Merge branch 'react' into react-documentation

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# Embed the viewer using a script tag
<iframe src="https://codesandbox.io/embed/lrjoo3znxm?fontsize=14" style="width:100%; height:600px; border:0; border-radius: 4px; overflow:hidden;" sandbox="allow-modals allow-forms allow-popups allow-scripts allow-same-origin"></iframe>
## Important notes:
- You must correctly specify `rootUrl` **and** the HTML `<base>` tag.
- If your application runs in a subdirectory (e.g. /viewer/), this must be specified in `routerBasename`
- Currently, the WADO Image Loader Codecs and Web Worker source code must also be server at the ROOT URL

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- Essentials
- [Getting Started](essentials/getting-started.md)
- [Configuration](essentials/configuration.md)
- [Themeing](essentials/themeing.md)
- [Troubleshooting](essentials/troubleshooting.md)
- [Architecture](architecture/index.md)
- Overview
- Deployment
- [Architecture](essentials/architecture.md)
- [Deployment](essentials/deployment.md)
---
- [Advanced](advanced/index.md)
- [Architecture](advanced/architecture.md)
- [Overview](advanced/architecture.md#overview)
@ -17,23 +18,34 @@
- [Extensions](advanced/architecture.md#misc-extensions)
- [Diagram](advanced/architecture.md#diagram)
- [Common Questions](advanced/architecture.md#common-questions)
- [Data](advanced/data.md)
- [Hierarchy](advanced/data.md#hierarchy)
- [Display Sets](advanced/data.md#display-sets)
- [Measurements & Annotations](advanced/data.md#measurements-and-annotations)
- [Extensions](advanced/extensions.md)
- [Overview](advanced/extensions.md#overview)
- [Modules](advanced/extensions.md#modules)
- [Registering](advanced/extensions.md#registering-extensions)
- [OHIF Maintained](advanced/extensions.md#ohif-maintained-extensions)
- [Custom Tools](advanced/custom-tools.md)
- Connecting to Image Archives
- [DICOM Web](connecting-to-image-archives/dicomweb.md)
---
----
- I Want To
- [Embed the viewer using a script tag](I-want-to/script-tag.md)
- [Deployment](deployment/index.md)
- [Embedded](deployment/index.md#embedded-viewer)
- [Stand-alone](deployment/index.md#stand-alone-viewer)
- [Data]()
- Recipes
- [Embedding the Viewer](deployment/recipes/embedded-viewer.md))
- [PWA: Static]()
- [PWA: Docker]()
- [PWA: Nginx + Orthanc]()
- [PWA: Nginx + dcm4chee]()
- [PWA: Nginx + DICOMCloud]()
- [PWA: User Access Control]()
---
----
- FAQ
- [General](faq/general.md)
----
- [Contributing](contributing.md)
- [FAQ](frequently-asked-questions.md)
- [Help](help.md)

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# Data
## Hierarchy
Studies, Series, Instances, Frames
## Display Sets
## Measurements and Annotation

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# Connecting to Image Archives
# DICOM Web
[DICOMWeb](https://en.wikipedia.org/wiki/DICOMweb) refers to RESTful DICOM Services and is 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.

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# Contributing
### I would like to contribute code - how do I do this?
## I would like to contribute code - how do I do this?
Fork the repository, make your change and submit a pull request.
### Any guidance on submitting changes?
## 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:
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 posting on the forum if you are not sure.
- Code quality is acceptable. We don't have coding standards defined, but make sure it passes ESLint and looks like the rest of the code in the repository.
- Quality of design is acceptable. This is a bit subjective so you should consider posting on the forum for specific guidance.
- 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.
- Functionality is appropriate for the repository. Consider posting on the forum
if you are not sure.
- Code quality is acceptable. We don't have coding standards defined, but make
sure it passes ESLint and looks like the rest of the code in the repository.
- Quality of design is acceptable. This is a bit subjective so you should
consider posting on the forum for specific guidance.
- 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.
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
## Testing contribution pull requests
OHIF uses [netlify](netlify.com) so that pull requests are autogenerated and available for testing.
OHIF uses [netlify](netlify.com) so that pull requests are autogenerated and
available for testing.
For example, [this url](https://deploy-preview-237--ohif.netlify.com/viewer/?url=https://s3.eu-central-1.amazonaws.com/ohif-viewer/sampleDICOM.json) allows you to test [pull request 237, the request that created this FAQ entry,](https://github.com/OHIF/Viewers/pull/237) using data pulled from Amazon S3.
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.
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.
```
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:
If you have made a documentation change, a link like this will let you preview
the gitbook generated by the pull request:
```
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
<!-- prettier-ignore-end -->

