ConceptNameCodeSequence.CodeValue ===
+      CodeNameCodeSequenceValues.Score
+    ) {
+      ContentSequence.forEach(item => {
+        if (
+          [
+            RELATIONSHIP_TYPE.SELECTED_FROM,
+            RELATIONSHIP_TYPE.INFERRED_FROM,
+          ].includes(item.RelationshipType)
+        ) {
+          if (item.ReferencedSOPSequence) {
+            measurement.coords.forEach(coord => {
+              coord.ReferencedSOPSequence = item.ReferencedSOPSequence;
+            });
+          }
+        }
+      });
+    }
+
+    if (MeasuredValueSequence) {
+      measurement.labels.push(
+        getLabelFromMeasuredValueSequence(
+          ConceptNameCodeSequence,
+          MeasuredValueSequence
+        )
+      );
+    }
+  });
+
+  return measurement;
+};
+
+export default processTID1410Measurement;

platform/core/src/DICOMSR/dataExchange.js

@@ -19,9 +19,10 @@ import findMostRecentStructuredReport from './utils/findMostRecentStructuredRepo
  * Function to be registered into MeasurementAPI to retrieve measurements from DICOM Structured Reports
  *
  * @param {serverType} server
+ * @param {object} external
  * @returns {Promise} Should resolve with OHIF measurementData object
  */
-const retrieveMeasurements = server => {
+const retrieveMeasurements = (server, external = {}) => {
   log.info('[DICOMSR] retrieveMeasurements');
 
   if (!server || server.type !== 'dicomWeb') {
@@ -36,7 +37,7 @@ const retrieveMeasurements = server => {
 
   if (!latestSeries) return Promise.resolve({});
 
-  return retrieveMeasurementFromSR(latestSeries, studies, serverUrl);
+  return retrieveMeasurementFromSR(latestSeries, studies, serverUrl, external);
 };
 
 /**

platform/core/src/DICOMSR/handleStructuredReport.js

@@ -17,9 +17,15 @@ const TRANSFER_SYNTAX_UID = '1.2.840.10008.1.2.1';
  * @param {Array} series - List of all series metaData loaded
  * @param {Array} studies - List of all studies metaData loaded
  * @param {string} serverUrl - Server URL to be used on request
+ * @param {object} external
  * @returns {Object} MeasurementData
  */
-const retrieveMeasurementFromSR = async (series, studies, serverUrl) => {
+const retrieveMeasurementFromSR = async (
+  series,
+  studies,
+  serverUrl,
+  external
+) => {
   const config = {
     url: serverUrl,
     headers: DICOMWeb.getAuthorizationHeader(),
@@ -40,7 +46,8 @@ const retrieveMeasurementFromSR = async (series, studies, serverUrl) => {
   const displaySets = getAllDisplaySets(studies);
   const measurementsData = parseDicomStructuredReport(
     part10SRArrayBuffer,
-    displaySets
+    displaySets,
+    external
   );
 
   return measurementsData;

platform/core/src/DICOMSR/parseDicomStructuredReport.js

@@ -1,7 +1,11 @@
 import dcmjs from 'dcmjs';
+import classes from '../classes';
+import parseSCOORD3D from './SCOORD3D/parseSCOORD3D';
 
 import findInstanceMetadataBySopInstanceUID from './utils/findInstanceMetadataBySopInstanceUid';
 
+const { LogManager } = classes;
+
 /**
  * Function to parse the part10 array buffer that comes from a DICOM Structured report into measurementData
  * measurementData format is a viewer specific format to be stored into the redux and consumed by other components
@@ -9,20 +13,40 @@ import findInstanceMetadataBySopInstanceUID from './utils/findInstanceMetadataBy
  *
  * @param {ArrayBuffer} part10SRArrayBuffer
  * @param {Array} displaySets
+ * @param {object} external
  * @returns
  */
-const parseDicomStructuredReport = (part10SRArrayBuffer, displaySets) => {
+const parseDicomStructuredReport = (
-  // Get the dicom data as an Object
+  part10SRArrayBuffer,
+  displaySets,
+  external
+) => {
+  if (external && external.servicesManager) {
+    parseSCOORD3D({ servicesManager: external.servicesManager, displaySets });
+  }
 
+  // Get the dicom data as an Object
   const dicomData = dcmjs.data.DicomMessage.readFile(part10SRArrayBuffer);
   const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
     dicomData.dict
   );
 
   const { MeasurementReport } = dcmjs.adapters.Cornerstone;
-  const storedMeasurementByToolType = MeasurementReport.generateToolState(
+
-    dataset
+  let storedMeasurementByToolType;
-  );
+  try {
+    storedMeasurementByToolType = MeasurementReport.generateToolState(dataset);
+  } catch (error) {
+    const seriesDescription = dataset.SeriesDescription || '';
+    LogManager.publish(LogManager.EVENTS.OnLog, {
+      title: `Failed to parse ${seriesDescription} measurement report`,
+      type: 'warning',
+      message: error.message || '',
+      notify: true,
+    });
+    return;
+  }
+
   const measurementData = {};
   let measurementNumber = 0;
 

platform/core/src/DICOMSR/utils/findMostRecentStructuredReport.js

@@ -41,6 +41,7 @@ const isStructuredReportSeries = series => {
   const supportedSopClassUIDs = [
     '1.2.840.10008.5.1.4.1.1.88.22',
     '1.2.840.10008.5.1.4.1.1.11.1',
+    '1.2.840.10008.5.1.4.1.1.88.34', // COMPREHENSIVE_3D_SR
   ];
 
   const firstInstance = series.getFirstInstance();

platform/core/src/classes/LogManager.js

@@ -0,0 +1,18 @@
+import PubSub from './PubSub';
+
+/** Log Events */
+export const LogEvents = Object.freeze({
+  OnLog: 'onLog',
+});
+
+/**
+ * Log manager that implements pub/sub.
+ * This manager can be used to send logs across different packages
+ * using previously registered events.
+ */
+class LogManager extends PubSub {
+  EVENTS = LogEvents;
+}
+
+/** Singleton */
+export default new LogManager();

platform/core/src/classes/MetadataProvider.js

@@ -231,26 +231,26 @@ class MetadataProvider {
         let columnCosines;
 
         if (PixelSpacing) {
-          rowPixelSpacing = PixelSpacing[0];
+          rowPixelSpacing = validNumber(PixelSpacing[0]);
-          columnPixelSpacing = PixelSpacing[1];
+          columnPixelSpacing = validNumber(PixelSpacing[1]);
         }
 
         if (ImageOrientationPatient) {
-          rowCosines = ImageOrientationPatient.slice(0, 3);
+          rowCosines = validNumber(ImageOrientationPatient.slice(0, 3));
-          columnCosines = ImageOrientationPatient.slice(3, 6);
+          columnCosines = validNumber(ImageOrientationPatient.slice(3, 6));
         }
 
         metadata = {
           frameOfReferenceUID: instance.FrameOfReferenceUID,
           rows: instance.Rows,
           columns: instance.Columns,
-          imageOrientationPatient: ImageOrientationPatient,
+          imageOrientationPatient: validNumber(ImageOrientationPatient),
           rowCosines,
           columnCosines,
-          imagePositionPatient: instance.ImagePositionPatient,
+          imagePositionPatient: validNumber(instance.ImagePositionPatient),
-          sliceThickness: instance.SliceThickness,
+          sliceThickness: validNumber(instance.SliceThickness),
-          sliceLocation: instance.SliceLocation,
+          sliceLocation: validNumber(instance.SliceLocation),
-          pixelSpacing: PixelSpacing,
+          pixelSpacing: validNumber(PixelSpacing),
           rowPixelSpacing,
           columnPixelSpacing,
         };

