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<div class='row'>
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<div class='column' style='text-align: right; padding: 0 20px'>
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<strong>Looking for a Live Demo?</strong>
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<a href="http://viewer.ohif.org/">Preview The OHIF Viewer</a>
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</div>
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<div class='column' style='text-align: left; padding: 0 20px'>
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<a href="https://www.netlify.com">
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<img src="https://www.netlify.com/img/global/badges/netlify-color-bg.svg"/>
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</a>
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</div>
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</div>
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> ATTENTION! You are looking at the docs for the `OHIF-v3` Viewer (third time is always a charm). If you're looking for the our `OHIF-v2` (React stable version) or OHIF-v1 (deprecated `Meteor` version) select it's version from the dropdown box in the top left corner
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> of this page.
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# Introduction
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The [Open Health Imaging Foundation][ohif-org] (OHIF) Viewer is an open source,
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web-based, medical imaging viewer. It can be configured to connect to Image
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Archives that support [DicomWeb][dicom-web], and offers support for mapping to
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proprietary API formats. OHIF maintained extensions add support for viewing,
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annotating, and reporting on DICOM images in 2D (slices) and 3D (volumes).
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<center><i>The <strong>OHIF Viewer v3</strong>: A general purpose DICOM Viewer (<a href="http://viewer.ohif.org/">Live Demo</a>)</center>
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## What's new in `OHIF-v3`
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`OHIF-v3` is our second try for a React-based viewer, and is the third version of
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our medical image web viewers from the start. The summary of changes include:
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- Addition of workflow modes
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- Often, medical imaging use cases involves lots of specific workflows that re-use
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functionalities. We have added the capability of workflow modes, that enable people
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to customize user interface and configure application for specific workflow.
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- The idea is to re-use the functionalities that extensions provide and create a workflow.
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Brain segmentation workflow is different from prostate segmentation in UI for sure; however, they share the segmentation tools that can be re-used.
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- Our vision is that technical people focus of developing extensions which provides
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core functionalities, and experts to build modes by picking the appropriate functionalities
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from each extension.
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- Redux store has been removed from the viewer, and a cleaner, more powerful
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- tailwind CSS
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- End-to-end test suite
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Below, you can find the gap analysis between the `OHIF-v2` and `OHIF-v3`:
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{% include "./_gap_analysis.md" %}
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## Where to next?
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The Open Health Imaging Foundation intends to provide a simple general purpose
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DICOM Viewer which can be easily extended for specific uses. If you find
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yourself unable to extend the viewer for your purposes, please reach out via our
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[GitHub issues][gh-issues]. We are actively seeking feedback on ways to improve
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our integration and extension points.
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Check out these helpful links:
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- Ready to dive into some code? Check out our
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[Getting Started Guide](./development/getting-started.md).
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- We're an active, vibrant community.
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[Learn how you can be more involved.](./development/contributing.md)
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- Feeling lost? Read our [help page](./help.md).
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<!--
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Links
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-->
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<!-- prettier-ignore-start -->
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[ohif-org]: http://www.ohif.org
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[ohif-demo]: http://viewer.ohif.org/
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[dicom-web]: https://en.wikipedia.org/wiki/DICOMweb
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[gh-issues]: https://github.com/OHIF/Viewers/issues
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<!-- prettier-ignore-end -->
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@@ -1,83 +0,0 @@
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# OHIF Viewers
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- [Our Process](our-process.md)
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- User Manuals
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- [Overview](userManuals/index.md)
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- [Study List](userManuals/studyList/index.md)
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- [Viewer](userManuals/viewer/index.md)
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- [Study Panel](userManuals/viewer/studyPanel/study-panel.md)
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- [Measurement Panel](userManuals/viewer/measurementPanel/measurement-panel.md)
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- [Viewport](userManuals/viewer/viewport/viewport.md)
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- [Toolbar](userManuals/viewer/toolbar/toolbar.md)
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- [Hot keys](userManuals/viewer/hotkeys/hotkeys.md)
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- [Language](userManuals/viewer/language/language.md)
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- Development
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- [Getting Started](development/getting-started.md)
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- [Contributing](development/contributing.md)
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- [Continuous Integration](development/continous-integration.md)
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- [Testing](development/testing.md)
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- [Configuring Data Source](configuring/index.md)
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- [Local DICOM Server](configuring/data-source.md)
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---
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- [Architecture](architecture/index.md)
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- [Viewer](viewer/index.md)
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- [Configuration](viewer/configuration.md)
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- [Theming](viewer/themeing.md)
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- [Internationalization](viewer/internationalization.md)
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- [Extensions](extensions/index.md#Overview)
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- [Registering](extensions/index.md#registering-an-extension)
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- [OHIF Maintained](extensions/index.md#ohif-maintained-extensions)
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- [Lifecycle Hooks](extensions/index.md#lifecycle-hooks)
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- [preRegistration](extensions/lifecycle/pre-registration.md)
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- [onModeEnter](extensions/lifecycle/on-mode-enter.md)
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- [onModeExit](extensions/lifecycle/on-mode-exit.md)
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- [Modules](extensions/index.md#modules)
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- [Toolbar](extensions/modules/toolbar.md)
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- [Commands](extensions/modules/commands.md)
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- [DataSource](extensions/modules/data-source.md)
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- [SOPClassHandler](extensions/modules/sop-class-handler.md)
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- [Viewport](extensions/modules/viewport.md)
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- [Panel](extensions/modules/panel.md)
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- [LayoutTemplate](extensions/modules/layout-template.md)
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- [HangingProtocol](extensions/modules/hpModule.md)
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- [Context](extensions/index.md#contexts)
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- [ExtensionManager](managers/extension.md)
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- [Modes](modes/index.md)
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- [LifeCycle](modes/lifeCycle.md#overview)
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- [Validity](modes/validity.md#overview)
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- [Routes](modes/routes.md#overview)
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- [Managers](managers/index.md)
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- [Extension Manager](managers/extension.md)
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- [Service Manager](managers/service.md)
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- [Commands Manager](managers/commands.md)
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- [Hotkeys Manager](managers/hotkeys.md)
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- [Services](services/index.md)
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- [Data Services](services/data/index.md)
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- [Dicom Metadata Store](services/data/DicomMetadataStore.md)
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- [DisplaySet Service](services/data/DisplaySetService.md)
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- [Hanging Protocol Service](services/data/HangingProtocolService.md)
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- [Toolbar Service](services/data/ToolbarService.md)
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- [Measurement Service](services/data/MeasurementService.md)
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- [UI Services](services/ui/index.md)
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- [UI Notification Service](services/ui/ui-notification-service.md)
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- [UI Modal Service](services/ui/ui-modal-service.md)
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- [UI Dialog Service](services/ui/ui-dialog-service.md)
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- [UI Viewport Dialog Service](services/ui/ui-viewport-dialog-service.md)
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- [Viewport Grid Service](services/ui/ViewportGridService.md)
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- [Pub/Sub Pattern](services/pubsub.md)
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- [Deployment](deployment/index.md)
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- [Build for Production](deployment/recipes/build-for-production.md)
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- [Static](deployment/recipes/static-assets.md)
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- [Nginx + Image Archive](deployment/recipes/nginx--image-archive.md)
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- [User Account Control](deployment/recipes/user-account-control.md)
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- [Google Cloud Healthcare](connecting-to-image-archives/google-cloud-healthcare.md)
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- [FAQ](faq/index.md)
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- [Scope of Project](faq/scope-of-project.md)
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- [Browser Support](faq/browser-support.md)
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- [PWA vs Packaged](faq/pwa-vs-packaged.md)
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- [Help](help.md) -->
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@@ -1,110 +0,0 @@
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<table>
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<thead>
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<tr>
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<th align="left" width="50%">OHIF-v2 functionalities</th>
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<th align="center">OHIF-v3</th>
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<th align="center">Comment</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td align="left">Rendering of 2D images via Cornerstone</td>
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<td align="center">✅</td>
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<td align="center"></td>
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</tr>
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<tr>
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<td align="left">Study List</td>
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<td align="center">✅</td>
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<td align="center"></td>
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</tr>
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<tr>
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<td align="left">Series Browser</td>
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<td align="center">✅</td>
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<td align="center"></td>
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</tr>
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<tr>
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<td align="left">DICOM JSON</td>
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<td align="center">✅</td>
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<td align="center"></td>
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</tr>
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<tr>
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<td align="left">2D Tools via CornerstoneTools</td>
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<td align="center">✅</td>
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<td align="center"></td>
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</tr>
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<tr>
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<td align="left">OpenID Connect standard authentication flow for connecting to identity providers</td>
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<td align="center">🔜</td>
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<td align="center">In Progress</td>
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</tr>
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<tr>
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<td align="left">Internationalization</td>
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<td align="center">🔜</td>
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<td align="center">Not Started</td>
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</tr>
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<tr>
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<td align="left">Drag/drop DICOM data into the viewer (see https://viewer.ohif.org/local)</td>
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<td align="center">🔜</td>
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<td align="center">Not Started</td>
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</tr>
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<tr>
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<td align="left">IHE Invoke Image Display - Standard-compliant launching of the viewer (e.g. from PACS or RIS)</td>
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<td align="center">🔜</td>
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<td align="center">Not Started</td>
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</tr>
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<tr>
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<td align="left">DICOM PDF support</td>
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<td align="center">🔜</td>
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<td align="center">Not Started</td>
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</tr>
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<tr>
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<td align="left">DICOM Whole-slide imaging viewport</td>
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<td align="center">🔜</td>
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<td align="center">Not Started</td>
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</tr>
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<tr>
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<td align="left">Displaying non-renderable DICOM as HTML</td>
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<td align="center">🔜</td>
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<td align="center">Not Started</td>
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</tr>
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<tr>
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<td align="left">Segmentation support</td>
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<td align="center">🔜</td>
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<td align="center">Not Started</td>
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</tr>
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<tr>
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<td align="left">RT STRUCT support</td>
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<td align="center">🔜</td>
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<td align="center">Not Started</td>
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</tr>
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<tr>
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<td align="left">White-labelling: Easily replace the OHIF Logo with your logo</td>
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<td align="center">🔜</td>
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<td align="center">Not Started</td>
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</tr>
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<tr>
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<td align="left">DICOM upload to PACS</td>
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<td align="center">🔜</td>
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<td align="center">Not Started</td>
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</tr>
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<tr>
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<td align="left">Google Cloud adapter</td>
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<td align="center">🔜</td>
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<td align="center">Not Started</td>
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</tr>
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<tr>
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<td align="left">VTK Extension + MIP / MPR layout</td>
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<td align="center">❌</td>
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<td align="center">Other plans</td>
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</tr>
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<tr>
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<td align="left">UMD Build (Embedded Viewer). </td>
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<td align="center">❌</td>
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<td align="center">The problem is that this breaks a bunch of extensions that rely on third party scripts (e.g. VTK) which have their own web worker loaders.</td>
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</tr>
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</tbody>
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</table>
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❌
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✅
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🔜
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@@ -1,213 +0,0 @@
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# Architecture
|
||||
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>New `OHIF-v3` architecture has made OHIF a general purpose extensible medical imaging **platform**, as opposed to a somewhat highly configurable viewer.
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In order to achieve a platform that can support various workflows and be extensible for the foreseeable future we went through extensive planning of possible use cases and decided to significantly change and improve the architecture.
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Below, we aim to demystify that complexity by providing insight into how `OHIF Platform` is
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architected, and the role each of it's dependent libraries plays.
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- [Architecture](#architecture)
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- [Overview](#overview)
|
||||
- [Extensions](#extensions)
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- [Modes](#modes)
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- [Platform](#platform)
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- [`@ohif/viewer`](#ohifviewer)
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- [`@ohif/core`](#ohifcore)
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- [`@ohif/ui`](#ohifui)
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- [Overview of the architecture](#overview-of-the-architecture)
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- [Common Questions](#common-questions)
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## Overview
|
||||
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The [OHIF Medical Image Viewing Platform][viewers-project] is maintained as a
|
||||
[`monorepo`][monorepo]. This means that this repository, instead of containing a
|
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single project, contains many projects. If you explore our project structure,
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you'll see the following:
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```bash
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.
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||||
│
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├── extensions
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||||
│ ├── _example # Skeleton of example extension
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||||
│ ├── default # default functionalities
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│ ├── cornerstone # 2D images w/ Cornerstone.js
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│ ├── measurement-tracking # measurement tracking
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│ ├── dicom-sr # Structured reports
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│ └── dicom-pdf # View DICOM wrapped PDFs in viewport
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│
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├── modes
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│ └── longitudinal # longitudinal measurement tracking mode
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│
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├── platform
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│ ├── core # Business Logic
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│ ├── i18n # Internationalization Support
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│ ├── ui # React component library
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│ └── viewer # Connects platform and extension projects
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│
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||||
├── ... # misc. shared configuration
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||||
├── lerna.json # MonoRepo (Lerna) settings
|
||||
├── package.json # Shared devDependencies and commands
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||||
└── README.md
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||||
```
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|
||||
OHIF v3 is comprised of the following components, described in detail in further sections:
|
||||
|
||||
- `@ohif/viewer`: The core framework that controls extension registration, mode composition and routing.
|
||||
- `@ohif/core`: A library of useful and reusable medical imaging functionality for the web.
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||||
- `@ohif/ui`: A library of reusable components to build OHIF-styled applications with.
|
||||
- `Extensions`: A set of building blocks for building applications. The OHIF org maintains a few core libraries.
|
||||
- `Modes`: Configuration objects that tell @ohif/viewer how to compose extensions to build applications on different routes of the platform.
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
## Extensions
|
||||
The `extensions` directory contains many packages that provides essential
|
||||
functionalities such as rendering, study/series browsers, measurement tracking that modes
|
||||
can consume to enable a certain workflow. Extensions have had their behavior changed
|
||||
in `OHIF-v3` and their api is expanded. In summary:
|
||||
|
||||
>In `OHIF-v3`, extensions no longer automatically hook themselves to the app. Now,
|
||||
>registering an extension makes its component available to `modes` that wish to use them.
|
||||
> Basically, extensions in `OHIF-v3` are **building blocks** for building applications.
|
||||
|
||||
|
||||
OHIF team maintains several high value and commonly used functionalities in its
|
||||
own extensions. For a list of extensions maintained by OHIF,
|
||||
[check out this helpful table](../extensions/index.md#maintained-extensions).
|
||||
As an example `default` extension provides a default viewer layout,
|
||||
a study/series browser and a datasource that maps to a DICOMWeb compliant backend.
|
||||
|
||||
|
||||
[Click here to read more about extensions!](../extensions/index.md)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
## Modes
|
||||
|
||||
The `modes` directory contains workflows that can be registered with OHIF
|
||||
within certain `routes`. The mode will get used once the user opens the viewer
|
||||
on the registered route.
|
||||
|
||||
OHIF extensions were designed to provide certain core functionalities for building
|
||||
your viewer. However, often in medical imaging we face a specific use case
|
||||
in which we are using some core functionalities, adding our specific UI, and
|
||||
use it in our workflows. Previously, to achieve this you had to create an
|
||||
extension to add have such feature. `OHIF-v3` introduces `Modes` to enable
|
||||
building such workflows by re-using the core functionalities from the extensions.
|
||||
|
||||
Some common workflows may include:
|
||||
|
||||
- Measurement tracking for lesions
|
||||
- Segmentation of brain abnormalities
|
||||
- AI probe mode for detecting prostate cancer
|
||||
|
||||
In the mentioned modes above, they will share the same core rendering module that
|
||||
the `default` extension provides. However, segmentation mode will require
|
||||
segmentation tools which is not needed for the other two.
|
||||
As you can see, modes are a layer on top of extensions, that you
|
||||
can configure in order to achieve certain workflows.
|
||||
|
||||
To summarize the difference between extensions and modes in `OHIF-v3` and extensions in `OHIF-v2`
|
||||
|
||||
> - `Modes` are configuration objects that tell *@ohif/viewer* how to compose extensions to build applications on different routes of the platform.
|
||||
> - In v2 extensions are “plugins” that add functionality to a core viewer.
|
||||
> - In v3 extensions are building blocks that a mode uses to build an entire viewer layout.
|
||||
|
||||
[Click here to read more about modes!](../modes/index.md)
|
||||
|
||||
|
||||
|
||||
## Platform
|
||||
|
||||
### `@ohif/viewer`
|
||||
|
||||
This library is the core library which consumes modes and extensions and builds an application. Extensions can be passed in as app configuration and will be consumed and initialized at the appropriate time by the application. Upon initialization the viewer will consume extensions and modes and build up the route desired, these can then be accessed via the study list, or directly via url parameters.
|
||||
|
||||
Upon release modes will also be plugged into the app via configuration, but this is still an area which is under development/discussion, and they are currently pulled from the window in beta.
|
||||
|
||||
Future ideas for this framework involve only adding modes and fetching the required extension versions at either runtime or build time, but this decision is still up for discussion.
|
||||
|
||||
### `@ohif/core`
|
||||
OHIF core is a carefully maintained and tested set of web-based medical imaging functions and classes. This library includes managers and services used from within the viewer app.
|
||||
|
||||
OHIF core is largely similar to the @ohif/core library in v2, however a lot of logic has been moved to extensions:
|
||||
however all logic about DICOMWeb and other data fetching mechanisms have been pulled out, as these now live in extensions, described later.
|
||||
|
||||
|
||||
|
||||
|
||||
### `@ohif/ui`
|
||||
Firstly, a large time-consumer/barrier for entry we discovered was building new UI in a timely manner that fit OHIF’s theme. For this reason we have built a new UI component library which contains all the components one needs to build their own viewer.
|
||||
|
||||
These components are presentational only, so you can reuse them with whatever logic you desire. As the components are presentational, you may swap out @ohif/ui for a custom UI library with conforming API if you wish to white label the viewer. The UI library is here to make development easier and quicker, but it is not mandatory for extension components to use.
|
||||
|
||||
[Check out our component library!](https://react.ohif.org/)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
## Overview of the architecture
|
||||
OHIF-v3 architecture can be seen in the following figure. We will explore each
|
||||
piece in more detail.