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# Data Hierarchy
## Studies, Series, Instances, Frames
## Display Sets

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# Image Viewport
### Main Viewport Component
The [imageViewerViewport](https://github.com/OHIF/Viewers/tree/master/Packages/ohif-viewerbase/client/components/viewer/imageViewerViewport) component

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# Measurements and Annotations

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<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>

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# Deployment
There are a few possible approaches for deploying the application:
-

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# Deployment
The OHIF Viewer can be embedded in other web applications via it's [packaged
script source][ohif-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 customizing, optimizing, 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
The quickest and easiest way to get the OHIF Viewer up and running is to embed
it into an existing web application. It allows us to forego a "build step", and
add a powerful medical imaging viewer to an existing web page using only a few
include tags.
- Read more about it here: [Embedded Viewer](./recipes/embedded-viewer.md)
- And check out our
[live demo on CodeSandbox](https://codesandbox.io/s/lrjoo3znxm)
{% include "./_embedded-viewer-diagram.md" %}
### 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](/advanced/extensions.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
_blocking:_ Generate files from `npm script` that we can host. IE. production
ready build output
- AWS S3 + Cloudfront
- GCP + Cloudflare
- Azure
- Netlify (can use private repo)
- Github pages
Note: Include SSL instructions.
...
#### Docker
- Why Docker?
- Ship your environment
- "It works on my machine"
_Ship Archive w/ Client:_ todo
...
## 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
...
### What if I don't have an imaging archive?
...
#### Making sure your archive is accessible
- CORS
- Proxy (dangers)
- Note: PACS not meant to be directly accesible from Web
#### Securing your data
- Reach out to experts
- Recipes
### What if my archive doesn't support DICOM Web?
- Mapping layer
- GraphQL?
<!--
Links
-->
<!-- prettier-ignore-start -->
[ohif-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
<!-- prettier-ignore-end -->