platform/core/src/classes/PubSub.js

@@ -0,0 +1,75 @@
+const _subscriptions = Symbol('subscriptions');
+const _lastSubscriptionId = Symbol('lastSubscriptionId');
+
+/**
+ * Class to implement publish/subscribe pattern
+ *
+ * @class
+ * @classdesc Pub/sub mechanism
+ */
+export default class PubSub {
+  constructor() {
+    this[_subscriptions] = {};
+    this[_lastSubscriptionId] = 0;
+  }
+
+  /**
+   * Subscribe to event
+   *
+   * @param {string} eventName Event name
+   * @param {Function} callback Callback function
+   * @returns {void}
+   */
+  subscribe(eventName, callback) {
+    if (eventName === undefined) {
+      throw new Error('Event name is required');
+    }
+
+    if (typeof callback !== 'function') {
+      throw new Error('Callback must be a function');
+    }
+
+    if (!this[_subscriptions].hasOwnProperty(eventName)) {
+      this[_subscriptions][eventName] = {};
+    }
+
+    const subscriptionId = `sub${this[_lastSubscriptionId]++}`;
+    this[_subscriptions][eventName][subscriptionId] = callback;
+  }
+
+  /**
+   * Removes a subscription
+   *
+   * @param {string} eventName Event name
+   * @param {Function} [callback] Callback function
+   * @returns {void}
+   */
+  unsubscribe(eventName, callback) {
+    const callbacks = this[_subscriptions][eventName] || {};
+    for (let subscriptionId in callbacks) {
+      if (!callback) {
+        delete callbacks[subscriptionId];
+      } else if (callbacks[subscriptionId] === callback) {
+        delete callbacks[subscriptionId];
+      }
+    }
+  }
+
+  /**
+   * Publish event to all subscriptions
+   *
+   * @param {String} eventName Event name
+   * @param {any} [payload] Data that will be published
+   * @returns {void}
+   */
+  publish(eventName, ...payload) {
+    if (eventName === undefined) {
+      throw new Error('Event name is required');
+    }
+
+    const callbacks = this[_subscriptions][eventName] || {};
+    for (let subscriptionId in callbacks) {
+      callbacks[subscriptionId](...payload);
+    }
+  }
+}

platform/core/src/classes/StudyLoadingListener.js

@@ -1,16 +1,14 @@
 import cornerstone from 'cornerstone-core';
 import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader';
-import {
+import debounce from 'lodash.debounce';
-  clearStudyLoadingProgress,
+
-  setStudyLoadingProgress,
-} from '../redux/actions';
 import StackManager from '../utils/StackManager';
+import { StudyPrefetcher } from './StudyPrefetcher';
 
 class BaseLoadingListener {
   constructor(stack, options = {}) {
     this.id = BaseLoadingListener.getNewId();
     this.stack = stack;
-    this.startListening();
     this.statsItemsLimit = options.statsItemsLimit || 2;
     this.stats = {
       items: [],
@@ -60,6 +58,9 @@ class BaseLoadingListener {
   }
 
   _getProgressId() {
+    /**
+     * TODO: The id key should be configurable.
+     */
     const displaySetInstanceUID = this.stack.displaySetInstanceUID;
     return 'StackProgress:' + displaySetInstanceUID;
   }
@@ -96,11 +97,18 @@ class BaseLoadingListener {
 class DICOMFileLoadingListener extends BaseLoadingListener {
   constructor(stack, options) {
     super(stack, options);
+
+    this.imageLoadProgressEventHandler = this._imageLoadProgressEventHandler.bind(
+      this
+    );
+
     this._dataSetUrl = this._getDataSetUrl(stack);
     this._lastLoaded = 0;
 
     // Check how many instances has already been download (cached)
     this._checkCachedData();
+
+    this.startListening();
   }
 
   _checkCachedData() {
@@ -127,10 +135,6 @@ class DICOMFileLoadingListener extends BaseLoadingListener {
   startListening() {
     const imageLoadProgressEventName = this._getImageLoadProgressEventName();
 
-    this.imageLoadProgressEventHandler = this._imageLoadProgressEventHandle.bind(
-      this
-    );
-
     this.stopListening();
 
     cornerstone.events.addEventListener(
@@ -200,17 +204,57 @@ class DICOMFileLoadingListener extends BaseLoadingListener {
   }
 }
 
+const StudyLoadingListenerEvents = {
+  OnProgress: 'StudyLoadingListenerEvents.OnProgress',
+};
+
+function promiseState(promise, callback) {
+  // Symbols and RegExps are never content-equal
+  var uniqueValue = window['Symbol'] ? Symbol('unique') : /unique/;
+
+  function notifyPendingOrResolved(value) {
+    if (value === uniqueValue) {
+      return callback('pending');
+    } else {
+      return callback('fulfilled');
+    }
+  }
+
+  function notifyRejected(reason) {
+    return callback('rejected');
+  }
+
+  var race = [promise, Promise.resolve(uniqueValue)];
+  Promise.race(race).then(notifyPendingOrResolved, notifyRejected);
+}
+
 class StackLoadingListener extends BaseLoadingListener {
   constructor(stack, options = {}) {
     options.statsItemsLimit = 20;
+
     super(stack, options);
 
+    this.imageLoadedEventHandler = this._imageLoadedEventHandler.bind(this);
+    this.imageCachePromiseRemovedEventHandler = this._imageCachePromiseRemovedEventHandler.bind(
+      this
+    );
+
     this.imageDataMap = this._convertImageIdsArrayToMap(stack.imageIds);
     this.framesStatus = this._createArray(stack.imageIds.length, false);
     this.loadedCount = 0;
 
     // Check how many instances has already been download (cached)
-    this._checkCachedData();
+    this._debouncedSetProgressData = debounce((...args) => {
+      this._setProgressData(...args);
+
+      /** After checking cache, continue prefetch */
+      const studyPrefetcher = StudyPrefetcher.getInstance();
+      studyPrefetcher.prefetch(studyPrefetcher.getElement());
+    }, 300);
+    const debounced = true;
+    this._checkCachedData(debounced);
+
+    this.startListening();
   }
 
   _convertImageIdsArrayToMap(imageIds) {
@@ -238,18 +282,37 @@ class StackLoadingListener extends BaseLoadingListener {
     return array;
   }
 
-  _checkCachedData() {
+  /**
-    // const imageIds = this.stack.imageIds;
+   * Check if image id is cached in cornerstone.
-    // TODO: No way to check status of Promise.
+   *
-    /*for(let i = 0; i < imageIds.length; i++) {
+   * @param {string} imageId
-            const imageId = imageIds[i];
+   * @returns
+   */
+  isImageCached(imageId) {
+    const image = cornerstone.imageCache.imageCache[imageId];
+    return image && image.sizeInBytes;
+  }
 
-            const imagePromise = cornerstone.imageCache.getImageLoadObject(imageId).promise;
+  _checkCachedData(debounced = false) {
+    const imageIds = this.stack.imageIds;
 