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
## Common Questions
|
||||
|
||||
|
||||
> Can I create my own Viewer using Vue.js or Angular.js?
|
||||
|
||||
You can, but you will not be able to leverage as much of the existing code and
|
||||
components. `@ohif/core` could still be used for business logic, and to provide
|
||||
a model for extensions. `@ohif/ui` would then become a guide for the components
|
||||
you would need to recreate.
|
||||
|
||||
|
||||
> When I want to implement a functionality, should it be in the mode or in an extension?
|
||||
|
||||
This is a great question. Modes are designed to consume extensions, so you should implement
|
||||
your functionality in one of the modules of your new extension, and let the mode to consume it.
|
||||
This way, in future, if you needed another mode that utilizes the same functionality, you can easily
|
||||
hook the extension to the new mode as well.
|
||||
|
||||
<!--
|
||||
Links
|
||||
-->
|
||||
|
||||
<!-- prettier-ignore-start -->
|
||||
[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/tree/master/platform/ui
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@@ -1,54 +0,0 @@
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{
|
||||
"title": "OHIF",
|
||||
"description": "Documentation for the OHIF framework",
|
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"gitbook": ">3.0.0",
|
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"plugins": [
|
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"edit-link",
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"theme-cornerstone",
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"-fontsettings",
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"github",
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"ga",
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"sitemap",
|
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"anchors",
|
||||
"versions"
|
||||
],
|
||||
"pluginsConfig": {
|
||||
"edit-link": {
|
||||
"base": "https://github.com/OHIF/Viewers/edit/master/docs",
|
||||
"label": "Edit This Page"
|
||||
},
|
||||
"github": {
|
||||
"url": "https://github.com/OHIF/Viewers"
|
||||
},
|
||||
"ga": {
|
||||
"token": "UA-110573590-2"
|
||||
},
|
||||
"sitemap": {
|
||||
"hostname": "https://docs.ohif.org"
|
||||
},
|
||||
"versions": {
|
||||
"gitbookConfigURL": "https://raw.githubusercontent.com/OHIF/Viewers/master/docs/book.json",
|
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"options": [
|
||||
{
|
||||
"value": "https://docs.ohif.org/history/v1/",
|
||||
"text": "Version 1.0.0 (Meteor)"
|
||||
},
|
||||
{
|
||||
"value": "https://docs.ohif.org/history/v2/",
|
||||
"text": "Version 2.0.0"
|
||||
},
|
||||
{
|
||||
"value": "https://docs.ohif.org/",
|
||||
"text": "Version 3.0.0",
|
||||
"selected": true
|
||||
}
|
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]
|
||||
}
|
||||
},
|
||||
"links": {
|
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"sharing": {
|
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"facebook": false,
|
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"twitter": false
|
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}
|
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}
|
||||
}
|
||||
@@ -1,194 +0,0 @@
|
||||
## Set up a local DICOM server
|
||||
|
||||
- [Set up a local DICOM server](#set-up-a-local-dicom-server)
|
||||
- [Requirements](#requirements)
|
||||
- [Open Source DICOM Image Archives](#open-source-dicom-image-archives)
|
||||
- [Running Orthanc](#running-orthanc)
|
||||
- [Orthanc: Learn More](#orthanc-learn-more)
|
||||
- [Connecting to Orthanc](#connecting-to-orthanc)
|
||||
- [Configuration: Learn More](#configuration-learn-more)
|
||||
- [Running DCM4CHEE](#running-dcm4chee)
|
||||
|
||||
|
||||
ATTENTION! Already have a remote or local server? Skip to the
|
||||
[configuration section](#configuration-learn-more) below.
|
||||
|
||||
While the OHIF Viewer can work with any data source, the easiest to configure
|
||||
are the ones that follow the [DICOMWeb][dicom-web] spec.
|
||||
|
||||
1. Choose and install an Image Archive
|
||||
2. Upload data to your archive (e.g. with DCMTK's [storescu][storescu] or your
|
||||
archive's web interface)
|
||||
3. Keep the server running
|
||||
|
||||
For our purposes, we will be using `Orthanc`, but you can see a list of
|
||||
[other Open Source options](#open-source-dicom-image-archives) below.
|
||||
|
||||
### Requirements
|
||||
|
||||
- Docker
|
||||
- [Docker for Mac](https://docs.docker.com/docker-for-mac/)
|
||||
- [Docker for Windows (recommended)](https://docs.docker.com/docker-for-windows/)
|
||||
- [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/)
|
||||
|
||||
_Not sure if you have `docker` installed already? Try running `docker --version`
|
||||
in command prompt or terminal_
|
||||
|
||||
> If you are using `Docker Toolbox` you need to change the _PROXY_DOMAIN_
|
||||
> parameter in _platform/viewer/package.json_ to http://192.168.99.100:8042 or
|
||||
> the ip docker-machine ip throws. This is the value [`WebPack`][webpack-proxy]
|
||||
> uses to proxy requests
|
||||
|
||||
|
||||
|
||||
## Open Source DICOM Image Archives
|
||||
|
||||
There are a lot of options available to you to use as a local DICOM server. Here are some of the more popular ones:
|
||||
|
||||
| Archive | Installation |
|
||||
| --------------------------------------------- | ---------------------------------- |
|
||||
| [DCM4CHEE Archive 5.x][dcm4chee] | [W/ Docker][dcm4chee-docker] |
|
||||
| [Orthanc][orthanc] | [W/ Docker][orthanc-docker] |
|
||||
| [DICOMcloud][dicomcloud] (**DICOM Web only**) | [Installation][dicomcloud-install] |
|
||||
| [OsiriX][osirix] (**Mac OSX only**) | Desktop Client |
|
||||
| [Horos][horos] (**Mac OSX only**) | Desktop Client |
|
||||
|
||||
_Feel free to make a Pull Request if you want to add to this list._
|
||||
|
||||
|
||||
Below, we will focus on `DCM4CHEE` and `Orthanc` usage:
|
||||
|
||||
|
||||
|
||||
### Running Orthanc
|
||||
|
||||
_Start Orthanc:_
|
||||
|
||||
```bash
|
||||
# Runs orthanc so long as window remains open
|
||||
yarn run orthanc:up
|
||||
```
|
||||
|
||||
_Upload your first Study:_
|
||||
|
||||
1. Navigate to
|
||||
[Orthanc's web interface](http://localhost:8042/app/explorer.html) at
|
||||
`http://localhost:8042/app/explorer.html` in a web browser.
|
||||
2. In the top right corner, click "Upload"
|
||||
3. Click "Select files to upload..." and select one or more DICOM files
|
||||
4. Click "Start the upload"
|
||||
|
||||
#### Orthanc: Learn More
|
||||
|
||||
You can see the `docker-compose.yml` file this command runs at
|
||||
[`<project-root>/.docker/Nginx-Orthanc/`][orthanc-docker-compose], and more on
|
||||
Orthanc for Docker in [Orthanc's documentation][orthanc-docker].
|
||||
|
||||
#### Connecting to Orthanc
|
||||
|
||||
Now that we have a local Orthanc instance up and running, we need to configure
|
||||
our web application to connect to it. Open a new terminal window, navigate to
|
||||
this repository's root directory, and run:
|
||||
|
||||
```bash
|
||||
# If you haven't already, enable yarn workspaces
|
||||
yarn config set workspaces-experimental true
|
||||
|
||||
# Restore dependencies
|
||||
yarn install
|
||||
|
||||
# Run our dev command, but with the local orthanc config
|
||||
yarn run dev:orthanc
|
||||
```
|
||||
|
||||
#### Configuration: Learn More
|
||||
|
||||
> For more configuration fun, check out the
|
||||
> [Essentials Configuration](./index.md) guide.
|
||||
|
||||
Let's take a look at what's going on under the hood here. `yarn run dev:orthanc`
|
||||
is running the `dev:orthanc` script in our project's `package.json` (inside `platform/viewer`). That script
|
||||
is:
|
||||
|
||||
```js
|
||||
cross-env NODE_ENV=development PROXY_TARGET=/dicom-web PROXY_DOMAIN=http://localhost:8042 APP_CONFIG=config/docker_nginx-orthanc.js webpack-dev-server --config .webpack/webpack.pwa.js -w
|
||||
```
|
||||
|
||||
- `cross-env` sets three environment variables
|
||||
- PROXY_TARGET: `/dicom-web`
|
||||
- PROXY_DOMAIN: `http://localhost:8042`
|
||||
- APP_CONFIG: `config/docker_nginx-orthanc.js`
|
||||
- `webpack-dev-server` runs using the `.webpack/webpack.pwa.js` configuration
|
||||
file. It will watch for changes and update as we develop.
|
||||
|
||||
`PROXY_TARGET` and `PROXY_DOMAIN` tell our development server to proxy requests
|
||||
to `Orthanc`. This allows us to bypass CORS issues that normally occur when
|
||||
requesting resources that live at a different domain.
|
||||
|
||||
The `APP_CONFIG` value tells our app which file to load on to `window.config`.
|
||||
By default, our app uses the file at
|
||||
`<project-root>/platform/viewer/public/config/default.js`. Here is what that
|
||||
configuration looks like:
|
||||
|
||||
```js
|
||||
window.config = {
|
||||
routerBasename: '/',
|
||||
extensions: [],
|
||||
modes: [],
|
||||
showStudyList: true,
|
||||
dataSources: [
|
||||
{
|
||||
friendlyName: 'dcmjs DICOMWeb Server',
|
||||
namespace: 'org.ohif.default.dataSourcesModule.dicomweb',
|
||||
sourceName: 'dicomweb',
|
||||
configuration: {
|
||||
name: 'DCM4CHEE',
|
||||
wadoUriRoot: 'https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/wado',
|
||||
qidoRoot: 'https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/rs',
|
||||
wadoRoot: 'https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/rs',
|
||||
qidoSupportsIncludeField: true,
|
||||
supportsReject: true,
|
||||
imageRendering: 'wadors',
|
||||
thumbnailRendering: 'wadors',
|
||||
enableStudyLazyLoad: true,
|
||||
supportsFuzzyMatching: true,
|
||||
supportsWildcard: true,
|
||||
},
|
||||
},
|
||||
],
|
||||
defaultDataSourceName: 'dicomweb',
|
||||
};
|
||||
```
|
||||
|
||||
To learn more about how you can configure the OHIF Viewer, check out our
|
||||
[Configuration Guide](./index.md).
|
||||
|
||||
|
||||
|
||||
### Running DCM4CHEE
|
||||
|
||||
dcm4che is a collection of open source applications for healthcare enterprise written in Java programming language
|
||||
which implements DICOM standard. dcm4chee (extra 'e' at the end) is dcm4che project
|
||||
for an Image Manager/Image Archive which provides storage, retrieval and other functionalities.
|
||||
You can read more about dcm4chee in their website [here](https://www.dcm4che.org/)
|
||||
|
||||
DCM4chee installation is out of scope for these tutorials and can be found [here](https://github.com/dcm4che/dcm4chee-arc-light/wiki/Run-minimum-set-of-archive-services-on-a-single-host)
|
||||
|
||||
An overview of steps for running OHIF Viewer using a local DCM4CHEE is shown below:
|
||||
|
||||
<div style="padding:56.25% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/557570043?badge=0&autopause=0&player_id=0&app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen style="position:absolute;top:0;left:0;width:100%;height:100%;" title="Local dcm4chee"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
[dcm4chee]: https://github.com/dcm4che/dcm4chee-arc-light
|
||||
[dcm4chee-docker]: https://github.com/dcm4che/dcm4chee-arc-light/wiki/Running-on-Docker
|
||||
[orthanc]: https://www.orthanc-server.com/
|
||||
[orthanc-docker]: http://book.orthanc-server.com/users/docker.html
|
||||
[dicomcloud]: https://github.com/DICOMcloud/DICOMcloud
|
||||
[dicomcloud-install]: https://github.com/DICOMcloud/DICOMcloud#running-the-code
|
||||
[osirix]: http://www.osirix-viewer.com/
|
||||
[horos]: https://www.horosproject.org/
|
||||
[default-config]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/public/config/default.js
|
||||
[html-templates]: https://github.com/OHIF/Viewers/tree/master/platform/viewer/public/html-templates
|
||||
[config-files]: https://github.com/OHIF/Viewers/tree/master/platform/viewer/public/config
|
||||
@@ -1,190 +0,0 @@
|
||||
# Configuring Data Source
|
||||
|
||||
|
||||
|
||||
- [Configuring Data Source](#configuring-data-source)
|
||||
- [Overview](#overview)
|
||||
- [Configuration Files](#configuration-files)
|
||||
- [Environment Variables](#environment-variables)
|
||||
|
||||
|
||||
## Overview
|
||||
|
||||
After following the steps outlined in
|
||||
[Getting Started](./../development/getting-started.md), you'll notice that the
|
||||
OHIF Viewer has data for several studies and their images. You didn't add this
|
||||
data, so where is it coming from?
|
||||
|
||||
By default, the viewer is configured to connect to a remote server hosted by the
|
||||
nice folks over at [dcmjs.org][dcmjs-org]. While convenient for getting started,
|
||||
the time may come when you want to develop using your own data either locally or
|
||||
remotely.
|
||||
|
||||
|
||||
## Configuration Files
|
||||
|
||||
The configuration for our viewer is in the `<root>platform/viewer/public/config`
|
||||
directory. Our build process knows which configuration file to use based on the
|
||||
`APP_CONFIG` environment variable. By default, its value is
|
||||
[`config/default.js`][default-config]. The majority of the viewer's features,
|
||||
and registered extension's features, are configured using this file.
