chore(release): publish [skip ci]

- @ohif/extension-vtk@1.5.2
 - @ohif/core@2.9.2
 - @ohif/viewer@3.11.4

.github/stale.yml

@@ -18,6 +18,9 @@ exemptLabels:
   - 'Triage :white_flag:'
   - 'Extension: Discussion'
   - 'Announcement 🎉'
+  - 'IDC:priority'
+  - 'IDC:candidate'
+  - 'IDC:collaboration'
 # Label to use when marking an issue as stale
 staleLabel: 'Stale :baguette_bread:'
 # Comment to post when marking an issue as stale. Set to `false` to disable

docs/latest/README.md

@@ -48,7 +48,7 @@ Check out these helpful links:
   -->
 
 <!-- prettier-ignore-start -->
-[ohif-org]: https://www.ohif.org
+[ohif-org]: http://www.ohif.org
 [dicom-web]: https://en.wikipedia.org/wiki/DICOMweb
 [gh-issues]: https://github.com/OHIF/Viewers/issues
 <!-- prettier-ignore-end -->

docs/latest/SUMMARY.md

@@ -5,6 +5,7 @@
   - [Getting Started](development/getting-started.md)
   - [Contributing](development/contributing.md)
   - [Continuous Integration](development/continous-integration.md)
+  - [Testing](development/testing.md)
 - [Configuring](configuring/index.md)
   - [Data Source](configuring/data-source.md)
 

docs/latest/architecture/index.md

@@ -13,7 +13,6 @@ architected, and the role each of it's dependent libraries plays.
 - [Overview](#overview)
 - [Business Logic](#business-logic)
 - [Component Library](#react-component-library)
-- [Internationalization](#internationalization-i18n)
 - [Extensions & Configuration](#extensions--configuration)
 - [Common Questions](#common-questions)
 
@@ -74,10 +73,10 @@ This diagram is a conceptual illustration of how the Viewer is architected.
 The [`@ohif/core`][core-github] project offers pre-packaged solutions for
 features common to Web-based medical imaging viewers. For example:
 
-- [Hotkeys](#)
+- Hotkeys
 - DICOM Web requests
 - Hanging Protocols
-- [Managing a study's measurements](../services/default/measurements.md)
+- Managing a study's measurements
 - Managing a study's DICOM metadata
 - [A flexible pattern for extensions](../extensions/index.md)
 - And many others
@@ -99,10 +98,6 @@ application.
 
 [Check out our component library!](https://react.ohif.org/)
 
-## Internationalization (i18n)
-
-...
-
 ## Extensions & Configuration
 
 While OHIF maintains several high value and commonly requested features in its
@@ -120,7 +115,7 @@ the viewer. Some common use cases include:
 We expose common integration points via [extensions](../extensions/index.md) to
 make this possible. The viewer and many of our own extensions also offer
 [configuration][configuration]. For a list of extensions maintained by OHIF,
-[check out this helpful table](../extensions/index.mdl#maintained-extensions).
+[check out this helpful table](../extensions/index.md#maintained-extensions).
 
 If you find yourself thinking "I wish the Viewer could do X", and you can't
 accomplish it with an extension today, create a GitHub issue! We're actively
@@ -147,12 +142,12 @@ you would need to recreate.
   -->
 
 <!-- prettier-ignore-start -->
-[monorepo]: #
+[monorepo]: https://github.com/OHIF/Viewers/issues/768
 [viewers-project]: https://github.com/OHIF/Viewers
 [viewer-npm]: https://www.npmjs.com/package/@ohif/viewer
 [pwa]: https://developers.google.com/web/progressive-web-apps/
 [configuration]: ../configuring/index.md
 [extensions]: ../extensions/index.md
 [core-github]: https://github.com/OHIF/viewers/platform/core
-[ui-github]: https://github.com/OHIF/Viewers/platform/ui
+[ui-github]: https://github.com/OHIF/Viewers/tree/master/platform/ui
 <!-- prettier-ignore-end -->

docs/latest/deployment/index.md

@@ -123,14 +123,111 @@ There are two important steps to making sure this setup works:
 Most image archives do not provide either of these features "out of the box".
 It's common to use IIS, Nginx, or Apache to route incoming requests and append
 appropriate headers. You can find an example of this setup in our
-[Nginx + Image Archive Deployment Recipe](deployment/recipes/nginx--image-archive.md).
+[Nginx + Image Archive Deployment Recipe](./recipes/nginx--image-archive.md).
 
 #### What if my archive doesn't support DicomWeb?
 
-> This is possible to do with the OHIF Viewer, but not as straightforward. Look
-> out for documentation on this subject in the near future.
+It's possible to supply all Study data via JSON format, in the event you do not have a DicomWeb endpoint.
+You can host all of the relevant files on any web accessible server (Amazon S3, Azure Blob Storage, Local file server etc.)
+
+This JSON is supplied via the '?url=' query parameter.
+It should reference an endpoint that returns **application/json** formatted text.
+
+If you do not have an API, you can simply return a text file containing the JSON from any web server.
+
+
+You tell the OHIF viewer to use JSON by appending the `'?url='` query to the `/Viewer` route:
+
+eg. `https://my-test-ohif-server/viewer?url=https://my-json-server/study-uid.json`
+
+The returned JSON object must contain a single root object with a 'studies' array.
+
+
+*Sample JSON format:*
+```JSON
+{
+    "studies": [
+      {
+        "StudyInstanceUID": "1.2.840.113619.2.5.1762583153.215519.978957063.78",
+        "StudyDescription": "BRAIN SELLA",
+        "StudyDate": "20010108",
+        "StudyTime": "120022",
+        "PatientName": "MISTER^MR",
+        "PatientId": "832040",
+        "series": [
+          {
+            "SeriesDescription": "SAG T-1",
+            "SeriesInstanceUID": "1.2.840.113619.2.5.1762583153.215519.978957063.121",
+            "SeriesNumber": 2,
+            "SeriesDate": "20010108",
+            "SeriesTime": "120318",
+            "Modality": "MR",
+            "instances": [
+              {
+                "metadata": {
+                    "Columns": 512,
+                    "Rows": 512,
+                    "InstanceNumber": 3,
+                    "AcquisitionNumber": 0,
+                    "PhotometricInterpretation": "MONOCHROME2",
+                    "BitsAllocated": 16,
+                    "BitsStored": 16,
+                    "PixelRepresentation": 1,
+                    "SamplesPerPixel": 1,
+                    "PixelSpacing": [0.390625, 0.390625],
+                    "HighBit": 15,
+                    "ImageOrientationPatient": [0,1,0,0,0,-1],
+                    "ImagePositionPatient": [11.600000,-92.500000, 98.099998],
+                    "FrameOfReferenceUID": "1.2.840.113619.2.5.1762583153.223134.978956938.470",
+                    "ImageType": ["ORIGINAL","PRIMARY","OTHER"],
+                    "Modality": "MR",
+                    "SOPInstanceUID": "1.2.840.113619.2.5.1762583153.215519.978957063.124",
+                    "SeriesInstanceUID": "1.2.840.113619.2.5.1762583153.215519.978957063.121",
+                    "StudyInstanceUID": "1.2.840.113619.2.5.1762583153.215519.978957063.78"
+                },
+                "url": "dicomweb://s3.amazonaws.com/lury/MRStudy/1.2.840.113619.2.5.1762583153.215519.978957063.124.dcm"
+             }
+           ]
+         }
+       ]
+     }
+   ]
+}
+```
+More info on this JSON format can be found here [Issue #1500](https://github.com/OHIF/Viewers/issues/1500)
+
+
+**Implementation Notes:**
+
+1. When hosting the viewer, you will also need to host a /viewer route on the server - or the browser may not be able to find the route.
+2. For each instance url (dicom object) in the returned JSON, you must prefix the `url` with `dicomweb:` in order for the cornerstone image loader to retrieve it correctly.
+ eg. `https://image-server/my-image.dcm` ---> `dicomweb:https://image-server/my-image.dcm`
+3. The JSON format above is compatible with >= v3.7.8 of the application. Older versions of the viewer used a different JSON format. As of 20/04/20 the public [https://viewer.ohif.org/] is a pre 3.0 version that does not support this format yet.
+4. The JSON format is case-sensitive. Please ensure you have matched casing with the naturalised Dicom format referenced in [Issue #1500](https://github.com/OHIF/Viewers/issues/1500).
+
+*CORS Issues (Cross-Origin Resource Sharing)*
+
+If you host a JSON API or Images on a different domain from the the app itself, you will likely have CORS issues. This will also happen when testing from Localhost and reaching out to remote servers.
+Even if the domain is the same, different ports, subdomains or protocols (https vs http) will also cause CORS errors.
+You will to need add a configuration on each server hosting these assets to allow your App server origin.
+
+For example:
+
+Lets assume your application is hosted on `https://my-ohif-server.com`.
+
+Your JSON API is hosted on `https://my-json-api.aws.com`
+
+And your images are stored on Amazon S3 at `https://my-s3-bucket.aws.com`
+
+When you first start your application, browsing to `https://my-ohif-server.com/viewer?url=https://my-json-api.aws.com/api/my-json-study-info.json`, you will likely get a CORS error in the browser console as it tries to connect to `https://my-json-api.aws.com`.
+
+Adding a setting on the JSON server to allow the CORS origin = `https://my-ohif-server.com` should solve this.
+
+Next, you will likely get a similar CORS error, as the browser tries to go to `https://my-s3-bucket.aws.com`.
+You will need to go to the S3 bucket configuration, and add a CORS setting to allow origin = `https://my-ohif-server.com`.
+
+Essentially, whenever the application connects to a remote resource, you will need to add the applications url to the allowed CORS Origins on that resource. Adding an origin similar to https://localhost:3000 will also allow for local testing.
 
-...
 
 ### Securing Your Data
 
@@ -166,7 +263,7 @@ window.config = {
 ```
 
 You can find an example of this setup in our
-[User Account Control Deployment Recipe](deployment/recipes/user-account-control.md).
+[User Account Control Deployment Recipe](./recipes/user-account-control.md).
 
 #### Choosing a Flow for the Viewer
 
@@ -183,12 +280,12 @@ many possible configurations, so please don't feel limited to these setups.
 Please feel free to suggest or contribute your own recipes.
 
 - Script Include
-  - [Embedding the Viewer](deployment/recipes/embedded-viewer.md)
+  - [Embedding the Viewer](./recipes/embedded-viewer.md)
 - Stand-Alone
-  - [Build for Production](deployment/recipes/build-for-production.md)
-  - [Static](deployment/recipes/static-assets.md)
-  - [Nginx + Image Archive](deployment/recipes/nginx--image-archive.md)
-  - [User Account Control](deployment/recipes/user-account-control.md)
+  - [Build for Production](./recipes/build-for-production.md)
+  - [Static](./recipes/static-assets.md)
+  - [Nginx + Image Archive](./recipes/nginx--image-archive.md)
+  - [User Account Control](./recipes/user-account-control.md)
 
 <!--
   Links

docs/latest/deployment/recipes/embedded-viewer.md

@@ -50,7 +50,7 @@ window.config = {
 ```
 
 To learn more about how you can configure the OHIF Viewer, check out our
-[Configuration Guide](./index.md).
+[Configuration Guide](../../configuring/index.md).
 
 <ol start="3"><li>
   Render the viewer in the web page's target <code>div</code>
@@ -126,12 +126,39 @@ globally defined styles/scripts.
 > We're trying to embed the OHIF Viewer into an existing React App, but seeing
 > react-dom and react conflicts. What can we do?
 
+If you are installing OHIF viewer inside another react app, you may use `installViewer` as follows:
+```
+import { installViewer } from '@ohif/viewer'
+
+const ohifViewerConfig = window.config // or set it here
+const containerId = 'ohif'
+const componentRenderedOrUpdatedCallback = function() {
+    console.log('OHIF Viewer rendered/updated');
+};
+
+componentDidMount() {
+   installViewer(
+      ohifViewerConfig,
+      containerId,
+      componentRenderedOrUpdatedCallback
+    );
+}
+
+render () {
+   ...
+   //you can render in any element you wish
+   <AnyTag id={containerId}/>
+}
+
+```
+
 `installViewer` is a convenience method that pulls in some dependencies that may
 not be compatible with existing `react` apps. `@ohif/viewer` also exports `App`
 which is a react component that takes the `configuration` outlined above as
 props. You can use it as a reusable component, and to avoid `react` version
 conflict issues.
 
+
 <!--
   LINKS
   -->

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

@@ -49,9 +49,7 @@ We can solve this one of two ways:
 1. Have our Image Archive located at the same domain as our Web App
 2. Add appropriate `Access-Control-Allow-*` HTTP headers
 
-This solution uses the first approach, but you can see an example of the second
-in the `docker-compose` bundled with this project for local development:
-[HERE](https://github.com/OHIF/Viewers/blob/master/platform/viewer/.recipes/Nginx-Orthanc/docker-compose.yml)
+**This solution uses the first approach.**
 
 You can read more about CORS in this Medium article: [Understanding
 CORS][understanding-cors]
@@ -121,7 +119,10 @@ 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 determined by the env variable: `APP_CONFIG`. You can see where we set its value in the `dockerfile` for this solution:
+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
+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`
 
@@ -138,11 +139,11 @@ Viewer's configuration, you can run:
 
 All other files are found in: `/docker/OpenResty-Orthanc/`
 
-| Service           | Configuration                                  | Docs                                        |
-| ----------------- | ---------------------------------------------- | ------------------------------------------- |
-| OHIF Viewer       | [dockerfile][dockerfile] / [config.js][config] | You're reading them now!                    |
-| OpenResty (Nginx) | [`/nginx.conf`][config-nginx]                  | [lua-resty-openidc][lua-resty-openidc-docs] |
-| Orthanc           | [`/orthanc.json`][config-orthanc]              | [Here][orthanc-docs]                        |
+| Service           | Configuration                     | Docs                                        |
+| ----------------- | --------------------------------- | ------------------------------------------- |
+| OHIF Viewer       | [dockerfile][dockerfile]          | You're reading them now!                    |
+| OpenResty (Nginx) | [`/nginx.conf`][config-nginx]     | [lua-resty-openidc][lua-resty-openidc-docs] |
+| Orthanc           | [`/orthanc.json`][config-orthanc] | [Here][orthanc-docs]                        |
 
 ## Next Steps
 
@@ -218,10 +219,11 @@ following resources helpful:
 - [OpenResty Guide](http://www.staticshin.com/programming/definitely-an-open-resty-guide/)
 - [Lua Ngx API](https://openresty-reference.readthedocs.io/en/latest/Lua_Nginx_API/)
 
-For a different take on this setup, check out the repository one of our
-community members put together:
+For a different take on this setup, check out the repositories our community
+members put together:
 
 - [mjstealey/ohif-orthanc-dimse-docker](https://github.com/mjstealey/ohif-orthanc-dimse-docker)
+- [trypag/ohif-orthanc-postgres-docker](https://github.com/trypag/ohif-orthanc-postgres-docker)
 
 <!--
   Links
@@ -234,8 +236,7 @@ community 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]: #
-[dockerfile]: #
-[config-nginx]: #
-[config-orthanc]: #
+[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
 <!-- prettier-ignore-end -->

docs/latest/deployment/recipes/user-account-control.md

@@ -122,7 +122,10 @@ 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 determined by the env variable: `APP_CONFIG`. You can see where we set its value in the `dockerfile` for this solution:
+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
+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-keycloak.js`
 
@@ -146,8 +149,8 @@ All other files are found in: `/docker/OpenResty-Orthanc-Keycloak/`
 | Orthanc           | [`/orthanc.json`][config-orthanc]                | [Here][orthanc-docs]                        |
 | Keycloak          | [`/ohif-keycloak-realm.json`][config-keycloak]\* |                                             |
 
-- \* These are the seed values for Keycloak. They can be manually updated at
-  `http://127.0.0.1/auth/admin`
+\* These are the seed values for Keycloak. They can be manually updated at
+`http://127.0.0.1/auth/admin`
 
 #### Keycloak Themeing
 
@@ -261,12 +264,12 @@ for OAuth:
 
 - [Diagrams of OpenID Connect Flows](https://medium.com/@darutk/diagrams-of-all-the-openid-connect-flows-6968e3990660)
 - [KeyCloak: OpenID Connect Flows](https://www.keycloak.org/docs/latest/securing_apps/index.html#authorization-code)
-  - [Good description on SSO Protocols](https://www.keycloak.org/docs/2.5/server_admin/topics/sso-protocols/oidc.html)
 
-For a different take on this setup, check out the repository one of our
-community members put together:
+For a different take on this setup, check out the repositories our community
+members put together:
 
 - [mjstealey/ohif-orthanc-dimse-docker](https://github.com/mjstealey/ohif-orthanc-dimse-docker)
+- [trypag/ohif-orthanc-postgres-docker](https://github.com/trypag/ohif-orthanc-postgres-docker)
 
 <!--
   Links
@@ -278,8 +281,8 @@ community members put together:
 [lua-resty-openidc-docs]: https://github.com/zmartzone/lua-resty-openidc
 <!-- SRC -->
 [config]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/src/config.js
-[dockerfile]: https://github.com/OHIF/Viewers/tree/master/platform/viewer/.recipes
-[config-nginx]: https://github.com/OHIF/Viewers/tree/master/platform/viewer/.recipes
-[config-orthanc]: https://github.com/OHIF/Viewers/tree/master/platform/viewer/.recipes
-[config-keycloak]: https://github.com/OHIF/Viewers/tree/master/platform/viewer/.recipes
+[dockerfile]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/.recipes/OpenResty-Orthanc-Keycloak/dockerfile
+[config-nginx]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/.recipes/OpenResty-Orthanc-Keycloak/config/nginx.conf
+[config-orthanc]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/.recipes/OpenResty-Orthanc-Keycloak/config/orthanc.json
+[config-keycloak]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/.recipes/OpenResty-Orthanc-Keycloak/config/ohif-keycloak-realm.json
 <!-- prettier-ignore-end -->

docs/latest/development/contributing.md

@@ -114,8 +114,8 @@ the tips above will help ensure your changes are reviewed.
 
 ## Testing contribution pull requests
 
-OHIF uses [netlify](netlify.com) so that pull requests are autogenerated and
-available for testing.
+OHIF uses [netlify](https://www.netlify.com/) so that pull requests are
+autogenerated and available for testing.
 
 For example, [this url][example-url] allows you to test [pull request 237, the
 request that created this FAQ entry,][pr-237] using data pulled from Amazon S3.

docs/latest/development/testing.md

@@ -132,7 +132,7 @@ feature `X` or scenario `Y`? Open an issue and let's discuss.
 [flow-org]: https://flow.org/
 <!-- Talks -->
 [assert-js-talks]: https://www.youtube.com/playlist?list=PLZ66c9_z3umNSrKSb5cmpxdXZcIPNvKGw
-[kent-talk]: https://www.youtube.com/watch?list=PLV5CVI1eNcJgNqzNwcs4UKrlJdhfDjshf
+[kent-talk]: https://www.youtube.com/watch?v=Fha2bVoC8SE
 [gleb-talk]: https://www.youtube.com/watch?v=5FnalKRjpZk
 [kent-blog]: https://kentcdodds.com/blog/unit-vs-integration-vs-e2e-tests
 <!-- Images -->

docs/latest/extensions/_maintained-extensions-table.md

@@ -31,6 +31,7 @@
             </td>
             <td>Viewport, Toolbar</td>
         </tr>
+        <!-- dicom-html -->
         <tr>
             <td>
                 <a href="https://www.npmjs.com/package/@ohif/extension-dicom-html">DICOM HTML</a>
@@ -40,6 +41,7 @@
             </td>
             <td>Viewport, SopClassHandler</td>
         </tr>
+        <!-- dicom-pdf -->
         <tr>
             <td>
                 <a href="https://www.npmjs.com/package/@ohif/extension-dicom-pdf">DICOM PDF</a>
@@ -49,6 +51,7 @@
             </td>
             <td>Viewport, SopClassHandler</td>
         </tr>
+        <!-- dicom-microscopy -->
         <tr>
             <td>
                 <a href="https://www.npmjs.com/package/@ohif/extension-dicom-microscopy">DICOM Microscopy</a>
@@ -58,5 +61,15 @@
             </td>
             <td>Viewport, SopClassHandler</td>
         </tr>
+        <!-- dicom-segmentation -->
+        <tr>
+            <td>
+                <a href="https://www.npmjs.com/package/@ohif/extension-dicom-segmentation">DICOM Segmentation</a>
+            </td>
+            <td>
+                Renders segmentation images for a <a href="https://github.com/OHIF/Viewers/blob/master/extensions/dicom-segmentation/src/OHIFDicomSegSopClassHandler.js#L5-L7">specific SopClassUID</a>.
+            </td>
+            <td>Panel, Toolbar</td>
+        </tr>
     </tbody>
 </table>

docs/latest/extensions/index.md

@@ -74,7 +74,8 @@ export default {
 ### Registering an Extension
 
 There are two different ways to register and configure extensions: At
-[runtime](#runtime-extensions) and at [build time](#bundled-extensions).
+[runtime](#registering-at-runtime) and at
+[build time](#registering-at-build-time).
 
 You can leverage one or both strategies. Which one(s) you choose depend on your
 application's requirements. Each [module](#modules) defined by the extension
@@ -82,9 +83,9 @@ becomes available to the core application via the `ExtensionManager`.
 
 #### Registering at Runtime
 
-The `@ohif/viewer` uses a [configuration file](#) at startup. The schema for
-that file includes an `Extensions` key that supports an array of extensions to
-register.
+The `@ohif/viewer` uses a [configuration file](../viewer/configuration.md) at
+startup. The schema for that file includes an `Extensions` key that supports an
+array of extensions to register.
 
 ```js
 // prettier-ignore
@@ -193,8 +194,8 @@ today, create a GitHub issue!
 
 The `ExtensionManager` is a class made available to us via the `@ohif/core`
 project (platform/core). Our application instantiates a single instance of it,
-and provides a `ServicesManager` and `CommandsManager` along with the application's
-configuration through the appConfig key (optional).
+and provides a `ServicesManager` and `CommandsManager` along with the
+application's configuration through the appConfig key (optional).
 
 ```js
 const commandsManager = new CommandsManager();
@@ -202,7 +203,7 @@ const servicesManager = new ServicesManager();
 const extensionManager = new ExtensionManager({
   commandsManager,
   servicesManager,
-  appConfig
+  appConfig,
 });
 ```
 
@@ -212,8 +213,9 @@ The `ExtensionManager` only has a few public members:
 - `registerExtensions` - Registers an array of extensions
 - `modules` - An object containing registered extensions by `MODULE_TYPE`
 
-During registration, lifecycle hooks and modules have access to the extension's config,
-the application's config and `ExtensionManager`'s `ServicesManager` and `CommandsManager` instances.
+During registration, lifecycle hooks and modules have access to the extension's
+config, the application's config and `ExtensionManager`'s `ServicesManager` and
+`CommandsManager` instances.
 
 Our `@ohif/viewer` uses the `modules` member to access registered extensions at
 appropriate places in our application.

docs/latest/extensions/modules/sop-class-handler.md

@@ -1,9 +1,9 @@
 # Module: SOP Class Handler
 
-An extension can register a SOP Class Handler Module by defining a
-`getSopClassHandlerModule` method. The SOP Class Handler is a bit different from
-the other modules, as it doesn't provide a `1:1` schema for UI or provide it's
-own components. It instead defines:
+An extension can register a [SOP Class][sop-class-link] Handler Module by
+defining a `getSopClassHandlerModule` method. The [SOP Class][sop-class-link]
+Handler is a bit different from the other modules, as it doesn't provide a `1:1`
+schema for UI or provide it's own components. It instead defines:
 
 - `sopClassUIDs`: an array of string SOP Class UIDs that the
   `getDisplaySetFromSeries` method should be applied to.
@@ -76,6 +76,13 @@ getSopClassHandlerModule({ servicesManager, commandsManager }) {
 };
 ```
 
+### More examples :
+
+- [Dicom-HTML SOP][dicom-html-sop]
+- [Dicom-PDF SOP][dicom-pdf-sop]
+- [Dicom-Microscopy SOP][dicom-micro-sop]
+- [Dicom-Segmentation SOP][dicom-seg-sop]
+
 ## `@ohif/viewer` usage
 
 We use the `sopClassHandlerModule`s in three different places:
@@ -88,3 +95,11 @@ Each time, it is used to map study and series data to `displaySets`. It does
 this by working alongside the `StudyMetadataManager` in `@ohif/core`. That
 manager has the method `createDisplaySets` that takes an array of
 `sopClassHandlerModules`.
+
+<!-- prettier-ignore-start -->
+[sop-class-link]: http://dicom.nema.org/dicom/2013/output/chtml/part04/sect_B.5.html
+[dicom-html-sop]: https://github.com/OHIF/Viewers/blob/master/extensions/dicom-html/src/OHIFDicomHtmlSopClassHandler.js#L4-L12
+[dicom-pdf-sop]: https://github.com/OHIF/Viewers/blob/master/extensions/dicom-pdf/src/OHIFDicomPDFSopClassHandler.js#L4-L6
+[dicom-micro-sop]: https://github.com/OHIF/Viewers/blob/master/extensions/dicom-microscopy/src/DicomMicroscopySopClassHandler.js#L5-L7
+[dicom-seg-sop]: https://github.com/OHIF/Viewers/blob/master/extensions/dicom-segmentation/src/OHIFDicomSegSopClassHandler.js#L5-L7
+<!-- prettier-ignore-end -->

docs/latest/our-process.md

@@ -75,7 +75,7 @@ items to our ["Active Development" GitHub Project Board][gh-board]. Items on
 this project board are either in active development by Core Team members, or
 queued up for development as in-progress items are completed.
 