-            if (imagePromise && (imagePromise.state() === 'resolved')) {
+    for (let i = 0; i < imageIds.length; i++) {
-                this._updateFrameStatus(imageId, true);
+      const imageId = imageIds[i];
-            }
+
-        }*/
+      const imageObject = cornerstone.imageCache.getImageLoadObject(imageId);
+
+      if (this.isImageCached(imageId)) {
+        this._updateFrameStatus(imageId, true, debounced);
+      }
+
+      if (imageObject && imageObject.promise) {
+        promiseState(imageObject.promise, state => {
+          if (state === 'fulfilled') {
+            this._updateFrameStatus(imageId, true, debounced);
+          }
+        });
+      }
+    }
   }
 
   _getImageLoadedEventName() {
@@ -272,11 +335,6 @@ class StackLoadingListener extends BaseLoadingListener {
     const imageLoadedEventName = this._getImageLoadedEventName();
     const imageCachePromiseRemovedEventName = this._getImageCachePromiseRemoveEventName();
 
-    this.imageLoadedEventHandler = this._imageLoadedEventHandler.bind(this);
-    this.imageCachePromiseRemovedEventHandler = this._imageCachePromiseRemovedEventHandler.bind(
-      this
-    );
-
     this.stopListening();
 
     cornerstone.events.addEventListener(
@@ -303,7 +361,7 @@ class StackLoadingListener extends BaseLoadingListener {
     );
   }
 
-  _updateFrameStatus(imageId, loaded) {
+  _updateFrameStatus(imageId, loaded, debounced) {
     const imageData = this.imageDataMap.get(imageId);
 
     if (!imageData || imageData.loaded === loaded) {
@@ -318,7 +376,7 @@ class StackLoadingListener extends BaseLoadingListener {
     imageData.loaded = loaded;
     this.framesStatus[imageData.index] = loaded;
     this.loadedCount += loaded ? 1 : -1;
-    this._updateProgress();
+    this._updateProgress(debounced);
   }
 
   _setProgressData(progressId, progressData) {
@@ -339,7 +397,7 @@ class StackLoadingListener extends BaseLoadingListener {
     );
   }
 
-  _updateProgress() {
+  _updateProgress(debounced) {
     const totalFramesCount = this.stack.imageIds.length;
     const loadedFramesCount = this.loadedCount;
     const loadingFramesCount = totalFramesCount - loadedFramesCount;
@@ -357,6 +415,11 @@ class StackLoadingListener extends BaseLoadingListener {
       framesStatus: this.framesStatus,
     };
 
+    if (debounced) {
+      this._debouncedSetProgressData(progressId, progressData);
+      return;
+    }
+
     this._setProgressData(progressId, progressData);
   }
 
@@ -371,11 +434,13 @@ class StackLoadingListener extends BaseLoadingListener {
     }
 
     progressBar += ']';
-    log.info(`${displaySetInstanceUID}: ${progressBar}`);
+    console.info(`${displaySetInstanceUID}: ${progressBar}`);
   }
 }
 
 class StudyLoadingListener {
+  static events = StudyLoadingListenerEvents;
+
   constructor(options) {
     this.listeners = {};
     this.options = options;
@@ -454,14 +519,36 @@ class StudyLoadingListener {
 
   _getSchema(stack) {
     const imageId = stack.imageIds[0];
+    if (!imageId) {
+      return;
+    }
     const colonIndex = imageId.indexOf(':');
     return imageId.substring(0, colonIndex);
   }
 
-  // Singleton
   static getInstance(options) {
+    /**
+     * TODO: Use a different alternative without the use of events.
+     */
+    const DEFAULT_OPTIONS = {
+      _setProgressData: (progressId, progressData) => {
+        const event = new CustomEvent(StudyLoadingListenerEvents.OnProgress, {
+          detail: { progressId, progressData },
+        });
+        document.dispatchEvent(event);
+      },
+      _clearProgressById: progressId => {
+        const event = new CustomEvent(StudyLoadingListenerEvents.OnProgress, {
+          detail: { progressId, percentComplete: 0 },
+        });
+        document.dispatchEvent(event);
+      },
+    };
+
     if (!StudyLoadingListener._instance) {
-      StudyLoadingListener._instance = new StudyLoadingListener(options);
+      StudyLoadingListener._instance = new StudyLoadingListener(
+        options || DEFAULT_OPTIONS
+      );
     }
 
     return StudyLoadingListener._instance;

platform/core/src/classes/StudyPrefetcher.js

@@ -1,14 +1,27 @@
-import log from '../log.js';
-import OHIFError from './OHIFError';
 import cornerstone from 'cornerstone-core';
-import cornerstoneTools from 'cornerstone-tools';
 import getImageId from '../utils/getImageId.js';
 
+const noop = () => {};
+
 export class StudyPrefetcher {
-  constructor(studies) {
+  options = {
+    order: 'closest',
+    displaySetCount: 1,
+    onImageCached: noop,
+    requestType: 'prefetch',
+    preventCache: false,
+    prefetchDisplaySetsTimeout: 300,
+    maxNumPrefetchRequests: 100,
+    includeActiveDisplaySet: false,
+  };
+
+  constructor(studies, options) {
     this.studies = studies || [];
-    this.prefetchDisplaySetsTimeout = 300;
+
-    this.lastActiveViewportElement = null;
+    if (options) {
+      this.options = { ...this.options, ...options };
+      this.options.requestType = 'prefetch';
+    }
 
     cornerstone.events.addEventListener(
       'cornerstoneimagecachefull.StudyPrefetcher',
@@ -16,6 +29,9 @@ export class StudyPrefetcher {
     );
   }
 
+  /**
+   * Remove previously set event listeners and stop prefetching.
+   */
   destroy() {
     this.stopPrefetching();
     cornerstone.events.removeEventListener(
@@ -24,95 +40,180 @@ export class StudyPrefetcher {
     );
   }
 
-  static getInstance() {
+  /**
+   * Get StudyPrefetcher singleton instance.
+   *
+   * @param {array} studies
+   * @param {object} options
+   * @returns
+   */
+  static getInstance(studies = [], options) {
     if (!StudyPrefetcher.instance) {
-      StudyPrefetcher.instance = new StudyPrefetcher([]);
+      StudyPrefetcher.instance = new StudyPrefetcher(studies, options);
+    }
+
+    if (options) {
+      this.options = { ...this.options, ...options };
+      this.options.requestType = 'prefetch';
     }
 
     return StudyPrefetcher.instance;
   }
 
+  /**
+   * OHIF study metadata instances.
+   *
+   * @param {array} studies
+   */
   setStudies(studies) {
     this.stopPrefetching();
     this.studies = studies;
   }
 
-  prefetch() {
+  /**
+   * Get previously prefetched element.
+   *
+   * @returns {HTMLElement} Previously prefetched element.
+   */
+  getElement() {
+    return this.element;
+  }
+
+  /**
+   * Prefetch related display sets based on cornerstone viewport element
+   * with previously set options.
+   *
+   * @param {*} element
+   * @param {string} displaySetInstanceUID the display set instance uid
+   * @returns
+   */
+  prefetch(element, displaySetInstanceUID) {
     if (!this.studies || !this.studies.length) {
       return;
     }
 
+    this.element = element;
+    try {
+      this.enabledElement = cornerstone.getEnabledElement(element);
+    } catch {
+      throw new Error('Failed to find the enabled element');
+    }
+
     this.stopPrefetching();
-    this.prefetchDisplaySets();
+    this.prefetchDisplaySets(displaySetInstanceUID);
   }
 