|
||||
|
||||
The simplest way is to update the existing default config:
|
||||
|
||||
> _/platform/viewer/public/config/default.js_
|
||||
|
||||
```js
|
||||
window.config = {
|
||||
routerBasename: '/',
|
||||
extensions: [],
|
||||
modes: [],
|
||||
showStudyList: true,
|
||||
dataSources: [
|
||||
{
|
||||
friendlyName: 'dcmjs DICOMWeb Server',
|
||||
namespace: 'org.ohif.default.dataSourcesModule.dicomweb',
|
||||
sourceName: 'dicomweb',
|
||||
configuration: {
|
||||
name: 'DCM4CHEE',
|
||||
wadoUriRoot: 'https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/wado',
|
||||
qidoRoot: 'https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/rs',
|
||||
wadoRoot: 'https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/rs',
|
||||
qidoSupportsIncludeField: true,
|
||||
supportsReject: true,
|
||||
imageRendering: 'wadors',
|
||||
thumbnailRendering: 'wadors',
|
||||
enableStudyLazyLoad: true,
|
||||
supportsFuzzyMatching: true,
|
||||
supportsWildcard: true,
|
||||
},
|
||||
},
|
||||
],
|
||||
defaultDataSourceName: 'dicomweb',
|
||||
};
|
||||
|
||||
```
|
||||
|
||||
|
||||
> As you can see a new change in `OHIF-v3` is the addition of `dataSources`.
|
||||
> You can build your own datasource and map it to the internal data structure of OHIF’s > metadata and enjoy using other peoples developed mode on your own data!
|
||||
>
|
||||
> You can read more about data sources at [Data Source section in Modes](../modes/index.md)
|
||||
>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
The configuration can also be written as a JS Function in case you need to inject dependencies like external services:
|
||||
|
||||
|
||||
```js
|
||||
window.config = ({ servicesManager } = {}) => {
|
||||
const { UIDialogService } = servicesManager.services;
|
||||
return {
|
||||
cornerstoneExtensionConfig: {
|
||||
tools: {
|
||||
ArrowAnnotate: {
|
||||
configuration: {
|
||||
getTextCallback: (callback, eventDetails) => UIDialogService.create({...
|
||||
}
|
||||
}
|
||||
},
|
||||
},
|
||||
routerBasename: '/',
|
||||
dataSources: [
|
||||
{
|
||||
friendlyName: 'dcmjs DICOMWeb Server',
|
||||
namespace: 'org.ohif.default.dataSourcesModule.dicomweb',
|
||||
sourceName: 'dicomweb',
|
||||
configuration: {
|
||||
name: 'DCM4CHEE',
|
||||
wadoUriRoot: 'https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/wado',
|
||||
qidoRoot: 'https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/rs',
|
||||
wadoRoot: 'https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/rs',
|
||||
qidoSupportsIncludeField: true,
|
||||
supportsReject: true,
|
||||
imageRendering: 'wadors',
|
||||
thumbnailRendering: 'wadors',
|
||||
enableStudyLazyLoad: true,
|
||||
supportsFuzzyMatching: true,
|
||||
supportsWildcard: true,
|
||||
},
|
||||
},
|
||||
],
|
||||
defaultDataSourceName: 'dicomweb',
|
||||
};
|
||||
};
|
||||
```
|
||||
|
||||
<!-- **Embedded Use Note:**
|
||||
|
||||
Alternatively, when using the `umd` bundle for embedded use cases, these same
|
||||
values are what you'll pass to `installViewer` method:
|
||||
|
||||
`OHIFStandaloneViewer.installViewer(window.config)` -->
|
||||
|
||||
## Environment Variables
|
||||
|
||||
We use environment variables at build and dev time to change the Viewer's
|
||||
behavior. We can update the `HTML_TEMPLATE` to easily change which extensions
|
||||
are registered, and specify a different `APP_CONFIG` to connect to an
|
||||
alternative data source (or even specify different default hotkeys).
|
||||
|
||||
| Environment Variable | Description | Default |
|
||||
| -------------------- | -------------------------------------------------------------------------------------------------- | ------------------- |
|
||||
| `HTML_TEMPLATE` | Which [HTML template][html-templates] to use as our web app's entry point. Specific to PWA builds. | `index.html` |
|
||||
| `PUBLIC_URL` | The route relative to the host that the app will be served from. Specific to PWA builds. | `/` |
|
||||
| `APP_CONFIG` | Which [configuration file][config-file] to copy to output as `app-config.js` | `config/default.js` |
|
||||
| `PROXY_TARGET` | When developing, proxy requests that match this pattern to `PROXY_DOMAIN` | `undefined` |
|
||||
| `PROXY_DOMAIN` | When developing, proxy requests from `PROXY_TARGET` to `PROXY_DOMAIN` | `undefined` |
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
You can also create a new config file and specify its path relative to the build
|
||||
output's root by setting the `APP_CONFIG` environment variable. You can set the
|
||||
value of this environment variable a few different ways:
|
||||
|
||||
- ~[Add a temporary environment variable in your shell](https://facebook.github.io/create-react-app/docs/adding-custom-environment-variables#adding-temporary-environment-variables-in-your-shell)~
|
||||
- Previous `react-scripts` functionality that we need to duplicate with
|
||||
`dotenv-webpack`
|
||||
- ~[Add environment specific variables in `.env` file(s)](https://facebook.github.io/create-react-app/docs/adding-custom-environment-variables#adding-development-environment-variables-in-env)~
|
||||
- Previous `react-scripts` functionality that we need to duplicate with
|
||||
`dotenv-webpack`
|
||||
- Using the `cross-env` package in an npm script:
|
||||
- `"build": "cross-env APP_CONFIG=config/my-config.js react-scripts build"`
|
||||
|
||||
After updating the configuration, `yarn run build` to generate updated build
|
||||
output.
|
||||
|
||||
|
||||
|
||||
<!--
|
||||
Links
|
||||
-->
|
||||
|
||||
<!-- prettier-ignore-start -->
|
||||
[dcmjs-org]: https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/wado
|
||||
[dicom-web]: https://en.wikipedia.org/wiki/DICOMweb
|
||||
[storescu]: http://support.dcmtk.org/docs/storescu.html
|
||||
[webpack-proxy]: https://webpack.js.org/configuration/dev-server/#devserverproxy
|
||||
[orthanc-docker-compose]: https://github.com/OHIF/Viewers/tree/master/.docker/Nginx-Orthanc
|
||||
<!-- Archives -->
|
||||
[dcm4chee]: https://github.com/dcm4che/dcm4chee-arc-light
|
||||
[dcm4chee-docker]: https://github.com/dcm4che/dcm4chee-arc-light/wiki/Running-on-Docker
|
||||
[orthanc]: https://www.orthanc-server.com/
|
||||
[orthanc-docker]: http://book.orthanc-server.com/users/docker.html
|
||||
[dicomcloud]: https://github.com/DICOMcloud/DICOMcloud
|
||||
[dicomcloud-install]: https://github.com/DICOMcloud/DICOMcloud#running-the-code
|
||||
[osirix]: http://www.osirix-viewer.com/
|
||||
[horos]: https://www.horosproject.org/
|
||||
[default-config]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/public/config/default.js
|
||||
[html-templates]: https://github.com/OHIF/Viewers/tree/master/platform/viewer/public/html-templates
|
||||
[config-files]: https://github.com/OHIF/Viewers/tree/master/platform/viewer/public/config
|
||||
<!-- prettier-ignore-end -->
|
||||
@@ -1,3 +0,0 @@
|
||||
# Google Cloud Healthcare
|
||||
|
||||
> Coming soon - We are working on bringing Google Cloud Healthcare to OHIF-v3
|
||||
@@ -1,4 +0,0 @@
|
||||
<div style="text-align: center;">
|
||||
<img src="/assets/img/embedded-viewer-diagram.png" alt="Embedded Viewer Diagram" style="margin: 0 auto;" />
|
||||
<div><i>embedded viewer diagram</i></div>
|
||||
</div>
|
||||
@@ -1,4 +0,0 @@
|
||||
<div style="text-align: center;">
|
||||
<img src="/assets/img/nginx-image-archive.png" alt="request flow example" style="margin: 0 auto;" />
|
||||
<div><i>simplified request flow diagram</i></div>
|
||||
</div>
|
||||
@@ -1,4 +0,0 @@
|
||||
<div style="text-align: center;">
|
||||
<img src="/assets/img/user-access-control-request-flow.png" alt="request flow example" style="margin: 0 auto;" />
|
||||
<div><i>simplified request flow diagram</i></div>
|
||||
</div>
|
||||
@@ -1,302 +0,0 @@
|
||||
# Deployment
|
||||
|
||||
The OHIF Viewer can be embedded in other web applications via it's [packaged
|
||||
script source][viewer-npm], or served up as a stand-alone PWA ([progressive web
|
||||
application][pwa-url]) by building and hosting a collection of static assets. In
|
||||
either case, you will need to configure your instance of the Viewer so that it
|
||||
can connect to your data source (the database or PACS that provides the data
|
||||
your Viewer will display).
|
||||
|
||||
## Overview
|
||||
|
||||
Our goal is to make deployment as simple and painless as possible; however,
|
||||
there is an inherent amount of complexity in configuring and deploying web
|
||||
applications. If you find yourself a little lost, please don't hesitate to
|
||||
[reach out for help](/help.md)
|
||||
|
||||
## Deployment Scenarios
|
||||
|
||||
### Embedded Viewer (deprecated)
|
||||
`OHIF-v3` has deprecated deploying the viewer as an embedded viewer the number of underlying
|
||||
libraries that run web workers are increasing for OHIF. An example of these libraries is
|
||||
OHIF's 3D rendering functionality that is provided by `vtk-js`.
|
||||
|
||||
### Stand-alone Viewer
|
||||
|
||||
Deploying the OHIF Viewer as a stand-alone web application provides many
|
||||
benefits, but comes at the cost of time and complexity. Some benefits include:
|
||||
|
||||
_Today:_
|
||||
|
||||
- Leverage [extensions](/extensions/index.md) and [modes](/modes/index.md) to drop-in powerful new features
|
||||
- Add routes and customize the viewer's workflow
|
||||
- Finer control over styling and whitelabeling
|
||||
|
||||
_In the future:_
|
||||
|
||||
- The ability to package the viewer for [App Store distribution][app-store]
|
||||
- Leverage `service-workers` for offline support and speed benefits from caching
|
||||
|
||||
#### Hosted Static Assets
|
||||
|
||||
At the end of the day, a production OHIF Viewer instance is a collection of
|
||||
HTML, CSS, JS, Font Files, and Images. We "build" those files from our
|
||||
`source code` with configuration specific to our project. We then make those
|
||||
files publicly accessible by hosting them on a Web Server.
|
||||
|
||||
If you have not deployed a web application before, this may be a good time to
|
||||
[reach out for help](/help.md), as these steps assume prior web development and
|
||||
deployment experience.
|
||||
|
||||
##### Part 1 - Build Production Assets
|
||||
|
||||
"Building", or creating, the files you will need is the same regardless of the
|
||||
web host you choose. You can find detailed instructions on how to configure and
|
||||
build the OHIF Viewer in our
|
||||
["Build for Production" guide](./recipes/build-for-production.md).
|
||||
|
||||
##### Part 2 - Host Your App
|
||||
|
||||
There are a lot of [benefits to hosting static assets][host-static-assets] over
|
||||
dynamic content. You can find instructions on how to host your build's output
|
||||
via one of these guides:
|
||||
|
||||
_Drag-n-drop_
|
||||
|
||||
- [Netlify: Drop](/deployment/recipes/static-assets.md#netlify-drop)
|
||||
|
||||
_Easy_
|
||||
|
||||
- [Surge.sh](/deployment/recipes/static-assets.md#surgesh)
|
||||
- [GitHub Pages](/deployment/recipes/static-assets.md#github-pages)
|
||||
|
||||
_Advanced_
|
||||
|
||||
- [AWS S3 + Cloudfront](/deployment/recipes/static-assets.md#aws-s3--cloudfront)
|
||||
- [GCP + Cloudflare](/deployment/recipes/static-assets.md#gcp--cloudflare)
|
||||
- [Azure](/deployment/recipes/static-assets.md#azure)
|
||||
|
||||
## Data
|
||||
|
||||
The OHIF Viewer is able to connect to any data source that implements the [DICOM
|
||||
Web Standard][dicom-web-standard]. [DICOM Web][dicom-web] refers to RESTful
|
||||
DICOM Services -- a recently standardized set of guidelines for exchanging
|
||||
medical images and imaging metadata over the internet. Not all archives fully
|
||||
support it yet, but it is gaining wider adoption.
|
||||
|
||||
### Configure Connection
|
||||
|
||||
If you have an existing archive and intend to host the OHIF Viewer at the same
|
||||
domain name as your archive, then connecting the two is as simple as following
|
||||
the steps layed out in our
|
||||
[Configuration Essentials Guide](./../configuring/index.md).
|
||||
|
||||
#### What if I don't have an imaging archive?
|
||||
|
||||
We provide some guidance on configuring a local image archive in our
|
||||
[Data Source Essentials](./../configuring/index.md#set-up-a-local-DICOM-server) guide. Hosting an
|
||||
archive remotely is a little trickier. You can check out some of our
|
||||
[advanced recipes](#recipes) for modeled setups that may work for you.
|
||||
|
||||
#### What if I intend to host the OHIF Viewer at a different domain?
|
||||
|
||||
There are two important steps to making sure this setup works:
|
||||
|
||||
1. Your Image Archive needs to be exposed, in some way, to the open web. This
|
||||
can be directly, or through a `reverse proxy`, but the Viewer needs _some
|
||||
way_ to request it's data.
|
||||
2. \* Your Image Archive needs to have appropriate CORS (Cross-Origin Resource
|
||||
Sharing) Headers
|
||||
|
||||
> \* Cross-Origin Resource Sharing (CORS) is a mechanism that uses additional
|
||||
> HTTP headers to tell a browser to let a web application running at one origin
|
||||
> (domain) have permission to access selected resources from a server at a
|
||||
> different origin. - [MDN Web Docs: Web - Http - CORS][cors]
|
||||
|
||||
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](./recipes/nginx--image-archive.md).
|
||||
|
||||
#### What if my archive doesn't support DicomWeb?
|
||||
|
||||
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 using the `dicomjson` datasource and appending `'?url='` query to your mode's route:
|
||||
|
||||
eg. `https://my-test-ohif-server/myMode/dicomjson?url=https://my-json-server/study-uid.json`
|
||||
|
||||
|
||||
The returned JSON object must contain a single root object with a 'studies' array.
|
||||
|
||||
You can read more about using different data sources for mode's routes [here](../modes/routes.md#route-path)
|
||||
|
||||
*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. -->
|
||||
1. For each instance url (dicom object) in the returned JSON, you must prefix the `url` with `dicomjson:` in order for the cornerstone image loader to retrieve it correctly.
|
||||
eg. `https://image-server/my-image.dcm` ---> `dicomjson:https://image-server/my-image.dcm`
|
||||
2. The JSON format above is compatible with >= v3.7.8 of the application in `V2` version. 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.
|
||||
3. 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/myMode/dicomjson?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
|
||||
Coming soon
|
||||
|
||||
<!--
|
||||
> Feeling lost? Securing your data is important, and it can be hard to tell if
|
||||
> you've gotten it right. Don't hesitate to work with professional auditors, or
|
||||
> [enlist help from experts](./../help.md).
|
||||
|
||||
The OHIF Viewer can be configured to work with authorization servers that
|
||||
support one or more of the OpenID-Connect authorization flows. The Viewer finds
|
||||
it's OpenID-Connect settings on the `oidc` configuration key. You can set these
|
||||
values following the instructions laid out in the
|
||||
[Configuration Essentials Guide](./../configuring/index.md).
|
||||
|
||||
_Example OpenID-Connect Settings:_
|
||||
|
||||
```js
|
||||
window.config = {
|
||||
...