-> :pencil: Want to contribute but not sure where to start? Check out [Up for
+> 🖋 Want to contribute but not sure where to start? Check out [Up for
 > grabs][label-grabs] issues and our [Contributing
 > documentation][contributing-docs]
 
@@ -156,5 +156,5 @@ addressed and a Stable version is released.
 [ohif-prod]: https://viewer.ohif.org
 [gh-board]: https://github.com/OHIF/Viewers/projects/4
 [label-grabs]: https://github.com/OHIF/Viewers/issues?q=is%3Aissue+is%3Aopen+label%3A%22Up+For+Grabs+%3Araising_hand_woman%3A%22
-[contributing-docs]: https://docs.ohif.org/contributing/
+[contributing-docs]: ./development/contributing.md
 <!-- prettier-ignore-end -->

docs/latest/services/index.md

@@ -62,7 +62,7 @@ able to fail or be removed. Related patterns that may reduce coupling include:
   -->
 
 <!-- prettier-ignore-start -->
-[commands]: #/
+[commands]: ../extensions/modules/commands.md
 [core-services]: https://github.com/OHIF/Viewers/tree/master/platform/core/src/services
 [services-manager]: https://github.com/OHIF/Viewers/blob/master/platform/core/src/services/ServicesManager.js
 [cross-cutting-concerns]: https://en.wikipedia.org/wiki/Cross-cutting_concern

docs/latest/services/ui/index.md

@@ -2,8 +2,8 @@
 
 - [Overview](#overview)
 - [Example](#example)
-- [Tips & Tricks](#/)
-- [Maintained Services](#/)
+- [Tips & Tricks](#tips--tricks)
+- [Maintained Services](#maintained-services)
 
 ## Overview
 

docs/latest/viewer/configuration.md

@@ -11,7 +11,59 @@ are:
 ```js
 window.config = {
   routerBasename: '/',
-  whiteLabelling: {},
+  /**
+   * "White Labeling" is used to change the branding, look, and feel of the OHIF
+   * Viewer. These settings, and the color variables that are used by our components,
+   * are the easiest way to rebrand the application.
+   *
+   * More extensive changes are made possible through swapping out the UI library,
+   * Viewer project, or extensions.
+   */
+  whiteLabeling: {
+    /* Optional: Should return a React component to be rendered in the "Logo" section of the application's Top Navigation bar */
+    createLogoComponentFn: function(React) {
+      return React.createElement('a', {
+        target: '_self',
+        rel: 'noopener noreferrer',
+        className: 'header-brand',
+        href: '/',
+        style: {
+          display: 'block',
+          textIndent: '-9999px',
+          background: 'url(/svg-file-hosted-at-domain-root.svg)',
+          backgroundSize: 'contain',
+          backgroundRepeat: 'no-repeat',
+          width: '200px',
+        },
+      });
+    },
+  },
+  /**
+   * Internally, the OHIF Viewer fetches data primarily with the
+   * `cornerstoneWADOImageLoader` and the `DICOMWebClient`. If either of these
+   * receive a non-200 response, this method allows you to handle that error.
+   *
+   * Common use cases include:
+   * - Showing a notification with the UINotificationService
+   * - Redirecting the user
+   * - Refreshing an auth token
+   *
+   * @param {Object} error - JS new Error()
+   * @param {XMLHttpRequest} error.request - The XHR request that's onreadystate change triggered this callback
+   * @param {string} error.response - The XHR's response property
+   * @param {number} error.status - The XHR's status property
+   */
+  httpErrorHandler: error => {
+    const { request: xhr, response, status } = err;
+    const { responseType, statusText } = xhr;
+
+    // In local files, status is 0 upon success in Firefox
+    if (xhr.readyState === XMLHttpRequest.DONE) {
+      console.log(statusText, response, responseType);
+    } else {
+      console.warn('Likely CORS error');
+    }
+  },
   extensions: [],
   showStudyList: true,
   filterQueryParam: false,

docs/latest/viewer/internationalization.md

@@ -135,7 +135,7 @@ console.log(T('$t(Common:Play) my translated text'));
 
 # Main Concepts While Translating
 
-## - Namespaces
+## Namespaces
 
 Namespaces are being used to organize translations in smaller portions, combined
 semantically or by use. Each `.json` file inside `@ohif/i18n` npm package
@@ -157,7 +157,7 @@ NameSpace, like this following example getting data from `Common` NameSpace:
 $t(Common:Reset)
 ```
 
-## - Extending Languages in @ohif/i18n
+## Extending Languages in @ohif/i18n
 
 Sometimes, even using the same language, some nouns or jargons can change
 according to the country, states or even from Hospital to Hospital.
@@ -212,7 +212,7 @@ object like this:
 Please check the `index.js` files inside locales folder for an example of this
 exporting structure.
 
-### - Extending languages dynamically
+### Extending languages dynamically
 
 You have access to the i18next instance, so you can use the
 [addResourceBundle](https://www.i18next.com/how-to/add-or-load-translations#add-after-init)
@@ -314,4 +314,4 @@ REACT_APP_I18N_DEBUG=true yarn run dev
 ### Contributing with new languages
 
 Contributions of any kind are welcome! Please check the
-[instructions](https://docs.ohif.org/contributing.html).
+[instructions](../development/contributing.md).

docs/latest/viewer/themeing.md

@@ -66,11 +66,11 @@ open to pull requests and discussion issues.
 
 Current white-labeling options are limited. We expose the ability to replace the
 "Logo" section of the application with a custom "Logo" component. You can do
-this by adding a `whiteLabelling` key to your
+this by adding a `whiteLabeling` key to your
 [configuration file](./configuration.md).
 
 ```js
-function RadicalImagingLogo() {
+function RadicalImagingLogo(React) {
   return React.createElement(
     'a',
     {
@@ -83,8 +83,8 @@ function RadicalImagingLogo() {
   );
 }
 
-props.whiteLabelling = {
-  logoComponent: RadicalImagingLogo(),
+props.whiteLabeling = {
+  createLogoComponentFn: RadicalImagingLogo,
 };
 ```
 

docs/latest/yarn.lock

@@ -20,10 +20,10 @@ abbrev@~1.0.9:
   resolved "https://registry.yarnpkg.com/abbrev/-/abbrev-1.0.9.tgz#91b4792588a7738c25f35dd6f63752a2f8776135"
   integrity sha1-kbR5JYinc4wl813W9jdSovh3YTU=
 
-agent-base@4, agent-base@^4.1.0:
-  version "4.2.1"
-  resolved "https://registry.yarnpkg.com/agent-base/-/agent-base-4.2.1.tgz#d89e5999f797875674c07d87f260fc41e83e8ca9"
-  integrity sha512-JVwXMr9nHYTUXsBFKUqhJwvlcYU/blreOEUkhNR2eXZIvwd+c+o5V4MgDPKWnMS/56awN3TRzIP+KoPn+roQtg==
+agent-base@4, agent-base@^4.1.0, agent-base@^4.3.0:
+  version "4.3.0"
+  resolved "https://registry.yarnpkg.com/agent-base/-/agent-base-4.3.0.tgz#8165f01c436009bccad0b1d122f05ed770efc6ee"
+  integrity sha512-salcGninV0nPrwpGNn4VTXBb1SOuXQBiqbrNXoeizJsHrsL6ERFM2Ne3JUSBWRE6aeNJI2ROP/WEEIDUiDe3cg==
   dependencies:
     es6-promisify "^5.0.0"
 
@@ -773,9 +773,9 @@ err-code@^1.0.0:
     prr "~1.0.1"
 
 es6-promise@^4.0.3:
-  version "4.2.6"
-  resolved "https://registry.yarnpkg.com/es6-promise/-/es6-promise-4.2.6.tgz#b685edd8258886365ea62b57d30de28fadcd974f"
-  integrity sha512-aRVgGdnmW2OiySVPUC9e6m+plolMAJKjZnQlCwNSuK5yQ0JN61DZSO1X1Ufd1foqWRAlig0rhduTCHe7sVtK5Q==
+  version "4.2.8"
+  resolved "https://registry.yarnpkg.com/es6-promise/-/es6-promise-4.2.8.tgz#4eb21594c972bc40553d276e510539143db53e0a"
+  integrity sha512-HJDGx5daxeIvxdBxvG2cb9g4tEvwIk3i8+nhX0yGrYmZUzbkdg8QbDevheDB8gd0//uPj4c1EQua8Q+MViT0/w==
 
 es6-promisify@^5.0.0:
   version "5.0.0"
@@ -1289,11 +1289,11 @@ http-signature@~1.2.0:
     sshpk "^1.7.0"
 
 https-proxy-agent@^2.1.0:
-  version "2.2.1"
-  resolved "https://registry.yarnpkg.com/https-proxy-agent/-/https-proxy-agent-2.2.1.tgz#51552970fa04d723e04c56d04178c3f92592bbc0"
-  integrity sha512-HPCTS1LW51bcyMYbxUIOO4HEOlQ1/1qRaFWcyxvwaqUS9TY88aoEuHUY33kuAh1YhVVaDQhLZsnPd+XNARWZlQ==
+  version "2.2.4"
+  resolved "https://registry.yarnpkg.com/https-proxy-agent/-/https-proxy-agent-2.2.4.tgz#4ee7a737abd92678a293d9b34a1af4d0d08c787b"
+  integrity sha512-OmvfoQ53WLjtA9HeYP9RNrWMJzzAz1JGaSFr1nijg0PVR1JaD/xbJq1mdEIIlxGpXp9eSe/O2LgU9DJmTPd0Eg==
   dependencies:
-    agent-base "^4.1.0"
+    agent-base "^4.3.0"
     debug "^3.1.0"
 
 humanize-ms@^1.2.1:
@@ -1807,11 +1807,16 @@ ms@2.0.0:
   resolved "https://registry.yarnpkg.com/ms/-/ms-2.0.0.tgz#5608aeadfc00be6c2901df5f9861788de0d597c8"
   integrity sha1-VgiurfwAvmwpAd9fmGF4jeDVl8g=
 
-ms@^2.0.0, ms@^2.1.1:
+ms@^2.0.0:
   version "2.1.1"
   resolved "https://registry.yarnpkg.com/ms/-/ms-2.1.1.tgz#30a5864eb3ebb0a66f2ebe6d727af06a09d86e0a"
   integrity sha512-tgp+dl5cGk28utYktBsrFqA7HKgrhgPsg6Z/EfhWI4gl1Hwq8B/GmY/0oXZ6nF8hDVesS/FpnYaD/kOWhYQvyg==
 
+ms@^2.1.1:
+  version "2.1.2"
+  resolved "https://registry.yarnpkg.com/ms/-/ms-2.1.2.tgz#d09d1f357b443f493382a8eb3ccd183872ae6009"
+  integrity sha512-sGkPx+VjMtmA6MX27oA4FBFELFCZZ4S4XqeGOXCv68tT+jb3vk/RyaKWP0PTKyWtmLSM0b+adUTEvbs1PEaH2w==
+
 mute-stream@~0.0.4:
   version "0.0.8"
   resolved "https://registry.yarnpkg.com/mute-stream/-/mute-stream-0.0.8.tgz#1630c42b2251ff81e2a283de96a5497ea92e5e0d"

extensions/cornerstone/CHANGELOG.md

@@ -3,6 +3,55 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+# [2.7.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.6.1...@ohif/extension-cornerstone@2.7.0) (2020-04-24)
+
+
+### Features
+
+* 🎸 Seg jump to slice + show/hide ([835f64d](https://github.com/OHIF/Viewers/commit/835f64d47a9994f6a25aaf3941a4974e215e7e7f))
+
+
+
+
+
+## [2.6.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.6.0...@ohif/extension-cornerstone@2.6.1) (2020-04-23)
+
+
+### Bug Fixes
+
+* 🐛 Multiframe fix ([#1661](https://github.com/OHIF/Viewers/issues/1661)) ([7120561](https://github.com/OHIF/Viewers/commit/71205618ecb8b592247c5acb32284bfe7e18fce5))
+
+
+
+
+
+# [2.6.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.5.2...@ohif/extension-cornerstone@2.6.0) (2020-04-23)
+
+
+### Features
+
+* configuration to hook into XHR Error handling ([e96205d](https://github.com/OHIF/Viewers/commit/e96205de35e5bec14dc8a9a8509db3dd4e6ecdb6))
+
+
+
+
+
+## [2.5.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.5.1...@ohif/extension-cornerstone@2.5.2) (2020-04-09)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
+## [2.5.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.5.0...@ohif/extension-cornerstone@2.5.1) (2020-04-02)
+
+**Note:** Version bump only for package @ohif/extension-cornerstone
+
+
+
+
+
 # [2.5.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.4.3...@ohif/extension-cornerstone@2.5.0) (2020-03-13)
 
 

extensions/cornerstone/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-cornerstone",
-  "version": "2.5.0",
+  "version": "2.7.0",
   "description": "OHIF extension for Cornerstone",
   "author": "OHIF",
   "license": "MIT",
@@ -35,8 +35,8 @@
     "cornerstone-core": "^2.2.8",
     "cornerstone-math": "^0.1.8",
     "cornerstone-tools": "4.12.5",
-    "cornerstone-wado-image-loader": "^3.0.0",
-    "dcmjs": "^0.10.1",
+    "cornerstone-wado-image-loader": "^3.1.0",
+    "dcmjs": "^0.12.2",
     "dicom-parser": "^1.8.3",
     "hammerjs": "^2.0.8",
     "prop-types": "^15.6.2",

extensions/cornerstone/src/asyncComponent.js

@@ -1,37 +0,0 @@
-/**
- * We use this component to leverage "Code Splitting"
- *
- * Link: https://serverless-stack.com/chapters/code-splitting-in-create-react-app.html
- */
-
-import React, { Component } from 'react';
-
-export default function asyncComponent(importComponent) {
-  class AsyncComponent extends Component {
-    constructor(props) {
-      super(props);
-
-      this.state = {
-        component: null,
-      };
-    }
-
-    async componentDidMount() {
-      // Add dynamically loaded component to state
-      const { default: component } = await importComponent();
-
-      this.setState({
-        component: component,
-      });
-    }
-
-    render() {
-      const C = this.state.component;
-
-      // Render the loaded component, or null
-      return C ? <C {...this.props} /> : null;
-    }
-  }
-
-  return AsyncComponent;
-}

extensions/cornerstone/src/commandsModule.js

@@ -7,6 +7,9 @@ import { getEnabledElement } from './state';
 import CornerstoneViewportDownloadForm from './CornerstoneViewportDownloadForm';
 const scroll = cornerstoneTools.import('util/scroll');
 
+const { studyMetadataManager } = OHIF.utils;
+const { setViewportSpecificData } = OHIF.redux.actions;
+
 const commandsModule = ({ servicesManager }) => {
   const actions = {
     rotateViewport: ({ viewports, rotation }) => {
@@ -255,9 +258,35 @@ const commandsModule = ({ servicesManager }) => {
         cornerstone.setViewport(enabledElement, viewport);
       }
     },
+    jumpToImage: ({
+      StudyInstanceUID,
+      SOPInstanceUID,
+      frameIndex,
+      activeViewportIndex
+    }) => {
+      const study = studyMetadataManager.get(StudyInstanceUID);
+
+      const displaySet = study.findDisplaySet(ds => {
+        return ds.images && ds.images.find(i => i.getSOPInstanceUID() === SOPInstanceUID)
+      });
+
+      displaySet.SOPInstanceUID = SOPInstanceUID;
+      displaySet.frameIndex = frameIndex;
+
+      window.store.dispatch(setViewportSpecificData(activeViewportIndex, displaySet));
+
+      cornerstone.getEnabledElements().forEach(enabledElement => {
+        cornerstone.updateImage(enabledElement.element);
+      });
+    }
   };
 
   const definitions = {
+    jumpToImage: {
+      commandFn: actions.jumpToImage,
+      storeContexts: [],
+      options: {},
+    },
     getNearbyToolData: {
       commandFn: actions.getNearbyToolData,
       storeContexts: [],

extensions/cornerstone/src/index.js

@@ -1,14 +1,20 @@
+import React from 'react';
 import init from './init.js';
-import asyncComponent from './asyncComponent.js';
 import commandsModule from './commandsModule.js';
 import toolbarModule from './toolbarModule.js';
 import CornerstoneViewportDownloadForm from './CornerstoneViewportDownloadForm';
 
-const OHIFCornerstoneViewport = asyncComponent(() =>
-  import(
-    /* webpackChunkName: "OHIFCornerstoneViewport" */ './OHIFCornerstoneViewport.js'
-  )
-);
+const Component = React.lazy(() => {
+  return import('./OHIFCornerstoneViewport');
+});
+
+const OHIFCornerstoneViewport = props => {
+  return (
+    <React.Suspense fallback={<div>Loading...</div>}>
+      <Component {...props} />
+    </React.Suspense>
+  );
+};
 
 /**
  *

extensions/cornerstone/src/initCornerstoneTools.js

@@ -2,6 +2,9 @@ import Hammer from 'hammerjs';
 import cornerstone from 'cornerstone-core';
 import cornerstoneMath from 'cornerstone-math';
 import cornerstoneTools from 'cornerstone-tools';
+import OHIF from '@ohif/core';
+
+const { log } = OHIF;
 
 export default function(configuration = {}) {
   // For debugging
@@ -12,6 +15,13 @@ export default function(configuration = {}) {
   cornerstoneTools.external.cornerstoneMath = cornerstoneMath;
   cornerstoneTools.init(configuration);
 
+  cornerstoneTools.loadHandlerManager.setErrorLoadingHandler(
+    (element, imageId, error) => {
+      log.error(imageId);
+      throw error;
+    }
+  );
+
   // Set the tool font and font size
   // context.font = "[style] [variant] [weight] [size]/[line height] [font family]";
   const fontFamily =

extensions/dicom-html/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.
 
+## [1.2.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.2.0...@ohif/extension-dicom-html@1.2.1) (2020-04-28)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
+# [1.2.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.1.2...@ohif/extension-dicom-html@1.2.0) (2020-04-24)
+
+
+### Features
+
+* 🎸 Seg jump to slice + show/hide ([835f64d](https://github.com/OHIF/Viewers/commit/835f64d47a9994f6a25aaf3941a4974e215e7e7f))
+
+
+
+
+
+## [1.1.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.1.1...@ohif/extension-dicom-html@1.1.2) (2020-04-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-html
+
+
+
+
+
 ## [1.1.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.1.0...@ohif/extension-dicom-html@1.1.1) (2020-03-09)
 
 **Note:** Version bump only for package @ohif/extension-dicom-html

extensions/dicom-html/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-html",
-  "version": "1.1.1",
+  "version": "1.2.1",
   "description": "OHIF extension for rendering structured reports to HTML",
   "author": "OHIF",
   "license": "MIT",
@@ -29,7 +29,7 @@
   },
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
-    "dcmjs": "^0.10.1",
+    "dcmjs": "^0.12.2",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6"

extensions/dicom-html/src/DicomHtmlViewport.js

@@ -1,6 +1,6 @@
 import React, { Component } from 'react';
 import PropTypes from 'prop-types';
-import * as dcmjs from 'dcmjs';
+import dcmjs from 'dcmjs';
 import TypedArrayProp from './TypedArrayProp';
 
 import './DicomHtmlViewport.css';

extensions/dicom-html/src/asyncComponent.js

@@ -1,37 +0,0 @@
-/**
- * We use this component to leverage "Code Splitting"
- *
- * Link: https://serverless-stack.com/chapters/code-splitting-in-create-react-app.html
- */
-
-import React, { Component } from 'react';
-
-export default function asyncComponent(importComponent) {
-  class AsyncComponent extends Component {
-    constructor(props) {
-      super(props);
-
-      this.state = {
-        component: null,
-      };
-    }
-
-    async componentDidMount() {
-      // Add dynamically loaded component to state
-      const { default: component } = await importComponent();
-
-      this.setState({
-        component: component,
-      });
-    }
-
-    render() {
-      const C = this.state.component;
-
-      // Render the loaded component, or null
-      return C ? <C {...this.props} /> : null;
-    }
-  }
-
-  return AsyncComponent;
-}

extensions/dicom-html/src/index.js

@@ -1,11 +1,17 @@
-import asyncComponent from './asyncComponent.js';
+import React from 'react';
 import OHIFDicomHtmlSopClassHandler from './OHIFDicomHtmlSopClassHandler.js';
 
-const OHIFDicomHtmlViewport = asyncComponent(() =>
-  import(
-    /* webpackChunkName: "OHIFDicomHtmlViewport" */ './OHIFDicomHtmlViewport.js'
-  )
-);
+const Component = React.lazy(() => {
+  return import('./OHIFDicomHtmlViewport');
+});
+
+const OHIFDicomHtmlViewport = props => {
+  return (
+    <React.Suspense fallback={<div>Loading...</div>}>
+      <Component {...props} />
+    </React.Suspense>
+  );
+};
 
 export default {
   /**

extensions/dicom-microscopy/CHANGELOG.md

@@ -3,6 +3,22 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [0.50.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.8...@ohif/extension-dicom-microscopy@0.50.9) (2020-04-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-microscopy
+
+
+
+
+
+## [0.50.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.7...@ohif/extension-dicom-microscopy@0.50.8) (2020-03-31)
+
+**Note:** Version bump only for package @ohif/extension-dicom-microscopy
+
+
+
+
+
 ## [0.50.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.6...@ohif/extension-dicom-microscopy@0.50.7) (2020-03-09)
 