+  /**
+   * Stop prefetching images.
+   */
   stopPrefetching() {
-    cornerstoneTools.requestPoolManager.clearRequestStack('prefetch');
+    cornerstone.imageLoadPoolManager.clearRequestStack('prefetch');
   }
 
-  prefetchDisplaySetsAsync(timeout) {
+  /**
-    timeout = timeout || this.prefetchDisplaySetsTimeout;
+   * Prefetch display sets async.
-
+   *
+   * @param {HTMLElement} element cornerstone viewport element
+   * @param {number} timeout
+   */
+  prefetchDisplaySetsAsync(element, timeout) {
+    try {
+      this.enabledElement = cornerstone.getEnabledElement(element);
+    } catch {
+      throw new Error('Failed to find the enabled element');
+    }
+    timeout = timeout || this.options.prefetchDisplaySetsTimeout;
     clearTimeout(this.prefetchDisplaySetsHandler);
     this.prefetchDisplaySetsHandler = setTimeout(() => {
-      this.prefetchDisplaySets();
+      this.prefetchDisplaySets(element);
     }, timeout);
   }
 
-  prefetchDisplaySets() {
+  /**
-    // TODO: Allow passing in config
+   * Extract all image ids from all display sets to be fetched and
-    let config = {
+   * call method to add images to request pool manager.
-      order: 'closest',
+   *
-      displaySetCount: 1,
+   * @param {string} displaySetInstanceUID the display set instance uid
-    };
+   */
-
+  prefetchDisplaySets(displaySetInstanceUID) {
-    const displaySetsToPrefetch = this.getDisplaySetsToPrefetch(config);
+    const displaySetsToPrefetch = this.getDisplaySetsToPrefetch(
+      displaySetInstanceUID
+    );
     const imageIds = this.getImageIdsFromDisplaySets(displaySetsToPrefetch);
-
     this.prefetchImageIds(imageIds);
   }
 
+  /**
+   * Add image ids to request pool manager.
+   *
+   * @param {array} imageIds
+   */
   prefetchImageIds(imageIds) {
     const nonCachedImageIds = this.filterCachedImageIds(imageIds);
-    const requestPoolManager = cornerstoneTools.requestPoolManager;
+    const imageLoadPoolManager = cornerstone.imageLoadPoolManager;
-    const requestType = 'prefetch';
+
-    const preventCache = false;
+    imageLoadPoolManager.maxNumRequests = {
-    const noop = () => {};
+      ...imageLoadPoolManager.maxNumRequests,
+      prefetch: this.options.maxNumPrefetchRequests,
+    };
+
+    let requestFn;
+    if (this.options.preventCache) {
+      requestFn = id => cornerstone.loadImage(id);
+    } else {
+      requestFn = id => cornerstone.loadAndCacheImage(id);
+    }
 
     nonCachedImageIds.forEach(imageId => {
-      requestPoolManager.addRequest(
+      imageLoadPoolManager.addRequest(
-        {},
+        requestFn.bind(this, imageId),
-        imageId,
+        this.options.requestType,
-        requestType,
+        {
-        preventCache,
+          imageId,
-        noop,
+        }
-        noop
       );
     });
-
-    requestPoolManager.startGrabbing();
   }
 
+  /**
+   * Get study by cornerstone image instance.
+   *
+   * @param {object} image
+   * @returns
+   */
   getStudy(image) {
     const StudyInstanceUID = cornerstone.metaData.get(
       'StudyInstanceUID',
       image.imageId
     );
-    return OHIF.viewer.Studies.find(
+    const studies = this.studies;
-      study => study.StudyInstanceUID === StudyInstanceUID
+    return studies.find(
+      study => study.getData().StudyInstanceUID === StudyInstanceUID
     );
   }
 
+  /**
+   * Get study series by cornerstone image instance.
+   *
+   * @param {object} study OHIF study instance
+   * @param {object} image cornerstone image instance object
+   * @returns
+   */
   getSeries(study, image) {
     const SeriesInstanceUID = cornerstone.metaData.get(
       'SeriesInstanceUID',
       image.imageId
     );
-    const studyMetadata = OHIF.viewerbase.getStudyMetadata(study);
+    return study.getSeriesByUID(SeriesInstanceUID);
-
-    return studyMetadata.getSeriesByUID(SeriesInstanceUID);
   }
 
+  /**
+   * Get sop instance by cornerstone image instance.
+   *
+   * @param {array} series
+   * @param {object} image
+   * @returns
+   */
   getInstance(series, image) {
     const instanceMetadata = cornerstone.metaData.get(
       'instance',
@@ -121,7 +222,33 @@ export class StudyPrefetcher {
     return series.getInstanceByUID(instanceMetadata.SOPInstanceUID);
   }
 
-  getActiveDisplaySet(displaySets, instance) {
+  /**
+   * Returns the display set with given uid.
+   *
+   * @param {string} displaySetInstanceUID the display set instance uid
+   * @returns {object} displaySet
+   */
+  getDisplaySetByUID(displaySetInstanceUID) {
+    let displaySet;
+    this.studies.forEach(study => {
+      const ds = study.displaySets.find(
+        ds => ds.displaySetInstanceUID === displaySetInstanceUID
+      );
+      if (ds) {
+        displaySet = ds;
+      }
+    });
+    return displaySet;
+  }
+
+  /**
+   * Get display set by SOPInstanceUID.
+   *
+   * @param {array} displaySets
+   * @param {object} instance
+   * @returns
+   */
+  getDisplaySetBySOPInstanceUID(displaySets, instance) {
     return displaySets.find(displaySet => {
       return displaySet.images.some(displaySetImage => {
         return displaySetImage.SOPInstanceUID === instance.SOPInstanceUID;
@@ -129,25 +256,48 @@ export class StudyPrefetcher {
     });
   }
 
-  getDisplaySetsToPrefetch(config) {
+  /**
+   * Get active viewport image based on cornerstone viewport element.
+   * @returns
+   */
+  getActiveViewportImage() {
+    if (!this.enabledElement) {
+      return;
+    }
+
+    return this.enabledElement.image;
+  }
+
+  /**
+   * Prefetch display sets based on cornerstone viewport element image.
+   *
+   * @param {string} displaySetInstanceUID the display set instance uid
+   * @returns {array} displaySets
+   */
+  getDisplaySetsToPrefetch(displaySetInstanceUID) {
     const image = this.getActiveViewportImage();
 
-    if (!image || !config || !config.displaySetCount) {
+    if (!image) {
       return [];
     }
 
-    /*const study = this.getStudy(image);
+    const study = this.getStudy(image);
     const series = this.getSeries(study, image);
-    const instance = this.getInstance(series, image);*/
+    const instance = this.getInstance(series, image);
     const displaySets = study.displaySets;
-    const activeDisplaySet = null; //this.getActiveDisplaySet(displaySets, instance);
+    const activeDisplaySet = displaySetInstanceUID
+      ? this.getDisplaySetByUID(displaySetInstanceUID)
+      : this.getDisplaySetBySOPInstanceUID(displaySets, instance);
+
     const prefetchMethodMap = {
       topdown: 'getFirstDisplaySets',
       downward: 'getNextDisplaySets',
+      upward: 'getPreviousDisplaySets',
       closest: 'getClosestDisplaySets',
+      all: 'getAllDisplaySets',
     };
 