|
||||
oidc: [
|
||||
{
|
||||
// ~ REQUIRED
|
||||
// Authorization Server URL
|
||||
authority: 'http://127.0.0.1/auth/realms/ohif',
|
||||
client_id: 'ohif-viewer',
|
||||
redirect_uri: 'http://127.0.0.1/callback', // `OHIFStandaloneViewer.js`
|
||||
response_type: 'code', // "Authorization Code Flow"
|
||||
scope: 'openid', // email profile openid
|
||||
// ~ OPTIONAL
|
||||
post_logout_redirect_uri: '/logout-redirect.html',
|
||||
},
|
||||
],
|
||||
}
|
||||
```
|
||||
|
||||
You can find an example of this setup in our
|
||||
[User Account Control Deployment Recipe](./recipes/user-account-control.md).
|
||||
|
||||
#### Choosing a Flow for the Viewer
|
||||
|
||||
In general, we recommend using the "Authorization Code Flow" ( [see
|
||||
`response_type=code` here][code-flows]); however, the "Implicit Flow" ( [see
|
||||
`response_type=token` here][code-flows]) can work if additonal precautions are
|
||||
taken. If the flow you've chosen produces a JWT Token, it's validity can be used
|
||||
to secure access to your Image Archive as well.
|
||||
|
||||
-->
|
||||
|
||||
### Recipes
|
||||
|
||||
We've included a few recipes for common deployment scenarios. There are many,
|
||||
many possible configurations, so please don't feel limited to these setups.
|
||||
Please feel free to suggest or contribute your own recipes.
|
||||
|
||||
|
||||
- [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
|
||||
-->
|
||||
|
||||
<!-- prettier-ignore-start -->
|
||||
[viewer-npm]: https://www.npmjs.com/package/@ohif/viewer
|
||||
[pwa-url]: https://developers.google.com/web/progressive-web-apps/
|
||||
[static-assets-url]: https://www.maxcdn.com/one/visual-glossary/static-content/
|
||||
[app-store]: https://medium.freecodecamp.org/i-built-a-pwa-and-published-it-in-3-app-stores-heres-what-i-learned-7cb3f56daf9b
|
||||
[dicom-web-standard]: https://www.dicomstandard.org/dicomweb/
|
||||
[dicom-web]: https://en.wikipedia.org/wiki/DICOMweb
|
||||
[host-static-assets]: https://www.netlify.com/blog/2016/05/18/9-reasons-your-site-should-be-static/
|
||||
[cors]: https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS
|
||||
[code-flows]: https://medium.com/@darutk/diagrams-of-all-the-openid-connect-flows-6968e3990660
|
||||
[code-sandbox]: https://codesandbox.io/s/viewer-script-tag-tprch
|
||||
<!-- prettier-ignore-end -->
|
||||
@@ -1,135 +0,0 @@
|
||||
# Build for Production
|
||||
|
||||
> If you've already followed the
|
||||
> ["Getting Started" Guide](/development/getting-started.md), you can skip ahead
|
||||
> to [Configuration](#configuration)
|
||||
|
||||
## Overview
|
||||
|
||||
### Build Machine Requirements
|
||||
|
||||
- [Node.js & NPM](https://nodejs.org/en/download/)
|
||||
- [Yarn](https://yarnpkg.com/lang/en/docs/install/)
|
||||
- [Git](https://www.atlassian.com/git/tutorials/install-git)
|
||||
|
||||
### Getting the Code
|
||||
|
||||
_With Git:_
|
||||
|
||||
```bash
|
||||
# Clone the remote repository to your local machine
|
||||
git clone https://github.com/OHIF/Viewers.git
|
||||
```
|
||||
|
||||
More on: _[`git clone`](https://git-scm.com/docs/git-clone),
|
||||
[`git checkout`](https://git-scm.com/docs/git-checkout)_
|
||||
|
||||
_From .zip:_
|
||||
|
||||
[OHIF/Viewers: react.zip](https://github.com/OHIF/Viewers/archive/master.zip)
|
||||
|
||||
### Restore Dependencies & Build
|
||||
|
||||
Open your terminal, and navigate to the directory containing the source files.
|
||||
Next run these commands:
|
||||
|
||||
```js
|
||||
// If you haven't already, enable yarn workspaces
|
||||
yarn config set workspaces-experimental true
|
||||
|
||||
// Restore dependencies
|
||||
yarn install
|
||||
|
||||
// Build source code for production
|
||||
yarn run build
|
||||
```
|
||||
|
||||
If everything worked as expected, you should have a new `dist/` directory in the
|
||||
project's folder. It should roughly resemble the following:
|
||||
|
||||
```bash
|
||||
<root>platform/viewer/dist/
|
||||
├── app-config.js
|
||||
├── app.bundle.js
|
||||
├── app.css
|
||||
├── index.html
|
||||
├── manifest.json
|
||||
├── service-worker.js
|
||||
└── ...
|
||||
```
|
||||
|
||||
By default, the build output will connect to OHIF's publicly accessible PACS. If
|
||||
this is your first time setting up the OHIF Viewer, it is recommended that you
|
||||
test with these default settings. After testing, you can find instructions on
|
||||
how to configure the project for your own imaging archive below.
|
||||
|
||||
### Configuration
|
||||
|
||||
The configuration for our viewer is in the `<root>platform/viewer/public/config`
|
||||
directory. Our build process knows which configuration file to use based on the
|
||||
`APP_CONFIG` environment variable. By default, its value is
|
||||
[`config/default.js`][default-config]. The majority of the viewer's features,
|
||||
and registered extension's features, are configured using this file.
|
||||
|
||||
The easiest way to apply your own configuration is to modify the `default.js`
|
||||
file. For more advanced cofiguration options, check out our
|
||||
[configuration essentials guide](/configuring/index.md).
|
||||
|
||||
## Next Steps
|
||||
|
||||
### Deploying Build Output
|
||||
|
||||
_Drag-n-drop_
|
||||
|
||||
- [Netlify: Drop](/deployment/recipes/static-assets.md#netlify-drop)
|
||||
|
||||
_Easy_
|
||||
|
||||
- [Surge.sh](/deployment/recipes/static-assets.md#surgesh)
|
||||
- [GitHub Pages](/deployment/recipes/static-assets.md#github-pages)
|
||||
|
||||
_Advanced_
|
||||
|
||||
- [AWS S3 + Cloudfront](/deployment/recipes/static-assets.md#aws-s3--cloudfront)
|
||||
- [GCP + Cloudflare](/deployment/recipes/static-assets.md#gcp--cloudflare)
|
||||
- [Azure](/deployment/recipes/static-assets.md#azure)
|
||||
|
||||
### Testing Build Output Locally
|
||||
|
||||
A quick way to test your build output locally is to spin up a small webserver.
|
||||
You can do this by running the following commands in the `dist/` output
|
||||
directory:
|
||||
|
||||
```js
|
||||
// Install http-server as a globally available package
|
||||
yarn global add http-server
|
||||
|
||||
// Change the directory to the platform/viewer
|
||||
|
||||
// Serve the files in our current directory
|
||||
// Accessible at: `http://localhost:8080`
|
||||
npx http-server ./dist
|
||||
```
|
||||
|
||||
<div style="padding:56.25% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/551957266?badge=0&autopause=0&player_id=0&app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen style="position:absolute;top:0;left:0;width:100%;height:100%;" title="HTTP Server Deploy"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script>
|
||||
|
||||
### Automating Builds and Deployments
|
||||
|
||||
If you found setting up your environment and running all of these steps to be a
|
||||
bit tedious, then you are in good company. Thankfully, there are a large number
|
||||
of tools available to assist with automating tasks like building and deploying
|
||||
web application. For a starting point, check out this repository's own use of:
|
||||
|
||||
- [CircleCI][circleci]: [config.yaml][circleci-config]
|
||||
- [Netlify][netlify]: [netlify.toml][netlify.toml] |
|
||||
[build-deploy-preview.sh][build-deploy-preview.sh]
|
||||
|
||||
|
||||
|
||||
<!-- prettier-ignore-start -->
|
||||
[circleci]: https://circleci.com/gh/OHIF/Viewers
|
||||
[circleci-config]: https://github.com/OHIF/Viewers/blob/master/.circleci/config.yml
|
||||
[netlify]: https://app.netlify.com/sites/ohif/deploys
|
||||
[netlify.toml]: https://github.com/OHIF/Viewers/blob/master/netlify.toml
|
||||
[build-deploy-preview.sh]: https://github.com/OHIF/Viewers/blob/master/.netlify/build-deploy-preview.sh
|
||||
<!-- prettier-ignore-end -->
|
||||
@@ -1,264 +0,0 @@
|
||||
# Nginx + Image Archive
|
||||
|
||||
> DISCLAIMER! We make no claims or guarantees of this approach's security. If in
|
||||
> doubt, enlist the help of an expert and conduct proper audits.
|
||||
|
||||
At a certain point, you may want others to have access to your instance of the
|
||||
OHIF Viewer and its medical imaging data. This post covers one of many potential
|
||||
setups that accomplish that. Please note, noticably absent is user account
|
||||
control.
|
||||
|
||||
Do not use this recipe to host sensitive medical data on the open web. Depending
|
||||
on your company's policies, this may be an appropriate setup on an internal
|
||||
network when protected with a server's basic authentication. For a more robust
|
||||
setup, check out our [user account control recipe](./user-account-control.md)
|
||||
that builds on the lessons learned here.
|
||||
|
||||
## Overview
|
||||
|
||||
Our two biggest hurdles when hosting our image archive and web client are:
|
||||
|
||||
- Risks related to exposing our PACS to the netowrk
|
||||
- Cross-Origin Resource Sharing (CORS) requests
|
||||
|
||||
### Handling Web Requests
|
||||
|
||||
We mittigate our first issue by allowing [Nginx][nginx] to handle incoming web
|
||||
requests. Nginx is open source software for web serving, reverse proxying,
|
||||
caching, and more. It's designed for maximum performance and stability --
|
||||
allowing us to more reliably serve content than Orthanc's built-in server can.
|
||||
|
||||
More specifically, we accomplish this by using a
|
||||
[`reverse proxy`](https://en.wikipedia.org/wiki/Reverse_proxy) to retrieve
|
||||
resources from our image archive (Orthanc), and when accessing its web admin.
|
||||
|
||||
> A reverse proxy is a type of proxy server that retrieves resources on behalf
|
||||
> of a client from one or more servers. These resources are then returned to the
|
||||
> client, appearing as if they originated from the proxy server itself.
|
||||
|
||||
### CORS Issues
|
||||
|
||||
Cross-Origin Resource Sharing (CORS) is a mechanism that uses HTTP headers to
|
||||
tell a browser which web applications have permission to access selected
|
||||
resources from a server at a different origin (domain, protocol, port). IE. By
|
||||
default, a Web App located at `http://my-website.com` can't access resources
|
||||
hosted at `http://not-my-website.com`
|
||||
|
||||
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.**
|
||||
|
||||
You can read more about CORS in this Medium article: [Understanding
|
||||
CORS][understanding-cors]
|
||||
|
||||
### Diagram
|
||||
|
||||
This setup allows us to create a setup similar to the one pictured below:
|
||||
|
||||
{% include "./../_nginx-image-archive-diagram.md" %}
|
||||
|
||||
- All web requests are routed through `nginx` on our `OpenResty` image
|
||||
- `/pacs` is a reverse proxy for `orthanc`'s `DICOM Web` endpoints
|
||||
- `/pacs-admin` is a reverse proxy for `orthanc`'s Web Admin
|
||||
- All static resources for OHIF Viewer are served up by `nginx` when a matching
|
||||
route for that resource is requested
|
||||
|
||||
## Getting Started
|
||||
|
||||
### Requirements
|
||||
|
||||
- Docker
|
||||
- [Docker for Mac](https://docs.docker.com/docker-for-mac/)
|
||||
- [Docker for Windows](https://docs.docker.com/docker-for-windows/)
|
||||
|
||||
_Not sure if you have `docker` installed already? Try running `docker --version`
|
||||
in command prompt or terminal_
|
||||
|
||||
### Setup
|
||||
|
||||
- Navigate to `viewer` folder inside `platform`
|
||||
- then: `cd .recipes/OpenResty-Orthanc`
|
||||
- run: `docker-compose up --build`
|
||||
- Navigate to `127.0.0.1` for the viewer
|
||||
- Navigate to `127.0.0.1/pacs-admin` for uploading studies
|
||||
|
||||
|
||||
You can see the overview of the mentioned steps:
|
||||
|
||||
|
||||
<div style="padding:56.25% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/554726410?badge=0&autopause=0&player_id=0&app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen style="position:absolute;top:0;left:0;width:100%;height:100%;" title="NginX Deployment"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script>
|
||||
|
||||
<!-- ### Setup
|
||||
|
||||
_Spin Things Up_
|
||||
|
||||
- Navigate to `<project-root>/docker/OpenResty-Orthanc` in your shell
|
||||
- Run `docker-compose up`
|
||||
|
||||
_Upload Your First Study_
|
||||
|
||||
- Navigate to `http://127.0.0.1/pacs-admin`
|
||||
- From the top right, select "Upload"
|
||||
- Click "Select files to upload..." (DICOM)
|
||||
- Click "Start the upload"
|
||||
- Navigate back to `http://127.0.0.1/` to view your studies in the Study List -->
|
||||
|
||||
### Troubleshooting
|
||||
|
||||
_Exit code 137_
|
||||
|
||||
This means Docker ran out of memory. Open Docker Desktop, go to the `advanced`
|
||||
tab, and increase the amount of Memory available.
|
||||
|
||||
_Cannot create container for service X_
|
||||
|
||||
Use this one with caution: `docker system prune`
|
||||
|
||||
_X is already running_
|
||||
|
||||
Stop running all containers:
|
||||
|
||||
- Win: `docker ps -a -q | ForEach { docker stop $_ }`
|
||||
- Linux: `docker stop $(docker ps -a -q)`
|
||||
|
||||
|
||||
_Traceback (most recent call last):_
|
||||
_File "urllib3/connectionpool.py", line 670, in urlopen_
|
||||
_...._
|
||||
|
||||
Are you sure your docker is running? see explanation [here](https://github.com/docker/compose/issues/7896)
|
||||
|
||||
|
||||
### Configuration
|
||||
|
||||
After verifying that everything runs with default configuration values, you will
|
||||
likely want to update:
|
||||
|
||||
- The domain: `http://127.0.0.1`
|
||||
|
||||
#### 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:
|
||||
|
||||
`ENV APP_CONFIG=config/docker_openresty-orthanc.js`
|
||||
|
||||
You can find the configuration we're using here:
|
||||
`/public/config/docker_openresty-orthanc.js`
|
||||
|
||||
To rebuild the `webapp` image created by our `dockerfile` after updating the
|
||||
Viewer's configuration, you can run:
|
||||
|
||||
- `docker-compose build` OR
|
||||
- `docker-compose up --build`
|
||||
|
||||
#### Other
|
||||
|
||||
All other files are found in: `/docker/OpenResty-Orthanc/`
|
||||
|
||||
| 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
|
||||
|
||||
### Deploying to Production
|
||||
|
||||
While these configuration and docker-compose files model an environment suitable
|
||||
for production, they are not easy to deploy "as is". You can either:
|
||||
|
||||
- Manually recreate this environment and deploy built application files **OR**
|
||||
- Deploy to a cloud kubernetes provider like
|
||||
[Digital Ocean](https://www.digitalocean.com/products/kubernetes/) **OR**
|
||||
- [See a full list of cloud providers here](https://landscape.cncf.io/category=cloud&format=card-mode&grouping=category)
|
||||
- Find and follow your preferred provider's guide on setting up
|
||||
[swarms and stacks](https://docs.docker.com/get-started/)
|
||||
|
||||
### Adding SSL
|
||||
|
||||
Adding SSL registration and renewal for your domain with Let's Encrypt that
|
||||
terminates at Nginx is an incredibly important step toward securing your data.
|
||||
Here are some resources, specific to this setup, that may be helpful:
|
||||
|
||||
- [lua-resty-auto-ssl](https://github.com/GUI/lua-resty-auto-ssl)
|
||||
- [Let's Encrypt + Nginx](https://www.nginx.com/blog/using-free-ssltls-certificates-from-lets-encrypt-with-nginx/)
|
||||
|
||||
While we terminate SSL at Nginx, it may be worth using self signed certificates
|
||||
for communication between services.