 **Note:** Version bump only for package @ohif/extension-dicom-microscopy

extensions/dicom-microscopy/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-microscopy",
-  "version": "0.50.7",
+  "version": "0.50.9",
   "description": "OHIF extension for Dicom Microscopy",
   "author": "OHIF",
   "license": "MIT",

extensions/dicom-microscopy/src/DicomMicroscopyViewport.js

@@ -34,11 +34,12 @@ class DicomMicroscopyViewport extends Component {
       .then(instances => {
         const promises = [];
         for (let i = 0; i < instances.length; i++) {
-          const sopInstanceUid = instances[i]['00080018']['Value'][0];
+          const sopInstanceUID = instances[i]['00080018']['Value'][0];
+
           const retrieveInstanceOptions = {
             studyInstanceUID: displaySet.StudyInstanceUID,
             seriesInstanceUID: displaySet.SeriesInstanceUID,
-            sopInstanceUid,
+            sopInstanceUID,
           };
 
           const promise = dicomWebClient

extensions/dicom-microscopy/src/asyncComponent.js

@@ -1,37 +0,0 @@
-/**
- * We use this component to leverage "Code Splitting"
- *
- * Link: https://serverless-stack.com/chapters/code-splitting-in-create-react-app.html
- */
-
-import React, { Component } from 'react';
-
-export default function asyncComponent(importComponent) {
-  class AsyncComponent extends Component {
-    constructor(props) {
-      super(props);
-
-      this.state = {
-        component: null,
-      };
-    }
-
-    async componentDidMount() {
-      // Add dynamically loaded component to state
-      const { default: component } = await importComponent();
-
-      this.setState({
-        component: component,
-      });
-    }
-
-    render() {
-      const C = this.state.component;
-
-      // Render the loaded component, or null
-      return C ? <C {...this.props} /> : null;
-    }
-  }
-
-  return AsyncComponent;
-}

extensions/dicom-microscopy/src/index.js

@@ -1,11 +1,17 @@
-import asyncComponent from './asyncComponent.js';
+import React from 'react';
 import DicomMicroscopySopClassHandler from './DicomMicroscopySopClassHandler.js';
 
-const DicomMicroscopyViewport = asyncComponent(() =>
-  import(
-    /* webpackChunkName: "DicomMicroscopyViewport" */ './DicomMicroscopyViewport.js'
-  )
-);
+const Component = React.lazy(() => {
+  return import('./DicomMicroscopyViewport');
+});
+
+const DicomMicroscopyViewport = props => {
+  return (
+    <React.Suspense fallback={<div>Loading...</div>}>
+      <Component {...props} />
+    </React.Suspense>
+  );
+};
 
 export default {
   /**

extensions/dicom-p10-downloader/.webpack/webpack.dev.js

@@ -0,0 +1,8 @@
+const path = require('path');
+const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+
+module.exports = (env, argv) => {
+  return webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
+};

extensions/dicom-p10-downloader/.webpack/webpack.prod.js

@@ -0,0 +1,38 @@
+const merge = require('webpack-merge');
+const path = require('path');
+const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
+const pkg = require('./../package.json');
+
+const ROOT_DIR = path.join(__dirname, './..');
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+
+module.exports = (env, argv) => {
+  const commonConfig = webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
+
+  return merge(commonConfig, {
+    devtool: 'source-map',
+    stats: {
+      colors: true,
+      hash: true,
+      timings: true,
+      assets: true,
+      chunks: false,
+      chunkModules: false,
+      modules: false,
+      children: false,
+      warnings: true,
+    },
+    optimization: {
+      minimize: true,
+      sideEffects: true,
+    },
+    output: {
+      path: ROOT_DIR,
+      library: 'OHIFExtDicomP10Downloader',
+      libraryTarget: 'umd',
+      libraryExport: 'default',
+      filename: pkg.main,
+    },
+  });
+};

extensions/dicom-p10-downloader/CHANGELOG.md

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

extensions/dicom-p10-downloader/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 Open Health Imaging Foundation
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

extensions/dicom-p10-downloader/README.md

@@ -0,0 +1 @@
+# @ohif/extension-dicom-p10-downloader

extensions/dicom-p10-downloader/package.json

@@ -0,0 +1,40 @@
+{
+  "name": "@ohif/extension-dicom-p10-downloader",
+  "version": "0.1.0",
+  "description": "OHIF extension for downloading DICOM P10 files",
+  "author": "OHIF",
+  "license": "MIT",
+  "repository": "OHIF/Viewers",
+  "main": "dist/index.umd.js",
+  "module": "src/index.js",
+  "publishConfig": {
+    "access": "public"
+  },
+  "engines": {
+    "node": ">=10",
+    "npm": ">=6",
+    "yarn": ">=1.16.0"
+  },
+  "files": [
+    "dist",
+    "README.md"
+  ],
+  "scripts": {
+    "dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --debug --output-pathinfo",
+    "build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
+    "build:package": "yarn run build",
+    "prepublishOnly": "yarn run build",
+    "start": "yarn run dev"
+  },
+  "peerDependencies": {
+    "@ohif/core": "^2.6.0",
+    "dicom-parser": "^1.8.3",
+    "dicomweb-client": "^0.5.2"
+  },
+  "dependencies": {
+    "@babel/runtime": "^7.5.5",
+    "dicomweb-client": "^0.6.0",
+    "file-saver": "^2.0.2",
+    "jszip": "^3.2.2"
+  }
+}

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

@@ -0,0 +1,105 @@
+import OHIF from '@ohif/core';
+import {
+  save,
+  getDicomWebClientFromContext,
+  getSOPInstanceReferenceFromActiveViewport,
+  getSOPInstanceReferencesFromViewports,
+} from './utils';
+import _downloadAndZip from './downloadAndZip';
+
+const {
+  utils: {
+    Queue,
+  },
+} = OHIF;
+
+export function getCommands(context) {
+  const queue = new Queue(1);
+  const actions = {
+    /**
+     * @example Running this command using Commands Manager
+     * commandsManager.runCommand(
+     *   'downloadAndZip',
+     *   {
+     *     listOfUIDs: [...],
+     *     options: {
+     *       progress(status) {
+     *         console.info('Progress:', (status.progress * 100).toFixed(2) + '%');
+     *       }
+     *     }
+     *   },
+     *   'VIEWER'
+     * );
+     */
+    downloadAndZip({ servers, dicomWebClient, listOfUIDs, options }) {
+      return save(
+        _downloadAndZip(
+          dicomWebClient || getDicomWebClientFromContext(context, servers),
+          listOfUIDs,
+          options
+        ),
+        listOfUIDs
+      );
+    },
+    downloadAndZipSeriesOnViewports({ servers, viewports, progress }) {
+      const dicomWebClient = getDicomWebClientFromContext(context, servers);
+      const listOfUIDs = getSOPInstanceReferencesFromViewports(viewports);
+      return save(
+        _downloadAndZip(dicomWebClient, listOfUIDs, { progress }),
+        listOfUIDs
+      );
+    },
+    downloadAndZipSeriesOnActiveViewport({ servers, viewports, progress }) {
+      const dicomWebClient = getDicomWebClientFromContext(context, servers);
+      const listOfUIDs = getSOPInstanceReferenceFromActiveViewport(viewports);
+      return save(
+        _downloadAndZip(dicomWebClient, listOfUIDs, { progress }),
+        listOfUIDs
+      );
+    },
+  };
+
+  const definitions = {
+    downloadAndZip: {
+      commandFn: queue.bindSafe(actions.downloadAndZip, error),
+      storeContexts: ['servers'],
+    },
+    downloadAndZipSeriesOnViewports: {
+      commandFn: queue.bindSafe(actions.downloadAndZipSeriesOnViewports, error),
+      storeContexts: ['servers', 'viewports'],
+      options: { progress },
+    },
+    downloadAndZipSeriesOnActiveViewport: {
+      commandFn: queue.bindSafe(
+        actions.downloadAndZipSeriesOnActiveViewport,
+        error
+      ),
+      storeContexts: ['servers', 'viewports'],
+      options: { progress },
+    },
+  };
+
+  return {
+    actions,
+    definitions,
+  };
+}
+
+/**
+ * Utils
+ */
+
+function progress(status) {
+  OHIF.log.info(
+    'Download and Zip Progress:',
+    (status.progress * 100.0).toFixed(2) + '%'
+  );
+}
+
+function error(e) {
+  if (e.message === 'Queue limit reached') {
+    OHIF.log.warn('A download is already in progress, please wait.');
+  } else {
+    OHIF.log.error(e);
+  }
+}

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

@@ -0,0 +1,244 @@
+import OHIF from '@ohif/core';
+import { api } from 'dicomweb-client';
+import dicomParser from 'dicom-parser';
+import JSZip from 'jszip';
+
+/**
+ * Constants
+ */
+
+const {
+  utils: {
+    isDicomUid,
+    hierarchicalListUtils,
+    progressTrackingUtils: progressUtils,
+  },
+} = OHIF;
+
+/**
+ * Public Methods
+ */
+
+/**
+ * Download and Zip all DICOM P10 instances from specified DICOM Web Client
+ * based on an hierarchical list of UIDs;
+ *
+ * @param {DICOMwebClient} dicomWebClient A DICOMwebClient instance through
+ *  which the referenced instances will be retrieved;
+ * @param {Array} listOfUIDs The hierarchical list of UIDs from the instances
+ *  that should be retrieved:
+ *  A hierarchical list of UIDs is a regular JS Array where the type of the UID
+ *  (study, series, instance) is determined by its nasting lavel. For example:
+ *    @ The following list instructs the library to download all the instances
+ *      from both studies "A" and "B":
+ *
+ *    ['studyUIDFromA', 'studyUIDFromB']
+ *
+ *    @ In the previous example both UIDs are treated as STUDY UIDs because both
+ *      of them are listed in the same (top) level of the list. If, on the other
+ *      hand, only instances from series "I" and "J" from the study "B"
+ *      are to be downloaded, the expected hierarchical list would be:
+ *
+ *    ['studyUIDFromA', ['studyUIDFromB', ['seriesUIDFromI', 'seriesUIDFromJ']]]
+ *
+ *    @ Which, when prettified, reads like this:
+ *
+ *    [
+ *      'studyUIDFromA',
+ *      ['studyUIDFromB', [
+ *        'seriesUIDFromI',
+ *        'seriesUIDFromJ'
+ *      ]]
+ *    ]
+ *
+ *    @ Furthermore, if only instances "X", "Y" and "Z" from series "J" need to
+ *      be downloaded (instead of all the instances from that series), the list
+ *      could be changed to:
+ *
+ *    [
+ *      'studyUIDFromA',
+ *      ['studyUIDFromB', [
+ *        'seriesUIDFromI',
+ *        ['seriesUIDFromJ', [
+ *          'instanceUIDFromX',
+ *          'instanceUIDFromY',
+ *          'instanceUIDFromZ'
+ *        ]]
+ *      ]]
+ *    ]
+ *
+ * Please refer to hierarchicalListUtils.js for more information and utilities;
+ *
+ * @param {Object} options A plain object with options;
+ * @param {function} options.progress A callback to retrieve notifications
+ * @returns {Promise} A promise that resolves to an URL from which the ZIP file
+ *  can be downloaded;
+ */
+
+async function downloadAndZip(dicomWebClient, listOfUIDs, options) {
+  if (dicomWebClient instanceof api.DICOMwebClient) {
+    const settings = buildSettings(listOfUIDs, options);
+    const { compression } = settings.tasks;
+    // Register user-provided progress handler as a task list observer
+    progressUtils.addObserver(settings.taskList, settings.options.progress);
+    const buffers = await downloadAll(dicomWebClient, settings).catch(error => {
+      // Reject promise from compression task on download failure
+      compression.deferred.reject(error);
+      throw error;
+    });
+    compression.deferred.resolve(zipAll(buffers, settings));
+    const url = await compression.deferred.promise;
+    return url;
+  }
+  throw new Error('A valid DICOM Web Client instance is expected');
+}
+
+/**
+ * Utils
+ */
+
+async function zipAll(buffers, settings) {
+  const zip = new JSZip();
+  OHIF.log.info('Adding DICOM P10 files to archive:', buffers.length);
+  buffers.forEach((buffer, i) => {
+    const path = buildPath(buffer) || `${i}.dcm`;
+    zip.file(path, buffer);
+  });
+  // Set compression task progress to 50%
+  progressUtils.update(settings.tasks.compression.task, 0.5);
+  const blob = await zip.generateAsync({ type: 'blob' });
+  return URL.createObjectURL(blob);
+}
+
+function buildSettings(listOfUIDs, options) {
+  const taskList = progressUtils.createList();
+  const compression = progressUtils.addDeferred(taskList);
+  const downloads = [];
+
+  // Build downloads list
+  hierarchicalListUtils.forEach(
+    listOfUIDs,
+    (StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID) => {
+      if (isDicomUid(StudyInstanceUID)) {
+        downloads.push({
+          tracking: progressUtils.addDeferred(taskList),
+          parameters: [StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID],
+        });
+      }
+    }
+  );
+
+  // Print tree of hierarchical references
+  OHIF.log.info('Downloading DICOM P10 files for references:');
+  OHIF.log.info(hierarchicalListUtils.print(listOfUIDs));
+
+  return {
+    options: Object(options),
+    taskList,
+    tasks: {
+      downloads,
+      compression,
+    },
+  };
+}
+
+function buildPath(buffer) {
+  let path;
+  try {
+    const byteArray = new Uint8Array(buffer);
+    const dataSet = dicomParser.parseDicom(byteArray, {
+      // Stop parsing after SeriesInstanceUID is found
+      untilTag: 'x0020000e',
+    });
+    const StudyInstanceUID = dataSet.string('x0020000d');
+    const SeriesInstanceUID = dataSet.string('x0020000e');
+    const SOPInstanceUID = dataSet.string('x00080018');
+    if (StudyInstanceUID && SeriesInstanceUID && SOPInstanceUID) {
+      path = `${StudyInstanceUID}/${SeriesInstanceUID}/${SOPInstanceUID}.dcm`;
+    }
+  } catch (e) {
+    OHIF.log.error('Error parsing downloaded DICOM P10 file...', e);
+  }
+  return path;
+}
+
+async function downloadAll(dicomWebClient, settings) {
+  const { downloads } = settings.tasks;
+
+  // Make sure at least one download was initiated
+  if (downloads.length < 1) {
+    throw new Error('No valid reference to be downloaded');
+  }
+
+  const promises = downloads.map(item => {
+    const {
+      parameters,
+      tracking: { deferred, task },
+    } = item;
+    deferred.resolve(download(task, dicomWebClient, ...parameters));
+    return deferred.promise;
+  });
+
+  // Wait on created download promises
+  return Promise.all(promises).then(results => {
+    const buffers = [];
+    // The "results" array may directly contain buffers (ArrayBuffer instances)
+    // or arrays of buffers, depending on the type of downloads initiated on the
+    // previous step (retrieveStudy, retrieveSeries or retrieveinstance). Ex:
+    // results = [buf1, [buf2, buf3], buf4, [buf5], ...];
+    results.forEach(
+      function select(nesting, result) {
+        if (result instanceof ArrayBuffer) {
+          buffers.push(result);
+        } else if (nesting && Array.isArray(result)) {
+          // "nesting" argument is important to make sure only two levels
+          // of arrays are visited. For example, "bufX" should not be visited:
+          // [buf1, [buf2, buf3, [bufX]], buf4, [buf5], ...];
+          result.forEach(select.bind(null, false));
+        }
+      }.bind(null, true)
+    );
+    return buffers;
+  });
+}
+
+async function download(
+  task,
+  dicomWebClient,
+  studyInstanceUID,
+  seriesInstanceUID,
+  sopInstanceUID
+) {
+  // Strict DICOM-formatted variable names COULDN'T be used here because the
+  // DICOM Web client interface expects them in this specific format.
+  // @TODO: Add support for download progress handler which will use the
+  // currently not use "task" param
+  if (!isDicomUid(studyInstanceUID)) {
+    throw new Error('Download requires at least a "StudyInstanceUID" property');
+  }
+  if (!isDicomUid(seriesInstanceUID)) {
+    // Download entire study
+    return dicomWebClient.retrieveStudy({
+      studyInstanceUID,
+    });
+  }
+  if (!isDicomUid(sopInstanceUID)) {
+    // Download entire series
+    return dicomWebClient.retrieveSeries({
+      studyInstanceUID,
+      seriesInstanceUID,
+    });
+  }
+  // Download specific instance
+  return dicomWebClient.retrieveInstance({
+    studyInstanceUID,
+    seriesInstanceUID,
+    sopInstanceUID,
+  });
+}
+
+/**
+ * Exports
+ */
+
+export { downloadAndZip as default, downloadAndZip };

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

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

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

@@ -0,0 +1,110 @@
+import OHIF from '@ohif/core';
+import { api } from 'dicomweb-client';
+import { saveAs } from 'file-saver';
+
+const {
+  utils: { isDicomUid, resolveObjectPath, hierarchicalListUtils },
+  DICOMWeb,
+} = OHIF;
+
+function validDicomUid(subject) {
+  if (isDicomUid(subject)) {
+    return subject;
+  }
+}
+
+function getActiveServerFromServersStore(store) {
+  const servers = resolveObjectPath(store, 'servers');
+  if (Array.isArray(servers) && servers.length > 0) {
+    return servers.find(server => resolveObjectPath(server, 'active') === true);
+  }
+}
+
+function getDicomWebClientFromConfig(config) {
+  const servers = resolveObjectPath(config, 'servers.dicomWeb');
+  if (Array.isArray(servers) && servers.length > 0) {
+    const server = servers[0];
+    return new api.DICOMwebClient({
+      url: server.wadoRoot,
+      headers: DICOMWeb.getAuthorizationHeader(server),
+    });
+  }
+}
+
+function getDicomWebClientFromContext(context, store) {
+  const activeServer = getActiveServerFromServersStore(store);
+  if (activeServer) {
+    return new api.DICOMwebClient({
+      url: activeServer.wadoRoot,
+      headers: DICOMWeb.getAuthorizationHeader(activeServer),
+    });
+  } else if (context.dicomWebClient instanceof api.DICOMwebClient) {
+    return context.dicomWebClient;
+  }
+}
+
+function getSOPInstanceReference(viewports, index) {
+  if (index >= 0) {
+    const { StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID } = Object(
+      resolveObjectPath(viewports, `viewportSpecificData.${index}`)
+    );
+    return Object.freeze(
+      hierarchicalListUtils.addToList(
+        [],
+        validDicomUid(StudyInstanceUID),
+        validDicomUid(SeriesInstanceUID),
+        validDicomUid(SOPInstanceUID)
+      )
+    );
+  }
+}
+
+function getSOPInstanceReferenceFromActiveViewport(viewports) {
+  return getSOPInstanceReference(
+    viewports,
+    resolveObjectPath(viewports, 'activeViewportIndex')
+  );
+}
+
+function getSOPInstanceReferencesFromViewports(viewports) {
+  const list = [];
+  const viewportSpecificData = resolveObjectPath(
+    viewports,
+    'viewportSpecificData'
+  );
+  Object.keys(viewportSpecificData).forEach(index => {
+    const { StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID } = Object(
+      viewportSpecificData[index]
+    );
+    hierarchicalListUtils.addToList(
+      list,
+      validDicomUid(StudyInstanceUID),
+      validDicomUid(SeriesInstanceUID),
+      validDicomUid(SOPInstanceUID)
+    );
+  });
+  return list;
+}
+
+function save(promise, listOfUIDs) {
+  return Promise.resolve(promise)
+    .then(url => {
+      OHIF.log.info('Files successfully compressed:', url);
+      const StudyInstanceUID = hierarchicalListUtils.getItem(listOfUIDs, 0);
+      saveAs(url, `${StudyInstanceUID}.zip`);
+      return url;
+    })
+    .catch(error => {
+      OHIF.log.error('Failed to create Zip file...', error);
+      return null;
+    });
+}
+
+export {
+  save,
+  validDicomUid,
+  getDicomWebClientFromConfig,
+  getDicomWebClientFromContext,
+  getSOPInstanceReferenceFromActiveViewport,
+  getSOPInstanceReferencesFromViewports,
+};

extensions/dicom-pdf/CHANGELOG.md

@@ -3,6 +3,14 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [1.0.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@1.0.2...@ohif/extension-dicom-pdf@1.0.3) (2020-04-02)
+
+**Note:** Version bump only for package @ohif/extension-dicom-pdf
+
+
+
+
+
 ## [1.0.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@1.0.1...@ohif/extension-dicom-pdf@1.0.2) (2020-03-09)
 
 **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": "1.0.2",
+  "version": "1.0.3",
   "description": "OHIF extension for Dicom PDF",
   "author": "OHIF",
   "license": "MIT",

extensions/dicom-pdf/src/asyncComponent.js

@@ -1,37 +0,0 @@
-/**
- * We use this component to leverage "Code Splitting"
- *
- * Link: https://serverless-stack.com/chapters/code-splitting-in-create-react-app.html
- */
-
-import React, { Component } from 'react';
-
-export default function asyncComponent(importComponent) {
-  class AsyncComponent extends Component {
-    constructor(props) {
-      super(props);
-
-      this.state = {
-        component: null,
-      };
-    }
-
-    async componentDidMount() {
-      // Add dynamically loaded component to state
-      const { default: component } = await importComponent();
-
-      this.setState({
-        component: component,
-      });
-    }
-
-    render() {
-      const C = this.state.component;
-
-      // Render the loaded component, or null
-      return C ? <C {...this.props} /> : null;
-    }
-  }
-
-  return AsyncComponent;
-}

extensions/dicom-pdf/src/index.js

@@ -1,11 +1,17 @@
-import asyncComponent from './asyncComponent.js';
+import React from 'react';
 import OHIFDicomPDFSopClassHandler from './OHIFDicomPDFSopClassHandler.js';
 