-    const prefetchOrder = config.order;
+    const prefetchOrder = this.options.order;
     const methodName = prefetchMethodMap[prefetchOrder];
     const getDisplaySets = this[methodName];
 
@@ -163,18 +313,59 @@ export class StudyPrefetcher {
       this,
       displaySets,
       activeDisplaySet,
-      config.displaySetCount
+      this.options.displaySetCount,
+      this.options.includeActiveDisplaySet
     );
   }
 
-  getFirstDisplaySets(displaySets, activeDisplaySet, displaySetCount) {
+  /**
+   * Get all display sets.
+   *
+   * @param {array} displaySets
+   * @param {object} activeDisplaySet
+   * @param {number} displaySetCount
+   * @param {boolean} includeActiveDisplaySet
+   * @returns
+   */
+  getAllDisplaySets(
+    displaySets,
+    activeDisplaySet,
+    displaySetCount,
+    includeActiveDisplaySet
+  ) {
+    const length = displaySets.length;
+    const selectedDisplaySets = [];
+
+    for (let i = 0; i < length; i++) {
+      const displaySet = displaySets[i];
+      selectedDisplaySets.push(displaySet);
+    }
+
+    return selectedDisplaySets;
+  }
+
+  /**
+   * Get all display sets in order after the active display set.
+   *
+   * @param {array} displaySets
+   * @param {object} activeDisplaySet
+   * @param {number} displaySetCount
+   * @param {boolean} includeActiveDisplaySet
+   * @returns
+   */
+  getFirstDisplaySets(
+    displaySets,
+    activeDisplaySet,
+    displaySetCount,
+    includeActiveDisplaySet
+  ) {
     const length = displaySets.length;
     const selectedDisplaySets = [];
 
     for (let i = 0; i < length && displaySetCount; i++) {
       const displaySet = displaySets[i];
 
-      if (displaySet !== activeDisplaySet) {
+      if (includeActiveDisplaySet || displaySet !== activeDisplaySet) {
         selectedDisplaySets.push(displaySet);
         displaySetCount--;
       }
@@ -183,21 +374,78 @@ export class StudyPrefetcher {
     return selectedDisplaySets;
   }
 
-  getNextDisplaySets(displaySets, activeDisplaySet, displaySetCount) {
+  /**
+   * Get all display sets before the active display set.
+   *
+   * @param {array} displaySets
+   * @param {object} activeDisplaySet
+   * @param {number} displaySetCount
+   * @param {boolean} includeActiveDisplaySet
+   * @returns
+   */
+  getPreviousDisplaySets(
+    displaySets,
+    activeDisplaySet,
+    displaySetCount,
+    includeActiveDisplaySet
+  ) {
     const activeDisplaySetIndex = displaySets.indexOf(activeDisplaySet);
-    const begin = activeDisplaySetIndex + 1;
+    const end = includeActiveDisplaySet
-    const end = Math.min(begin + displaySetCount, displaySets.length);
+      ? activeDisplaySetIndex + 1
+      : activeDisplaySetIndex;
+    const previousDisplaySets = displaySets.slice(0, end);
+    return previousDisplaySets.reverse().slice(0, displaySetCount);
+  }
 
+  /**
+   * Get all display sets after the active display set.
+   *
+   * @param {array} displaySets
+   * @param {object} activeDisplaySet
+   * @param {number} displaySetCount
+   * @param {boolean} includeActiveDisplaySet
+   * @returns
+   */
+  getNextDisplaySets(
+    displaySets,
+    activeDisplaySet,
+    displaySetCount,
+    includeActiveDisplaySet
+  ) {
+    const activeDisplaySetIndex = displaySets.indexOf(activeDisplaySet);
+    const begin = includeActiveDisplaySet
+      ? activeDisplaySetIndex
+      : activeDisplaySetIndex + 1;
+    const end = Math.min(begin + displaySetCount, displaySets.length);
     return displaySets.slice(begin, end);
   }
 
-  getClosestDisplaySets(displaySets, activeDisplaySet, displaySetCount) {
+  /**
+   * Get all display set closest to the active display set.
+   *
+   * @param {array} displaySets
+   * @param {object} activeDisplaySet
+   * @param {number} displaySetCount
+   * @param {boolean} includeActiveDisplaySet
+   * @returns
+   */
+  getClosestDisplaySets(
+    displaySets,
+    activeDisplaySet,
+    displaySetCount,
+    includeActiveDisplaySet
+  ) {
     const activeDisplaySetIndex = displaySets.indexOf(activeDisplaySet);
     const length = displaySets.length;
     const selectedDisplaySets = [];
     let left = activeDisplaySetIndex - 1;
     let right = activeDisplaySetIndex + 1;
 
+    if (includeActiveDisplaySet) {
+      selectedDisplaySets.push(displaySets[activeDisplaySetIndex]);
+      displaySetCount--;
+    }
+
     while ((left >= 0 || right < length) && displaySetCount) {
       if (left >= 0) {
         selectedDisplaySets.push(displaySets[left]);
@@ -215,6 +463,12 @@ export class StudyPrefetcher {
     return selectedDisplaySets;
   }
 
+  /**
+   * Get all image ids from display sets.
+   *
+   * @param {array} displaySets
+   * @returns {array} image ids
+   */
   getImageIdsFromDisplaySets(displaySets) {
     let imageIds = [];
 
@@ -225,9 +479,19 @@ export class StudyPrefetcher {
     return imageIds;
   }
 
+  /**
+   * Get all image ids from a given display set.
+   *
+   * @param {array} displaySet
+   * @returns
+   */
   getImageIdsFromDisplaySet(displaySet) {
     const imageIds = [];
 
+    if (!displaySet.images || displaySet.images.length < 1) {
+      return [];
+    }
+
     // TODO: This duplicates work done by the stack manager
     displaySet.images.forEach(image => {
       const numFrames = image.numFrames;
@@ -245,15 +509,30 @@ export class StudyPrefetcher {
     return imageIds;
   }
 
+  /**
+   * Filter cached image ids from a set of image ids.
+   *
+   * @param {array} imageIds
+   * @returns {array} images not cached
+   */
   filterCachedImageIds(imageIds) {
     return imageIds.filter(imageId => !this.isImageCached(imageId));
   }
 
+  /**
+   * Check if image id is cached in cornerstone.
+   *
+   * @param {string} imageId
+   * @returns
+   */
   isImageCached(imageId) {
     const image = cornerstone.imageCache.imageCache[imageId];
     return image && image.sizeInBytes;
   }
 