|
||||
|
||||
- [SSL Termination for TCP Upstream Servers](https://docs.nginx.com/nginx/admin-guide/security-controls/terminating-ssl-tcp/)
|
||||
|
||||
### Use PostgresSQL w/ Orthanc
|
||||
|
||||
Orthanc can handle a large amount of data and requests, but if you find that
|
||||
requests start to slow as you add more and more studies, you may want to
|
||||
configure your Orthanc instance to use PostgresSQL. Instructions on how to do
|
||||
that can be found in the
|
||||
[`Orthanc Server Book`](http://book.orthanc-server.com/users/docker.html), under
|
||||
"PostgreSQL and Orthanc inside Docker"
|
||||
|
||||
### Improving This Guide
|
||||
|
||||
Here are some improvements this guide would benefit from, and that we would be
|
||||
more than happy to accept Pull Requests for:
|
||||
|
||||
- SSL Support
|
||||
- Complete configuration with `.env` file (or something similar)
|
||||
- Any security issues
|
||||
- One-click deploy to a cloud provider
|
||||
|
||||
## Resources
|
||||
|
||||
### Misc. Helpful Commands
|
||||
|
||||
_Check if `nginx.conf` is valid:_
|
||||
|
||||
```bash
|
||||
docker run --rm -t -a stdout --name my-openresty -v $PWD/config/:/usr/local/openresty/nginx/conf/:ro openresty/openresty:alpine-fat openresty -c /usr/local/openresty/nginx/conf/nginx.conf -t
|
||||
```
|
||||
|
||||
_Interact w/ running container:_
|
||||
|
||||
`docker exec -it CONTAINER_NAME bash`
|
||||
|
||||
_List running containers:_
|
||||
|
||||
`docker ps`
|
||||
|
||||
### Referenced Articles
|
||||
|
||||
For more documentation on the software we've chosen to use, you may find the
|
||||
following resources helpful:
|
||||
|
||||
- [Orthanc for Docker](http://book.orthanc-server.com/users/docker.html)
|
||||
- [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 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
|
||||
-->
|
||||
|
||||
<!-- prettier-ignore-start -->
|
||||
<!-- DOCS -->
|
||||
[nginx]: https://www.nginx.com/resources/glossary/nginx/
|
||||
[understanding-cors]: https://medium.com/@baphemot/understanding-cors-18ad6b478e2b
|
||||
[orthanc-docs]: http://book.orthanc-server.com/users/configuration.html#configuration
|
||||
[lua-resty-openidc-docs]: https://github.com/zmartzone/lua-resty-openidc
|
||||
<!-- SRC -->
|
||||
[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 -->
|
||||
@@ -1,153 +0,0 @@
|
||||
# Deploy Static Assets
|
||||
|
||||
> WARNING! All of these solutions stand-up a publicly accessible web viewer. Do
|
||||
> not hook your hosted viewer up to a sensitive source of data without
|
||||
> implementing authentication.
|
||||
|
||||
There are a lot of options for deploying static assets. Some services, like
|
||||
`netlify` and `surge.sh`, specialize in static websites. You'll notice that
|
||||
deploying with them requires much less time and effort, but comes at the cost of
|
||||
less product offerings.
|
||||
|
||||
While not required, it can simplify things to host your Web Viewer alongside
|
||||
your image archive. Services with more robust product offerings, like
|
||||
`Google Cloud`, `Microsoft's Azure`, and `Amazon Web Services (AWS)`, are able
|
||||
to accomodate this setup.
|
||||
|
||||
_Drag-n-drop_
|
||||
|
||||
- [Netlify: Drop](#netlify-drop)
|
||||
|
||||
_Easy_
|
||||
|
||||
- [Surge.sh](#surgesh)
|
||||
- [GitHub Pages](#github-pages)
|
||||
|
||||
_Advanced_
|
||||
|
||||
- [Deploy Static Assets](#deploy-static-assets)
|
||||
- [Drag-n-drop](#drag-n-drop)
|
||||
- [Netlify: Drop](#netlify-drop)
|
||||
- [Easy](#easy)
|
||||
- [Surge.sh](#surgesh)
|
||||
- [GitHub Pages](#github-pages)
|
||||
- [Advanced](#advanced)
|
||||
- [AWS S3 + Cloudfront](#aws-s3--cloudfront)
|
||||
- [GCP + Cloudflare](#gcp--cloudflare)
|
||||
- [Azure](#azure)
|
||||
|
||||
## Drag-n-drop
|
||||
|
||||
### Netlify: Drop
|
||||
|
||||
<div style="padding:56.25% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/551957463?badge=0&autopause=0&player_id=0&app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen style="position:absolute;top:0;left:0;width:100%;height:100%;" title="Netlify Drop"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script>
|
||||
|
||||
|
||||
_GIF demonstrating deployment with Netlify Drop_
|
||||
|
||||
1. https://app.netlify.com/drop
|
||||
2. Drag your `build/` folder on to the drop target
|
||||
3. ...
|
||||
4. _annnd you're done_
|
||||
|
||||
**Features:**
|
||||
|
||||
- Custom domains & HTTPS
|
||||
- Instant Git integration
|
||||
- Continuous deployment
|
||||
- Deploy previews
|
||||
- Access to add-ons
|
||||
|
||||
(Non-free tiers include identity, FaaS, Forms, etc.)
|
||||
|
||||
Learn more about [Netlify on their website](https://www.netlify.com/)
|
||||
|
||||
## Easy
|
||||
|
||||
### Surge.sh
|
||||
|
||||
> Static web publishing for Front-End Developers. Simple, single-command web
|
||||
> publishing. Publish HTML, CSS, and JS for free, without leaving the command
|
||||
> line.
|
||||
|
||||
|
||||
|
||||
_GIF demonstrating deployment with surge_
|
||||
|
||||
```shell
|
||||
# Add surge command
|
||||
yarn global add surge
|
||||
|
||||
# In the build directory
|
||||
surge
|
||||
```
|
||||
|
||||
**Features:**
|
||||
|
||||
- Free custom domain support
|
||||
- Free SSL for surge.sh subdomains
|
||||
- pushState support for single page apps
|
||||
- Custom 404.html pages
|
||||
- Barrier-free deployment through the CLI
|
||||
- Easy integration into your Grunt toolchain
|
||||
- Cross-origin resource support
|
||||
- And more…
|
||||
|
||||
Learn more about [surge.sh on their website](https://surge.sh/)
|
||||
|
||||
### GitHub Pages
|
||||
|
||||
> WARNING! While great for project sites and light use, it is not advised to use
|
||||
> GitHub Pages for production workloads. Please consider using a different
|
||||
> service for mission critical applications.
|
||||
|
||||
> Websites for you and your projects. Hosted directly from your GitHub
|
||||
> repository. Just edit, push, and your changes are live.
|
||||
|
||||
This deploy strategy makes more sense if you intend to maintain your project in
|
||||
a GitHub repository. It allows you to specify a `branch` or `folder` as the
|
||||
target for a GitHub Page's website. As you push code changes, the hosted content
|
||||
updates to reflect those changes.
|
||||
|
||||
1. Head over to GitHub.com and create a new repository, or go to an existing
|
||||
one. Click on the Settings tab.
|
||||
2. Scroll down to the GitHub Pages section. Choose the `branch` or `folder` you
|
||||
would like as the "root" of your website.
|
||||
3. Fire up a browser and go to `http://username.github.io/repository`
|
||||
|
||||
Configuring Your Site:
|
||||
|
||||
- [Setting up a custom domain](https://help.github.com/en/articles/using-a-custom-domain-with-github-pages)
|
||||
- [Setting up SSL](https://help.github.com/en/articles/securing-your-github-pages-site-with-https)
|
||||
|
||||
Learn more about [GitHub Pages on its website](https://pages.github.com/)
|
||||
|
||||
## Advanced
|
||||
|
||||
All of these options, while using providers with more service offerings,
|
||||
demonstrate how to host the viewer with their respective file storage and CDN
|
||||
offerings. While you can serve your static assets this way, if you're going
|
||||
through the trouble of using AWS/GCP/Azure, it's more likely you're doing so to
|
||||
avoid using a proxy or to simplify authentication.
|
||||
|
||||
If that is the case, check out some of our more advanced `docker` deployments
|
||||
that target these providers from the left-hand sidepanel.
|
||||
|
||||
These guides can be a bit longer and a update more frequently. To provide
|
||||
accurate documentation, we will link to each provider's own recommended steps:
|
||||
|
||||
### AWS S3 + Cloudfront
|
||||
|
||||
- [Host a Static Website](https://docs.aws.amazon.com/AmazonS3/latest/dev/website-hosting-custom-domain-walkthrough.html)
|
||||
- [Speed Up Your Website with Cloudfront](https://docs.aws.amazon.com/AmazonS3/latest/dev/website-hosting-cloudfront-walkthrough.html)
|
||||
|
||||
### GCP + Cloudflare
|
||||
|
||||
- [Things to Know Before Getting Started](https://code.luasoftware.com/tutorials/google-cloud-storage/things-to-know-before-hosting-static-website-on-google-cloud-storage/)
|
||||
- [Hosting a Static Website on GCP](https://cloud.google.com/storage/docs/hosting-static-website)
|
||||
|
||||
### Azure
|
||||
|
||||
- [Host a Static Website](https://docs.microsoft.com/en-us/azure/storage/blobs/storage-blob-static-website)
|
||||
- [Add SSL Support](https://docs.microsoft.com/en-us/azure/storage/blobs/storage-https-custom-domain-cdn)
|
||||
- [Configure a Custom Domain](https://docs.microsoft.com/en-us/azure/storage/blobs/storage-custom-domain-name)
|
||||
@@ -1,3 +0,0 @@
|
||||
# User Account Control
|
||||
|
||||
> Coming soon - We are working on bringing the User Account Control to OHIF-v3
|
||||
@@ -1,109 +0,0 @@
|
||||
# Continous Integration (CI)
|
||||
|
||||
This repository uses `CircleCI` and `Netlify` for continous integration.
|
||||
|
||||
## Deploy Previews
|
||||
|
||||
[Netlify Deploy previews][deploy-previews] are generated for every pull request.
|
||||
They allow pull request authors and reviewers to "Preview" the OHIF Viewer as if
|
||||
the changes had been merged.
|
||||
|
||||
Deploy previews can be configured by modifying the `netlify.toml` file in the
|
||||
root of the repository. Some additional scripts/assets for netlify are included
|
||||
in the root `.netlify` directory.
|
||||
|
||||
## Workflows
|
||||
|
||||
[CircleCI Workflows][circleci-workflows] are a set of rules for defining a
|
||||
collection of jobs and their run order. They are self-documenting and their
|
||||
configuration can be found in our CircleCI configuration file:
|
||||
`.circleci/config.yml`.
|
||||
|
||||
### Workflow: PR_CHECKS
|
||||
|
||||
The PR_CHECKS workflow (Pull Request Checks) runs our automated unit and
|
||||
end-to-end tests for every code check-in. These tests must all pass before code
|
||||
can be merged to our `master` branch.
|
||||
|
||||
<div style="text-align: center;">
|
||||
<a href="/assets/img/WORKFLOW_PR_CHECKS.png">
|
||||
<img src="/assets/img/WORKFLOW_PR_CHECKS.png" alt="workflow diagram" style="margin: 0 auto; max-width: 500px;" />
|
||||
</a>
|
||||
<div><i>Workflow diagram for PR_CHECKS</i></div>
|
||||
</div>
|
||||
|
||||
### Workflow: PR_OPTIONAL_DOCKER_PUBLISH
|
||||
|
||||
The PR_OPTIONAL_DOCKER_PUBLISH workflow allows for "manual approval" to publish
|
||||
the pull request as a tagged docker image. This is helpful when changes need to
|
||||
be tested with the Google Adapter before merging to `master`.
|
||||
|
||||
<div style="text-align: center;">
|
||||
<a href="/assets/img/WORKFLOW_PR_OPTIONAL_DOCKER_PUBLISH.png">
|
||||
<img src="/assets/img/WORKFLOW_PR_OPTIONAL_DOCKER_PUBLISH.png" alt="workflow diagram" style="margin: 0 auto; max-width: 500px;" />
|
||||
</a>
|
||||
<div><i>Workflow diagram for PR_WORKFLOW_PR_OPTIONAL_DOCKER_PUBLISH</i></div>
|
||||
</div>
|
||||
|
||||
> NOTE: This workflow will fail unless it's for a branch on our `upstream`
|
||||
> repository. If you need this functionality, but the branch is from a fork,
|
||||
> merge the changes to a short-lived `feature/` branch on `upstream`
|
||||
|
||||
### Workflow: DEPLOY
|
||||
|
||||
The DEPLOY workflow deploys the OHIF Viewer when changes are merged to master.
|
||||
It uses the Netlify CLI to deploy assets created as part of the repository's PWA
|
||||
Build process (`yarn run build`). The workflow allows for "Manual Approval" to
|
||||
promote the build to `STAGING` and `PRODUCTION` environments.
|
||||
|
||||
<div style="text-align: center;">
|
||||
<a href="/assets/img/WORKFLOW_DEPLOY.png">
|
||||
<img src="/assets/img/WORKFLOW_DEPLOY.png" alt="workflow diagram" style="margin: 0 auto; max-width: 500px;" />
|
||||
</a>
|
||||
<div><i>Workflow diagram for WORKFLOW_DEPLOY</i></div>
|
||||
</div>
|
||||
|
||||
| Environment | Description | URL |
|
||||
| ----------- | ---------------------------------------------------------------------------------- | --------------------------------------------- |
|
||||
| Development | Always reflects latest changes on `master` branch. | [Netlify][netlify-dev] / [OHIF][ohif-dev] |
|
||||
| Staging | For manual testing before promotion to prod. Keeps development workflow unblocked. | [Netlify][netlify-stage] / [OHIF][ohif-stage] |
|
||||
| Production | Stable, tested, updated less frequently. | [Netlify][netlify-prod] / [OHIF][ohif-prod] |
|
||||
|
||||
### Workflow: RELEASE
|
||||
|
||||
The RELEASE workflow publishes our `npm` packages, updated documentation, and
|
||||
`docker` image when changes are merged to master. `Lerna` and "Semantic Commit
|
||||
Syntax" are used to independently version and publish the many packages in our
|
||||
monorepository. If a new version is cut/released, a Docker image is created.
|
||||
Documentation is generated with `gitbook` and pushed to our `gh-pages` branch.
|
||||
GitHub hosts the `gh-pages` branch with GitHub Pages.
|
||||
|
||||
- Platform Packages: https://github.com/ohif/viewers/#platform
|
||||
- Extension Packages: https://github.com/ohif/viewers/#extensions
|
||||
- Documentation: https://docs.ohif.org/
|
||||
|
||||
<div style="text-align: center;">
|
||||
<a href="/assets/img/WORKFLOW_RELEASE.png">
|
||||
<img src="/assets/img/WORKFLOW_RELEASE.png" alt="workflow diagram" style="margin: 0 auto; max-width: 500px;" />
|
||||
</a>
|
||||
<div><i>Workflow diagram for WORKFLOW_RELEASE</i></div>
|
||||
</div>
|
||||
|
||||
### HOTFIX
|
||||
|
||||
_Not yet implemented_
|
||||
|
||||
<!--
|
||||
LINKS
|
||||
-->
|
||||
|
||||
<!-- prettier-ignore-start -->
|
||||
[deploy-previews]: https://www.netlify.com/blog/2016/07/20/introducing-deploy-previews-in-netlify/
|
||||
[circleci-workflows]: https://circleci.com/docs/2.0/workflows/
|
||||
[netlify-dev]: https://ohif-dev.netlify.com
|
||||
[netlify-stage]: https://ohif-stage.netlify.com
|
||||
[netlify-prod]: https://ohif-prod.netlify.com
|
||||
[ohif-dev]: https://viewer-dev.ohif.org
|
||||
[ohif-stage]: https://viewer-stage.ohif.org
|
||||
[ohif-prod]: https://viewer-prod.ohif.org
|
||||
<!-- prettier-ignore-end -->
|
||||
@@ -1,154 +0,0 @@
|
||||
# Contributing
|
||||
|
||||
## How can I help?
|
||||
|
||||
Fork the repository, make your change and submit a pull request. If you would
|
||||
like to discuss the changes you intend to make to clarify where or how they
|
||||
should be implemented, please don't hesitate to create a new issue. At a
|
||||
minimum, you may want to read the following documentation:
|
||||
|
||||
- [Getting Started](/development/getting-started.md)
|
||||
- [Architecture](/architecture/index.md)
|
||||
|
||||
Pull requests that are:
|
||||
|
||||
- Small
|
||||
- [Well tested](./testing.md)
|
||||
- Decoupled
|
||||
|
||||
Are much more likely to get reviewed and merged in a timely manner.