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# Embedded Viewer
The quickest and easiest way to get the OHIF Viewer up and running is to embed
it into an existing web application. It allows us to forego a "build step", and
add a powerful medical imaging viewer to an existing web page using only a few
include tags. Here's how it works:
{% include "./../_embedded-viewer-diagram.md" %}
1. Create a new web page or template that includes the following external
dependencies:
<ul>
<li>
<a href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css">
<code>bootstrap@3.3.7</code>
</a>
</li>
<li>
<a href="https://fonts.googleapis.com/css?family=Sanchez">
<code>Google Font @ Sanchez</code>
</a>
</li>
<li>
<a href="https://use.fontawesome.com/releases/v5.7.2/css/all.css">
<code>fontawesome@5.7.2</code>
</a>
</li>
<li>
<a href="https://unpkg.com/react@16/umd/react.production.min.js">
<code>react@16.8.6</code>
</a>
</li>
<li>
<a href="https://unpkg.com/react-dom@16/umd/react-dom.production.min.js">
<code>react-dom@16.8.6</code>
</a>
</li>
<li>
<a href="https://unpkg.com/ohif-viewer/dist/index.umd.js">
<code>ohif-viewer@latest</code>
</a>
</li>
</ul>
<ol start="2">
<li>the HTML <code>base</code> tag</li>
<li>The <a href="">WADO Image Loader Codecs and Web Worker source code</a>
should be accessible from your server's root</li>
<li>Create a JS Object to hold the OHIF Viewer's configuration. Here are some
example values that would allow the viewer to hit our public PACS:</li>
</ol>
```js
var props = {
// Directory your application runs in (e.g. /viewer/)
routerBasename: '/',
rootUrl: 'https://lrjoo3znxm.codesandbox.io',
servers: {
dicomWeb: [
{
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,
imageRendering: 'wadors',
thumbnailRendering: 'wadors',
requestOptions: {
requestFromBrowser: true,
},
},
],
},
}
```
<ol start="5"><li>
Render the viewer in the web page's target <code>div</code>
</li></ol>
```js
// Made available by the `ohif-viewer` script included in step 1
var Viewer = window.OHIFStandaloneViewer.App
var app = React.createElement(Viewer, props, null)
ReactDOM.render(app, document.getElementById('ohif-viewer-target'))
```
#### Tips & Tricks
> I'm having trouble getting this to work. Where can I go for help?
First, check out this fully functional
[CodeSandbox](https://codesandbox.io/s/lrjoo3znxm) example. If you're still
having trouble, feel free to search or GitHub issues. Can't find anything
related your problem? Create a new one.
> When I include bootstrap, other styles on my page no longer work correctly.
> What can I do?
When we include `bootsrap` (and the other dependencies), they are added
globally. This has the potential of causing conflicts with other scripts and
styles on the page. To prevent this, `embed` the viewer in a new/empty web page.
Have that working? Good. Now `embed` that new page using an
[`<iframe>` element](https://developer.mozilla.org/en-US/docs/Web/HTML/Element/iframe).
This should produce the expected result while also protecting your page from any
globally defined styles/scripts.

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# Security

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# Deployment

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# Themeing

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# Frequently Asked Questions - General
### How do I file a bug?
We accept and triage bug reports through Github primarily.
1. [Create a Github account](https://github.com/join)
2. Search the current [Issue List](https://github.com/OHIF/Viewers/issues) to ensure you are not creating a duplicate issue.
If your issue already exists, post a comment to show us that this issue also affects you.
3. If no prior issue exists, [Create a New Issue](https://github.com/OHIF/Viewers/issues/new) on the repository.
Some tips for filing a new issue:
* **Make sure your issue is reproducible**: If we try to reproduce your issue given your provided steps and we cannot reproduce it, we will not be able to fix it. *Nobody wants to spend time guessing how to reproduce your issue!* Before filing, please reproduce your issue more than once and clearly describe the steps taken.
* **If you are reporting a user interface issue, provide screenshots**: A picture is worth a thousand words. If your issue concerns the UI, screenshots will help us identify the issue dramatically faster since it can be extremely challenging to describe UI bugs with text. *You should still clearly describe the steps that you took to produce the issue*.
* **Include platform & environment**: Your operating system, web browser, and web browser version are highly relevant for many bugs. Please provide these with all bug reports.
* **Include expected and actual result**: Tell us what you expected to happen, and what actually happened. If you don't do this, we might not consider it a bug.
### How can I request a new feature?
At the moment we are in the process of defining our roadmap and will do our best to communicate this to the community. If your requested feature is on the roadmap, then it will most likely be built at some point. If it is not, you are welcome to build it yourself and [contribute it](../contributing.md). If you have resources and would like to fund the development of a feature, please [contact us](http://www.ohif.org).
### Who should I contact about Academic Collaborations?
[Gordon J. Harris](http://www.dfhcc.harvard.edu/insider/member-detail/member/gordon-j-harris-phd/) at Massachusetts General Hospital is the primary contact for any academic collaborators. We are always happy to hear about new groups interested in using the OHIF framework, and may be able to provide development support if the proposed collaboration has an impact on cancer research.
### Do you offer commercial support?
The Open Health Imaging Foundation does not offer commercial support, however, some community members do offer consulting services. The following contacts may be useful:
* Rob Lewis ([Radical Imaging](http://radicalimaging.com/))
**Please file a Pull Request if you wish to add your name or organization to this list.**
### I emailed my question to you directly and you did not respond. Why not?
Emailing developers directly is not a shortcut to faster support. Please file your issues and questions on Github so that everyone can benefit from the discussion and solutions.
### Do your Viewers have [510(k) Clearance](https://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/HowtoMarketYourDevice/PremarketSubmissions/PremarketNotification510k/) from the U.S. F.D.A or [CE Marking](https://ec.europa.eu/growth/single-market/ce-marking_en) from the European Commission?
**NO.** The OHIF Viewer, Lesion Tracker, and Standalone Viewer, **NOT** F.D.A. cleared or CE Marked. It is the users responsibility to ensure compliance with applicable rules and regulations. The [License](https://github.com/OHIF/Viewers/blob/master/LICENSE) for the OHIF Framework does not prevent your company or group from seeking F.D.A. clearance for a product built using the framework.
If you have gone this route (or are going there), please let us know because we would be interested to hear about your experience.
### Are your Viewers [HIPAA](https://en.wikipedia.org/wiki/Health_Insurance_Portability_and_Accountability_Act) Compliant?
**NO.** The OHIF Viewer, Lesion Tracker, and Standalone Viewer **DO NOT** fulfill all of the criteria to become HIPAA Compliant. It is the users responsibility to ensure compliance with applicable rules and regulations.