+  /**
+   * Warns that cache is full and stops prefetching.
+   */
   cacheFullHandler = () => {
     log.warn('Cache full');
     this.stopPrefetching();

platform/core/src/classes/index.js

@@ -4,6 +4,8 @@ import CommandsManager from './CommandsManager.js';
 import { DICOMFileLoadingListener } from './StudyLoadingListener';
 import HotkeysManager from './HotkeysManager.js';
 import ImageSet from './ImageSet';
+import LogManager from './LogManager';
+import PubSub from './PubSub';
 import MetadataProvider from './MetadataProvider';
 import OHIFError from './OHIFError.js';
 import { OHIFStudyMetadataSource } from './OHIFStudyMetadataSource';
@@ -36,7 +38,9 @@ const classes = {
   MetadataProvider,
   CommandsManager,
   HotkeysManager,
+  LogManager,
   ImageSet,
+  PubSub,
   StudyPrefetcher,
   StudyLoadingListener,
   StackLoadingListener,

platform/core/src/classes/metadata/StudyMetadata.js

@@ -9,7 +9,10 @@ import { SeriesMetadata } from './SeriesMetadata';
 import { api } from 'dicomweb-client';
 // - createStacks
 import { isImage } from '../../utils/isImage';
-import { isDisplaySetReconstructable, isSpacingUniform } from '../../utils/isDisplaySetReconstructable';
+import {
+  isDisplaySetReconstructable,
+  isSpacingUniform,
+} from '../../utils/isDisplaySetReconstructable';
 import errorHandler from '../../errorHandler';
 import isLowPriorityModality from '../../utils/isLowPriorityModality';
 import getXHRRetryRequestHook from '../../utils/xhrRetryRequestHook';
@@ -159,41 +162,64 @@ class StudyMetadata extends Metadata {
     // series into another display set.
     const stackableInstances = [];
     series.forEachInstance(instance => {
+      let displaySet;
+
       // All imaging modalities must have a valid value for SOPClassUID (x00080016) or Rows (x00280010)
       if (
         !isImage(instance.getTagValue('SOPClassUID')) &&
         !instance.getTagValue('Rows')
       ) {
-        return;
+        // we set an empty display and we add a isModalitySupported variable to
-      }
+        // print a warning that the modality is not supported in the thumbnail.
-
+        const displaySet = new ImageSet([]);
-      let displaySet;
+        const seriesData = series.getData();
-
-      if (isMultiFrame(instance)) {
-        displaySet = makeDisplaySet(series, [instance]);
-
         displaySet.setAttributes({
-          sopClassUIDs,
+          displaySetInstanceUID: displaySet.uid,
-          isClip: true,
+          SeriesDate: seriesData.SeriesDate,
+          SeriesTime: seriesData.SeriesTime,
           SeriesInstanceUID: series.getSeriesInstanceUID(),
-          StudyInstanceUID: study.getStudyInstanceUID(), // Include the study instance UID for drag/drop purposes
+          SeriesNumber: instance.getTagValue('SeriesNumber'),
-          numImageFrames: instance.getTagValue('NumberOfFrames'), // Override the default value of instances.length
+          SeriesDescription: instance.getTagValue('SeriesDescription'),
-          InstanceNumber: instance.getTagValue('InstanceNumber'), // Include the instance number
+          numImageFrames: instance.getTagValue('NumberOfFrames'),
-          AcquisitionDatetime: instance.getTagValue('AcquisitionDateTime'), // Include the acquisition datetime
+          frameRate: instance.getTagValue('FrameTime'),
-        });
+          Modality: instance.getTagValue('Modality'),
-        displaySets.push(displaySet);
+          isMultiFrame: false,
-      } else if (isSingleImageModality(instance.Modality)) {
-        displaySet = makeDisplaySet(series, [instance]);
-        displaySet.setAttributes({
-          sopClassUIDs,
           StudyInstanceUID: study.getStudyInstanceUID(), // Include the study instance UID
-          SeriesInstanceUID: series.getSeriesInstanceUID(),
           InstanceNumber: instance.getTagValue('InstanceNumber'), // Include the instance number
           AcquisitionDatetime: instance.getTagValue('AcquisitionDateTime'), // Include the acquisition datetime
+          isReconstructable: false,
+          isModalitySupported: false,
+          metadata: instance.getData().metadata,
         });
+
         displaySets.push(displaySet);
       } else {
-        stackableInstances.push(instance);
+        if (isMultiFrame(instance)) {
+          displaySet = makeDisplaySet(series, [instance]);
+
+          displaySet.setAttributes({
+            sopClassUIDs,
+            isClip: true,
+            SeriesInstanceUID: series.getSeriesInstanceUID(),
+            StudyInstanceUID: study.getStudyInstanceUID(), // Include the study instance UID for drag/drop purposes
+            numImageFrames: instance.getTagValue('NumberOfFrames'), // Override the default value of instances.length
+            InstanceNumber: instance.getTagValue('InstanceNumber'), // Include the instance number
+            AcquisitionDatetime: instance.getTagValue('AcquisitionDateTime'), // Include the acquisition datetime
+          });
+          displaySets.push(displaySet);
+        } else if (isSingleImageModality(instance.Modality)) {
+          displaySet = makeDisplaySet(series, [instance]);
+          displaySet.setAttributes({
+            sopClassUIDs,
+            StudyInstanceUID: study.getStudyInstanceUID(), // Include the study instance UID
+            SeriesInstanceUID: series.getSeriesInstanceUID(),
+            InstanceNumber: instance.getTagValue('InstanceNumber'), // Include the instance number
+            AcquisitionDatetime: instance.getTagValue('AcquisitionDateTime'), // Include the acquisition datetime
+          });
+          displaySets.push(displaySet);
+        } else {
+          stackableInstances.push(instance);
+        }
       }
     });
 
@@ -227,7 +253,6 @@ class StudyMetadata extends Metadata {
     displaySets.map(displaySet => this._derivedDisplaySets.push(displaySet));
   }
 
-
   /**
    * Returns the source display set of the derivated display set.
    * @param {object} derivatedDisplaySet
@@ -242,40 +267,45 @@ class StudyMetadata extends Metadata {
     });
 
     const otherDisplaySets = allDisplaySets.filter(
-      ds => ds.displaySetInstanceUID !== derivatedDisplaySet.displaySetInstanceUID
+      ds =>
+        ds.displaySetInstanceUID !== derivatedDisplaySet.displaySetInstanceUID
     );
 
     const { metadata } = derivatedDisplaySet;
 
-    let referencedSeriesInstanceUIDs = _findReferencedSeriesInstanceUIDsFromSourceImageSequence
+    let referencedSeriesInstanceUIDs = _findReferencedSeriesInstanceUIDsFromSourceImageSequence(
-    (metadata, otherDisplaySets);
+      metadata,
+      otherDisplaySets
+    );
 
-    let noReferencedSeriesAvailable = !referencedSeriesInstanceUIDs ||
+    let noReferencedSeriesAvailable =
+      !referencedSeriesInstanceUIDs ||
       referencedSeriesInstanceUIDs.length === 0;
     if (noReferencedSeriesAvailable) {
-      referencedSeriesInstanceUIDs =
+      referencedSeriesInstanceUIDs = _findReferencedSeriesInstanceUIDsFromReferencedSeriesSequence(
-        _findReferencedSeriesInstanceUIDsFromReferencedSeriesSequence
+        metadata
-          (metadata);
+      );
     }
 
-    noReferencedSeriesAvailable = !referencedSeriesInstanceUIDs ||
+    noReferencedSeriesAvailable =
+      !referencedSeriesInstanceUIDs ||
       referencedSeriesInstanceUIDs.length === 0;
     if (noReferencedSeriesAvailable) {
-      referencedSeriesInstanceUIDs =
+      referencedSeriesInstanceUIDs = _findReferencedSeriesInstanceUIDsFromReferencedImageSequence(
-      _findReferencedSeriesInstanceUIDsFromReferencedImageSequence
+        metadata,
-          (metadata, otherDisplaySets);
+        otherDisplaySets
+      );
     }
 