-const ConnectedOHIFDicomPDFViewer = asyncComponent(() =>
-  import(
-    /* webpackChunkName: "ConnectedOHIFDicomPDFViewer" */ './ConnectedOHIFDicomPDFViewer'
-  )
-);
+const Component = React.lazy(() => {
+  return import('./ConnectedOHIFDicomPDFViewer');
+});
+
+const ConnectedOHIFDicomPDFViewer = props => {
+  return (
+    <React.Suspense fallback={<div>Loading...</div>}>
+      <Component {...props} />
+    </React.Suspense>
+  );
+};
 
 export default {
   /**

extensions/dicom-rt/.webpack/webpack.dev.js

@@ -0,0 +1,8 @@
+const path = require('path');
+const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+
+module.exports = (env, argv) => {
+  return webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
+};

extensions/dicom-rt/.webpack/webpack.prod.js

@@ -0,0 +1,44 @@
+const webpack = require('webpack');
+const merge = require('webpack-merge');
+const path = require('path');
+const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
+const pkg = require('./../package.json');
+
+const ROOT_DIR = path.join(__dirname, './..');
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+
+module.exports = (env, argv) => {
+  const commonConfig = webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
+
+  return merge(commonConfig, {
+    devtool: 'source-map',
+    stats: {
+      colors: true,
+      hash: true,
+      timings: true,
+      assets: true,
+      chunks: false,
+      chunkModules: false,
+      modules: false,
+      children: false,
+      warnings: true,
+    },
+    optimization: {
+      minimize: true,
+      sideEffects: true,
+    },
+    output: {
+      path: ROOT_DIR,
+      library: 'OHIFExtDicomSeg',
+      libraryTarget: 'umd',
+      libraryExport: 'default',
+      filename: pkg.main,
+    },
+    plugins: [
+      new webpack.optimize.LimitChunkCountPlugin({
+        maxChunks: 1,
+      }),
+    ],
+  });
+};

extensions/dicom-rt/CHANGELOG.md

@@ -0,0 +1,27 @@
+# Change Log
+
+All notable changes to this project will be documented in this file.
+See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+## [0.1.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.1.0...@ohif/extension-dicom-rt@0.1.1) (2020-04-28)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt
+
+
+
+
+
+# [0.1.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.0.2...@ohif/extension-dicom-rt@0.1.0) (2020-04-24)
+
+
+### Features
+
+* 🎸 Seg jump to slice + show/hide ([835f64d](https://github.com/OHIF/Viewers/commit/835f64d47a9994f6a25aaf3941a4974e215e7e7f))
+
+
+
+
+
+## 0.0.2 (2020-04-09)
+
+**Note:** Version bump only for package @ohif/extension-dicom-rt

extensions/dicom-rt/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 Open Health Imaging Foundation
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

extensions/dicom-rt/README.md

@@ -0,0 +1 @@
+# @ohif/extension-dicom-rt

extensions/dicom-rt/package.json

@@ -0,0 +1,43 @@
+{
+  "name": "@ohif/extension-dicom-rt",
+  "version": "0.1.1",
+  "description": "OHIF extension for rendering DICOM RTSTRUCTs on top of cornerstone images.",
+  "author": "OHIF",
+  "license": "MIT",
+  "repository": "OHIF/Viewers",
+  "main": "dist/index.umd.js",
+  "module": "src/index.js",
+  "engines": {
+    "node": ">=10",
+    "npm": ">=6",
+    "yarn": ">=1.16.0"
+  },
+  "files": [
+    "dist",
+    "README.md"
+  ],
+  "publishConfig": {
+    "access": "public"
+  },
+  "scripts": {
+    "dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --debug --output-pathinfo",
+    "dev:dicom-html": "yarn run dev",
+    "build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
+    "build:package": "yarn run build",
+    "prepublishOnly": "yarn run build",
+    "start": "yarn run dev"
+  },
+  "peerDependencies": {
+    "@ohif/core": "^0.50.0",
+    "cornerstone-core": "^2.2.8",
+    "cornerstone-tools": "^4.0.9",
+    "dcmjs": "^0.12.2",
+    "prop-types": "^15.6.2",
+    "react": "^16.8.6",
+    "react-dom": "^16.8.6"
+  },
+  "dependencies": {
+    "@babel/runtime": "^7.5.5",
+    "react-select": "^3.0.8"
+  }
+}

extensions/dicom-rt/src/OHIFDicomRTStructSopClassHandler.js

@@ -0,0 +1,237 @@
+import { MODULE_TYPES, utils, DICOMWeb } from '@ohif/core';
+import loadRTStruct from './loadRTStruct';
+
+import id from './id';
+
+// TODO: Should probably use dcmjs for this
+const SOP_CLASS_UIDS = {
+  DICOM_RT_STRUCT: '1.2.840.10008.5.1.4.1.1.481.3',
+};
+
+const sopClassUIDs = Object.values(SOP_CLASS_UIDS);
+
+const OHIFDicomRTStructSopClassHandler = {
+  id: 'OHIFDicomRTStructSopClassHandler',
+  type: MODULE_TYPES.SOP_CLASS_HANDLER,
+  sopClassUIDs,
+  getDisplaySetFromSeries: function (
+    series,
+    study,
+    dicomWebClient,
+    authorizationHeaders
+  ) {
+    const instance = series.getFirstInstance();
+
+    const metadata = instance.getData().metadata;
+    const {
+      SeriesDate,
+      SeriesTime,
+      SeriesDescription,
+      FrameOfReferenceUID,
+      SOPInstanceUID,
+      SeriesInstanceUID,
+      StudyInstanceUID,
+    } = metadata;
+
+    // TODO -> GET REFERENCED FRAME OF REFERENCE SEQUENCE.
+
+    const rtStructDisplaySet = {
+      Modality: 'RTSTRUCT',
+      displaySetInstanceUID: utils.guid(),
+      wadoRoot: study.getData().wadoRoot,
+      wadoUri: instance.getData().wadouri,
+      SOPInstanceUID,
+      SeriesInstanceUID,
+      StudyInstanceUID,
+      FrameOfReferenceUID,
+      authorizationHeaders,
+      metadata,
+      isDerived: true,
+      referencedDisplaySetUID: null, // Assigned when loaded.
+      labelmapIndex: null, // Assigned when loaded.
+      isLoaded: false,
+      SeriesDate,
+      SeriesTime,
+      SeriesDescription,
+    };
+
+    if (!metadata.ReferencedSeriesSequence) {
+      const ReferencedFrameOfReferenceSequence =
+        metadata.ReferencedFrameOfReferenceSequence;
+
+      if (ReferencedFrameOfReferenceSequence) {
+        // TODO -> @dannyrb Do we augment metadata or add a (potentially large? fallback list in filterDerivedDisplaySets )
+        metadata.ReferencedSeriesSequence = _deriveReferencedSeriesSequenceFromFrameOfReferenceSequence(
+          ReferencedFrameOfReferenceSequence
+        );
+      }
+    }
+
+    rtStructDisplaySet.load = function (referencedDisplaySet, studies) {
+      return loadRTStruct(
+        rtStructDisplaySet,
+        referencedDisplaySet,
+        studies
+      ).catch(error => {
+        rtStructDisplaySet.isLoaded = false;
+        throw new Error(error);
+      });
+    };
+
+    return rtStructDisplaySet;
+  },
+};
+
+function _deriveReferencedSeriesSequenceFromFrameOfReferenceSequence(
+  ReferencedFrameOfReferenceSequence
+) {
+  const ReferencedSeriesSequence = [];
+
+  _getSequenceAsArray(ReferencedFrameOfReferenceSequence).forEach(
+    referencedFrameOfReference => {
+      const { RTReferencedStudySequence } = referencedFrameOfReference;
+
+      _getSequenceAsArray(RTReferencedStudySequence).forEach(
+        rtReferencedStudy => {
+          const { RTReferencedSeriesSequence } = rtReferencedStudy;
+
+          _getSequenceAsArray(RTReferencedSeriesSequence).forEach(
+            rtReferencedSeries => {
+              const ReferencedInstanceSequence = [];
+              const {
+                ContourImageSequence,
+                SeriesInstanceUID,
+              } = rtReferencedSeries;
+
+              _getSequenceAsArray(ContourImageSequence).forEach(
+                contourImage => {
+                  ReferencedInstanceSequence.push({
+                    ReferencedSOPInstanceUID:
+                      contourImage.ReferencedSOPInstanceUID,
+                    ReferencedSOPClassUID: contourImage.ReferencedSOPClassUID,
+                  });
+                }
+              );
+
+              const referencedSeries = {
+                SeriesInstanceUID,
+                ReferencedInstanceSequence,
+              };
+
+              ReferencedSeriesSequence.push(referencedSeries);
+            }
+          );
+        }
+      );
+    }
+  );
+
+  return ReferencedSeriesSequence;
+}
+
+function _getSequenceAsArray(sequence) {
+  return Array.isArray(sequence) ? sequence : [sequence];
+}
+
+function _getReferencedFrameOfReferenceSequence(instance) {
+  const referencedFrameOfReferenceSequenceRaw = instance['30060010'];
+
+  const referencedFrameOfReferenceSequence = [];
+
+  if (
+    !referencedFrameOfReferenceSequenceRaw ||
+    !referencedFrameOfReferenceSequenceRaw.Value
+  ) {
+    return undefined;
+  }
+
+  referencedFrameOfReferenceSequenceRaw.Value.forEach(
+    referencedFrameOfReferenceRaw => {
+      const frameOfReferenceUID = DICOMWeb.getString(
+        referencedFrameOfReferenceRaw['00200052']
+      );
+
+      const referencedFrameOfReference = { frameOfReferenceUID };
+      const RTReferencedStudySequenceRaw =
+        referencedFrameOfReferenceRaw['30060012'];
+
+      referencedFrameOfReferenceSequence.push(referencedFrameOfReference);
+
+      if (RTReferencedStudySequenceRaw && RTReferencedStudySequenceRaw.Value) {
+        referencedFrameOfReference.rtReferencedStudySequence = [];
+
+        const { rtReferencedStudySequence } = referencedFrameOfReference;
+
+        RTReferencedStudySequenceRaw.Value.forEach(rtReferencedStudyRaw => {
+          const referencedSopClassUID = DICOMWeb.getString(
+            rtReferencedStudyRaw['00081150']
+          );
+
+          const referencedSOPInstanceUID = DICOMWeb.getString(
+            rtReferencedStudyRaw['00081155']
+          );
+
+          const rtReferencedStudy = {
+            referencedSopClassUID,
+            referencedSOPInstanceUID,
+            rtReferencedSeriesSequence: [],
+          };
+
+          rtReferencedStudySequence.push(rtReferencedStudy);
+
+          const { rtReferencedSeriesSequence } = rtReferencedStudy;
+
+          const rtReferencedSeriesSequenceRaw =
+            rtReferencedStudyRaw['30060014'];
+
+          rtReferencedSeriesSequenceRaw.Value.forEach(rtReferencedSeriesRaw => {
+            const seriesInstanceUID = DICOMWeb.getString(
+              rtReferencedSeriesRaw['0020000E']
+            );
+
+            const rtReferencedSeries = {
+              seriesInstanceUID,
+              contourImageSequence: [],
+            };
+
+            rtReferencedSeriesSequence.push(rtReferencedSeries);
+
+            const { contourImageSequence } = rtReferencedSeries;
+
+            const contourImageSequenceRaw = rtReferencedSeriesRaw['30060016'];
+
+            contourImageSequenceRaw.Value.forEach(contourImageRaw => {
+              const referencedSOPClassUID = DICOMWeb.getString(
+                contourImageRaw['00081150']
+              );
+
+              const referencedSOPInstanceUID = DICOMWeb.getString(
+                contourImageRaw['00081155']
+              );
+
+              const referencedFrameNumber = DICOMWeb.getString(
+                contourImageRaw['00081160']
+              );
+              const referencedSegmentNumber = DICOMWeb.getString(
+                contourImageRaw['0062000B']
+              );
+
+              const contourImage = {
+                referencedSOPClassUID,
+                referencedSOPInstanceUID,
+                referencedFrameNumber,
+                referencedSegmentNumber,
+              };
+
+              contourImageSequence.push(contourImage);
+            });
+          });
+        });
+      }
+    }
+  );
+
+  return referencedFrameOfReferenceSequence;
+}
+
+export default OHIFDicomRTStructSopClassHandler;

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

@@ -0,0 +1,61 @@
+import React from 'react';
+
+const LoadingIndicator = ({ height = "200px", width = "200px", expand = false }) => {
+  return (
+    <div style={expand ? { height: "100%", width: "100%" } : {}}>
+      <svg style={{ margin: 'auto', background: 'none', display: 'block', shapeRendering: 'auto' }} width={width} height={height} viewBox="0 0 100 100" preserveAspectRatio="xMidYMid">
+        <g transform="rotate(0 50 50)">
+          <rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
+            <animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.9166666666666666s" repeatCount="indefinite"></animate>
+          </rect>
+        </g><g transform="rotate(30 50 50)">
+          <rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
+            <animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.8333333333333334s" repeatCount="indefinite"></animate>
+          </rect>
+        </g><g transform="rotate(60 50 50)">
+          <rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
+            <animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.75s" repeatCount="indefinite"></animate>
+          </rect>
+        </g><g transform="rotate(90 50 50)">
+          <rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
+            <animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.6666666666666666s" repeatCount="indefinite"></animate>
+          </rect>
+        </g><g transform="rotate(120 50 50)">
+          <rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
+            <animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.5833333333333334s" repeatCount="indefinite"></animate>
+          </rect>
+        </g><g transform="rotate(150 50 50)">
+          <rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
+            <animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.5s" repeatCount="indefinite"></animate>
+          </rect>
+        </g><g transform="rotate(180 50 50)">
+          <rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
+            <animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.4166666666666667s" repeatCount="indefinite"></animate>
+          </rect>
+        </g><g transform="rotate(210 50 50)">
+          <rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
+            <animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.3333333333333333s" repeatCount="indefinite"></animate>
+          </rect>
+        </g><g transform="rotate(240 50 50)">
+          <rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
+            <animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.25s" repeatCount="indefinite"></animate>
+          </rect>
+        </g><g transform="rotate(270 50 50)">
+          <rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
+            <animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.16666666666666666s" repeatCount="indefinite"></animate>
+          </rect>
+        </g><g transform="rotate(300 50 50)">
+          <rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
+            <animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.08333333333333333s" repeatCount="indefinite"></animate>
+          </rect>
+        </g><g transform="rotate(330 50 50)">
+          <rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
+            <animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="0s" repeatCount="indefinite"></animate>
+          </rect>
+        </g>
+      </svg>
+    </div>
+  );
+};
+
+export default LoadingIndicator;

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

@@ -0,0 +1,44 @@
+.dcmrt-panel-section {
+  display: flex;
+  flex-direction: column;
+  color: var(--text-primary-color);
+  font-size: 12px;
+}
+
+.dcmrt-panel-section .header {
+  display: flex;
+  flex-direction: row;
+  align-items: center;
+  justify-content: space-between;
+  background-color: var(--ui-gray-dark);
+  border-radius: 5px;
+  font-weight: bold;
+  padding: 10px 15px;
+}
+
+.dcmrt-panel-section .header .eye-icon,
+.dcmrt-panel-section .header .angle-double-down,
+.dcmrt-panel-section .header .angle-double-up {
+  cursor: pointer;
+  color: var(--active-color);
+}
+
+.dcmrt-panel-section .header .eye-icon:hover,
+.dcmrt-panel-section .header .angle-double-down:hover,
+.dcmrt-panel-section .header .angle-double-up:hover {
+  color: var(--hover-color);
+}
+
+.dcmrt-panel-section .header .eye-icon.expanded {
+  color: var(--default-color);
+}
+
+.icons {
+  display: flex;
+  align-items: center;
+  border-radius: 5px;
+}
+
+.icons .angle-double-down, .icons .angle-double-up {
+  margin-left: 15px;
+}

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

@@ -0,0 +1,82 @@
+import React, { useState, useEffect } from 'react';
+import PropTypes from 'prop-types';
+import { Icon } from '@ohif/ui';
+
+import './PanelSection.css';
+import LoadingIndicator from '../LoadingIndicator/LoadingIndicator';
+
+const PanelSection = ({
+  title,
+  children,
+  visible = false,
+  expanded = false,
+  loading = false,
+  hideVisibleButton = false,
+  onVisibilityChange = () => { },
+  onExpandChange = () => { }
+}) => {
+  const [isExpanded, setIsExpanded] = useState(expanded);
+  const [isVisible, setIsVisible] = useState(visible);
+
+  useEffect(() => {
+    setIsVisible(visible);
+  }, [visible]);
+
+  return (
+    <div
+      className="dcmrt-panel-section"
+      style={{
+        marginBottom: isExpanded ? 0 : 2,
+        height: isExpanded ? '100%' : 'unset'
+      }}
+    >
+      <div className="header">
+        <div>{title}</div>
+        <div className="icons">
+          {!hideVisibleButton && (
+            <Icon
+              className={`eye-icon ${isVisible && 'expanded'}`}
+              name={isVisible ? "eye" : "eye-closed"}
+              width="20px"
+              height="20px"
+              onClick={() => {
+                const newVisibility = !isVisible;
+                setIsVisible(newVisibility);
+                onVisibilityChange(newVisibility);
+              }}
+            />
+          )}
+          <Icon
+            className={`angle-double-${isExpanded ? 'down' : 'up'} ${isExpanded && 'expanded'}`}
+            name={`angle-double-${isExpanded ? 'down' : 'up'}`}
+            width="20px"
+            height="20px"
+            onClick={() => {
+              const newExpandValue = !isExpanded;
+              setIsExpanded(newExpandValue);
+              onExpandChange(newExpandValue);
+            }}
+          />
+        </div>
+      </div>
+      {loading && isExpanded && <LoadingIndicator expand height="70px" width="70px" />}
+      {children}
+    </div>
+  );
+};
+
+PanelSection.propTypes = {
+  title: PropTypes.string.isRequired,
+  children: PropTypes.oneOfType([PropTypes.node, PropTypes.func]).isRequired,
+  visible: PropTypes.bool,
+  expanded: PropTypes.bool,
+  onVisibilityChange: PropTypes.func
+};
+
+PanelSection.defaultProps = {
+  visible: false,
+  expanded: false,
+  onVisibilityChange: () => { }
+};
+
+export default PanelSection;

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

@@ -0,0 +1,26 @@
+.dcmrt-panel {
+  display: flex;
+  flex-direction: column;
+  background-color: var(--primary-background-color);
+  height: 100%;
+  width: 100%;
+  padding: 20px;
+}
+
+.dcmrt-panel .dcmrt-panel-header {
+  display: flex;
+  flex-direction: row;
+  justify-content: space-between;
+  color: white;
+}
+
+.dcmrt-panel .dcmrt-panel-header .cog-icon {
+  align-self: flex-end;
+  color: var(--default-color);
+  cursor: pointer;
+  margin-bottom: 20px;
+}
+
+.dcmrt-panel .dcmrt-panel-header .cog-icon:hover {
+  color: var(--hover-color);
+}

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

@@ -0,0 +1,258 @@
+import React, { useState, useEffect } from 'react';
+import PropTypes from 'prop-types';
+import cornerstoneTools from 'cornerstone-tools';
+import cornerstone from 'cornerstone-core';
+
+import { ScrollableArea, TableList, Icon } from '@ohif/ui';
+
+import { utils } from '@ohif/core';
+
+import './RTPanel.css';
+import StructureSetItem from '../StructureSetItem/StructureSetItem';
+import RTPanelSettings from '../RTSettings/RTSettings';
+import PanelSection from '../PanelSection/PanelSection';
+import LoadingIndicator from '../LoadingIndicator/LoadingIndicator';
+
+const { studyMetadataManager } = utils;
+
+const refreshViewport = () => {
+  cornerstone.getEnabledElements().forEach(enabledElement => {
+    cornerstone.updateImage(enabledElement.element);
+  });
+};
+
+/**
+ * RTPanel component
+ *
+ * @param {Object} props
+ * @param {Array} props.studies
+ * @param {Array} props.viewports - viewportSpecificData
+ * @param {number} props.activeIndex - activeViewportIndex
+ * @param {number} props.isOpen - isOpen
+ * @returns component
+ */
+const RTPanel = ({ studies, viewports, activeIndex, isOpen, onContourItemClick }) => {
+  const [selectedContour, setSelectedContour] = useState();
+  const DEFAULT_SET_INDEX = 0;
+  const DEFAULT_STATE = {
+    referencedDisplaysets: [],
+    sets: [],
+    selectedSet: null,
+  };
+
+  const [state, setState] = useState(DEFAULT_STATE);
+  const [showSettings, setShowSettings] = useState(false);
+  const activeViewport = viewports[activeIndex];
+
+  /*
+   * TODO: Improve the way we notify parts of the app that depends on rts to be loaded.
+   *
+   * Currently we are using a non-ideal implementation through a custom event to notify the rtstruct panel
+   * or other components that could rely on loaded rtstructs that
+   * the first batch of structs were loaded so that e.g. when the user opens the panel
+   * before the structs are fully loaded, the panel can subscribe to this custom event
+   * and update itself with the new structs.
+   *
+   * This limitation is due to the fact that the rtmodule is an object (which will be
+   * updated after the structs are loaded) that React its not aware of its changes
+   * because the module object its not passed in to the panel component as prop but accessed externally.
+   *
+   * Improving this event approach to something reactive that can be tracked inside the react lifecycle,
+   * allows us to easily watch the module or the rtstruct loading process in any other component
+   * without subscribing to external events.
+   */
+  useEffect(() => {
+    document.addEventListener('extensiondicomrtrtloaded', updateStructureSets);
+
+    return () => {
+      document.removeEventListener('extensiondicomrtrtloaded', updateStructureSets);
+    };
+  }, []);
+
+  const updateStructureSets = () => {
+    const module = cornerstoneTools.getModule('rtstruct');
+    const StructureSets = module.state.StructureSets;
+
+    if (StructureSets && StructureSets.length) {
+      const viewportSets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(
+        activeViewport.SeriesInstanceUID
+      );
+
+      const studyMetadata = studyMetadataManager.get(activeViewport.StudyInstanceUID);
+      const referencedDisplaysets = studyMetadata.getDerivedDatasets({
+        referencedSeriesInstanceUID: activeViewport.SeriesInstanceUID,
+        Modality: 'RTSTRUCT',
+      });
+
+      if (viewportSets.length) {
+        const defaultSet = viewportSets[DEFAULT_SET_INDEX];
+        setState({
+          referencedDisplaysets,
+          selectedSet: defaultSet,
+          sets: viewportSets
+        });
+      } else {
+        setState(DEFAULT_STATE);
+      }
+    }
+  };
+
+  useEffect(() => {
+    updateStructureSets();
+  }, [studies, viewports, activeIndex]);
+
+  useEffect(() => {
+    setShowSettings(showSettings && !isOpen);
+  }, [isOpen]);
+
+  const toContourItem = ({ ROINumber, ROIName, RTROIObservations, colorArray, visible }, loadedSet) => {
+    let interpretedType = '';
+    if (RTROIObservations && RTROIObservations.RTROIInterpretedType) {
+      interpretedType = `(${RTROIObservations.RTROIInterpretedType})`;
+    }
+
+    const isSameContour = selectedContour && selectedContour === ROINumber;
+    return (
+      <StructureSetItem
+        key={ROINumber}
+        selected={isSameContour}
+        onClick={() => {
+          setSelectedContour(isSameContour ? null : ROINumber);
+
+          const enabledElements = cornerstone.getEnabledElements();
+          const element = enabledElements[activeIndex].element;
+          const toolState = cornerstoneTools.getToolState(element, 'stack');
+
+          if (!toolState) {
+            return;
+          }
+
+          const imageIds = toolState.data[0].imageIds;
+
+          const module = cornerstoneTools.getModule('rtstruct');
+          const imageId = module.getters.imageIdOfCenterFrameOfROIContour(
+            state.selectedSet.SeriesInstanceUID,
+            ROINumber,
+            imageIds
+          );
+
+          const frameIndex = imageIds.indexOf(imageId);
+          const SOPInstanceUID = cornerstone.metaData.get('SOPInstanceUID', imageId);
+          const StudyInstanceUID = cornerstone.metaData.get('StudyInstanceUID', imageId);
+
+          onContourItemClick({
+            StudyInstanceUID,
+            SOPInstanceUID,
+            frameIndex,
+            activeViewportIndex: activeIndex
+          });
+        }}
+        label={`${ROIName} ${interpretedType}`}
+        index={ROINumber}
+        color={colorArray}
+        visible={visible}
+        onVisibilityChange={() => {
+          const module = cornerstoneTools.getModule('rtstruct');
+          module.setters.toggleROIContour(state.selectedSet.SeriesInstanceUID, ROINumber);
+        }}
+      />
+    );
+  };
+
+  const configurationChangeHandler = newConfiguration => {
+    const module = cornerstoneTools.getModule('rtstruct');
+    module.configuration.lineWidth = newConfiguration.lineWidth;
+    module.configuration.opacity = newConfiguration.opacity;
+    refreshViewport();
+  };
+
+  if (showSettings) {
+    const module = cornerstoneTools.getModule('rtstruct');
+    return (
+      <RTPanelSettings
+        configuration={module.configuration}
+        onBack={() => setShowSettings(false)}
+        onChange={configurationChangeHandler}
+      />
+    );
+  }
+
+  return (
+    <div className="dcmrt-panel">
+      <div className="dcmrt-panel-header">
+        <h3>RT Structure Sets</h3>
+        <Icon
+          className="cog-icon"
+          name="cog"
+          width="25px"
+          height="25px"
+          onClick={() => setShowSettings(true)}
+        />
+      </div>
+      {!state.referencedDisplaysets.length && <LoadingIndicator expand height="70px" width="70px" />}
+      {state.referencedDisplaysets.map(displaySet => {
+        const { SeriesInstanceUID, metadata, isLoaded } = displaySet;
+
+        const module = cornerstoneTools.getModule('rtstruct');
+        const sets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(viewports[activeIndex].SeriesInstanceUID);
+
+        const loadedSet = sets.find(set => set.SeriesInstanceUID === SeriesInstanceUID);
+        return (
+          <PanelSection
+            key={SeriesInstanceUID}
+            title={metadata.StructureSetLabel}
+            loading={!isLoaded || !loadedSet}
+            visible={isLoaded && loadedSet.visible}
+            hideVisibleButton={!isLoaded}
+            expanded={isLoaded && loadedSet.SeriesInstanceUID === state.selectedSet.SeriesInstanceUID}
+            onVisibilityChange={() => {
+              const module = cornerstoneTools.getModule('rtstruct');
+              module.setters.toggleStructureSet(SeriesInstanceUID);
+            }}
+            onExpandChange={async () => {
+              if (!isLoaded) {
+                await displaySet.load(viewports[activeIndex], studies);
+                const module = cornerstoneTools.getModule('rtstruct');
+                const sets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(viewports[activeIndex].SeriesInstanceUID);
+                const selectedSet = sets.find(set => set.SeriesInstanceUID === SeriesInstanceUID);
+                setState(state => ({ ...state, selectedSet, sets }));
+              }
+            }}
+          >
+            <ScrollableArea>
+              <TableList headless>
+                {isLoaded && loadedSet.ROIContours.map(c => toContourItem(c, loadedSet))}
+              </TableList>
+            </ScrollableArea>
+          </PanelSection>
+        );
+      })}
+    </div>
+  );
+};
+
+RTPanel.propTypes = {
+  viewports: PropTypes.shape({
+    displaySetInstanceUID: PropTypes.string,
+    frameRate: PropTypes.any,
+    InstanceNumber: PropTypes.number,
+    isMultiFrame: PropTypes.bool,
+    isReconstructable: PropTypes.bool,
+    Modality: PropTypes.string,
+    plugin: PropTypes.string,
+    SeriesDate: PropTypes.string,
+    SeriesDescription: PropTypes.string,
+    SeriesInstanceUID: PropTypes.string,
+    SeriesNumber: PropTypes.any,
+    SeriesTime: PropTypes.string,
+    sopClassUIDs: PropTypes.arrayOf(PropTypes.string),
+    StudyInstanceUID: PropTypes.string,
+  }),
+  activeIndex: PropTypes.number.isRequired,
+  studies: PropTypes.array.isRequired,
+  isOpen: PropTypes.bool.isRequired,
+};
+
+RTPanel.defaultProps = {};
+
+export default RTPanel;