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# Frequently Asked Questions - Technical

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# Frequently Asked Questions
## How do I file a bug?
We accept and triage bug reports through Github primarily.
1. [Create a Github account](https://github.com/join)
2. Search the current [Issue List](https://github.com/OHIF/Viewers/issues) to
ensure you are not creating a duplicate issue.
If your issue already exists, post a comment to show us that this issue also
affects you.
3. If no prior issue exists,
[Create a New Issue](https://github.com/OHIF/Viewers/issues/new) on the
repository.
Some tips for filing a new issue:
- **Make sure your issue is reproducible**: If we try to reproduce your issue
given your provided steps and we cannot reproduce it, we will not be able to
fix it. _Nobody wants to spend time guessing how to reproduce your issue!_
Before filing, please reproduce your issue more than once and clearly describe
the steps taken.
- **If you are reporting a user interface issue, provide screenshots**: A
picture is worth a thousand words. If your issue concerns the UI, screenshots
will help us identify the issue dramatically faster since it can be extremely
challenging to describe UI bugs with text. _You should still clearly describe
the steps that you took to produce the issue_.
- **Include platform & environment**: Your operating system, web browser, and
web browser version are highly relevant for many bugs. Please provide these
with all bug reports.
- **Include expected and actual result**: Tell us what you expected to happen,
and what actually happened. If you don't do this, we might not consider it a
bug.
### How can I request a new feature?
At the moment we are in the process of defining our roadmap and will do our best
to communicate this to the community. If your requested feature is on the
roadmap, then it will most likely be built at some point. If it is not, you are
welcome to build it yourself and [contribute it](../contributing.md). If you
have resources and would like to fund the development of a feature, please
[contact us](http://www.ohif.org).
### Who should I contact about Academic Collaborations?
[Gordon J. Harris](http://www.dfhcc.harvard.edu/insider/member-detail/member/gordon-j-harris-phd/)
at Massachusetts General Hospital is the primary contact for any academic
collaborators. We are always happy to hear about new groups interested in using
the OHIF framework, and may be able to provide development support if the
proposed collaboration has an impact on cancer research.
### Do you offer commercial support?
The Open Health Imaging Foundation does not offer commercial support, however,
some community members do offer consulting services. The following contacts may
be useful:
- Rob Lewis ([Radical Imaging](http://radicalimaging.com/))
**Please file a Pull Request if you wish to add your name or organization to
this list.**
### I emailed my question to you directly and you did not respond. Why not?
Emailing developers directly is not a shortcut to faster support. Please file
your issues and questions on Github so that everyone can benefit from the
discussion and solutions.
### Do your Viewers have [510(k) Clearance][501k-clearance] from the U.S. F.D.A or [CE Marking][ce-marking] from the European Commission?
**NO.** The OHIF Viewer, Lesion Tracker, and Standalone Viewer, **NOT** F.D.A.
cleared or CE Marked. It is the users responsibility to ensure compliance with
applicable rules and regulations. The
[License](https://github.com/OHIF/Viewers/blob/master/LICENSE) for the OHIF
Framework does not prevent your company or group from seeking F.D.A. clearance
for a product built using the framework.
If you have gone this route (or are going there), please let us know because we
would be interested to hear about your experience.
### Are your Viewers [HIPAA][hipaa] Compliant?
**NO.** The OHIF Viewer, Lesion Tracker, and Standalone Viewer **DO NOT**
fulfill all of the criteria to become HIPAA Compliant. It is the users
responsibility to ensure compliance with applicable rules and regulations.
<!--
Links
-->
<!-- prettier-ignore-start -->
[501k-clearance]: https://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/HowtoMarketYourDevice/PremarketSubmissions/PremarketNotification510k/
[ce-marking]: https://ec.europa.eu/growth/single-market/ce-marking_en
[hipaa]: https://en.wikipedia.org/wiki/Health_Insurance_Portability_and_Accountability_Act
<!-- prettier-ignore-end -->

