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Update docs for docs.ohif.org

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swederik committed Jan 30, 2018
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# Add a Tool to the Viewer
To add a tool to the Viewer there are a few steps:
1. Add the tool itself to the repository.
If you're using something from Cornerstone Tools you can skip this step.
Some examples of custom tools can be found in the lesion tracker: https://github.com/OHIF/Viewers/tree/master/Packages/ohif-lesiontracker/client/compatibility
2. Add the toolbar button itself to the array of tools in the Toolbar:
https://github.com/OHIF/Viewers/blob/574a6d02b090b8b2f020430c5919f8377b8316c6/OHIFViewer/client/components/toolbarSection/toolbarSection.js
3. **A:** Add it to the toolManager (if it's a tool, such as length / angle):
https://github.com/OHIF/Viewers/blob/574a6d02b090b8b2f020430c5919f8377b8316c6/Packages/lesiontracker/client/tools.js#L2
** --- OR --- **
**B:** Add it to the functionList if it's a command (e.g. toggle CINE play, or Invert the current viewport):
https://github.com/OHIF/Viewers/blob/574a6d02b090b8b2f020430c5919f8377b8316c6/OHIFViewer/client/components/viewer/viewer.js#L12
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{% include "./SUMMARY.md" %}
# Introduction
The [Open Health Imaging Foundation](https://www.ohif.org) is developing an open source framework for constructing web-based medical imaging applications. The application framework is built using modern HTML / CSS / JavaScript and uses [Cornerstone](https://cornerstonejs.org/) at its core to display and manipulate medical images. It is built with Meteor, a Node.js-based full-stack JavaScript platform.
This documentation concerns the OHIF framework itself and its three example applications: the OHIF Viewer, Lesion Tracker, and the Standalone Viewer.
## The **OHIF Viewer**: A general purpose DICOM Viewer ([demo](http://viewer.ohif.org/))
![OHIF Viewer Screenshot](../assets/img/viewer.png)
The Open Health Imaging Foundation intends to provide a simple general purpose DICOM Viewer which can be easily extended for specific uses. The primary purpose of the OHIF Viewer is to serve as a testing ground for the underlying packages and the [Cornerstone](https://cornerstonejs.org/) family of libraries.
## **Lesion Tracker**: An oncology-focused imaging application ([demo](http://lesiontracker.ohif.org/))
![Lesion Tracker Screenshot](../assets/img/lesionTracker.png)
The Lesion Tracker is designed to facilitate quantitative assessments of tumour burden over time. It is similar in scope to the ePAD Imaging Platform (https://epad.stanford.edu/), developed at Stanford Medicine.
## Study List & DICOM Connectivity
![Study List Screenshot](../assets/img/worklist.png)
The solution provides a study list and other resources for connecting to PACS and other Image Archives through standard communication approaches (DICOM Web, DICOM Messages).
## Standalone Viewer ([demo](ohif-viewer.s3-website.eu-central-1.amazonaws.com/?url=https://raw.githubusercontent.com/OHIF/Viewers/master/StandaloneViewer/etc/sampleDICOM.json))
The Standalone Viewer offers only the client-side portions of the OHIF Viewer with the Study List pages removed. This single-page viewer can be hosted as a static site (e.g. on Amazon S3, Azure Blob Storage, or Github Pages), and easily integrated with existing back-end DICOM storage systems. Alternative [Cornerstone](https://cornerstonejs.org/) Image Loaders can be included to allow your viewer to support non-DICOM objects (e.g. PNG, JPEG).