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

@@ -0,0 +1,88 @@
+.dcmrt-settings {
+  display: flex;
+  flex-direction: column;
+  padding: 20px;
+  color: white;
+}
+
+.dcmrt-settings .settings-title {
+  display: flex;
+  flex-direction: row;
+  align-items: center;
+  justify-content: space-between;
+  padding-bottom: 20px;
+}
+
+.dcmrt-settings .settings-title h3 {
+  color: var(--text-primary-color);
+  margin: 0;
+  padding: 0;
+}
+
+.dcmrt-settings .settings-section .content {
+  padding: 10px;
+  background-color: var(--ui-gray-dark);
+  border-radius: 5px;
+}
+
+.dcmrt-settings .settings-section .header {
+  border-bottom: 2px solid black;
+  display: flex;
+  flex-direction: row;
+  align-items: center;
+  justify-content: space-between;
+  background-color: var(--ui-gray-dark);
+  border-radius: 5px;
+  font-weight: bold;
+  font-size: 12px;
+  padding: 10px 15px;
+}
+
+.dcmrt-settings .settings-section p {
+  font-weight: bold;
+}
+
+.dcmrt-settings .range {
+  display: flex;
+  padding: 10px 10px;
+  font-size: 12px;
+}
+
+.dcmrt-settings .range:not(:last-of-type) {
+  padding-bottom: 0;
+}
+
+.dcmrt-settings .range label {
+  margin: 0;
+  display: unset;
+  min-width: 40px;
+  max-width: 40px;
+}
+
+.dcmrt-settings .range input {
+  width: 100%;
+  padding: 0 20px 0 20px;
+}
+
+.dcmrt-settings .return-button {
+  color: #333;
+  background-color: #fff;
+  padding: 4px 12px;
+  line-height: 1.4;
+  text-align: center;
+  white-space: nowrap;
+  vertical-align: middle;
+  cursor: pointer;
+  user-select: none;
+  border: 1px solid #ccc;
+  border-radius: 4px;
+  transition: all 0.15s ease;
+}
+
+.dcmrt-settings .return-button:hover,
+.dcmrt-settings .return-button:active,
+.dcmrt-settings .return-button.active {
+  background-color: var(--active-color);
+  border-color: var(--ui-border-color-active);
+  color: #fff;
+}

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

@@ -0,0 +1,71 @@
+import React, { useState, useEffect } from 'react';
+import PropTypes from 'prop-types';
+import { Range } from '@ohif/ui';
+
+import './RTSettings.css';
+
+const RTSettings = ({ configuration, onBack, onChange }) => {
+  const toFloat = value => parseFloat(value / 100).toFixed(2);
+
+  const save = (field, value) => {
+    onChange({ ...configuration, [field]: value });
+  };
+
+  const SettingsSection = ({ title, children }) => {
+    return (
+      <div className="settings-section">
+        <div className="header">{title}</div>
+        <div className="content">
+          {children}
+        </div>
+      </div>
+    );
+  };
+
+  return (
+    <div className="dcmrt-settings">
+      <div className="settings-title">
+        <h3>RT Structure Set Settings</h3>
+        <button className="return-button" onClick={onBack}>
+          Back
+        </button>
+      </div>
+
+      <SettingsSection title="Segment Outline">
+        <div className="range">
+          <label htmlFor="range">Opacity</label>
+          <Range
+            showPercentage
+            step={1}
+            min={0}
+            max={100}
+            value={configuration.opacity * 100}
+            onChange={event => save('opacity', toFloat(event.target.value))}
+          />
+        </div>
+        <div className="range">
+          <label htmlFor="range">Width</label>
+          <Range
+            showValue
+            step={1}
+            min={1}
+            max={5}
+            value={configuration.lineWidth}
+            onChange={event => save('lineWidth', parseInt(event.target.value))}
+          />
+        </div>
+      </SettingsSection>
+    </div>
+  );
+};
+
+RTSettings.propTypes = {
+  configuration: PropTypes.shape({
+    lineWidth: PropTypes.oneOfType([PropTypes.number, PropTypes.string]).isRequired,
+    opacity: PropTypes.oneOfType([PropTypes.number, PropTypes.string]).isRequired,
+  }).isRequired,
+  onBack: PropTypes.func.isRequired,
+  onChange: PropTypes.func.isRequired,
+};
+
+export default RTSettings;

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

@@ -0,0 +1,88 @@
+.dcmrt-structure-set-item .item-color-section {
+  display: flex;
+  justify-content: center;
+  align-items: center;
+  flex-direction: column;
+}
+
+.dcmrt-structure-set-item .item-color {
+  margin-top: 8px;
+  border-radius: 100%;
+  width: 20px;
+  height: 20px;
+}
+
+.dcmrt-structure-set-item .item-info {
+  display: inline-block;
+  margin-top: 9px;
+  padding-left: 9px;
+  width: 90px;
+  border-left: 1px solid var(--text-secondary-color);
+  color: var(--text-primary-color);
+  width: 100%;
+}
+
+.dcmrt-structure-set-item.selected .item-actions {
+  height: 35px;
+  visibility: visible;
+}
+
+.dcmrt-structure-set-item .item-actions {
+  margin-left: -1px;
+  background-color: var(--ui-gray-darker);
+  height: 0;
+  overflow: hidden;
+  transition: all 0.3s ease;
+  visibility: hidden;
+  padding-left: 14px;
+}
+
+.dcmrt-structure-set-item .item-actions .btnAction {
+  background-color: transparent;
+  border: none;
+  color: var(--default-color);
+  cursor: pointer;
+  line-height: 35px;
+  height: 35px;
+  transition: all 0.3s ease;
+}
+
+.dcmrt-structure-set-item .item-actions .btnAction:hover, .dcmrt-structure-set-item .item-actions .btnAction:active {
+  color: var(--text-primary-color);
+}
+
+.dcmrt-structure-set-item .item-actions .btnAction i {
+  margin-right: 4px;
+}
+
+.dcmrt-structure-set-item.selected .item-actions {
+  height: 35px;
+  visibility: visible;
+}
+
+.dcmrt-structure-set-item .item-label {
+  display: flex;
+  justify-content: space-between;
+  padding-right: 10px;
+}
+
+.dcmrt-structure-set-item .item-label span {
+  overflow-wrap: normal;
+  white-space: nowrap;
+  overflow: hidden;
+  max-width: calc(100% - 40px); /* calc(100% - 50px); 20px = eye icon */
+  text-overflow: ellipsis;
+}
+
+.dcmrt-structure-set-item .item-label .eye-icon {
+  cursor: pointer;
+  color: var(--active-color);
+}
+
+.dcmrt-structure-set-item .item-label .eye-icon:hover {
+  color: var(--hover-color);
+}
+
+.dcmrt-structure-set-item .item-label .eye-icon.--visible {
+  color: var(--default-color);
+}

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

@@ -0,0 +1,100 @@
+import React, { useState } from 'react';
+import PropTypes from 'prop-types';
+import { TableListItem, Icon } from '@ohif/ui';
+
+import './StructureSetItem.css';
+
+const ColoredCircle = ({ color }) => {
+  return (
+    <div
+      className="item-color"
+      style={{ backgroundColor: `rgba(${color.join(',')})` }}
+    ></div>
+  );
+};
+
+ColoredCircle.propTypes = {
+  color: PropTypes.array.isRequired,
+};
+
+const StructureSetItem = ({
+  index,
+  label,
+  onClick,
+  itemClass,
+  color,
+  visible = true,
+  onVisibilityChange,
+  selected = false,
+}) => {
+  const [isVisible, setIsVisible] = useState(visible);
+  return (
+    <div className={`dcmrt-structure-set-item ${selected && 'selected'}`}>
+      <TableListItem
+        key={index}
+        itemKey={index}
+        itemIndex={index}
+        itemClass={itemClass}
+        itemMeta={<ColoredCircle color={color} />}
+        itemMetaClass="item-color-section"
+        onItemClick={onClick}
+      >
+        <div>
+          <div className="item-label" style={{ marginBottom: 4 }}>
+            <span>{label}</span>
+            <Icon
+              className={`eye-icon ${isVisible && '--visible'}`}
+              name={isVisible ? 'eye' : 'eye-closed'}
+              width="20px"
+              height="20px"
+              onClick={event => {
+                event.stopPropagation();
+                const newVisibility = !isVisible;
+                setIsVisible(newVisibility);
+                onVisibilityChange(newVisibility);
+              }}
+            />
+          </div>
+          {false && <div className="item-info">{'...'}</div>}
+          {false && (
+            <div className="item-actions">
+              <button
+                className="btnAction"
+                onClick={() => console.log('Relabelling...')}
+              >
+                <span style={{ marginRight: '4px' }}>
+                  <Icon name="edit" width="14px" height="14px" />
+                </span>
+                Relabel
+              </button>
+              <button
+                className="btnAction"
+                onClick={() => console.log('Editing description...')}
+              >
+                <span style={{ marginRight: '4px' }}>
+                  <Icon name="edit" width="14px" height="14px" />
+                </span>
+                Description
+              </button>
+            </div>
+          )}
+        </div>
+      </TableListItem>
+    </div>
+  );
+};
+
+StructureSetItem.propTypes = {
+  index: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired,
+  label: PropTypes.string.isRequired,
+  onClick: PropTypes.func,
+  itemClass: PropTypes.string,
+  color: PropTypes.array.isRequired,
+};
+
+StructureSetItem.defaultProps = {
+  itemClass: '',
+  onClick: () => { },
+};
+
+export default StructureSetItem;

extensions/dicom-rt/src/id.js

@@ -0,0 +1,3 @@
+const id = 'rt';
+
+export default id;

extensions/dicom-rt/src/index.js

@@ -0,0 +1,77 @@
+import React from 'react';
+
+import init from './init.js';
+import sopClassHandlerModule from './OHIFDicomRTStructSopClassHandler';
+import id from './id.js';
+import RTPanel from './components/RTPanel/RTPanel';
+
+export default {
+  /**
+   * Only required property. Should be a unique value across all extensions.
+   */
+  id,
+
+  /**
+   *
+   *
+   * @param {object} [configuration={}]
+   * @param {object|array} [configuration.csToolsConfig] - Passed directly to `initCornerstoneTools`
+   */
+  preRegistration({ servicesManager, configuration = {} }) {
+    init({ servicesManager, configuration });
+  },
+  getPanelModule({ commandsManager }) {
+    const ExtendedRTPanel = props => {
+      const contourItemClickHandler = contourData => {
+        commandsManager.runCommand('jumpToImage', contourData);
+      };
+
+      return (
+        <RTPanel {...props} onContourItemClick={contourItemClickHandler} />
+      );
+    };
+
+    return {
+      menuOptions: [
+        {
+          icon: 'list',
+          label: 'RTSTRUCT',
+          target: 'rt-panel',
+          isDisabled: studies => {
+            if (!studies) {
+              return true;
+            }
+
+            for (let i = 0; i < studies.length; i++) {
+              const study = studies[i];
+
+              if (study && study.series) {
+                for (let j = 0; j < study.series.length; j++) {
+                  const series = study.series[j];
+                  if (
+                    /* Could be expanded to contain RTPLAN and RTDOSE information in the future */
+                    ['RTSTRUCT'].includes(series.Modality)
+                  ) {
+                    return false;
+                  }
+                }
+              }
+            }
+
+            return true;
+          },
+        },
+      ],
+      components: [
+        {
+          id: 'rt-panel',
+          component: ExtendedRTPanel,
+        },
+      ],
+      defaultContext: ['VIEWER'],
+    };
+  },
+  getSopClassHandlerModule({ servicesManager }) {
+    return sopClassHandlerModule;
+  },
+};

extensions/dicom-rt/src/init.js

@@ -0,0 +1,25 @@
+import cornerstoneTools from 'cornerstone-tools';
+import RTStructDisplayTool from './tools/RTStructDisplayTool';
+import rtStructModule from './tools/modules/rtStructModule';
+
+import TOOL_NAMES from './utils/toolNames';
+
+const defaultConfig = {
+  TOOL_NAMES: {
+    RT_STRUCT_DISPLAY_TOOL: 'RTStructDisplayTool',
+  },
+};
+
+/**
+ *
+ * @param {object} configuration
+ * @param {Object|Array} configuration.csToolsConfig
+ */
+export default function init({ servicesManager, configuration = {} }) {
+  const conifg = Object.assign({}, defaultConfig, configuration);
+
+  TOOL_NAMES.RT_STRUCT_DISPLAY_TOOL = conifg.TOOL_NAMES.RT_STRUCT_DISPLAY_TOOL;
+
+  cornerstoneTools.register('module', 'rtstruct', rtStructModule);
+  cornerstoneTools.addTool(RTStructDisplayTool);
+}

extensions/dicom-rt/src/loadRTStruct.js

@@ -0,0 +1,309 @@
+import OHIF from '@ohif/core';
+import dcmjs from 'dcmjs';
+import cornerstone from 'cornerstone-core';
+import cornerstoneTools from 'cornerstone-tools';
+import transformPointsToImagePlane from './utils/transformPointsToImagePlane';
+import TOOL_NAMES from './utils/toolNames';
+
+const dicomlab2RGB = dcmjs.data.Colors.dicomlab2RGB;
+const globalImageIdSpecificToolStateManager =
+  cornerstoneTools.globalImageIdSpecificToolStateManager;
+const { DicomLoaderService } = OHIF.utils;
+
+export default async function loadRTStruct(
+  rtStructDisplaySet,
+  referencedDisplaySet,
+  studies
+) {
+  const rtStructModule = cornerstoneTools.getModule('rtstruct');
+
+  // Set here is loading is asynchronous.
+  // If this function throws its set back to false.
+  rtStructDisplaySet.isLoaded = true;
+
+  const { StudyInstanceUID, SeriesInstanceUID } = referencedDisplaySet;
+
+  const segArrayBuffer = await DicomLoaderService.findDicomDataPromise(
+    rtStructDisplaySet,
+    studies
+  );
+
+  const dicomData = dcmjs.data.DicomMessage.readFile(segArrayBuffer);
+  const rtStructDataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
+    dicomData.dict
+  );
+
+  rtStructDataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(
+    dicomData.meta
+  );
+
+  // global cornerstone tools state to attach measurements to.
+  const toolState = globalImageIdSpecificToolStateManager.saveToolState();
+
+  const {
+    StructureSetROISequence,
+    ROIContourSequence,
+    RTROIObservationsSequence,
+    StructureSetLabel,
+  } = rtStructDataset;
+
+  // Define our structure set entry and add it to the rtstruct module state.
+  const structureSet = {
+    StructureSetLabel,
+    SeriesInstanceUID: rtStructDataset.SeriesInstanceUID,
+    ROIContours: [],
+    referencedSeriesSequence:
+      rtStructDisplaySet.metadata.ReferencedSeriesSequence,
+    visible: true,
+  };
+
+  rtStructModule.setters.structureSet(structureSet);
+
+  const imageIdSopInstanceUidPairs = _getImageIdSopInstanceUidPairsForDisplaySet(
+    studies,
+    StudyInstanceUID,
+    SeriesInstanceUID
+  );
+
+  const rtStructDisplayToolName = TOOL_NAMES.RTSTRUCT_DISPLAY_TOOL;
+
+  for (let i = 0; i < ROIContourSequence.length; i++) {
+
+    const ROIContour = ROIContourSequence[i];
+    const { ReferencedROINumber, ContourSequence } = ROIContour;
+
+    if (!ContourSequence) {
+      continue;
+    }
+
+    _setROIContourMetadata(
+      structureSet,
+      StructureSetROISequence,
+      RTROIObservationsSequence,
+      ROIContour
+    );
+
+    for (let c = 0; c < ContourSequence.length; c++) {
+      const {
+        ContourImageSequence,
+        ContourData,
+        NumberOfContourPoints,
+        ContourGeometricType,
+      } = ContourSequence[c];
+
+      if (ContourGeometricType !== 'CLOSED_PLANAR') {
+        // TODO: Do we want to visualise types other than closed planar?
+        // We could easily do open planar.
+        continue;
+      }
+
+      const sopInstanceUID = ContourImageSequence.ReferencedSOPInstanceUID;
+      const imageId = _getImageId(imageIdSopInstanceUidPairs, sopInstanceUID);
+      const imageIdSpecificToolData = _getOrCreateImageIdSpecificToolData(
+        toolState,
+        imageId,
+        rtStructDisplayToolName
+      );
+
+      const imagePlane = cornerstone.metaData.get('imagePlaneModule', imageId);
+      const points = [];
+
+      for (let p = 0; p < NumberOfContourPoints * 3; p += 3) {
+        points.push({
+          x: ContourData[p],
+          y: ContourData[p + 1],
+          z: ContourData[p + 2],
+        });
+      }
+
+      transformPointsToImagePlane(points, imagePlane);
+
+      const measurementData = {
+        handles: {
+          points,
+        },
+        structureSetSeriesInstanceUid: rtStructDataset.SeriesInstanceUID,
+        ROINumber: ReferencedROINumber,
+      };
+
+      imageIdSpecificToolData.push(measurementData);
+    }
+  }
+
+  _setToolEnabledIfNotEnabled(rtStructDisplayToolName);
+
+  /*
+   * TODO: Improve the way we notify parts of the app that depends on rts to be loaded.
+   *
+   * Currently we are using a non-ideal implementation through a custom event to notify the rtstruct panel
+   * or other components that could rely on loaded rtstructs that
+   * the first batch of structs were loaded so that e.g. when the user opens the panel
+   * before the structs are fully loaded, the panel can subscribe to this custom event
+   * and update itself with the new structs.
+   *
+   * This limitation is due to the fact that the rtmodule is an object (which will be
+   * updated after the structs are loaded) that React its not aware of its changes
+   * because the module object its not passed in to the panel component as prop but accessed externally.
+   *
+   * Improving this event approach to something reactive that can be tracked inside the react lifecycle,
+   * 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');
+  document.dispatchEvent(event);
+}
+
+function _setROIContourMetadata(
+  structureSet,
+  StructureSetROISequence,
+  RTROIObservationsSequence,
+  ROIContour
+) {
+  const StructureSetROI = StructureSetROISequence.find(
+    structureSetROI =>
+      structureSetROI.ROINumber === ROIContour.ReferencedROINumber
+  );
+
+  const ROIContourData = {
+    ROINumber: StructureSetROI.ROINumber,
+    ROIName: StructureSetROI.ROIName,
+    ROIGenerationAlgorithm: StructureSetROI.ROIGenerationAlgorithm,
+    ROIDescription: StructureSetROI.ROIDescription,
+    visible: true,
+  };
+
+  _setROIContourDataColor(ROIContour, ROIContourData);
+
+  if (RTROIObservationsSequence) {
+    // If present, add additional RTROIObservations metadata.
+    _setROIContourRTROIObservations(
+      ROIContourData,
+      RTROIObservationsSequence,
+      ROIContour.ReferencedROINumber
+    );
+  }
+
+  structureSet.ROIContours.push(ROIContourData);
+}
+
+function _setROIContourDataColor(ROIContour, ROIContourData) {
+  let { ROIDisplayColor, RecommendedDisplayCIELabValue } = ROIContour;
+
+  if (!ROIDisplayColor && RecommendedDisplayCIELabValue) {
+    // If ROIDisplayColor is absent, try using the RecommendedDisplayCIELabValue color.
+    ROIDisplayColor = dicomlab2RGB(RecommendedDisplayCIELabValue);
+  }
+
+  if (ROIDisplayColor) {
+    ROIContourData.colorArray = [...ROIDisplayColor];
+  } else {
+    //Choose a color from the cornerstoneTools colorLUT
+    // We sample from the default color LUT here (i.e. 0), as we have nothing else to go on.
+    const { getters } = cornerstoneTools.getModule('segmentation');
+    const color = getters.colorForSegmentIndexColorLUT(
+      0,
+      ROIContourData.ROINumber
+    );
+
+    ROIContourData.colorArray = [...color];
+  }
+}
+
+function _setROIContourRTROIObservations(
+  ROIContourData,
+  RTROIObservationsSequence,
+  ROINumber
+) {
+  const RTROIObservations = RTROIObservationsSequence.find(
+    RTROIObservations => RTROIObservations.ReferencedROINumber === ROINumber
+  );
+
+  if (RTROIObservations) {
+    // Deep copy so we don't keep the reference to the dcmjs dataset entry.
+    const {
+      ObservationNumber,
+      ROIObservationDescription,
+      RTROIInterpretedType,
+      ROIInterpreter,
+    } = RTROIObservations;
+
+    ROIContourData.RTROIObservations = {
+      ObservationNumber,
+      ROIObservationDescription,
+      RTROIInterpretedType,
+      ROIInterpreter,
+    };
+  }
+}
+
+function _setToolEnabledIfNotEnabled(toolName) {
+  cornerstone.getEnabledElements().forEach(enabledElement => {
+    const { element } = enabledElement;
+    const tool = cornerstoneTools.getToolForElement(element, toolName);
+
+    if (tool.mode !== 'enabled') {
+      // If not already active or passive, set passive so contours render.
+      cornerstoneTools.setToolEnabled(toolName);
+    }
+
+    cornerstone.updateImage(element);
+  });
+}
+
+function _getOrCreateImageIdSpecificToolData(toolState, imageId, toolName) {
+  if (toolState.hasOwnProperty(imageId) === false) {
+    toolState[imageId] = {};
+  }
+
+  const imageIdToolState = toolState[imageId];
+
+  // If we don't have tool state for this type of tool, add an empty object
+  if (imageIdToolState.hasOwnProperty(toolName) === false) {
+    imageIdToolState[toolName] = {
+      data: [],
+    };
+  }
+
+  return imageIdToolState[toolName].data;
+}
+
+const _getImageId = (imageIdSopInstanceUidPairs, sopInstanceUID) => {
+  const imageIdSopInstanceUidPairsEntry = imageIdSopInstanceUidPairs.find(
+    imageIdSopInstanceUidPairsEntry =>
+      imageIdSopInstanceUidPairsEntry.sopInstanceUID === sopInstanceUID
+  );
+
+  return imageIdSopInstanceUidPairsEntry.imageId;
+};
+
+function _getImageIdSopInstanceUidPairsForDisplaySet(
+  studies,
+  StudyInstanceUID,
+  SeriesInstanceUID
+) {
+  const study = studies.find(
+    study => study.StudyInstanceUID === StudyInstanceUID
+  );
+
+  const displaySets = study.displaySets.filter(set => {
+    return set.SeriesInstanceUID === SeriesInstanceUID;
+  });
+
+  if (displaySets.length > 1) {
+    console.warn(
+      'More than one display set with the same SeriesInstanceUID. This is not supported yet...'
+    );
+    // TODO -> We could make check the instance list and see if any match?
+    // Do we split the segmentation into two cornerstoneTools segmentations if there are images in both series?
+    // ^ Will that even happen?
+  }
+
+  const referencedDisplaySet = displaySets[0];
+
+  return referencedDisplaySet.images.map(image => {
+    return {
+      imageId: image.getImageId(),
+      sopInstanceUID: image.getSOPInstanceUID(),
+    };
+  });
+}