-    const referencedSeriesAvailable = referencedSeriesInstanceUIDs &&
+    const referencedSeriesAvailable =
-      referencedSeriesInstanceUIDs.length !== 0;
+      referencedSeriesInstanceUIDs && referencedSeriesInstanceUIDs.length !== 0;
     if (referencedSeriesAvailable) {
       const referencedDisplaySet = otherDisplaySets.find(ds =>
         referencedSeriesInstanceUIDs.includes(ds.SeriesInstanceUID)
       );
-      ;
       return referencedDisplaySet;
     }
-  };
+  }
 
   /**
    * Returns a list of derived datasets in the study, filtered by the given filter.
@@ -303,7 +333,10 @@ class StudyMetadata extends Metadata {
     if (referencedSeriesInstanceUID) {
       filteredDerivedDisplaySets = filteredDerivedDisplaySets.filter(
         displaySet => {
-          return StudyMetadata.getReferencedDisplaySet(displaySet, [this]).SeriesInstanceUID === referencedSeriesInstanceUID;
+          return (
+            StudyMetadata.getReferencedDisplaySet(displaySet, [this])
+              .SeriesInstanceUID === referencedSeriesInstanceUID
+          );
         }
       );
     }
@@ -311,8 +344,7 @@ class StudyMetadata extends Metadata {
     if (referencedFrameOfReferenceUID) {
       filteredDerivedDisplaySets = filteredDerivedDisplaySets.filter(
         displaySet =>
-          displaySet.FrameOfReferenceUID ===
+          displaySet.FrameOfReferenceUID === referencedFrameOfReferenceUID
-          referencedFrameOfReferenceUID
       );
     }
 
@@ -497,6 +529,14 @@ class StudyMetadata extends Metadata {
       }
     }
 
+    if (
+      this._displaySets.some(
+        ds => ds.displaySetInstanceUID === displaySet.displaySetInstanceUID
+      )
+    ) {
+      return;
+    }
+
     this._displaySets.splice(insertIndex, 0, displaySet);
     this.displaySets = this._displaySets;
   }
@@ -861,8 +901,9 @@ const makeDisplaySet = (series, instances) => {
     imageSet.sortByImagePositionPatient();
 
     // check if the spacing is uniform and update isReconstructable
-    const datasetIs4D = displayReconstructableInfo.reconstructionIssues.find
+    const datasetIs4D = displayReconstructableInfo.reconstructionIssues.find(
-      (issue => issue === ReconstructionIssues.DATASET_4D);
+      issue => issue === ReconstructionIssues.DATASET_4D
+    );
     displaySpacingInfo = isSpacingUniform(imageSet.images, datasetIs4D);
     imageSet.isReconstructable = displaySpacingInfo.isUniform;
 
@@ -875,11 +916,15 @@ const makeDisplaySet = (series, instances) => {
 
   if (!imageSet.displayReconstructableInfo) {
     // It is not reconstrabale Save type of warning
-    imageSet.reconstructionIssues = displaySpacingInfo ?
+    imageSet.reconstructionIssues = displaySpacingInfo
-      displayReconstructableInfo.reconstructionIssues.concat(displaySpacingInfo.reconstructionIssues) :
+      ? displayReconstructableInfo.reconstructionIssues.concat(
-        displayReconstructableInfo.reconstructionIssues;
+          displaySpacingInfo.reconstructionIssues
+        )
+      : displayReconstructableInfo.reconstructionIssues;
   }
 
+  imageSet.isModalitySupported = true;
+
   return imageSet;
 };
 
@@ -957,38 +1002,36 @@ function _getDisplaySetFromSopClassModule(
 }
 
 /**
-  * Returns the referenced series instance UIDs by searching the information in the
+ * Returns the referenced series instance UIDs by searching the information in the
-  * ReferencedSeriesSequence.
+ * ReferencedSeriesSequence.
-  * @param {object} derivatedDisplaySet.metadata
+ * @param {object} derivatedDisplaySet.metadata
-  * @return {array[string]} referenced series instance UIDs.
+ * @return {array[string]} referenced series instance UIDs.
-  */
+ */
-function _findReferencedSeriesInstanceUIDsFromReferencedSeriesSequence (
+function _findReferencedSeriesInstanceUIDsFromReferencedSeriesSequence(
-  metadata,
+  metadata
 ) {
   if (!metadata.ReferencedSeriesSequence) {
     return;
   }
 
   let referencedSeriesInstanceUIDs;
-  const ReferencedSeriesSequence = _toArray(
+  const ReferencedSeriesSequence = _toArray(metadata.ReferencedSeriesSequence);
-    metadata.ReferencedSeriesSequence
-  );
 
   referencedSeriesInstanceUIDs = ReferencedSeriesSequence.map(
     ReferencedSeries => ReferencedSeries.SeriesInstanceUID
   );
 
   return referencedSeriesInstanceUIDs;
-};
+}
 
 /**
-  * Returns the referenced series instance UIDs by searching the information in the
+ * Returns the referenced series instance UIDs by searching the information in the
-  * ReferencedImageSequence.
+ * ReferencedImageSequence.
-  * @param {object} derivatedDisplaySet.metadata
+ * @param {object} derivatedDisplaySet.metadata
-  * @param {array[object]} displaysets
+ * @param {array[object]} displaysets
-  * @return {array[string]} referenced series instance UIDs.
+ * @return {array[string]} referenced series instance UIDs.
-  */
+ */
-function _findReferencedSeriesInstanceUIDsFromReferencedImageSequence (
+function _findReferencedSeriesInstanceUIDsFromReferencedImageSequence(
   metadata,
   displaySets
 ) {
@@ -1009,22 +1052,25 @@ function _findReferencedSeriesInstanceUIDsFromReferencedImageSequence (
       ReferencedSOPInstanceUID
     );
 
-    if (referencedSeriesInstanceUIDs && referencedSeriesInstanceUIDs.length !== 0) {
+    if (
+      referencedSeriesInstanceUIDs &&
+      referencedSeriesInstanceUIDs.length !== 0
+    ) {
       break;
     }
   }
 
   return referencedSeriesInstanceUIDs;
-};
+}
 
 /**
-  * Returns the referenced series instance UIDs by searching the information in the
+ * Returns the referenced series instance UIDs by searching the information in the
-  * SourceImageSequence.
+ * SourceImageSequence.
-  * @param {object} derivatedDisplaySet.metadata
+ * @param {object} derivatedDisplaySet.metadata
-  * @param {array[object]} displaysets
+ * @param {array[object]} displaysets
-  * @return {array[string]} referenced series instance UIDs.
+ * @return {array[string]} referenced series instance UIDs.
-  */
+ */
-function _findReferencedSeriesInstanceUIDsFromSourceImageSequence (
+function _findReferencedSeriesInstanceUIDsFromSourceImageSequence(
   metadata,
   displaySets
 ) {
@@ -1034,9 +1080,7 @@ function _findReferencedSeriesInstanceUIDsFromSourceImageSequence (
     SourceImageSequence = metadata.SourceImageSequence;
   } else {
     const { PerFrameFunctionalGroupsSequence } = metadata;
-    const firstFunctionalGroups = _toArray(
+    const firstFunctionalGroups = _toArray(PerFrameFunctionalGroupsSequence)[0];
-      PerFrameFunctionalGroupsSequence
-    )[0];
     if (firstFunctionalGroups) {
       const { DerivationImageSequence } = firstFunctionalGroups;
       SourceImageSequence = DerivationImageSequence;
@@ -1056,22 +1100,25 @@ function _findReferencedSeriesInstanceUIDsFromSourceImageSequence (
       displaySets,
       ReferencedSOPInstanceUID
     );
-    if (referencedSeriesInstanceUIDs && referencedSeriesInstanceUIDs.length !== 0) {
+    if (
+      referencedSeriesInstanceUIDs &&
+      referencedSeriesInstanceUIDs.length !== 0
+    ) {
       break;
     }
   }
 