|
||||
|
||||
## When changes impact multiple repositories
|
||||
|
||||
While this can be tricky, we've tried to reduce how often this situation crops
|
||||
up this with our [recent switch to a monorepo][monorepo]. Our maintained
|
||||
extensions, ui components, internationalization library, and business logic can
|
||||
all be developed by simply running `yarn run dev` from the repository root.
|
||||
|
||||
Testing the viewer with locally developed, unpublished package changes from a
|
||||
package outside of the monorepo is most common with extension development. Let's
|
||||
demonstrate how to accomplish this with two commonly forked extension
|
||||
dependencies:
|
||||
|
||||
### `cornerstone-tools`
|
||||
|
||||
On your local file system:
|
||||
|
||||
```bash
|
||||
# code/my-projects/
|
||||
.
|
||||
├── cornerstonejs/cornerstone-tools
|
||||
└── ohif/viewers
|
||||
```
|
||||
|
||||
- Open a terminal/shell
|
||||
- Navigate to `cornerstonejs/cornerstone-tools`
|
||||
- `yarn install`
|
||||
- [`yarn link`](https://yarnpkg.com/en/docs/cli/link)
|
||||
- `yarn run dev`
|
||||
|
||||
|
||||
- Open a new terminal/shell
|
||||
- Navigate to `ohif/viewers` (the root of ohif project)
|
||||
- `yarn install`
|
||||
- [`yarn link cornerstone-tools`](https://yarnpkg.com/en/docs/cli/link)
|
||||
- `yarn run dev`
|
||||
|
||||
As you make changed to `cornerstone-tools`, and it's output is rebuilt, you
|
||||
should see the following behavior:
|
||||
|
||||
<div style="text-align: center;">
|
||||
<a href="/assets/img/cornerstone-tools-link.gif">
|
||||
<img src="/assets/img/cornerstone-tools-link.gif" alt="Example of linked cornerstone-tools package" style="margin: 0 auto; max-width: 500px;" />
|
||||
</a>
|
||||
<div><i>example of linked cornerstone-tools package</i></div>
|
||||
</div>
|
||||
|
||||
If you wish to stop using your local package, run the following commands in the
|
||||
`ohif/viewers` repository root:
|
||||
|
||||
- `yarn unlink cornerstone-tools`
|
||||
- `yarn install --force`
|
||||
|
||||
<!--
|
||||
### `react-vtkjs-viewport`
|
||||
|
||||
On your local file system:
|
||||
|
||||
```bash
|
||||
# code/my-projects/
|
||||
.
|
||||
├── ohif/react-vtkjs-viewport
|
||||
└── ohif/viewers
|
||||
```
|
||||
|
||||
- Open a terminal/shell
|
||||
- Navigate to `ohif/react-vtkjs-viewport`
|
||||
- `yarn install`
|
||||
- [`yarn link`](https://yarnpkg.com/en/docs/cli/link)
|
||||
- `yarn run start`
|
||||
- Open a new terminal/shell
|
||||
- Navigate to `ohif/viewers`.
|
||||
- `yarn install`
|
||||
- [`yarn link react-vtkjs-viewport`](https://yarnpkg.com/en/docs/cli/link)
|
||||
- `yarn run dev` -->
|
||||
|
||||
#### Other linkage notes
|
||||
|
||||
We're still working out some of the kinks with local package development as
|
||||
there are a lot of factors that can influence the behavior of our development
|
||||
server and bundler. If you encounter issues not addressed here, please don't
|
||||
hesitate to reach out on GitHub.
|
||||
|
||||
Sometimes you might encounter a situation where the linking doesn't work as expected.
|
||||
This might happen when there are multiple linked packages with the same name.
|
||||
You can [remove][unlink] the linked packages inside yarn and try again.
|
||||
|
||||
## Any guidance on submitting changes?
|
||||
|
||||
While we do appreciate code contributions, triaging and integrating contributed
|
||||
code changes can be very time consuming. Please consider the following tips when
|
||||
working on your pull requests:
|
||||
|
||||
- Functionality is appropriate for the repository. Consider creating a GitHub
|
||||
issue to discuss your suggested changes.
|
||||
- The scope of the pull request is not too large. Please consider separate pull
|
||||
requests for each feature as big pull requests are very time consuming to
|
||||
understand.
|
||||
|
||||
We will provide feedback on your pull requests as soon as possible. Following
|
||||
the tips above will help ensure your changes are reviewed.
|
||||
|
||||
<!-- ## Testing contribution pull requests
|
||||
|
||||
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.
|
||||
|
||||
Replacing the number 237 in the link below with your pull request number should
|
||||
let you test it as well and you can use this link for discussions on github
|
||||
without requiring reviewers to download and build your branch.
|
||||
|
||||
```bash
|
||||
https://deploy-preview-237--ohif.netlify.com/viewer/?url=https://s3.eu-central-1.amazonaws.com/ohif-viewer/sampleDICOM.json
|
||||
```
|
||||
|
||||
If you have made a documentation change, a link like this will let you preview
|
||||
the gitbook generated by the pull request:
|
||||
|
||||
```bash
|
||||
https://deploy-preview-237--ohif.netlify.com/contributing.html
|
||||
``` -->
|
||||
|
||||
<!--
|
||||
Links
|
||||
-->
|
||||
|
||||
<!-- prettier-ignore-start -->
|
||||
[example-url]: https://deploy-preview-237--ohif.netlify.com/viewer/?url=https://s3.eu-central-1.amazonaws.com/ohif-viewer/sampleDICOM.json
|
||||
[pr-237]: https://github.com/OHIF/Viewers/pull/237
|
||||
[monorepo]: https://github.com/OHIF/Viewers/issues/768
|
||||
[unlink]: https://stackoverflow.com/questions/58459698/is-there-a-command-to-unlink-all-yarn-packages-yarn-unlink-all
|
||||
<!-- prettier-ignore-end -->
|
||||
@@ -1,107 +0,0 @@
|
||||
# Getting Started
|
||||
|
||||
## Setup
|
||||
|
||||
### Fork & Clone
|
||||
|
||||
If you intend to contribute back changes, or if you would like to pull updates
|
||||
we make to the OHIF Viewer, then follow these steps:
|
||||
|
||||
- [Fork][fork-a-repo] the [OHIF/Viewers][ohif-viewers-repo] repository
|
||||
- [Create a local clone][clone-a-repo] of your fork
|
||||
- `git clone https://github.com/YOUR-USERNAME/Viewers`
|
||||
- Add OHIF/Viewers as a [remote repository][add-remote-repo] labled `upstream`
|
||||
- Navigate to the cloned project's directory
|
||||
- `git remote add upstream https://github.com/OHIF/Viewers.git`
|
||||
|
||||
With this setup, you can now [sync your fork][sync-changes] to keep it
|
||||
up-to-date with the upstream (original) repository. This is called a "Triangular
|
||||
Workflow" and is common for Open Source projects. The GitHub blog has a [good
|
||||
graphic that illustrates this setup][triangular-workflow].
|
||||
|
||||
### Private
|
||||
|
||||
Alternatively, if you intend to use the OHIF Viewer as a starting point, and you
|
||||
aren't as concerned with syncing updates, then follow these steps:
|
||||
|
||||
1. Navigate to the [OHIF/Viewers][ohif-viewers] repository
|
||||
2. Click `Clone or download`, and then `Download ZIP`
|
||||
3. Use the contents of the `.zip` file as a starting point for your viewer
|
||||
|
||||
> NOTE: It is still possible to sync changes using this approach. However,
|
||||
> submitting pull requests for fixes and features are best done with the
|
||||
> separate, forked repository setup described in "Fork & Clone"
|
||||
|
||||
## Developing
|
||||
|
||||
### Requirements
|
||||
|
||||
- [Node.js & NPM](https://nodejs.org/en/)
|
||||
- [Yarn](https://yarnpkg.com/en/)
|
||||
- Yarn workspaces should be enabled:
|
||||
- `yarn config set workspaces-experimental true`
|
||||
|
||||
### Kick the tires
|
||||
|
||||
Navigate to the root of the project's directory in your terminal and run the
|
||||
following commands:
|
||||
|
||||
```bash
|
||||
# Switch to the v3 branch
|
||||
git switch feat/v2-main
|
||||
|
||||
# Restore dependencies
|
||||
yarn install
|
||||
|
||||
# Start local development server
|
||||
yarn run dev
|
||||
```
|
||||
|
||||
You should see the following output:
|
||||
|
||||
```bash
|
||||
@ohif/viewer: i ｢wds｣: Project is running at http://localhost:3000/
|
||||
@ohif/viewer: i ｢wds｣: webpack output is served from /
|
||||
@ohif/viewer: i ｢wds｣: Content not from webpack is served from D:\code\ohif\Viewers\platform\viewer
|
||||
@ohif/viewer: i ｢wds｣: 404s will fallback to /index.html
|
||||
|
||||
# And a list of all generated files
|
||||
```
|
||||
|
||||
### 🎉 Celebrate 🎉
|
||||
|
||||
<div style="padding:56.25% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/545988245?badge=0&autopause=0&player_id=0&app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen style="position:absolute;top:0;left:0;width:100%;height:100%;" title="getting-started"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script>
|
||||
|
||||
### Building for Production
|
||||
|
||||
> More comprehensive guides for building and publishing can be found in our
|
||||
> [deployment docs](./../deployment/index.md)
|
||||
|
||||
```bash
|
||||
# Build static assets to host a PWA
|
||||
yarn run build
|
||||
|
||||
# Build packaged output (script-tag use)
|
||||
yarn run build:package
|
||||
```
|
||||
|
||||
## Troubleshooting
|
||||
|
||||
- If you receive a _"No Studies Found"_ message and do not see your studies, try
|
||||
changing the Study Date filters to a wider range.
|
||||
- If you see a 'Loading' message which never resolves, check your browser
|
||||
JavaScript console inside the Developer Tools to identify any errors.
|
||||
|
||||
<!--
|
||||
Links
|
||||
-->
|
||||
|
||||
<!-- prettier-ignore-start -->
|
||||
[fork-a-repo]: https://help.github.com/en/articles/fork-a-repo
|
||||
[clone-a-repo]: https://help.github.com/en/articles/fork-a-repo#step-2-create-a-local-clone-of-your-fork
|
||||
[add-remote-repo]: https://help.github.com/en/articles/fork-a-repo#step-3-configure-git-to-sync-your-fork-with-the-original-spoon-knife-repository
|
||||
[sync-changes]: https://help.github.com/en/articles/syncing-a-fork
|
||||
[triangular-workflow]: https://github.blog/2015-07-29-git-2-5-including-multiple-worktrees-and-triangular-workflows/#improved-support-for-triangular-workflows
|
||||
[ohif-viewers-repo]: https://github.com/OHIF/Viewers
|
||||
[ohif-viewers]: https://github.com/OHIF/Viewers
|
||||
<!-- prettier-ignore-end -->
|
||||
@@ -1,211 +0,0 @@
|
||||
# Running Tests for OHIF
|
||||
|
||||
We introduce here various test types that is available
|
||||
for OIHF, and how to run each test in order to make sure your contribution
|
||||
hasn't broken any existing functionalities. Idea and philosophy of each testing category is discussed in the second
|
||||
part of this page.
|
||||
|
||||
## Unit test
|
||||
To run the unit test:
|
||||
```
|
||||
yarn run test:unit:ci
|
||||
```
|
||||
|
||||
Note: You should have already installed all the packages with `yarn install`.
|
||||
|
||||
|
||||
Running unit test will generate a report at the end showing the successful and
|
||||
unsuccessful tests with detailed explanations.
|
||||
|
||||
## End-to-end test
|
||||
For running the OHIF e2e test you need to run the following steps:
|
||||
|
||||
- Create a mini-pacs for OHIF to access the images for testing. We download
|
||||
and run our lightweight implementation which provides a collection of DICOM studies ([source code][mini-pacs]).
|
||||
|
||||
```
|
||||
docker run -p 5985:5985 -p 5984:5984 -e USE_POUCHDB=true -e DB_SERVER=http://0.0.0.0 ohif/viewer-testdata:0.1-test
|
||||
```
|
||||
|
||||
Successful execution should be
|
||||
|
||||
|
||||
|
||||
- Open a new terminal, navigate to the OHIF project, and run OHIF with the dicom-server config
|
||||
|
||||
```
|
||||
APP_CONFIG=config/dicomweb-server.js yarn start
|
||||
```
|
||||
|
||||
You should be able to see test studies in the study list
|
||||
|
||||
|
||||
|
||||
- Open a new terminal inside the OIHF project, and run the e2e cypress test
|
||||
|
||||
```
|
||||
yarn run test:e2e
|
||||
```
|
||||
|
||||
You should be able to see the cypress window open
|
||||
|
||||
|
||||
|
||||
Run the tests by clicking on the `Run #number integration tests` .
|
||||
|
||||
A new window will open and you will see e2e tests being executed one after
|
||||
each other.