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

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+import { importInternal, getToolState, toolColors } from 'cornerstone-tools';
+
+import TOOL_NAMES from '../utils/toolNames';
+
+// Cornerstone 3rd party dev kit imports
+const draw = importInternal('drawing/draw');
+const drawJoinedLines = importInternal('drawing/drawJoinedLines');
+const getNewContext = importInternal('drawing/getNewContext');
+const BaseTool = importInternal('base/BaseTool');
+
+/**
+ * @class RTStructDisplayTool - Renders RTSTRUCT data in a read only manner (i.e. as an overlay).
+ * @extends cornerstoneTools.BaseTool
+ */
+export default class RTStructDisplayTool extends BaseTool {
+  constructor(props = {}) {
+    const defaultProps = {
+      mixins: ['enabledOrDisabledBinaryTool'],
+      name: TOOL_NAMES.RTSTRUCT_DISPLAY_TOOL,
+    };
+
+    const initialProps = Object.assign(defaultProps, props);
+
+    super(initialProps);
+
+    this._rtStructModule = cornerstoneTools.getModule('rtstruct');
+  }
+
+  renderToolData(evt) {
+    const eventData = evt.detail;
+    const rtstructModule = this._rtStructModule;
+
+    const toolState = getToolState(evt.currentTarget, this.name);
+
+    if (!toolState) {
+      return;
+    }
+
+    const { lineWidth, opacity } = rtstructModule.configuration;
+
+    // We have tool data for this element - iterate over each one and draw it
+    const context = getNewContext(eventData.canvasContext.canvas);
+
+    for (let i = 0; i < toolState.data.length; i++) {
+      const data = toolState.data[i];
+
+      const structureSet = rtstructModule.getters.structureSet(
+        data.structureSetSeriesInstanceUid
+      );
+
+      // Don't render if entire StructureSet is hidden.
+      if (structureSet.visible === false) {
+        continue;
+      }
+
+      const ROIContourData = rtstructModule.getters.ROIContour(
+        data.structureSetSeriesInstanceUid,
+        data.ROINumber
+      );
+
+      // Don't render if ROIContour is hidden.
+      if (ROIContourData.visible === false) {
+        continue;
+      }
+
+      const points = data.handles.points;
+
+      if (!points.length) {
+        continue;
+      }
+
+      const colorArray = ROIContourData.colorArray;
+      const color = `rgba(${colorArray[0]},${colorArray[1]},${
+        colorArray[2]
+        },${opacity})`;
+
+      lineWidth;
+
+      draw(context, context => {
+        drawJoinedLines(
+          context,
+          eventData.element,
+          points[points.length - 1],
+          points,
+          {
+            color,
+            lineWidth,
+          }
+        );
+      });
+    }
+  }
+}

extensions/dicom-rt/src/tools/modules/lib/getImageIdOfCenterFrameOfROIContour.js

@@ -0,0 +1,67 @@
+import cornerstoneTools from 'cornerstone-tools';
+import TOOL_NAMES from '../../../utils/toolNames';
+
+const globalImageIdSpecificToolStateManager =
+  cornerstoneTools.globalImageIdSpecificToolStateManager;
+
+/**
+ * getImageIdOfCenterFrameOfROIContour - Returns the imageId nearest to the center of the
+ * volumes extent in the stack's Z direction which contains one of the ROIContour's Contours.
+ * @param {string} structureSetSeriesInstanceUid The SeriesInstanceUID of the structure set.
+ * @param {number} ROINumber The ROINumber of the region.
+ * @param {string} imageIdsInStack The stack of imageIds.
+ *
+ * @returns The imageId
+ */
+export default function getImageIdOfCenterFrameOfROIContour(
+  structureSetSeriesInstanceUid,
+  ROINumber,
+  imageIdsInStack
+) {
+  const rtStructDisplayToolName = TOOL_NAMES.RTSTRUCT_DISPLAY_TOOL;
+  const toolState = globalImageIdSpecificToolStateManager.saveToolState();
+  const imageIdIndicies = [];
+
+  for (let i = 0; i < imageIdsInStack.length; i++) {
+    const imageId = imageIdsInStack[i];
+
+    const imageIdSpecificToolState = toolState[imageId];
+
+    if (
+      !imageIdSpecificToolState ||
+      !imageIdSpecificToolState[rtStructDisplayToolName] ||
+      !imageIdSpecificToolState[rtStructDisplayToolName].data
+    ) {
+      continue;
+    }
+
+    const toolData = imageIdSpecificToolState[rtStructDisplayToolName].data;
+
+    if (
+      _toolDataContainsROIContour(
+        toolData,
+        structureSetSeriesInstanceUid,
+        ROINumber
+      )
+    ) {
+      imageIdIndicies.push(i);
+    }
+  }
+
+  const centerImageIdIndex =
+    imageIdIndicies[Math.floor(imageIdIndicies.length / 2)];
+
+  return imageIdsInStack[centerImageIdIndex];
+}
+
+function _toolDataContainsROIContour(
+  toolData,
+  structureSetSeriesInstanceUid,
+  ROINumber
+) {
+  return !!toolData.some(
+    toolDataI =>
+      toolDataI.structureSetSeriesInstanceUid ===
+        structureSetSeriesInstanceUid && toolDataI.ROINumber === ROINumber
+  );
+}

extensions/dicom-rt/src/tools/modules/lib/structureSetReferencesSeriesInstanceUid.js

@@ -0,0 +1,17 @@
+/**
+ * structureSetReferencesSeriesInstanceUid - Returns true if the structure set
+ * references the given SeriesInstanceUID.
+ * @param {*} StructureSet
+ * @param {*} SeriesInstanceUID
+ */
+export default function structureSetReferencesSeriesInstanceUid(
+  StructureSet,
+  SeriesInstanceUID
+) {
+  const { referencedSeriesSequence } = StructureSet;
+  return referencedSeriesSequence.some(
+    referencedSeries =>
+      referencedSeries.SeriesInstanceUID ===
+      SeriesInstanceUID
+  );
+}

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

@@ -0,0 +1,187 @@
+import cornerstone from 'cornerstone-core';
+import getImageIdOfCenterFrameOfROIContour from './lib/getImageIdOfCenterFrameOfROIContour';
+import structureSetReferencesSeriesInstanceUid from './lib/structureSetReferencesSeriesInstanceUid';
+
+// We should put this as a helper somewhere as we are using it in mutliple places.
+function refreshViewport() {
+  cornerstone.getEnabledElements().forEach(enabledElement => {
+    cornerstone.updateImage(enabledElement.element);
+  });
+}
+
+const configuration = {
+  lineWidth: 3,
+  opacity: 1.0,
+};
+
+const state = {
+  StructureSets: [],
+};
+
+/**
+ * Adds a structure set to the module.
+ * @param {Object} structureSetData The structure set data.
+ */
+function setStructureSet(structureSetData) {
+  state.StructureSets.push(structureSetData);
+}
+
+/**
+ * Returns the StructureSet with the given SeriesInstanceUID.
+ * @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
+ *
+ * @returns {Object} The StructureSet.
+ */
+function getStructureSet(SeriesInstanceUID) {
+  return state.StructureSets.find(
+    structureSet => structureSet.SeriesInstanceUID === SeriesInstanceUID
+  );
+}
+
+/**
+ * Returns the ROI Contour with the given ROINumber on the StructureSet defined by the given
+ * SeriesInstanceUID.
+ * @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
+ * @param {number} ROINumber The ROINUmber of the ROIContour to fetch.
+ */
+function getROIContour(SeriesInstanceUID, ROINumber) {
+  const structureSet = getStructureSet(SeriesInstanceUID);
+
+  if (!structureSet) {
+    return;
+  }
+
+  return structureSet.ROIContours.find(
+    ROIContour => ROIContour.ROINumber === ROINumber
+  );
+}
+
+/**
+ * Hides the StructureSet.
+ * @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
+ */
+function setHideStructureSet(SeriesInstanceUID) {
+  _setStructureSetVisible(SeriesInstanceUID, false);
+}
+
+/**
+ * Shows the StructureSet.
+ * @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
+ */
+function setShowStructureSet(SeriesInstanceUID) {
+  _setStructureSetVisible(SeriesInstanceUID, true);
+}
+
+/**
+ * Sets the visibility of the StructureSet.
+ * @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
+ * @param {boolean} visible Whether the StructureSet should visible or not.
+ */
+function _setStructureSetVisible(SeriesInstanceUID, visible = true) {
+  const StructureSet = getStructureSet(SeriesInstanceUID);
+
+  if (StructureSet) {
+    StructureSet.visible = visible;
+
+    refreshViewport();
+  }
+}
+
+/**
+ * Toggles the visibility of the StructureSet.
+ * @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
+ */
+function setToggleStructureSet(SeriesInstanceUID) {
+  const StructureSet = getStructureSet(SeriesInstanceUID);
+
+  if (StructureSet) {
+    StructureSet.visible = !StructureSet.visible;
+
+    refreshViewport();
+  }
+}
+
+/**
+ * Hides the ROIContour.
+ * @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
+ * @param {number} ROINumber The ROINUmber of the ROIContour.
+ */
+function setHideROIContour(SeriesInstanceUID, ROINumber) {
+  _setROIContourVisible(SeriesInstanceUID, ROINumber, false);
+}
+
+/**
+ * Shows the ROIContour.
+ * @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
+ * @param {number} ROINumber The ROINUmber of the ROIContour.
+ */
+function setShowROIContour(SeriesInstanceUID, ROINumber) {
+  _setROIContourVisible(SeriesInstanceUID, ROINumber, true);
+}
+
+/**
+ * Sets the visibility of the ROIContour.
+ * @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
+ * @param {number} ROINumber The ROINUmber of the ROIContour.
+ * @param {boolean} visible Whether the StructureSet should visible or not.
+ */
+function _setROIContourVisible(SeriesInstanceUID, ROINumber, visible = true) {
+  const ROIContour = getROIContour(SeriesInstanceUID, ROINumber);
+
+  if (ROIContour) {
+    ROIContour.visible = visible;
+
+    refreshViewport();
+  }
+}
+
+/**
+ * Toggles the visibility of the ROIContour.
+ * @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
+ * @param {number} ROINumber The ROINUmber of the ROIContour.
+ */
+function setToggleROIContour(SeriesInstanceUID, ROINumber) {
+  const ROIContour = getROIContour(SeriesInstanceUID, ROINumber);
+
+  if (ROIContour) {
+    ROIContour.visible = !ROIContour.visible;
+
+    refreshViewport();
+  }
+}
+
+/**
+ * Returns an array of StructureSets which reference the given SeriesInstanceUID.
+ * @param {string} SeriesInstanceUID The SeriesInstanceUID to check.
+ */
+function getStructuresSetsWhichReferenceSeriesInstanceUid(
+  SeriesInstanceUID
+) {
+  const { StructureSets } = state;
+  return StructureSets.filter(StructureSet =>
+    structureSetReferencesSeriesInstanceUid(
+      StructureSet,
+      SeriesInstanceUID
+    )
+  );
+}
+
+export default {
+  getters: {
+    structureSet: getStructureSet,
+    ROIContour: getROIContour,
+    structuresSetsWhichReferenceSeriesInstanceUid: getStructuresSetsWhichReferenceSeriesInstanceUid,
+    imageIdOfCenterFrameOfROIContour: getImageIdOfCenterFrameOfROIContour,
+  },
+  setters: {
+    structureSet: setStructureSet,
+    hideROIContour: setHideROIContour,
+    showROIContour: setShowROIContour,
+    toggleROIContour: setToggleROIContour,
+    hideStructureSet: setHideStructureSet,
+    showStructureSet: setShowStructureSet,
+    toggleStructureSet: setToggleStructureSet,
+  },
+  state,
+  configuration,
+};

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

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

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

@@ -0,0 +1,91 @@
+export default function transformPointsToImagePlane(points, imagePlane) {
+  // See Equation C.7.6.2.1-1 of the DICOM standard
+
+  const {
+    rowCosines,
+    columnCosines,
+    rowPixelSpacing: deltaI,
+    columnPixelSpacing: deltaJ,
+    imagePositionPatient,
+  } = imagePlane;
+
+  const X = [rowCosines[0], rowCosines[1], rowCosines[2]];
+  const Y = [columnCosines[0], columnCosines[1], columnCosines[2]];
+  const S = [
+    imagePositionPatient[0],
+    imagePositionPatient[1],
+    imagePositionPatient[2],
+  ];
+
+  // 9 sets of simulataneous equations to choose from, choose which set to solve
+  // Based on the largest component of each direction cosine.
+  // This avoids NaNs or floating point errors caused by dividing by very small numbers and ensures a safe mapping
+  // when mapping between planes that are close to orthogonal.
+
+  let ix = 0;
+  let iy = 0;
+  let largestDirectionCosineMagnitude = {
+    x: 0,
+    y: 0,
+  };
+
+  // Find the element with the largest magnitude in each direction cosine vector.
+  for (let i = 0; i < X.length; i++) {
+    if (Math.abs(X[i]) > largestDirectionCosineMagnitude.x) {
+      ix = i;
+      largestDirectionCosineMagnitude.x = Math.abs(X[i]);
+    }
+    if (Math.abs(Y[i]) > largestDirectionCosineMagnitude.y) {
+      iy = i;
+      largestDirectionCosineMagnitude.y = Math.abs(Y[i]);
+    }
+  }
+
+  const ci = {
+    // Index of max elements in X and Y
+    ix,
+    iy,
+  };
+
+  // Sanity Check
+  const directionCosineMagnitude = {
+    x: Math.pow(X[0], 2) + Math.pow(X[1], 2) + Math.pow(X[2], 2),
+    y: Math.pow(Y[0], 2) + Math.pow(Y[1], 2) + Math.pow(Y[2], 2),
+  };
+
+  if (directionCosineMagnitude.x < 0.99 || directionCosineMagnitude.y < 0.99) {
+    throw Error(
+      `Direction cosines do not sum to 1 in quadrature. There is likely a mistake in the DICOM metadata.` +
+        `directionCosineMagnitudes: ${directionCosineMagnitude.x}, ${directionCosineMagnitude.y}`
+    );
+  }
+
+  // Fill in elements that won't change between points
+  const c = [undefined, Y[ci.ix], X[ci.ix], undefined, X[ci.iy], Y[ci.iy]];
+
+  for (let pointI = 0; pointI < points.length; pointI++) {
+    // Subtract imagePositionPatient from the coordinate
+    const r = [
+      points[pointI].x - S[0],
+      points[pointI].y - S[1],
+      points[pointI].z - S[2],
+    ];
+
+    // Set the variable terms in c.
+    c[0] = r[ci.ix];
+    c[3] = r[ci.iy];
+
+    // General case: Solves the two choosen simulataneous equations to go from the patient coordinate system to the imagePlane.
+    const i =
+      (c[0] - (c[1] * c[3]) / c[5]) /
+      (c[2] * deltaI * (1 - (c[1] * c[4]) / (c[2] * c[5])));
+    const j = (c[3] - c[4] * i * deltaI) / (c[5] * deltaJ);
+
+    // NOTE: Add (0.5, 0.5) to the coordinate, as PCS reference frame is with respect to the centre of the first pixel.
+    points[pointI].x = i + 0.5;
+    points[pointI].y = j + 0.5;
+    delete points[pointI].z;
+  }
+
+  return;
+}

extensions/dicom-segmentation/CHANGELOG.md

@@ -3,6 +3,55 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [0.2.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.2.1...@ohif/extension-dicom-segmentation@0.2.2) (2020-04-28)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.2.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.2.0...@ohif/extension-dicom-segmentation@0.2.1) (2020-04-27)
+
+
+### Bug Fixes
+
+* 🐛 Dropdown not updating when selecting segment ([#1675](https://github.com/OHIF/Viewers/issues/1675)) ([20e366f](https://github.com/OHIF/Viewers/commit/20e366ffbd76781f48dc99c9f59e24b255b5e5df)), closes [#1669](https://github.com/OHIF/Viewers/issues/1669)
+
+
+
+
+
+# [0.2.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.1.2...@ohif/extension-dicom-segmentation@0.2.0) (2020-04-24)
+
+
+### Features
+
+* 🎸 Seg jump to slice + show/hide ([835f64d](https://github.com/OHIF/Viewers/commit/835f64d47a9994f6a25aaf3941a4974e215e7e7f))
+
+
+
+
+
+## [0.1.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.1.1...@ohif/extension-dicom-segmentation@0.1.2) (2020-04-09)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
+## [0.1.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.1.0...@ohif/extension-dicom-segmentation@0.1.1) (2020-04-01)
+
+
+### Bug Fixes
+
+* segmentation not loading ([#1566](https://github.com/OHIF/Viewers/issues/1566)) ([4a7ce1c](https://github.com/OHIF/Viewers/commit/4a7ce1c09324d74c61048393e3a2427757e4001a))
+
+
+
+
+
 # 0.1.0 (2020-03-13)
 
 

extensions/dicom-segmentation/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-segmentation",
-  "version": "0.1.0",
+  "version": "0.2.2",
   "description": "OHIF extension for viewing segmentations in the 2D MPR view",
   "author": "OHIF",
   "license": "MIT",
@@ -31,7 +31,7 @@
     "@ohif/core": "^0.50.0",
     "cornerstone-core": "^2.2.8",
     "cornerstone-tools": "4.12.5",
-    "dcmjs": "^0.6.1",
+    "dcmjs": "^0.12.2",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",
     "react-dom": "^16.8.6"

extensions/dicom-segmentation/src/OHIFDicomSegSopClassHandler.js

@@ -14,7 +14,7 @@ const OHIFDicomSegSopClassHandler = {
   id: 'OHIFDicomSegSopClassHandler',
   type: MODULE_TYPES.SOP_CLASS_HANDLER,
   sopClassUIDs,
-  getDisplaySetFromSeries: function(
+  getDisplaySetFromSeries: function (
     series,
     study,
     dicomWebClient,
@@ -53,7 +53,7 @@ const OHIFDicomSegSopClassHandler = {
       SeriesDescription,
     };
 
-    segDisplaySet.load = function(referencedDisplaySet, studies) {
+    segDisplaySet.load = function (referencedDisplaySet, studies) {
       return loadSegmentation(
         segDisplaySet,
         referencedDisplaySet,

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

@@ -12,14 +12,6 @@
   height: 20px;
 }
 
-.dcmseg-segment-item .segment-label {
-  overflow: hidden;
-  max-width: calc(100% - 50px);
-  text-overflow: ellipsis;
-  overflow-wrap: normal;
-  white-space: nowrap;
-}
-
 .dcmseg-segment-item .segment-info {
   display: inline-block;
   margin-top: 9px;
@@ -62,3 +54,30 @@
 .dcmseg-segment-item .segment-actions .btnAction i {
   margin-right: 4px;
 }
+
+.dcmseg-segment-item .segment-label {
+  display: flex;
+  justify-content: space-between;
+  padding-right: 20px;
+}
+
+.dcmseg-segment-item .segment-label span {
+  overflow-wrap: normal;
+  white-space: nowrap;
+  overflow: hidden;
+  max-width: calc(100% - 40px); /* calc(100% - 50px); 20px = eye icon */
+  text-overflow: ellipsis;
+}
+
+.dcmseg-segment-item .segment-label .eye-icon {
+  cursor: pointer;
+  color: var(--active-color);
+}
+
+.dcmseg-segment-item .segment-label .eye-icon:hover {
+  color: var(--hover-color);
+}
+
+.dcmseg-segment-item .segment-label .eye-icon.--visible {
+  color: var(--default-color);
+}

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

@@ -1,4 +1,4 @@
-import React from 'react';
+import React, { useState } from 'react';
 import PropTypes from 'prop-types';
 import { TableListItem, Icon } from '@ohif/ui';
 
@@ -17,48 +17,63 @@ ColoredCircle.propTypes = {
   color: PropTypes.array.isRequired,
 };
 
-const SegmentItem = ({ index, label, onClick, itemClass, color }) => (
-  <div className="dcmseg-segment-item">
-    <TableListItem
-      key={index}
-      itemKey={index}
-      itemIndex={index}
-      itemClass={itemClass}
-      itemMeta={<ColoredCircle color={color} />}
-      itemMetaClass="segment-color-section"
-      onItemClick={onClick}
-    >
-      <div>
-        <div className="segment-label" style={{ marginBottom: 4 }}>
-          {label}
-        </div>
-        {false && <div className="segment-info">{'...'}</div>}
-        {false && (
-          <div className="segment-actions">
-            <button
-              className="btnAction"
-              onClick={() => console.log('Relabelling...')}
-            >
-              <span style={{ marginRight: '4px' }}>
-                <Icon name="edit" width="14px" height="14px" />
-              </span>
+const SegmentItem = ({ index, label, onClick, itemClass, color, visible = true, onVisibilityChange }) => {
+  const [isVisible, setIsVisible] = useState(visible);
+  return (
+    <div className="dcmseg-segment-item">
+      <TableListItem
+        key={index}
+        itemKey={index}
+        itemIndex={index}
+        itemClass={itemClass}
+        itemMeta={<ColoredCircle color={color} />}
+        itemMetaClass="segment-color-section"
+        onItemClick={onClick}
+      >
+        <div>
+          <div className="segment-label" style={{ marginBottom: 4 }}>
+            <span>{label}</span>
+            <Icon
+              className={`eye-icon ${isVisible && '--visible'}`}
+              name={isVisible ? 'eye' : 'eye-closed'}
+              width="20px"
+              height="20px"
+              onClick={event => {
+                event.stopPropagation();
+                const newVisibility = !isVisible;
+                setIsVisible(newVisibility);
+                onVisibilityChange(newVisibility);
+              }}
+            />
+          </div>
+          {false && <div className="segment-info">{'...'}</div>}
+          {false && (
+            <div className="segment-actions">
+              <button
+                className="btnAction"
+                onClick={() => console.log('Relabelling...')}
+              >
+                <span style={{ marginRight: '4px' }}>
+                  <Icon name="edit" width="14px" height="14px" />
+                </span>
               Relabel
               </button>
-            <button
-              className="btnAction"
-              onClick={() => console.log('Editing description...')}
-            >
-              <span style={{ marginRight: '4px' }}>
-                <Icon name="edit" width="14px" height="14px" />
-              </span>
+              <button
+                className="btnAction"
+                onClick={() => console.log('Editing description...')}
+              >
+                <span style={{ marginRight: '4px' }}>
+                  <Icon name="edit" width="14px" height="14px" />
+                </span>
               Description
               </button>
-          </div>
-        )}
-      </div>
-    </TableListItem>
-  </div>
-);
+            </div>
+          )}
+        </div>
+      </TableListItem>
+    </div>
+  );
+};
 
 SegmentItem.propTypes = {
   index: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired,