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# Help
We all need a little help sometimes. Don't let a few roadblocks stand in the way
of you building something awesome.
## Free
If you're a developer looking to contribute code, documentation, or discussion;
we are more than happy to help provide clarification and answer questions via
[GitHub issues][gh-issues] or our [community forum][google-group]. Regular
contributors may also be invited to join our Slack Group to streamline
discussion.
For bug reports and feature requests (including incomplete or confusing
documentation), [GitHub issues][gh-issues] continue to be your best avenue of
communication.
Complex issues specific to your organization/situation are still okay to post,
but they're less likely to receive a response. Unfortunately, we have limited
resources and must be judicious with how we allocate them. If you find yourself
in this situation and in need of assistance, it may be in your best interest to
persue paid support.
## Paid / Commercial
The Open Health Imaging Foundation does not offer commercial support, however,
some community members do offer consulting services:
- Rob Lewis ([Radical Imaging](http://radicalimaging.com/))
**Please file a Pull Request if you wish to add your name or organization to
this list.**
<!--
Links
-->
[gh-issues]: https://github.com/OHIF/Viewers/issues/
[google-group]: https://groups.google.com/forum/#!forum/cornerstone-platform

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# Hanging Protocols

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# Layout Management

14
img/designs/cloud.svg Normal file
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 16 16">
<defs id="defs3051">
<style type="text/css" id="current-color-scheme">
.ColorScheme-Text {
color:#4d4d4d;
}
</style>
</defs>
<path
style="fill:currentColor;fill-opacity:1;stroke:none"
d="M 7.5 2 A 4.5 4.5 0 0 0 3 6.5 A 4.5 4.5 0 0 0 3.0527344 7.15625 A 3 3 0 0 0 1 10 A 3 3 0 0 0 4 13 L 11.5 13 A 3.5 3.5 0 0 0 15 9.5 A 3.5 3.5 0 0 0 11.970703 6.0351562 A 4.5 4.5 0 0 0 7.5 2 z M 7.5 3 A 3.5 3.5 0 0 1 11 6.5 A 3.5 3.5 0 0 1 10.949219 7.0644531 A 2.5 2.5 0 0 1 11.5 7 A 2.5 2.5 0 0 1 14 9.5 A 2.5 2.5 0 0 1 11.5 12 L 4 12 A 2 2 0 0 1 2 10 A 2 2 0 0 1 4 8 A 2 2 0 0 1 4.3574219 8.0332031 A 3.5 3.5 0 0 1 4 6.5 A 3.5 3.5 0 0 1 7.5 3 z "
id="path4139"
class="ColorScheme-Text"/>
</svg>

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<?xml version="1.0" encoding="utf-8"?>
<svg version="1.1" id="npm" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
viewBox="0 0 780 250" style="enable-background:new 0 0 780 250;" xml:space="preserve">
<style type="text/css">
.st0{fill:#C12127;}
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