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# Testing Philosiphy
|
||||
|
||||
> Testing is an opinionated topic. Here is a rough overview of our testing
|
||||
> philosophy. See something you want to discuss or think should be changed? Open
|
||||
> a PR and let's discuss.
|
||||
|
||||
You're an engineer. You know how to write code, and writing tests isn't all that
|
||||
different. But do you know why we write tests? Do you know when to write one, or
|
||||
what kind of test to write? How do you know if a test is a _"good"_ test? This
|
||||
document's goal is to give you the tools you need to make those determinations.
|
||||
|
||||
Okay. So why do we write tests? To increase our... **CONFIDENCE**
|
||||
|
||||
- If I do a large refactor, does everything still work?
|
||||
- If I changed some critical piece of code, is it safe to push to production?
|
||||
|
||||
Gaining the confidence we need to answer these questions after every change is
|
||||
costly. Good tests allow us to answer them without manual regression testing.
|
||||
What and how we choose to test to increase that confidence is nuanced.
|
||||
|
||||
## Kinds of Tests
|
||||
|
||||
Test's buy us confidence, but not all tests are created equal. Each kind of test
|
||||
has a different cost to write and maintain. An expensive test is worth it if it
|
||||
gives us confidence that a payment is processed, but it may not be the best
|
||||
choice for asserting an element's border color.
|
||||
|
||||
| Test Type | Example | Speed | Cost |
|
||||
| ----------- | ------------------------------------------------------------------------ | ---------------- | ------------------------------------------------------------------------ |
|
||||
| Static | `addNums(1, '2')` called with `string`, expected `int`. | :rocket: Instant | :money_with_wings: |
|
||||
| Unit | `addNums(1, 2)` returns expected result `3` | :airplane: Fast | :money_with_wings::money_with_wings: |
|
||||
| Integration | Clicking "Sign In", navigates to the dashboard (mocked network requests) | :running: Okay | :money_with_wings::money_with_wings::money_with_wings: |
|
||||
| End-to-end | Clicking "Sign In", navigates to the dashboard (no mocks) | :turtle: Slow | :money_with_wings::money_with_wings::money_with_wings::money_with_wings: |
|
||||
|
||||
- :rocket: Speed: How quickly tests run
|
||||
- :money_with_wings: Cost: Time to write, and to debug when broken (more points
|
||||
of failure)
|
||||
|
||||
### Static Code Analysis
|
||||
|
||||
Modern tooling gives us this "for free". It can catch invalid regular
|
||||
expressions, unused variables, and guarantee we're calling methods/functions
|
||||
with the expected paramater types.
|
||||
|
||||
Example Tooling:
|
||||
|
||||
- [ESLint][eslint-rules]
|
||||
- [TypeScript][typescript-docs] or [Flow][flow-org]
|
||||
|
||||
### Unit Tests
|
||||
|
||||
The building blocks of our libraries and applications. For these, you'll often
|
||||
be testing a single function or method. Conceptually, this equates to:
|
||||
|
||||
_Pure Function Test:_
|
||||
|
||||
- If I call `sum(2, 2)`, I expect the output to be `4`
|
||||
|
||||
_Side Effect Test:_
|
||||
|
||||
- If I call `resetViewport(viewport)`, I expect `cornerstone.reset` to be called
|
||||
with `viewport`
|
||||
|
||||
#### When to use
|
||||
|
||||
Anything that is exposed as public API should have unit tests.
|
||||
|
||||
#### When to avoid
|
||||
|
||||
You're actually testing implementation details. You're testing implementation
|
||||
details if:
|
||||
|
||||
- Your test does something that the consumer of your code would never do.
|
||||
- IE. Using a private function
|
||||
- A refactor can break your tests
|
||||
|
||||
### Integration Tests
|
||||
|
||||
We write integration tests to gain confidence that several units work together.
|
||||
Generally, we want to mock as little as possible for these tests. In practice,
|
||||
this means only mocking network requests.
|
||||
|
||||
#### When to use
|
||||
|
||||
...
|
||||
|
||||
### End-to-End Tests
|
||||
|
||||
These are the most expensive tests to write and maintain. Largely because, when
|
||||
they fail, they have the largest number of potential points of failure. So why
|
||||
do we write them? Because they also buy us the most confidence.
|
||||
|
||||
#### When to use
|
||||
|
||||
Mission critical features and functionality, or to cover a large breadth of
|
||||
functionality until unit tests catch up. Unsure if we should have a test for
|
||||
feature `X` or scenario `Y`? Open an issue and let's discuss.
|
||||
|
||||
## Summary
|
||||
|
||||
- Does your test increase confidence?
|
||||
- Does the test type chosen balance the cost-to-confidence ratio?
|
||||
|
||||
## Further Reading
|
||||
|
||||
### General
|
||||
|
||||
- [Assert(js) Conf 2018 Talks][assert-js-talks]
|
||||
- [Write tests. Not too many. Mostly integration.][kent-talk] - Kent C. Dodds
|
||||
- [I see your point, but…][gleb-talk] - Gleb Bahmutov
|
||||
- [Static vs Unit vs Integration vs E2E Testing][kent-blog] - Kent C. Dodds
|
||||
(Blog)
|
||||
|
||||
### End-to-end Testing w/ Cypress
|
||||
|
||||
- [Getting Started](https://docs.cypress.io/guides/overview/why-cypress.html)
|
||||
- Be sure to check out `Getting Started` and `Core Concepts`
|
||||
- [Best Practices](https://docs.cypress.io/guides/references/best-practices.html)
|
||||
- [Example Recipes](https://docs.cypress.io/examples/examples/recipes.html)
|
||||
|
||||
## Testing Dorito
|
||||
|
||||
[![testing dorito][testing-dorito-img]][testing-dorito]
|
||||
|
||||
<!--
|
||||
Links
|
||||
-->
|
||||
|
||||
<!-- prettier-ignore-start -->
|
||||
[eslint-rules]: https://eslint.org/docs/rules/
|
||||
[mini-pacs]: https://github.com/OHIF/viewer-testdata
|
||||
[typescript-docs]: https://www.typescriptlang.org/docs/home.html
|
||||
[flow-org]: https://flow.org/
|
||||
<!-- Talks -->
|
||||
[assert-js-talks]: https://www.youtube.com/playlist?list=PLZ66c9_z3umNSrKSb5cmpxdXZcIPNvKGw
|
||||
[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 -->
|
||||
[testing-trophy]: https://twitter.com/kentcdodds/status/960723172591992832?ref_src=twsrc%5Etfw%7Ctwcamp%5Etweetembed%7Ctwterm%5E960723172591992832&ref_url=https%3A%2F%2Fkentcdodds.com%2Fblog%2Fwrite-tests
|
||||
[aaron-square]: https://twitter.com/Carofine247/status/966727489274961920
|
||||
[gleb-pyramid]: https://twitter.com/Carofine247/status/966764532046684160/photo/3
|
||||
[testing-pyramid]: https://dojo.ministryoftesting.com/dojo/lessons/the-mobile-test-pyramid
|
||||
[testing-dorito]: https://twitter.com/denvercoder/status/960752578198843392
|
||||
[testing-dorito-img]: https://pbs.twimg.com/media/DVVHXycUMAAcN-F?format=jpg&name=4096x4096
|
||||
<!-- prettier-ignore-end -->
|
||||
@@ -1,67 +0,0 @@
|
||||
<table>
|
||||
<thead>
|
||||
<tr>
|
||||
<th>Extension</th>
|
||||
<th>Description</th>
|
||||
<th>Modules</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<!-- CORNERSTONE.js -->
|
||||
<tr>
|
||||
<td>
|
||||
<a href="">
|
||||
Default
|
||||
</a>
|
||||
</td>
|
||||
<td>
|
||||
Default extension provides default viewer layout, a study/series
|
||||
browser, and a datasource that maps to a DICOMWeb compliant backend
|
||||
</td>
|
||||
<td>commandsModule, ContextModule, DataSourceModule, HangingProtocolModule, LayoutTemplateModule, PanelModule, SOPClassHandlerModule, ToolbarModule</td>
|
||||
</tr>
|
||||
<!-- CORNERSTONE.js -->
|
||||
<tr>
|
||||
<td>
|
||||
<a href="https://www.npmjs.com/package/@ohif/extension-cornerstone">
|
||||
Cornerstone
|
||||
</a>
|
||||
</td>
|
||||
<td>
|
||||
Provides rendering functionalities for 2D images.
|
||||
</td>
|
||||
<td>ViewportModule, CommandsModule</td>
|
||||
</tr>
|
||||
<!-- dicom-pdf -->
|
||||
<!-- <tr>
|
||||
<td>
|
||||
<a href="https://www.npmjs.com/package/@ohif/extension-dicom-pdf">DICOM PDF</a>
|
||||
</td>
|
||||
<td>
|
||||
Renders PDFs for a <a href="https://github.com/OHIF/Viewers/blob/master/extensions/dicom-pdf/src/OHIFDicomPDFSopClassHandler.js#L4-L6">specific SopClassUID</a>.
|
||||
</td>
|
||||
<td>Viewport, SopClassHandler</td>
|
||||
</tr> -->
|
||||
<!-- dicom-sr -->
|
||||
<tr>
|
||||
<td>
|
||||
<a href="">DICOM SR</a>
|
||||
</td>
|
||||
<td>
|
||||
Maintained extensions for cornerstone and visualization of DICOM Structured Reports
|
||||
</td>
|
||||
<td>ViewportModule, CommandsModule, SOPClassHandlerModule</td>
|
||||
</tr>
|
||||
<!-- Measurement-tracking -->
|
||||
<tr>
|
||||
<td>
|
||||
<a href="">Measurement tracking</a>
|
||||
</td>
|
||||
<td>
|
||||
Tracking measurements in the measurement panel
|
||||
</td>
|
||||
<td> ContextModule,PanelModule,ViewportModule,CommandsModule</td>
|
||||
</tr>
|
||||
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -1,94 +0,0 @@
|
||||
<table>
|
||||
<thead>
|
||||
<tr>
|
||||
<th align="left" width="30%">
|
||||
Types
|
||||
</th>
|
||||
<th align="left">Description</th>
|
||||
<th align="left">Examples</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td align="left">
|
||||
<a href="./modules/layout-template.md">
|
||||
LayoutTemplate (NEW)
|
||||
</a>
|
||||
</td>
|
||||
<td align="left">Control Layout of a route</td>
|
||||
<td align="left"></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td align="left">
|
||||
<a href="./modules/data-source.md">
|
||||
DataSource (NEW)
|
||||
</a>
|
||||
</td>
|
||||
<td align="left">Control the mapping from DICOM metadata to OHIF-metadata</td>
|
||||
<td align="left"></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td align="left">
|
||||
<a href="./modules/sop-class-handler.md">
|
||||
SOPClassHandler
|
||||
</a>
|
||||
</td>
|
||||
<td align="left">Determines how retrieved study data is split into "DisplaySets"</td>
|
||||
<td align="left"></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td align="left">
|
||||
<a href="./modules/panel.md">
|
||||
Panel
|
||||
</a>
|
||||
</td>
|
||||
<td align="left">Adds left or right hand side panels</td>
|
||||
<td align="left"></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td align="left">
|
||||
<a href="./modules/viewport.md">
|
||||
Viewport
|
||||
</a>
|
||||
</td>
|
||||
<td align="left">Adds a component responsible for rendering a "DisplaySet"</td>
|
||||
<td align="left"></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td align="left">
|
||||
<a href="./modules/commands.md">
|
||||
Commands
|
||||
</a>
|
||||
</td>
|
||||
<td align="left">Adds named commands, scoped to a context, to the CommandsManager</td>
|
||||
<td align="left"></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td align="left">
|
||||
<a href="./modules/toolbar.md">
|
||||
Toolbar
|
||||
</a>
|
||||
</td>
|
||||
<td align="left">Adds buttons or custom components to the toolbar</td>
|
||||
<td align="left"></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td align="left">
|
||||
<a href="./modules/context.md">
|
||||
Context
|
||||
</a>
|
||||
</td>
|
||||
<td align="left">Shared state for a workflow or set of extension module definitions</td>
|
||||
<td align="left"></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td align="left">
|
||||
<a href="./modules/hpModule.md">
|
||||
HangingProtocol
|
||||
</a>
|
||||
</td>
|
||||
<td align="left">Adds hanging protocol rules</td>
|
||||
<td align="left"></td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -1,263 +0,0 @@
|
||||
# Extensions
|
||||
|
||||
- [Extensions](#extensions)
|
||||
- [Overview](#overview)
|
||||
- [Extension Skeleton](#extension-skeleton)
|
||||
- [OHIF-Maintained Extensions](#ohif-maintained-extensions)
|
||||
- [Registering an Extension](#registering-an-extension)
|
||||
- [Registering at Runtime](#registering-at-runtime)
|
||||
- [Registering at Build Time](#registering-at-build-time)
|
||||
- [Lifecycle Hooks](#lifecycle-hooks)
|
||||
- [Modules](#modules)
|
||||
- [Contexts](#contexts)
|
||||
|
||||
## Overview
|
||||
We have re-designed the architecture of the `OHIF-v3` to enable building applications
|
||||
that are easily extensible to various use cases (modes) that behind the scene would utilize desired functionalities (extensions) to reach the goal of the use case.
|
||||
|
||||
Previously, extensions were “additive” and could not easily be mixed and matched within the same viewer for different use cases. Previous `OHIF-v2` architecture meant that
|
||||
any minor extension alteration usually would require the user to hard fork. E.g. removing some of the tools from the toolbar of the cornerstone extension meant you had to hard fork it, which was frustrating if the implementation was otherwise the same as master.
|
||||
|
||||
|
||||
> - Developers should make packages of *reusable* functionality as extensions, and can consume
|
||||
> publicly available extensions.
|
||||
> - Any conceivable radiological workflow or viewer setup will be able to be built with the platform through *modes*.
|
||||
|
||||
|
||||
|
||||
Practical examples of extensions include:
|
||||
|
||||
- A set of segmentation tools that build on top of the `cornerstone` viewport
|
||||
- A set of rendering functionalities to volume render the data
|
||||
- [See our maintained extensions for more examples of what's possible](#maintained-extensions)
|
||||
|
||||
|
||||
|
||||
<mark>Diagram showing how extensions are configured and accessed.
|
||||
<!--
|
||||
<div style="text-align: center;">
|
||||
<a href="/assets/img/extensions-diagram.png">
|
||||
<img src="/assets/img/extensions-diagram.png" alt="Extensions Diagram" style="margin: 0 auto; max-width: 500px;" />
|
||||
</a>
|
||||
<div><i>Diagram showing how extensions are configured and accessed.</i></div>
|
||||
</div> -->
|
||||
|
||||
|
||||
|
||||
## Extension Skeleton
|
||||
|
||||
An extension is a plain JavaScript object that has an `id` property, and one or
|
||||
more [modules](#modules) and/or [lifecycle hooks](#lifecycle-hooks).
|
||||
|
||||
```js
|
||||
// prettier-ignore
|
||||
export default {
|
||||
/**
|
||||
* Only required property. Should be a unique value across all extensions.
|
||||
*/
|
||||
id: 'example-extension',
|
||||
|
||||
// Lifecyle
|
||||
preRegistration() { /* */ },
|
||||
onModeEnter() { /* */ },
|
||||
onModeExit() { /* */ },
|
||||
// Modules
|
||||
getLayoutTemplateModule() { /* */ },
|
||||
getDataSourcesModule() { /* */ },
|
||||
getSopClassHandlerModule() { /* */ },
|
||||
getPanelModule() { /* */ },
|
||||
getViewportModule() { /* */ },
|
||||
getCommandsModule() { /* */ },
|
||||
getContextModule() { /* */ },
|
||||
getToolbarModule() { /* */ },
|
||||
getHangingProtocolModule() { /* */ },
|
||||
}
|
||||
```
|
||||
|
||||
## OHIF-Maintained Extensions
|
||||
A small number of powerful extensions for popular use cases are maintained by
|
||||
OHIF. They're co-located in the [`OHIF/Viewers`][viewers-repo] repository, in
|
||||
the top level [`extensions/`][ext-source] directory.
|
||||
|
||||
{% include "./_maintained-extensions-table.md" %}
|
||||
|
||||
|
||||
## Registering an Extension
|
||||
|
||||
Extensions are building blocks that need to be registered. There are two different ways to register and configure extensions: At
|
||||
[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
|
||||
becomes available to the modes via the `ExtensionManager` by requesting it via
|
||||
its id. [Read more about Extension Manager](#extension-manager)
|
||||
|
||||
|
||||
|
||||
### Registering at Runtime
|
||||
|
||||
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
|
||||
import MyFirstExtension from '@ohif/extension-first'
|
||||
import MySecondExtension from '@ohif/extension-second'
|
||||
|
||||
const extensionConfig = {/* extension configuration */}
|
||||
|
||||
// prettier-ignore
|
||||
const config = {
|
||||
routerBasename: '/',
|
||||
extensions: [
|
||||
MyFirstExtension,
|
||||
[
|
||||
MySecondExtension,
|
||||
extensionConfig
|
||||
],
|
||||
],
|
||||
modes: [/* modes */],
|
||||
showStudyList: true,
|
||||
dataSources: [ /* data source config */]
|
||||
}
|
||||
```
|
||||
|
||||
Then, behind the scene, the runtime-added extensions will get merged with the
|
||||
default app extensions (note: default app extensions include: `OHIFDefaultExtension`,
|
||||
`OHIFCornerstoneExtension`, `OHIFDICOMSRExtension`,
|
||||
`OHIFMeasurementTrackingExtension`)
|
||||
|
||||
### Registering at Build Time
|
||||
|
||||
The `@ohif/viewer` works best when built as a "Progressive Web Application"
|
||||
(PWA). If you know the extensions your application will need, you can specify
|
||||
them at "build time" to leverage advantages afforded to us by modern tooling:
|
||||
|
||||
- Code Splitting (dynamic imports)
|
||||
- Tree Shaking
|
||||
- Dependency deduplication
|
||||
|
||||
You can update the list of bundled extensions by:
|
||||
|
||||
1. Having your `@ohif/viewer` project depend on the extension
|
||||
2. Importing and adding it to the list of extensions in the
|
||||
`<repo-root>/platform/src/index.js` entrypoint:
|
||||
|
||||
```js
|
||||
import OHIFDefaultExtension from '@ohif/extension-default';
|
||||
import OHIFCornerstoneExtension from '@ohif/extension-cornerstone';
|
||||
import OHIFMeasurementTrackingExtension from '@ohif/extension-measurement-tracking';
|
||||
import OHIFDICOMSRExtension from '@ohif/extension-dicom-sr';
|
||||
import MyFirstExtension from '@ohif/extension-first'
|
||||
|
||||
/** Combine our appConfiguration and "baked-in" extensions */
|
||||
const appProps = {
|
||||
config: window ? window.config : {},
|
||||
defaultExtensions: [
|
||||
OHIFDefaultExtension,
|
||||
OHIFCornerstoneExtension,
|
||||
OHIFMeasurementTrackingExtension,
|
||||
OHIFDICOMSRExtension,
|
||||
MyFirstExtension
|
||||
],
|
||||
};
|
||||
```
|
||||
|
||||
## Lifecycle Hooks
|
||||
|
||||
Currently, there are three lifecycle hook for extensions:
|
||||
|
||||
|
||||
[`preRegistration`](./lifecycle/pre-registration.md)
|
||||
This hook is called once on initialization of the entire viewer application, used to initialize the extensions state, and consume user defined extension configuration. If an extension defines the [`preRegistration`](./lifecycle/pre-registration.md)
|
||||
lifecycle hook, it is called before any modules are registered in the
|
||||
`ExtensionManager`. It's most commonly used to wire up extensions to
|
||||
[services](./../services/index.md) and [commands](./modules/commands.md), and to
|
||||
bootstrap 3rd party libraries.