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

@@ -1,4 +1,4 @@
-import React, { useState, useEffect } from 'react';
+import React, { useState, useEffect, useCallback } from 'react';
 import PropTypes from 'prop-types';
 import cornerstoneTools from 'cornerstone-tools';
 import cornerstone from 'cornerstone-core';
@@ -28,61 +28,50 @@ const refreshViewport = () => {
 /**
  * SegmentationPanel component
  *
- * @param {Object} props
- * @param {Array} props.studies
- * @param {Array} props.viewports - viewportSpecificData
- * @param {number} props.activeIndex - activeViewportIndex
+ * @param {Array} props.studies - Studies data
+ * @param {Array} props.viewports - Viewports data (viewportSpecificData)
+ * @param {number} props.activeIndex - Active viewport index
+ * @param {boolean} props.isOpen - Boolean that indicates if the panel is expanded
+ * @param {Function} props.onSegItemClick - Segment click handler
  * @returns component
  */
-const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
+const SegmentationPanel = ({
+  studies,
+  viewports,
+  activeIndex,
+  isOpen,
+  onSegItemClick,
+}) => {
   /*
    * TODO: wrap get/set interactions with the cornerstoneTools
    * store with context to make these kind of things less blurry.
    */
-  const segmentationModule = cornerstoneTools.getModule('segmentation');
-  const { configuration } = segmentationModule;
+  const { configuration } = cornerstoneTools.getModule('segmentation');
   const DEFAULT_BRUSH_RADIUS = configuration.radius || 10;
-
-  const [brushRadius, setBrushRadius] = useState(DEFAULT_BRUSH_RADIUS);
-
-  /* TODO: We shouldn't hardcode this color, in the future the SEG may set the colorLUT to whatever it wants. */
-  const [brushColor, setBrushColor] = useState('rgba(221, 85, 85, 1)');
-  const [selectedSegment, setSelectedSegment] = useState();
-  const [showSegSettings, setShowSegSettings] = useState(false);
-  const [selectedSegmentation, setSelectedSegmentation] = useState();
-
-  const viewport = viewports[activeIndex];
-
-  const {
-    StudyInstanceUID,
-    SeriesInstanceUID,
-    displaySetInstanceUID,
-  } = viewport;
-
-  const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
-  const firstImageId = studyMetadata.getFirstImageId(displaySetInstanceUID);
-
-  /* CornerstoneTools */
-  const [brushStackState, setBrushStackState] = useState(
-    segmentationModule.state.series[firstImageId]
-  );
+  const [state, setState] = useState({
+    brushRadius: DEFAULT_BRUSH_RADIUS,
+    brushColor:
+      'rgba(221, 85, 85, 1)' /* TODO: We shouldn't hardcode this color, in the future the SEG may set the colorLUT to whatever it wants. */,
+    selectedSegment: null,
+    selectedSegmentation: null,
+    showSegSettings: false,
+    brushStackState: null,
+    labelmapList: [],
+    segmentList: [],
+  });
 
   useEffect(() => {
-    setShowSegSettings(showSegSettings && !isOpen);
-  }, [isOpen]);
-
-  useEffect(() => {
-    setBrushStackState(segmentationModule.state.series[firstImageId]);
-  }, [studies, viewports, activeIndex, firstImageId]);
-
-  useEffect(() => {
-    if (brushStackState) {
-      setSelectedSegmentation(brushStackState.activeLabelmapIndex);
-    }
-
     const labelmapModifiedHandler = event => {
-      log.warn('labelmap modified', event);
-      setBrushStackState(segmentationModule.state.series[firstImageId]);
+      log.warn('Segmentation Panel: labelmap modified', event);
+      const module = cornerstoneTools.getModule('segmentation');
+      const activeViewport = viewports[activeIndex];
+      const studyMetadata = studyMetadataManager.get(
+        activeViewport.StudyInstanceUID
+      );
+      const firstImageId = studyMetadata.getFirstImageId(
+        activeViewport.displaySetInstanceUID
+      );
+      updateState('brushStackState', module.state.series[firstImageId]);
     };
 
     /*
@@ -107,142 +96,247 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
     };
   });
 
-  if (!brushStackState) {
-    return null;
-  }
-
-  const labelmap3D =
-    brushStackState.labelmaps3D[brushStackState.activeLabelmapIndex];
-
-  /*
-   * 2. UseEffect to update state? or to a least trigger a re-render
-   * 4. Toggle visibility of labelmap?
-   * 5. Toggle visibility of seg?
-   *
-   * If the port is cornerstone, just need to call a re-render.
-   * If the port is vtkjs, its a bit more tricky as we now need to create a new
-   */
-
-  const getLabelmapList = () => {
-    /* Get list of SEG labelmaps specific to active viewport (reference series) */
-    const referencedSegDisplaysets = _getReferencedSegDisplaysets(
-      StudyInstanceUID,
-      SeriesInstanceUID
+  useEffect(() => {
+    const module = cornerstoneTools.getModule('segmentation');
+    const activeViewport = viewports[activeIndex];
+    const studyMetadata = studyMetadataManager.get(
+      activeViewport.StudyInstanceUID
     );
+    const firstImageId = studyMetadata.getFirstImageId(
+      activeViewport.displaySetInstanceUID
+    );
+    const brushStackState = module.state.series[firstImageId];
 
-    return referencedSegDisplaysets.map((displaySet, index) => {
-      const { labelmapIndex, SeriesDate, SeriesTime } = displaySet;
+    if (brushStackState) {
+      const labelmap3D =
+        brushStackState.labelmaps3D[brushStackState.activeLabelmapIndex];
+      const labelmapList = getLabelmapList(
+        brushStackState,
+        firstImageId,
+        activeViewport
+      );
+      const segmentList = getSegmentList(labelmap3D, firstImageId, brushStackState);
+      setState(state => ({
+        ...state,
+        brushStackState,
+        selectedSegmentation: brushStackState.activeLabelmapIndex,
+        labelmapList,
+        segmentList,
+      }));
+    } else {
+      setState(state => ({
+        ...state,
+        labelmapList: [],
+        segmentList: [],
+      }));
+    }
+  }, [studies, viewports, activeIndex, getLabelmapList, getSegmentList, state.selectedSegmentation]);
 
-      /* Map to display representation */
-      const dateStr = `${SeriesDate}:${SeriesTime}`.split('.')[0];
-      const date = moment(dateStr, 'YYYYMMDD:HHmmss');
-      const isActiveLabelmap =
-        labelmapIndex === brushStackState.activeLabelmapIndex;
-      const displayDate = date.format('ddd, MMM Do YYYY');
-      const displayTime = date.format('h:mm:ss a');
-      const displayDescription = displaySet.SeriesDescription;
+  /* Handle open/closed panel behaviour */
+  useEffect(() => {
+    setState(state => ({
+      ...state,
+      showSegSettings: state.showSegSettings && !isOpen,
+    }));
+  }, [isOpen]);
 
-      return {
-        value: labelmapIndex,
-        title: displayDescription,
-        description: displayDate,
-        onClick: async () => {
-          const activatedLabelmapIndex = await _setActiveLabelmap(
-            viewport,
-            studies,
-            displaySet,
-            firstImageId,
-            brushStackState.activeLabelmapIndex
-          );
-          setSelectedSegmentation(activatedLabelmapIndex);
-        },
-      };
-    });
-  };
+  const getLabelmapList = useCallback(
+    (brushStackState, firstImageId, activeViewport) => {
+      /* Get list of SEG labelmaps specific to active viewport (reference series) */
+      const referencedSegDisplaysets = _getReferencedSegDisplaysets(
+        activeViewport.StudyInstanceUID,
+        activeViewport.SeriesInstanceUID
+      );
 
-  const labelmapList = getLabelmapList();
+      return referencedSegDisplaysets.map((displaySet, index) => {
+        const { labelmapIndex, SeriesDate, SeriesTime } = displaySet;
 
-  const segmentList = [];
+        /* Map to display representation */
+        const dateStr = `${SeriesDate}:${SeriesTime}`.split('.')[0];
+        const date = moment(dateStr, 'YYYYMMDD:HHmmss');
+        const isActiveLabelmap =
+          labelmapIndex === brushStackState.activeLabelmapIndex;
+        const displayDate = date.format('ddd, MMM Do YYYY');
+        const displayTime = date.format('h:mm:ss a');
+        const displayDescription = displaySet.SeriesDescription;
 
-  if (labelmap3D) {
-    /*
-     * Newly created segments have no `meta`
-     * So we instead build a list of all segment indexes in use
-     * Then find any associated metadata
-     */
-    const uniqueSegmentIndexes = labelmap3D.labelmaps2D
-      .reduce((acc, labelmap2D) => {
-        if (labelmap2D) {
-          const segmentIndexes = labelmap2D.segmentsOnLabelmap;
+        return {
+          value: labelmapIndex,
+          title: displayDescription,
+          description: displayDate,
+          onClick: async () => {
+            const activatedLabelmapIndex = await _setActiveLabelmap(
+              activeViewport,
+              studies,
+              displaySet,
+              firstImageId,
+              brushStackState.activeLabelmapIndex
+            );
+            updateState('selectedSegmentation', activatedLabelmapIndex);
+          },
+        };
+      });
+    },
+    [studies]
+  );
 
-          for (let i = 0; i < segmentIndexes.length; i++) {
-            if (!acc.includes(segmentIndexes[i]) && segmentIndexes[i] !== 0) {
-              acc.push(segmentIndexes[i]);
+  const getSegmentList = useCallback(
+    (labelmap3D, firstImageId, brushStackState) => {
+      /*
+       * Newly created segments have no `meta`
+       * So we instead build a list of all segment indexes in use
+       * Then find any associated metadata
+       */
+      const uniqueSegmentIndexes = labelmap3D.labelmaps2D
+        .reduce((acc, labelmap2D) => {
+          if (labelmap2D) {
+            const segmentIndexes = labelmap2D.segmentsOnLabelmap;
+
+            for (let i = 0; i < segmentIndexes.length; i++) {
+              if (!acc.includes(segmentIndexes[i]) && segmentIndexes[i] !== 0) {
+                acc.push(segmentIndexes[i]);
+              }
             }
           }
+
+          return acc;
+        }, [])
+        .sort((a, b) => a - b);
+
+      const module = cornerstoneTools.getModule('segmentation');
+      const colorLutTable =
+        module.state.colorLutTables[labelmap3D.colorLUTIndex];
+      const hasLabelmapMeta = labelmap3D.metadata && labelmap3D.metadata.data;
+
+      const segmentList = [];
+      for (let i = 0; i < uniqueSegmentIndexes.length; i++) {
+        const segmentIndex = uniqueSegmentIndexes[i];
+
+        const color = colorLutTable[segmentIndex];
+        let segmentLabel = '(unlabeled)';
+        let segmentNumber = segmentIndex;
+
+        /* Meta */
+        if (hasLabelmapMeta) {
+          const segmentMeta = labelmap3D.metadata.data[segmentIndex];
+
+          if (segmentMeta) {
+            segmentNumber = segmentMeta.SegmentNumber;
+            segmentLabel = segmentMeta.SegmentLabel;
+          }
         }
 
-        return acc;
-      }, [])
-      .sort((a, b) => a - b);
+        const sameSegment = state.selectedSegment === segmentNumber;
+        const setCurrentSelectedSegment = () => {
+          _setActiveSegment(
+            firstImageId,
+            segmentNumber,
+            labelmap3D.activeSegmentIndex
+          );
+          updateState('selectedSegment', sameSegment ? null : segmentNumber);
 
-    const colorLutTable =
-      segmentationModule.state.colorLutTables[labelmap3D.colorLUTIndex];
-    const hasLabelmapMeta = labelmap3D.metadata && labelmap3D.metadata.data;
+          const validIndexList = [];
+          labelmap3D.labelmaps2D.forEach((labelMap2D, index) => {
+            if (labelMap2D.segmentsOnLabelmap.includes(segmentNumber)) {
+              validIndexList.push(index);
+            }
+          });
+          const avg = array => array.reduce((a, b) => a + b) / array.length;
+          const average = avg(validIndexList);
+          const closest = validIndexList.reduce((prev, curr) => {
+            return Math.abs(curr - average) < Math.abs(prev - average)
+              ? curr
+              : prev;
+          });
 
-    for (let i = 0; i < uniqueSegmentIndexes.length; i++) {
-      const segmentIndex = uniqueSegmentIndexes[i];
+          const enabledElements = cornerstone.getEnabledElements();
+          const element = enabledElements[activeIndex].element;
+          const toolState = cornerstoneTools.getToolState(element, 'stack');
 
-      const color = colorLutTable[segmentIndex];
-      let segmentLabel = '(unlabeled)';
-      let segmentNumber = segmentIndex;
+          if (!toolState) {
+            return;
+          }
 
-      /* Meta */
-      if (hasLabelmapMeta) {
-        const segmentMeta = labelmap3D.metadata.data[segmentIndex];
+          const imageIds = toolState.data[0].imageIds;
+          const imageId = imageIds[closest];
+          const frameIndex = imageIds.indexOf(imageId);
 
-        if (segmentMeta) {
-          segmentNumber = segmentMeta.SegmentNumber;
-          segmentLabel = segmentMeta.SegmentLabel;
+          const SOPInstanceUID = cornerstone.metaData.get(
+            'SOPInstanceUID',
+            imageId
+          );
+          const StudyInstanceUID = cornerstone.metaData.get(
+            'StudyInstanceUID',
+            imageId
+          );
+
+          onSegItemClick({
+            StudyInstanceUID,
+            SOPInstanceUID,
+            frameIndex,
+            activeViewportIndex: activeIndex,
+          });
+        };
+
+        const enabledElements = cornerstone.getEnabledElements();
+        const enabledElementViewport = enabledElements[activeIndex];
+
+        let isVisible = true;
+        if (enabledElementViewport) {
+          const element = enabledElementViewport.element;
+          const module = cornerstoneTools.getModule('segmentation');
+          isVisible = module.getters.isSegmentVisible(
+            element,
+            segmentNumber,
+            brushStackState.activeLabelmapIndex
+          );
         }
+
+        segmentList.push(
+          <SegmentItem
+            key={segmentNumber}
+            itemClass={`segment-item ${sameSegment && 'selected'}`}
+            onClick={setCurrentSelectedSegment}
+            label={segmentLabel}
+            index={segmentNumber}
+            color={color}
+            visible={isVisible}
+            onVisibilityChange={() => {
+              const element = enabledElements[activeIndex].element;
+              module.setters.toggleSegmentVisibility(
+                element,
+                segmentNumber,
+                brushStackState.activeLabelmapIndex
+              );
+              refreshViewport();
+            }}
+          />
+        );
       }
 
-      const sameSegment = selectedSegment === segmentNumber;
-      const setCurrentSelectedSegment = () => {
-        _setActiveSegment(
-          firstImageId,
-          segmentNumber,
-          labelmap3D.activeSegmentIndex
-        );
-        setSelectedSegment(sameSegment ? null : segmentNumber);
-      };
+      return segmentList;
 
-      segmentList.push(
-        <SegmentItem
-          key={segmentNumber}
-          itemClass={`segment-item ${sameSegment && 'selected'}`}
-          onClick={setCurrentSelectedSegment}
-          label={segmentLabel}
-          index={segmentNumber}
-          color={color}
-        />
-      );
-    }
+      /*
+       * Let's iterate over segmentIndexes ^ above
+       * If meta has a match, use it to show info
+       * If now, add "no-meta" class
+       * Show default name
+       */
+    },
+    [activeIndex, onSegItemClick, state.selectedSegment]
+  );
 
-    /*
-     * Let's iterate over segmentIndexes ^ above
-     * If meta has a match, use it to show info
-     * If now, add "no-meta" class
-     * Show default name
-     */
-  }
+  const updateState = (field, value) => {
+    setState(state => ({ ...state, [field]: value }));
+  };
 
   const updateBrushSize = evt => {
     const updatedRadius = Number(evt.target.value);
 
     if (updatedRadius !== brushRadius) {
-      setBrushRadius(updatedRadius);
-      segmentationModule.setters.radius(updatedRadius);
+      updateState('brushRadius', updatedRadius);
+      const module = cornerstoneTools.getModule('segmentation');
+      module.setters.radius(updatedRadius);
     }
   };
 
@@ -251,29 +345,29 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
     if (labelmap3D.activeSegmentIndex > 1) {
       labelmap3D.activeSegmentIndex--;
     }
-    setSelectedSegment(labelmap3D.activeSegmentIndex);
+    updateState('selectedSegment', labelmap3D.activeSegmentIndex);
     updateActiveSegmentColor();
   };
 
   const incrementSegment = event => {
     event.preventDefault();
     labelmap3D.activeSegmentIndex++;
-    setSelectedSegment(labelmap3D.activeSegmentIndex);
+    updateState('selectedSegment', labelmap3D.activeSegmentIndex);
     updateActiveSegmentColor();
   };
 
   const updateActiveSegmentColor = () => {
     const color = getActiveSegmentColor();
-    setBrushColor(color);
+    updateState('brushColor', color);
   };
 
   const getActiveSegmentColor = () => {
-    if (!brushStackState) {
+    if (!state.brushStackState) {
       return 'rgba(255, 255, 255, 1)';
     }
 
-    const colorLutTable =
-      segmentationModule.state.colorLutTables[labelmap3D.colorLUTIndex];
+    const module = cornerstoneTools.getModule('segmentation');
+    const colorLutTable = module.state.colorLutTables[labelmap3D.colorLUTIndex];
     const color = colorLutTable[labelmap3D.activeSegmentIndex];
 
     return `rgba(${color.join(',')})`;
@@ -293,11 +387,11 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
     refreshViewport();
   };
 
-  if (showSegSettings) {
+  if (state.showSegSettings) {
     return (
       <SegmentationSettings
         configuration={configuration}
-        onBack={() => setShowSegSettings(false)}
+        onBack={() => updateState('showSegSettings', false)}
         onChange={updateConfiguration}
       />
     );
@@ -309,13 +403,13 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
           name="cog"
           width="25px"
           height="25px"
-          onClick={() => setShowSegSettings(true)}
+          onClick={() => updateState('showSegSettings', true)}
         />
         {false && (
           <form className="selector-form">
             <BrushColorSelector
               defaultColor={brushColor}
-              index={labelmap3D.activeSegmentIndex}
+              index={state.selectedSegment}
               onNext={incrementSegment}
               onPrev={decrementSegment}
             />
@@ -330,18 +424,16 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
         <h3>Segmentations</h3>
         <div className="segmentations">
           <SegmentationSelect
-            value={
-              labelmapList.find(i => i.value === selectedSegmentation) || null
-            }
+            value={state.labelmapList.find(i => i.value === state.selectedSegmentation)}
             formatOptionLabel={SegmentationItem}
-            options={labelmapList}
+            options={state.labelmapList}
           />
         </div>
         <ScrollableArea>
           <TableList
-            customHeader={<SegmentsHeader count={segmentList.length} />}
+            customHeader={<SegmentsHeader count={state.segmentList.length} />}
           >
-            {segmentList}
+            {state.segmentList}
           </TableList>
         </ScrollableArea>
       </div>
@@ -373,6 +465,7 @@ SegmentationPanel.propTypes = {
   }),
   activeIndex: PropTypes.number.isRequired,
   studies: PropTypes.array.isRequired,
+  isOpen: PropTypes.bool.isRequired,
 };
 SegmentationPanel.defaultProps = {};
 
@@ -420,7 +513,7 @@ const _setActiveLabelmap = async (
 ) => {
   if (displaySet.labelmapIndex === activeLabelmapIndex) {
     log.warn(`${activeLabelmapIndex} is already the active labelmap`);
-    return;
+    return displaySet.labelmapIndex;
   }
 
   if (!displaySet.isLoaded) {
@@ -431,7 +524,6 @@ const _setActiveLabelmap = async (
 
   const { state } = cornerstoneTools.getModule('segmentation');
   const brushStackState = state.series[firstImageId];
-
   brushStackState.activeLabelmapIndex = displaySet.labelmapIndex;
 
   refreshViewport();

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

@@ -17,6 +17,10 @@ const defaultColor = computedstyle.getPropertyValue('--default-color');
 const uiGrayDark = computedstyle.getPropertyValue('--ui-gray-dark');
 
 const segmentationSelectStyles = {
+  singleValue: (base, state) => ({
+    ...base,
+    width: '100%'
+  }),
   control: (base, state) => ({
     ...base,
     cursor: 'pointer',

extensions/dicom-segmentation/src/index.js

@@ -1,7 +1,9 @@
+import React from 'react';
+
 import init from './init.js';
 import toolbarModule from './toolbarModule.js';
-import panelModule from './panelModule.js';
 import sopClassHandlerModule from './OHIFDicomSegSopClassHandler.js';
+import SegmentationPanel from './components/SegmentationPanel/SegmentationPanel.js';
 
 export default {
   /**
@@ -21,8 +23,54 @@ export default {
   getToolbarModule({ servicesManager }) {
     return toolbarModule;
   },
-  getPanelModule({ servicesManager }) {
-    return panelModule;
+  getPanelModule({ commandsManager }) {
+    const ExtendedSegmentationPanel = props => {
+      const segItemClickHandler = segData => {
+        commandsManager.runCommand('jumpToImage', segData);
+      };
+
+      return (
+        <SegmentationPanel {...props} onSegItemClick={segItemClickHandler} />
+      );
+    };
+
+    return {
+      menuOptions: [
+        {
+          icon: 'list',
+          label: 'Segmentations',
+          target: 'segmentation-panel',
+          isDisabled: studies => {
+            if (!studies) {
+              return true;
+            }
+
+            for (let i = 0; i < studies.length; i++) {
+              const study = studies[i];
+
+              if (study && study.series) {
+                for (let j = 0; j < study.series.length; j++) {
+                  const series = study.series[j];
+
+                  if (series.Modality === 'SEG') {
+                    return false;
+                  }
+                }
+              }
+            }
+
+            return true;
+          },
+        },
+      ],
+      components: [
+        {
+          id: 'segmentation-panel',
+          component: ExtendedSegmentationPanel,
+        },
+      ],
+      defaultContext: ['VIEWER'],
+    };
   },
   getSopClassHandlerModule({ servicesManager }) {
     return sopClassHandlerModule;

extensions/dicom-segmentation/src/loadSegmentation.js

@@ -1,5 +1,5 @@
 import OHIF from '@ohif/core';
-import * as dcmjs from 'dcmjs';
+import dcmjs from 'dcmjs';
 import cornerstone from 'cornerstone-core';
 import cornerstoneTools from 'cornerstone-tools';
 

extensions/dicom-segmentation/src/panelModule.js

@@ -1,39 +0,0 @@
-import SegmentationPanel from './components/SegmentationPanel/SegmentationPanel.js';
-
-export default {
-  menuOptions: [
-    {
-      icon: 'list',
-      label: 'Segmentations',
-      target: 'segmentation-panel',
-      isDisabled: studies => {
-        if (!studies) {
-          return true;
-        }
-
-        for (let i = 0; i < studies.length; i++) {
-          const study = studies[i];
-
-          if (study && study.series) {
-            for (let j = 0; j < study.series.length; j++) {
-              const series = study.series[j];
-
-              if (series.Modality === 'SEG') {
-                return false;
-              }
-            }
-          }
-        }
-
-        return true;
-      },
-    },
-  ],
-  components: [
-    {
-      id: 'segmentation-panel',
-      component: SegmentationPanel,
-    },
-  ],
-  defaultContext: ['VIEWER'],
-};

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.
 