   return referencedSeriesInstanceUIDs;
-};
+}
 
 /**
-  * Returns the referenced series instance UIDs by searching the information in the
+ * Returns the referenced series instance UIDs by searching the information in the
-  * SOPInstanceUID of the displaySets.
+ * SOPInstanceUID of the displaySets.
-  * @param {array[object]} displaysets
+ * @param {array[object]} displaysets
-  * @param {string} SOPInstanceUID
+ * @param {string} SOPInstanceUID
-  * @return {array[string]} referenced series instance UIDs.
+ * @return {array[string]} referenced series instance UIDs.
-  */
+ */
-function _findReferencedSeriesInstanceUIDsFromSOPInstanceUID (
+function _findReferencedSeriesInstanceUIDsFromSOPInstanceUID(
   displaySets,
   SOPInstanceUID
 ) {
@@ -1092,10 +1139,10 @@ function _findReferencedSeriesInstanceUIDsFromSOPInstanceUID (
       }
     }
   }
-};
+}
 
 function _toArray(arrayOrObject) {
   return Array.isArray(arrayOrObject) ? arrayOrObject : [arrayOrObject];
 }
 
-export {StudyMetadata};
+export { StudyMetadata };

platform/core/src/index.js

@@ -20,6 +20,7 @@ import ui from './ui';
 import user from './user.js';
 import errorHandler from './errorHandler.js';
 import utils, { hotkeys } from './utils/';
+import str2ab from './utils/str2ab';
 
 import {
   UINotificationService,
@@ -96,6 +97,8 @@ export {
   UIDialogService,
   MeasurementService,
   LoggerService,
+
+  str2ab,
 };
 
 export { OHIF };

platform/core/src/index.test.js

@@ -26,6 +26,7 @@ describe('Top level exports', () => {
       'cornerstone',
       'default', //
       'errorHandler',
+      'str2ab',
       'string',
       'ui',
       'user',

platform/core/src/measurements/classes/MeasurementApi.js

@@ -802,6 +802,10 @@ export default class MeasurementApi {
       collection.push(addedMeasurement);
     }
 
+    if (measurement.isReadOnly) {
+      addedMeasurement.isReadOnly = measurement.isReadOnly;
+    }
+
     if (!emptyItem) {
       // Reflect the entry in the tool group collection
       groupCollection.push({

platform/core/src/measurements/lib/getImageAttributes.js

@@ -1,9 +1,11 @@
 import cornerstone from 'cornerstone-core';
 
-export default function(element) {
+export default function(element, imageId) {
-  // Get the Cornerstone imageId
+  if (!imageId) {
-  const enabledElement = cornerstone.getEnabledElement(element);
+    // Get the Cornerstone imageId
-  const imageId = enabledElement.image.imageId;
+    const enabledElement = cornerstone.getEnabledElement(element);
+    imageId = enabledElement.image.imageId;
+  }
 
   // Get StudyInstanceUID & PatientID
   const {

platform/core/src/measurements/tools/dicomSRDisplayTool.js

@@ -0,0 +1,22 @@
+export const dicomSRDisplayTool = {
+  id: 'DICOMSRDisplayTool',
+  name: 'DICOMSRDisplayTool',
+  toolGroup: 'allTools',
+  cornerstoneToolType: 'DICOMSRDisplayTool',
+  options: {
+    measurementTable: {
+      displayFunction: data => {
+        return `(SR) ${data.lesionNamingNumber ||
+          data.measurementNumber ||
+          data.text ||
+          ''}`;
+      },
+    },
+    caseProgress: {
+      include: true,
+      evaluate: true,
+    },
+  },
+};
+
+export default dicomSRDisplayTool;

platform/core/src/measurements/tools/index.js

@@ -10,6 +10,7 @@ import { angle } from './angle';
 import { targetCR } from './targetCR';
 import { targetNE } from './targetNE';
 import { targetUN } from './targetUN';
+import dicomSRDisplayTool from './dicomSRDisplayTool';
 
 export {
   arrowAnnotate,
@@ -24,4 +25,5 @@ export {
   targetCR,
   targetNE,
   targetUN,
+  dicomSRDisplayTool,
 };

platform/core/src/redux/actions.js

@@ -78,17 +78,6 @@ export const setActiveViewportSpecificData = viewportSpecificData => ({
 /**
  * NOT-VIEWPORT
  */
-export const setStudyLoadingProgress = (progressId, progressData) => ({
-  type: 'SET_STUDY_LOADING_PROGRESS',
-  progressId,
-  progressData,
-});
-
-export const clearStudyLoadingProgress = progressId => ({
-  type: 'CLEAR_STUDY_LOADING_PROGRESS',
-  progressId,
-});
-
 export const setUserPreferences = state => ({
   type: SET_USER_PREFERENCES,
   state,
@@ -134,8 +123,6 @@ const actions = {
   /**
    * NOT-VIEWPORT
    */
-  setStudyLoadingProgress,
-  clearStudyLoadingProgress,
   setUserPreferences,
   setExtensionData,
   setTimepoints,

platform/core/src/redux/actions.test.js

@@ -11,8 +11,6 @@ describe('actions', () => {
       'setLayout',
       'clearViewportSpecificData',
       'setActiveViewportSpecificData',
-      'setStudyLoadingProgress',
-      'clearStudyLoadingProgress',
       'setUserPreferences',
       'setExtensionData',
       'setTimepoints',

platform/core/src/redux/reducers/index.js

@@ -1,5 +1,4 @@
 import extensions from './extensions';
-import loading from './loading';
 import preferences from './preferences';
 import servers from './servers';
 import studies from './studies';
@@ -8,7 +7,6 @@ import viewports from './viewports';
 
 const reducers = {
   extensions,
-  loading,
   preferences,
   servers,
   studies,

platform/core/src/redux/reducers/loading.js

@@ -1,33 +0,0 @@
-import cloneDeep from 'lodash.clonedeep';
-
-const defaultState = {
-  progress: {},
-  lastUpdated: null,
-};
-
-const loading = (state = defaultState, action) => {
-  let progress;
-  let lastUpdated;
-  switch (action.type) {
-    case 'SET_STUDY_LOADING_PROGRESS':
-      progress = cloneDeep(state).progress;
-      progress[action.progressId] = action.progressData;
-
-      // This is a workaround so we can easily identify changes
-      // to the progress object without doing deep comparison.
-      lastUpdated = new Date().getTime();
-
-      return Object.assign({}, state, { progress, lastUpdated });
-    case 'CLEAR_STUDY_LOADING_PROGRESS':
-      progress = cloneDeep(state).progress;
-      delete progress[action.progressId];
-
-      lastUpdated = new Date().getTime();
-
-      return Object.assign({}, state, { progress, lastUpdated });
-    default:
-      return state;
-  }
-};
-
-export default loading;