|
||||
|
||||
|
||||
[`onModeEnter`](./lifecycle/on-mode-enter.md): This hook is called whenever a new mode is entered, or a mode’s data or datasource is switched. This hook can be used to initialize data.
|
||||
|
||||
[`onModeExit`](./lifecycle/on-mode-exit.md): Similarly to onModeEnter, this hook is called when navigating away from a mode, or before a mode’s data or datasource is changed. This can be used to clean up data (e.g. remove annotations that do not need to be persisted)
|
||||
|
||||
|
||||
|
||||
## Modules
|
||||
Modules are the meat of extensions, the `blocks` that we have been talking about a lot.
|
||||
They provide "definitions", components, and filtering/mapping logic that are then made available to modes and services.
|
||||
|
||||
Each module type has a special purpose, and is consumed by our viewer
|
||||
differently.
|
||||
|
||||
|
||||
{% include "./_modules.md" %}
|
||||
|
||||
|
||||
<figure style="text-align: center; font-style: italic;">Tbl. Module types with abridged descriptions and examples. Each module links to a dedicated documentation page.</figure>
|
||||
|
||||
|
||||
|
||||
|
||||
### Contexts
|
||||
|
||||
The `@ohif/viewer` tracks "active contexts" that extensions can use to scope
|
||||
their functionality. Some example contexts being:
|
||||
|
||||
- Route: `ROUTE:VIEWER`, `ROUTE:STUDY_LIST`
|
||||
- Active Viewport: `ACTIVE_VIEWPORT:CORNERSTONE`, `ACTIVE_VIEWPORT:VTK`
|
||||
|
||||
An extension module can use these to say "Only show this Toolbar Button if the
|
||||
active viewport is a Cornerstone viewport." This helps us use the appropriate UI
|
||||
and behaviors depending on the current contexts.
|
||||
|
||||
For example, if we have hotkey that "rotates the active viewport", each Viewport
|
||||
module that supports this behavior can add a command with the same name, scoped
|
||||
to the appropriate context. When the `command` is fired, the "active contexts"
|
||||
are used to determine the appropriate implementation of the rotate behavior.
|
||||
|
||||
|
||||
<!-- <mark>do we want the followings?
|
||||
## Consuming Extensions
|
||||
|
||||
We consume extensions, via the `ExtensionManager`, in our `@ohif/viewer`
|
||||
project.
|
||||
|
||||
```js
|
||||
const extensionManager = new ExtensionManager({
|
||||
commandsManager,
|
||||
servicesManager,
|
||||
hotkeysManager
|
||||
});
|
||||
|
||||
// prettier-ignore
|
||||
extensionManager.registerExtensions([ /** **/ ]);
|
||||
```
|
||||
|
||||
The `@ohif/viewer` project handles data fetching, basic routing, wires up UI
|
||||
services, and is the home to the more bespoke application logic that doesn't
|
||||
make as much sense to make reusable.
|
||||
|
||||
Long-term, replacing the `@ohif/viewer` application and consuming extensions
|
||||
(and the `ExtensionManager`) in your own project is the ideal path for
|
||||
applications requiring a high degree of customization that can't be achieved
|
||||
with current theming, configuration, extension, and services support.
|
||||
|
||||
If you're not sure how to achieve your goals with the extensibility available
|
||||
today, create a GitHub issue! -->
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<!--
|
||||
LINKS
|
||||
-->
|
||||
|
||||
<!-- prettier-ignore-start -->
|
||||
[viewers-repo]: https://github.com/OHIF/Viewers
|
||||
[ext-source]: https://github.com/OHIF/Viewers/tree/master/extensions
|
||||
[module-types]: https://github.com/OHIF/Viewers/blob/master/platform/core/src/extensions/MODULE_TYPES.js
|
||||
<!-- prettier-ignore-end -->
|
||||
@@ -1,29 +0,0 @@
|
||||
# Lifecycle Hook: onModeEnter
|
||||
|
||||
If an extension defines the `onModeEnter` lifecycle hook, it is called
|
||||
when a new mode is enters, or a mode's data or datasource is switched.
|
||||
|
||||
For instance, in DICOM structured report extension (`dicom-sr`), we are using
|
||||
`onModeEnter` to re-create the displaySets after a new mode is entered.
|
||||
|
||||
_Example `onModeEnter` hook implementation_
|
||||
|
||||
```js
|
||||
export default {
|
||||
id: 'org.ohif.dicom-sr',
|
||||
|
||||
onModeEnter({ servicesManager}) {
|
||||
const { DisplaySetService } = servicesManager.services;
|
||||
const displaySetCache = DisplaySetService.getDisplaySetCache();
|
||||
|
||||
const srDisplaySets = displaySetCache.filter(
|
||||
ds => ds.SOPClassHandlerId === SOPClassHandlerId
|
||||
);
|
||||
|
||||
srDisplaySets.forEach(ds => {
|
||||
// New mode route, allow SRs to be hydrated again
|
||||
ds.isHydrated = false;
|
||||
});
|
||||
},
|
||||
};
|
||||
```
|
||||
@@ -1,17 +0,0 @@
|
||||
# Lifecylce Hook: onModeExit
|
||||
|
||||
If an extension defines the `onModeExit` lifecycle hook, it is called when navigating
|
||||
away from a mode. This hook can be used to clean up data tasks such as unregistering services,
|
||||
removing annotations that do not need to be persisted.
|
||||
|
||||
_Example `onModeExit` hook implementation_
|
||||
|
||||
```js
|
||||
export default {
|
||||
id: 'myExampleExtension',
|
||||
|
||||
onModeExit({ servicesManager, commandsManager}) {
|
||||
myCacheServie.purge()
|
||||
},
|
||||
};
|
||||
```
|
||||
@@ -1,65 +0,0 @@
|
||||
# Lifecylce Hook: preRegistration
|
||||
|
||||
If an extension defines the `preRegistration` lifecycle hook, it is called
|
||||
before any modules are registered in the `ExtensionManager`. This hook can be
|
||||
used to:
|
||||
|
||||
- initialize 3rd party libraries
|
||||
- register event listeners
|
||||
- add or call services
|
||||
- add or call commands
|
||||
|
||||
The `preRegistration` hook receives an object containing the
|
||||
`ExtensionManager`'s associated `ServicesManager`, `CommandsManager`, and any
|
||||
`configuration` that was provided with the extension at time of registration.
|
||||
|
||||
Example `preRegistration` implementation that register a new service and make it
|
||||
available in the app. We will talk more in details for creating a new service for
|
||||
`OHIF-v3`.
|
||||
|
||||
```js
|
||||
|
||||
// new service inside new extension
|
||||
import MyNewService from './MyNewService';
|
||||
|
||||
export default function MyNewServiceWithServices(serviceManager) {
|
||||
return {
|
||||
name: 'MyNewService',
|
||||
create: ({ configuration = {} }) => {
|
||||
return new MyNewService(serviceManager);
|
||||
},
|
||||
};
|
||||
}
|
||||
```
|
||||
|
||||
and
|
||||
|
||||
```js
|
||||
import MyNewService from './MyNewService'
|
||||
|
||||
export default {
|
||||
id: 'MyExampleExtension',
|
||||
|
||||
/**
|
||||
* @param {object} params
|
||||
* @param {object} params.configuration
|
||||
* @param {ServicesManager} params.servicesManager
|
||||
* @param {CommandsManager} params.commandsManager
|
||||
* @returns void
|
||||
*/
|
||||
preRegistration({ servicesManager, commandsManager, configuration }) {
|
||||
console.log('Wiring up important stuff.');
|
||||
|
||||
window.importantStuff = () => {
|
||||
console.log(configuration);
|
||||
};
|
||||
|
||||
console.log('Important stuff has been wired.');
|
||||
window.importantStuff();
|
||||
|
||||
// Registering new services
|
||||
servicesManager.registerService(MyNewService(servicesManager));
|
||||
},
|
||||
},
|
||||
};
|
||||
```
|
||||
@@ -1,125 +0,0 @@
|
||||
# Module: Commands
|
||||
|
||||
|
||||
|
||||
- [Module: Commands](#module-commands)
|
||||
- [Overview](#overview)
|
||||
- [Command Definitions](#command-definitions)
|
||||
- [Command Behavior](#command-behavior)
|
||||
- [`CommandsManager` Public API](#commandsmanager-public-api)
|
||||
- [Contexts](#contexts)
|
||||
|
||||
## Overview
|
||||
`CommandsModule` includes list of arbitrary functions. These may activate tools, communicate with a server, open a modal, etc.
|
||||
The significant difference between `OHIF-v3` and `OHIF-v2` is that in `v3` a `mode` defines
|
||||
its toolbar, and which commands each tool call is inside in its toolDefinition
|
||||
|
||||
An extension can register a Commands Module by defining a `getCommandsModule`
|
||||
method. The Commands Module allows us to register one or more commands scoped to
|
||||
specific [contexts](./../index.md#contexts). Commands have several unique
|
||||
characteristics that make them tremendously powerful:
|
||||
|
||||
- Multiple implementations for the same command can be defined
|
||||
- Only the correct command's implementation will be run, dependent on the
|
||||
application's "context"
|
||||
- Commands are used by hotkeys, toolbar buttons and render settings
|
||||
|
||||
Here is a simple example commands module:
|
||||
|
||||
```js
|
||||
const getCommandsModule = () => ({
|
||||
definitions: {
|
||||
exampleActionDef: {
|
||||
commandFn: ({ param1 }) => {
|
||||
console.log(`param1's value is: ${param1}`);
|
||||
},
|
||||
// storeContexts: ['viewports'],
|
||||
options: { param1: 'param1' },
|
||||
context: 'VIEWER', // optional
|
||||
},
|
||||
},
|
||||
defaultContext: 'ACTIVE_VIEWPORT::DICOMSR',
|
||||
});
|
||||
```
|
||||
|
||||
|
||||
Each definition returned by the Commands Module is registered to the
|
||||
`ExtensionManager`'s `CommandsManager`.
|
||||
|
||||
> `storeContexts` has been removed in `OHIF-v3` and now modules have access to all commands and services. This change enables support for user-registered services.
|
||||
|
||||
## Command Definitions
|
||||
|
||||
The command definition consists of a named command (`exampleActionDef` below) and a
|
||||
`commandFn`. The command name is used to call the command, and the `commandFn`
|
||||
is the "command" that is actioned. T
|
||||
|
||||
```js
|
||||
exampleActionDef: {
|
||||
commandFn: ({ param1, options }) => { },
|
||||
options: { param1: 'measurement' },
|
||||
context: 'DEFAULT',
|
||||
}
|
||||
```
|
||||
|
||||
| Property | Type | Description |
|
||||
| --------------- | ------------------ | --------------------------------------------------------------------------------------------------------------------------------------- |
|
||||
| `commandFn` | func | The function to call when command is run. Receives `options` and `storeContexts`. |
|
||||
| `options` | object | (optional) Arguments to pass at the time of calling to the `commandFn` |
|
||||
| `context` | string[] or string | (optional) Overrides the `defaultContext`. Let's us know if command is currently "available" to be run. |
|
||||
|
||||
## Command Behavior
|
||||
|
||||
|
||||
|
||||
**If there are multiple valid commands for the application's active contexts**
|
||||
|
||||
- What happens: all commands are run
|
||||
- When to use: A `clearData` command that cleans up state for multiple
|
||||
extensions
|
||||
|
||||
**If no commands are valid for the application's active contexts**
|
||||
|
||||
- What happens: a warning is printed to the console
|
||||
- When to use: a `hotkey` (like "invert") that doesn't make sense for the
|
||||
current viewport (PDF or HTML)
|
||||
|
||||
## `CommandsManager` Public API
|
||||
|
||||
If you would like to run a command in the consuming app or an extension, you can
|
||||
use `CommandsManager.runCommand(commandName, options = {}, contextName)`
|
||||
|
||||
|
||||
```js
|
||||
// Returns all commands for a given context
|
||||
commandsManager.getContext('string');
|
||||
|
||||
// Run a command, it will run all the `speak` commands in all contexts
|
||||
commandsManager.runCommand('speak', { command: 'hello' });
|
||||
|
||||
// Run command, from Default context
|
||||
commandsManager.runCommand('speak', { command: 'hello' }, ['DEFAULT']);
|
||||
```
|
||||
|
||||
The `ExtensionManager` handles registering commands and creating contexts, so
|
||||
most consumer's won't need these methods. If you find yourself using these, ask
|
||||
yourself "why can't I register these commands via an extension?"
|
||||
|
||||
```js
|
||||
// Used by the `ExtensionManager` to register new commands
|
||||
commandsManager.registerCommand('context', 'name', commandDefinition);
|
||||
|
||||
// Creates a new context; clears the context if it already exists
|
||||
commandsManager.createContext('string');
|
||||
```
|
||||
|
||||
### Contexts
|
||||
|
||||
It is up to the consuming application to define what contexts are possible, and
|
||||
which ones are currently active. As extensions depend heavily on these, we will
|
||||
likely publish guidance around creating contexts, and ways to override extension
|
||||
defined contexts in the near future. If you would like to discuss potential
|
||||
changes to how contexts work, please don't hesitate to create a new GitHub
|
||||
issue.
|
||||
|
||||
[Some additional information on Contexts can be found here.](./../index.md#contexts)
|
||||
@@ -1,30 +0,0 @@
|
||||
# Module: Context
|
||||
|
||||
- [Module: Context](#module-context)
|
||||
- [Overview](#overview)
|
||||
|
||||
|
||||
## Overview
|
||||
This new module type allows you to connect components via a shared context. You can create a context that two components, e.g. a viewport and a panel can use to synchronize and communicate. An extensive example of this can be seen in the longitudinal mode’s custom extensions.
|
||||
|
||||
|
||||
|
||||
```jsx
|
||||
const ExampleContext = React.createContext();
|
||||
|
||||
function ExampleContextProvider({ children }) {
|
||||
return (
|
||||
<ExampleContext.Provider value={{ example: 'value' }}>
|
||||
{children}
|
||||
</ExampleContext.Provider>
|
||||
);
|
||||
}
|
||||
|
||||
const getContextModule = () => [
|
||||
{
|
||||
name: 'ExampleContext',
|
||||
context: ExampleContext,
|
||||
provider: ExampleContextProvider,
|
||||
},
|
||||
];
|
||||
```
|
||||
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