+## [1.5.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.5.1...@ohif/extension-vtk@1.5.2) (2020-05-04)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.5.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.5.0...@ohif/extension-vtk@1.5.1) (2020-04-28)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+# [1.5.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.4.1...@ohif/extension-vtk@1.5.0) (2020-04-24)
+
+
+### Features
+
+* 🎸 Seg jump to slice + show/hide ([835f64d](https://github.com/OHIF/Viewers/commit/835f64d47a9994f6a25aaf3941a4974e215e7e7f))
+
+
+
+
+
+## [1.4.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.4.0...@ohif/extension-vtk@1.4.1) (2020-04-23)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+# [1.4.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.14...@ohif/extension-vtk@1.4.0) (2020-04-23)
+
+
+### Features
+
+* configuration to hook into XHR Error handling ([e96205d](https://github.com/OHIF/Viewers/commit/e96205de35e5bec14dc8a9a8509db3dd4e6ecdb6))
+
+
+
+
+
+## [1.3.14](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.13...@ohif/extension-vtk@1.3.14) (2020-04-22)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.3.13](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.12...@ohif/extension-vtk@1.3.13) (2020-04-17)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.3.12](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.11...@ohif/extension-vtk@1.3.12) (2020-04-15)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.3.11](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.10...@ohif/extension-vtk@1.3.11) (2020-04-09)
+
+
+### Bug Fixes
+
+* Revert "refactor: Reduce bundle size ([#1575](https://github.com/OHIF/Viewers/issues/1575))" ([#1622](https://github.com/OHIF/Viewers/issues/1622)) ([d21af3f](https://github.com/OHIF/Viewers/commit/d21af3f133492fa31492413b8782936c9ff18b44))
+
+
+
+
+
+## [1.3.10](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.9...@ohif/extension-vtk@1.3.10) (2020-04-09)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+# Change Log
+
+All notable changes to this project will be documented in this file. See
+[Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+## [1.3.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.8...@ohif/extension-vtk@1.3.9) (2020-04-06)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.3.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.7...@ohif/extension-vtk@1.3.8) (2020-04-02)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.3.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.6...@ohif/extension-vtk@1.3.7) (2020-04-02)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.3.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.5...@ohif/extension-vtk@1.3.6) (2020-04-01)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.3.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.4...@ohif/extension-vtk@1.3.5) (2020-03-25)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.3.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.3...@ohif/extension-vtk@1.3.4) (2020-03-24)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.3.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.2...@ohif/extension-vtk@1.3.3) (2020-03-24)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.3.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.1...@ohif/extension-vtk@1.3.2) (2020-03-23)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.3.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.0...@ohif/extension-vtk@1.3.1) (2020-03-17)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
 # [1.3.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.2.24...@ohif/extension-vtk@1.3.0) (2020-03-13)
 
 

extensions/vtk/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-vtk",
-  "version": "1.3.0",
+  "version": "1.5.2",
   "description": "OHIF extension for VTK.js",
   "author": "OHIF",
   "license": "MIT",
@@ -34,8 +34,8 @@
     "@ohif/ui": "^0.50.0",
     "cornerstone-core": "^2.2.8",
     "cornerstone-tools": "4.12.5",
-    "cornerstone-wado-image-loader": "^3.0.0",
-    "dcmjs": "^0.10.1",
+    "cornerstone-wado-image-loader": "^3.1.0",
+    "dcmjs": "^0.12.2",
     "dicom-parser": "^1.8.3",
     "i18next": "^17.0.3",
     "i18next-browser-languagedetector": "^3.0.1",
@@ -53,10 +53,10 @@
     "react-vtkjs-viewport": "^0.8.3"
   },
   "devDependencies": {
-    "@ohif/core": "^2.6.0",
-    "@ohif/ui": "^1.4.0",
+    "@ohif/core": "^2.9.2",
+    "@ohif/ui": "^1.4.3",
     "cornerstone-tools": "4.12.5",
-    "cornerstone-wado-image-loader": "^3.0.0",
+    "cornerstone-wado-image-loader": "^3.1.0",
     "dicom-parser": "^1.8.3",
     "gh-pages": "^2.0.1",
     "i18next": "^17.0.3",

platform/core/CHANGELOG.md

@@ -3,6 +3,195 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [2.9.2](https://github.com/OHIF/Viewers/compare/@ohif/core@2.9.1...@ohif/core@2.9.2) (2020-05-04)
+
+
+### Bug Fixes
+
+* use bit-appropriate array for palette lookup tables ([#1698](https://github.com/OHIF/Viewers/issues/1698)) ([7033886](https://github.com/OHIF/Viewers/commit/70338866978a76fa026c18d7c3c05257c5ece762))
+
+
+
+
+
+## [2.9.1](https://github.com/OHIF/Viewers/compare/@ohif/core@2.9.0...@ohif/core@2.9.1) (2020-04-28)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+# [2.9.0](https://github.com/OHIF/Viewers/compare/@ohif/core@2.8.1...@ohif/core@2.9.0) (2020-04-24)
+
+
+### Features
+
+* 🎸 Seg jump to slice + show/hide ([835f64d](https://github.com/OHIF/Viewers/commit/835f64d47a9994f6a25aaf3941a4974e215e7e7f))
+
+
+
+
+
+## [2.8.1](https://github.com/OHIF/Viewers/compare/@ohif/core@2.8.0...@ohif/core@2.8.1) (2020-04-23)
+
+
+### Bug Fixes
+
+* 🐛 Multiframe fix ([#1661](https://github.com/OHIF/Viewers/issues/1661)) ([7120561](https://github.com/OHIF/Viewers/commit/71205618ecb8b592247c5acb32284bfe7e18fce5))
+
+
+
+
+
+# [2.8.0](https://github.com/OHIF/Viewers/compare/@ohif/core@2.7.1...@ohif/core@2.8.0) (2020-04-23)
+
+
+### Features
+
+* configuration to hook into XHR Error handling ([e96205d](https://github.com/OHIF/Viewers/commit/e96205de35e5bec14dc8a9a8509db3dd4e6ecdb6))
+
+
+
+
+
+## [2.7.1](https://github.com/OHIF/Viewers/compare/@ohif/core@2.7.0...@ohif/core@2.7.1) (2020-04-22)
+
+
+### Bug Fixes
+
+* whiteLabeling should support component creation by passing React to defined fn ([#1659](https://github.com/OHIF/Viewers/issues/1659)) ([2093a00](https://github.com/OHIF/Viewers/commit/2093a0036584b2cc698c8f06fe62b334523b1029))
+
+
+
+
+
+# [2.7.0](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.11...@ohif/core@2.7.0) (2020-04-17)
+
+
+### Features
+
+* set the authorization header for DICOMWeb requests if provided in query string ([#1646](https://github.com/OHIF/Viewers/issues/1646)) ([450c80b](https://github.com/OHIF/Viewers/commit/450c80b9d5f172be8b5713b422370360325a0afc))
+
+
+
+
+
+## [2.6.11](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.10...@ohif/core@2.6.11) (2020-04-15)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.6.10](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.9...@ohif/core@2.6.10) (2020-04-09)
+
+
+### Bug Fixes
+
+* Revert "refactor: Reduce bundle size ([#1575](https://github.com/OHIF/Viewers/issues/1575))" ([#1622](https://github.com/OHIF/Viewers/issues/1622)) ([d21af3f](https://github.com/OHIF/Viewers/commit/d21af3f133492fa31492413b8782936c9ff18b44))
+
+
+
+
+
+## [2.6.9](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.8...@ohif/core@2.6.9) (2020-04-09)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+# Change Log
+
+All notable changes to this project will be documented in this file. See
+[Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+
+## [2.6.8](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.7...@ohif/core@2.6.8) (2020-04-06)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.6.7](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.6...@ohif/core@2.6.7) (2020-04-02)
+
+
+### Bug Fixes
+
+* 🐛 Fix multiframe images ([#1595](https://github.com/OHIF/Viewers/issues/1595)) ([9e0bd52](https://github.com/OHIF/Viewers/commit/9e0bd52c6a86648eb6673344a8555ad787043e5c))
+
+
+
+
+
+## [2.6.6](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.5...@ohif/core@2.6.6) (2020-04-02)
+
+**Note:** Version bump only for package @ohif/core
+
+
+
+
+
+## [2.6.5](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.4...@ohif/core@2.6.5) (2020-04-01)
+
+
+### Bug Fixes
+
+* segmentation not loading ([#1566](https://github.com/OHIF/Viewers/issues/1566)) ([4a7ce1c](https://github.com/OHIF/Viewers/commit/4a7ce1c09324d74c61048393e3a2427757e4001a))
+
+
+
+
+
+## [2.6.4](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.3...@ohif/core@2.6.4) (2020-03-25)
+
+
+### Bug Fixes
+
+* Add support for single entries in SequenceOfUltrasoundRegions. M… ([#1559](https://github.com/OHIF/Viewers/issues/1559)) ([c1a0d3c](https://github.com/OHIF/Viewers/commit/c1a0d3c662d143b62dfbf1c01f6ce394af3756ca))
+* disable autoFreeze of immer, even in dev mode ([#1560](https://github.com/OHIF/Viewers/issues/1560)) ([d604eba](https://github.com/OHIF/Viewers/commit/d604ebaffd93f688eadd0081e402f27074dd226b))
+
+
+
+
+
+## [2.6.3](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.2...@ohif/core@2.6.3) (2020-03-24)
+
+
+### Bug Fixes
+
+* Ensure we take into account pixel spacing fields properly ([#1555](https://github.com/OHIF/Viewers/issues/1555)) ([77ab0ad](https://github.com/OHIF/Viewers/commit/77ab0ad9a14a135b5560741fc1600704df08c141))
+
+
+
+
+
+## [2.6.2](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.1...@ohif/core@2.6.2) (2020-03-24)
+
+
+### Bug Fixes
+
+* OverlayPlane module usage for ArrayBuffer, BulkDataURI, and InlineBinary cases, as well as PaletteColor LUTs for ArrayBuffer (i.e. local drag/drop) case ([#1546](https://github.com/OHIF/Viewers/issues/1546)) ([404d52f](https://github.com/OHIF/Viewers/commit/404d52fe5c0442dd13e4d407bb0687d72fa5f32c))
+
+
+
+
+
+## [2.6.1](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.0...@ohif/core@2.6.1) (2020-03-23)
+
+
+### Bug Fixes
+
+* avoid-wasteful-renders ([#1544](https://github.com/OHIF/Viewers/issues/1544)) ([e41d339](https://github.com/OHIF/Viewers/commit/e41d339f5faef6b93700bc860f37f29f32ad5ed6))
+
+
+
+
+
 # [2.6.0](https://github.com/OHIF/Viewers/compare/@ohif/core@2.5.3...@ohif/core@2.6.0) (2020-03-13)
 
 

platform/core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/core",
-  "version": "2.6.0",
+  "version": "2.9.2",
   "description": "Generic business logic for web-based medical imaging applications",
   "author": "OHIF Core Team",
   "license": "MIT",
@@ -33,14 +33,15 @@
   "peerDependencies": {
     "cornerstone-core": "^2.2.8",
     "cornerstone-tools": "4.12.5",
-    "cornerstone-wado-image-loader": "^3.0.0",
+    "cornerstone-wado-image-loader": "^3.1.0",
     "dicom-parser": "^1.8.3"
   },
   "dependencies": {
     "@babel/runtime": "^7.5.5",
     "ajv": "^6.10.0",
-    "dcmjs": "^0.8.3",
-    "dicomweb-client": "^0.5.2",
+    "dcmjs": "^0.12.2",
+    "dicomweb-client": "^0.6.0",
+    "immer": "6.0.2",
     "isomorphic-base64": "^1.0.2",
     "lodash.clonedeep": "^4.5.0",
     "lodash.merge": "^4.6.1",

platform/core/src/DICOMSR/handleStructuredReport.js

@@ -1,10 +1,11 @@
-import * as dcmjs from 'dcmjs';
+import dcmjs from 'dcmjs';
 import { api } from 'dicomweb-client';
 
 import DICOMWeb from '../DICOMWeb';
 import parseDicomStructuredReport from './parseDicomStructuredReport';
 import parseMeasurementsData from './parseMeasurementsData';
 import getAllDisplaySets from './utils/getAllDisplaySets';
+import errorHandler from '../errorHandler';
 
 const VERSION_NAME = 'dcmjs-0.0';
 const TRANSFER_SYNTAX_UID = '1.2.840.10008.1.2.1';
@@ -21,6 +22,7 @@ const retrieveMeasurementFromSR = async (series, studies, serverUrl) => {
   const config = {
     url: serverUrl,
     headers: DICOMWeb.getAuthorizationHeader(),
+    errorInterceptor: errorHandler.getHTTPErrorHandler(),
   };
 
   const dicomWeb = new api.DICOMwebClient(config);
@@ -71,6 +73,7 @@ const stowSRFromMeasurements = async (measurements, serverUrl) => {
   const config = {
     url: serverUrl,
     headers: DICOMWeb.getAuthorizationHeader(),
+    errorInterceptor: errorHandler.getHTTPErrorHandler(),
   };
 
   const dicomWeb = new api.DICOMwebClient(config);

platform/core/src/DICOMSR/parseDicomStructuredReport.js

@@ -1,4 +1,4 @@
-import * as dcmjs from 'dcmjs';
+import dcmjs from 'dcmjs';
 
 import findInstanceMetadataBySopInstanceUID from './utils/findInstanceMetadataBySopInstanceUid';
 

platform/core/src/DICOMSR/parseMeasurementsData.js

@@ -1,4 +1,4 @@
-import * as dcmjs from 'dcmjs';
+import dcmjs from 'dcmjs';
 import cornerstone from 'cornerstone-core';
 
 import log from '../log';

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

@@ -10,6 +10,13 @@ const findMostRecentStructuredReport = studies => {
   studies.forEach(study => {
     const allSeries = study.getSeries ? study.getSeries() : [];
     allSeries.forEach(series => {
+      // Skip series that may not have instances yet
+      // This can happen if we have retrieved just the initial
+      // details about the series via QIDO-RS, but not the full metadata
+      if (!series.instances.length) {
+        return;
+      }
+
       if (isStructuredReportSeries(series)) {
         if (
           !mostRecentStructuredReport ||

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

@@ -1,4 +1,4 @@
-import * as dcmjs from 'dcmjs';
+import dcmjs from 'dcmjs';
 
 /**
  *  Checks if dcmjs has support to determined tool

platform/core/src/DICOMWeb/getAuthorizationHeader.js

@@ -1,6 +1,3 @@
-// Commenting this out for now since it looks like Rollup is pulling in the
-// Node.js version instead of the Browser version of this package
-//import { btoa } from 'isomorphic-base64';
 import user from '../user';
 
 /**
@@ -18,6 +15,7 @@ export default function getAuthorizationHeader({ requestOptions } = {}) {
   // Check for OHIF.user since this can also be run on the server
   const accessToken = user && user.getAccessToken && user.getAccessToken();
 
+  // Auth for a specific server
   if (requestOptions && requestOptions.auth) {
     if (typeof requestOptions.auth === 'function') {
       // Custom Auth Header
@@ -26,7 +24,9 @@ export default function getAuthorizationHeader({ requestOptions } = {}) {
       // HTTP Basic Auth (user:password)
       headers.Authorization = `Basic ${btoa(requestOptions.auth)}`;
     }
-  } else if (accessToken) {
+  }
+  // Auth for the user's default
+  else if (accessToken) {
     headers.Authorization = `Bearer ${accessToken}`;
   }
 

platform/core/src/classes/MetadataProvider.js

@@ -1,7 +1,7 @@
-import * as dcmjs from 'dcmjs';
+import dcmjs from 'dcmjs';
 import queryString from 'query-string';
 import dicomParser from 'dicom-parser';
-import { getFallbackTagFromInstance } from '../utils/metadataProvider/metadataProviderFallbackTags';
+import getPixelSpacingInformation from '../utils/metadataProvider/getPixelSpacingInformation';
 import fetchPaletteColorLookupTableData from '../utils/metadataProvider/fetchPaletteColorLookupTableData';
 import fetchOverlayData from '../utils/metadataProvider/fetchOverlayData';
 
@@ -58,9 +58,7 @@ class MetadataProvider {
 
     Object.assign(instance, naturalizedDataset);
 
-    if (options.server) {
-      await this._checkBulkDataAndInlineBinaries(instance, options.server);
-    }
+    await this._checkBulkDataAndInlineBinaries(instance, options.server);
 
     return instance;
   }
@@ -163,18 +161,6 @@ class MetadataProvider {
       return instance[naturalizedTagOrWADOImageLoaderTag];
     }
 
-    if (options.fallback) {
-      // Perhaps the tag has fallbacks?
-      const fallbackTag = getFallbackTagFromInstance(
-        naturalizedTagOrWADOImageLoaderTag,
-        instance
-      );
-
-      if (fallbackTag) {
-        return fallbackTag;
-      }
-    }
-
     // Maybe its a legacy CornerstoneWADOImageLoader tag then:
     return this._getCornerstoneWADOImageLoaderTag(
       naturalizedTagOrWADOImageLoaderTag,
@@ -220,10 +206,9 @@ class MetadataProvider {
         const { ImageOrientationPatient } = instance;
 
         // Fallback for DX images.
-        const PixelSpacing = getFallbackTagFromInstance(
-          'PixelSpacing',
-          instance
-        );
+        // TODO: We should use the rest of the results of this function
+        // to update the UI somehow
+        const { PixelSpacing } = getPixelSpacingInformation(instance);
 
         let rowPixelSpacing;
         let columnPixelSpacing;
@@ -344,7 +329,7 @@ class MetadataProvider {
 
         break;
       case WADO_IMAGE_LOADER_TAGS.OVERLAY_PLANE_MODULE:
-        metadata = [];
+        const overlays = [];
 
         for (
           let overlayGroup = 0x00;
@@ -389,9 +374,13 @@ class MetadataProvider {
             roiStandardDeviation: instance[ROIStandardDeviationTag],
           };
 
-          metadata.push(overlay);
+          overlays.push(overlay);
         }
 
+        metadata = {
+          overlays,
+        };
+
         break;
 
       case WADO_IMAGE_LOADER_TAGS.PATIENT_MODULE:
@@ -411,6 +400,7 @@ class MetadataProvider {
 
       case WADO_IMAGE_LOADER_TAGS.GENERAL_IMAGE_MODULE:
         metadata = {
+          sopInstanceUid: instance.SOPInstanceUID,
           instanceNumber: instance.InstanceNumber,
           lossyImageCompression: instance.LossyImageCompression,
           lossyImageCompressionRatio: instance.LossyImageCompressionRatio,

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

@@ -11,6 +11,7 @@ import { api } from 'dicomweb-client';
 import { isImage } from '../../utils/isImage';
 import isDisplaySetReconstructable from '../../utils/isDisplaySetReconstructable';
 import isLowPriorityModality from '../../utils/isLowPriorityModality';
+import errorHandler from '../../errorHandler';
 
 export class StudyMetadata extends Metadata {
   constructor(data, uid) {
@@ -100,20 +101,29 @@ export class StudyMetadata extends Metadata {
    * Split a series metadata object into display sets
    * @param {Array} sopClassHandlerModules List of SOP Class Modules
    * @param {SeriesMetadata} series The series metadata object from which the display sets will be created
-   * @param {Array} [givenDisplaySets] An optional list to which the display sets will be appended
    * @returns {Array} The list of display sets created for the given series object
    */
-  _createDisplaySetsForSeries(
-    sopClassHandlerModules,
-    series,
-    givenDisplaySets
-  ) {
+  _createDisplaySetsForSeries(sopClassHandlerModules, series) {
     const study = this;
-    const displaySets = Array.isArray(givenDisplaySets) ? givenDisplaySets : [];
+    const displaySets = [];
+
     const anyInstances = series.getInstanceCount() > 0;
 
     if (!anyInstances) {
-      return;
+      const displaySet = new ImageSet([]);
+      const seriesData = series.getData();
+
+      displaySet.setAttributes({
+        displaySetInstanceUID: displaySet.uid,
+        SeriesInstanceUID: seriesData.SeriesInstanceUID,
+        SeriesDescription: seriesData.SeriesDescription,
+        SeriesNumber: seriesData.SeriesNumber,
+        Modality: seriesData.Modality,
+      });
+
+      displaySets.push(displaySet);
+
+      return displaySets;
     }
 
     const sopClassUIDs = getSopClassUIDs(series);
@@ -208,20 +218,21 @@ export class StudyMetadata extends Metadata {
   /**
    * Returns a list of derived datasets in the study, filtered by the given filter.
    * @param {object} filter An object containing search filters
-   * @param {object} filter.modality
+   * @param {object} filter.Modality
    * @param {object} filter.referencedSeriesInstanceUID
    * @param {object} filter.referencedFrameOfReferenceUID
    * @return {Array} filtered derived display sets
    */
   getDerivedDatasets(filter) {
     const {
-      modality,
+      Modality,
       referencedSeriesInstanceUID,
       referencedFrameOfReferenceUID,
     } = filter;
+
     let filteredDerivedDisplaySets = this._derivedDisplaySets;
 
-    if (modality) {
+    if (Modality) {
       filteredDerivedDisplaySets = filteredDerivedDisplaySets.filter(
         displaySet => displaySet.Modality === Modality
       );
@@ -280,14 +291,14 @@ export class StudyMetadata extends Metadata {
     }
 
     // Loop through the series (SeriesMetadata)
-    this.forEachSeries(
-      series =>
-        void this._createDisplaySetsForSeries(
-          sopClassHandlerModules,
-          series,
-          displaySets
-        )
-    );
+    this.forEachSeries(series => {
+      const displaySetsForSeries = this._createDisplaySetsForSeries(
+        sopClassHandlerModules,
+        series
+      );
+
+      displaySets.push(...displaySetsForSeries);
+    });
 
     return sortDisplaySetList(displaySets);
   }
@@ -303,13 +314,30 @@ export class StudyMetadata extends Metadata {
    * @returns {boolean} Returns true on success or false on failure (e.g., the series does not belong to this study)
    */
   createAndAddDisplaySetsForSeries(sopClassHandlerModules, series) {
-    if (this.containsSeries(series)) {
-      this.setDisplaySets(
-        this._createDisplaySetsForSeries(sopClassHandlerModules, series)
-      );
-      return true;
+    if (!this.containsSeries(series)) {
+      return false;
     }
-    return false;
+
+    const displaySets = this._createDisplaySetsForSeries(
+      sopClassHandlerModules,
+      series
+    );
+
+    // Note: filtering in place because this._displaySets has writable: false
+    for (let i = this._displaySets.length - 1; i >= 0; i--) {
+      const displaySet = this._displaySets[i];
+      if (displaySet.SeriesInstanceUID === series.getSeriesInstanceUID()) {
+        this._displaySets.splice(i, 1);
+      }
+    }
+
+    displaySets.forEach(displaySet => {
+      this.addDisplaySet(displaySet);
+    });
+
+    this.sortDisplaySets();
+
+    return true;
   }
 
   /**
@@ -318,6 +346,9 @@ export class StudyMetadata extends Metadata {
    */
   setDisplaySets(displaySets) {
     if (Array.isArray(displaySets) && displaySets.length > 0) {
+      // TODO: This is weird, can we just switch it to writable: true?
+      this._displaySets.splice(0);
+
       displaySets.forEach(displaySet => this.addDisplaySet(displaySet));
       this.sortDisplaySets();
     }
@@ -406,6 +437,30 @@ export class StudyMetadata extends Metadata {
     return result;
   }
 
+  /**
+   * Update a series in the current study by SeriesInstanceUID.
+   * @param {String} SeriesInstanceUID The SeriesInstanceUID to be updated
+   * @param {SeriesMetadata} series The series to be added to the current study.
+   * @returns {boolean} Returns true on success, false otherwise.
+   */
+  updateSeries(SeriesInstanceUID, series) {
+    const index = this._series.findIndex(series => {
+      return series.getSeriesInstanceUID() === SeriesInstanceUID;
+    });
+
+    if (index < 0) {
+      return false;
+    }
+
+    if (!(series instanceof SeriesMetadata)) {
+      throw new Error('Series must be an instance of SeriesMetadata');
+    }
+
+    this._series[index] = series;
+
+    return true;
+  }
+
   /**
    * Find a series by index.
    * @param {number} index An integer representing a list index.
@@ -780,9 +835,11 @@ function _getDisplaySetFromSopClassModule(
 
   const plugin = handlersForSopClassUID[0];
   const headers = DICOMWeb.getAuthorizationHeader();
+  const errorInterceptor = errorHandler.getHTTPErrorHandler();
   const dicomWebClient = new dwc({
     url: study.getData().wadoRoot,
     headers,
+    errorInterceptor,
   });
 
   let displaySet = plugin.getDisplaySetFromSeries(

platform/core/src/errorHandler.js

@@ -0,0 +1,6 @@
+// These should be overridden by the implementation
+const errorHandler = {
+  getHTTPErrorHandler: () => null,
+};
+
+export default errorHandler;

platform/core/src/index.js

@@ -18,6 +18,7 @@ import string from './string.js';
 import studies from './studies/';
 import ui from './ui';
 import user from './user.js';
+import errorHandler from './errorHandler.js';
 import utils, { hotkeys } from './utils/';
 
 import {
@@ -46,6 +47,7 @@ const OHIF = {
   string,
   ui,
   user,
+  errorHandler,
   object,
   log,
   DICOMWeb,
@@ -79,6 +81,7 @@ export {
   string,
   ui,
   user,
+  errorHandler,
   object,
   log,
   DICOMWeb,