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# OHIF Viewers
- [Installation](installation.md)
- Essentials
- [Installation](essentials/installation.md)
- [Getting Started](essentials/getting-started.md)
- [Architecture](essentials/architecture.md)
- [Configuration](essentials/configuration.md)
- [Troubleshooting](essentials/troubleshooting.md)
- Connecting to Image Archives
- [What are my options?](connecting-to-image-archives/options.md)
- [DICOM Web](connecting-to-image-archives/dicomweb.md)
- [DICOM Message Service Element](connecting-to-image-archives/dimse.md)
- Examples
- [dcm4chee w/ Docker](connecting-to-image-archives/dcm4chee-with-docker.md)
- [Orthanc w/ Docker](connecting-to-image-archives/orthanc-with-docker.md)
- [Osirix](connecting-to-image-archives/osirix.md)
- Data Organization
- [Data Hierarchy](data/data-hierarchy.md)
- [Image Viewport](data/image-viewport.md)
- Viewport Layout
- [Layout Management](layout/layout-management.md)
- [Hanging Protocols](layout/hanging-protocols.md)
- Packages
- [Measurements Package (ohif-measurements)](packages/measurements.md)
- Deployment
- [Building for Production](deployment/building-for-production.md)
- [Security](deployment/security.md)
- I Want To...
- [Add a Tool to the Viewer](I-want-to/add-a-tool-to-the-viewer.md)
----
- Example Applications
- [OHIF Viewer](example-applications/ohif-viewer.md)
- [Lesion Tracker](example-applications/lesion-tracker.md)
- [Standalone Viewer](example-applications/standalone-viewer.md)
----
- Standalone Viewer Integration
- [Usage](standalone-viewer/usage.md)
----
- Lesion Tracker
- [User Manual](lesion-tracker/user-manual.md)
- [Installation on Windows](lesion-tracker/installation-on-windows.md)
- [Manage Studies in Orthanc](lesion-tracker/manage-studies-in-orthanc.md)
- [User Accounts](lesion-tracker/user-accounts.md)
- [Study and Timepoint Management](lesion-tracker/study-and-timepoint-management.md)
- [Using the Viewer](lesion-tracker/using-the-viewer.md)
- [User Preferences](lesion-tracker/user-preferences.md)
- [Server Management](lesion-tracker/server-management.md)
- [Audit Trail](lesion-tracker/audit-trail.md)
----
- FAQ
- [General](faq/general.md)
- [Technical](faq/technical.md)
----
- [Contributing](contributing.md)
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# DCM4CHEE with Docker
1. Install Docker (https://www.docker.com/)
2. Follow the DCM4CHEE Guidelines for Running on Docker.
The easiest path is to use Docker-Compose which will start and stop multiple containers for you. There are excellent instructions provided by the DCM4CHEE team on the 'light archive' repository:
https://github.com/dcm4che/dcm4chee-arc-light/wiki/Running-on-Docker#use-docker-compose
* Create docker-compose.yml and docker-compose.env files
* Start the containers:
```` bash
docker-compose start
````
**Note:** If you are running this on Mac OSX you will probably need to change the default docker-compose.yml file slightly. Specifically, the paths that refer to /var/local/ will likely need to be changed to /opt/
3. Run the OHIF Viewer or Lesion Tracker using the dcm4cheeDIMSE.json configuration file
````bash
cd OHIFViewer
PACKAGE_DIRS="../Packages" meteor --settings ../config/dcm4cheeDIMSE.json
````
## Web Service URLs from DCM4CHEE:
Original source here: https://github.com/dcm4che/dcm4chee-arc-light/wiki/Running-on-Docker#web-service-urls
> - Archive UI: <http://localhost:8080/dcm4chee-arc/ui> - if secured, login with
> Username | Password | Role
> --- | --- | ---
> `user` | `user` | `user`
> `admin` | `admin` | `user` + `admin`
> - Keycloak Administration Console: <http://localhost:8080/auth>, login with Username: `admin`, Password: `admin`.
> - Wildfly Administration Console: <http://localhost:9990>, login with Username: `admin`, Password: `admin`.
> - Kibana UI: <http://localhost:5601>
> - DICOM QIDO-RS Base URL: <http://localhost:8080/dcm4chee-arc/aets/DCM4CHEE/rs>
> - DICOM STOW-RS Base URL: <http://localhost:8080/dcm4chee-arc/aets/DCM4CHEE/rs>
> - DICOM WADO-RS Base URL: <http://localhost:8080/dcm4chee-arc/aets/DCM4CHEE/rs>
> - DICOM WADO-URI: <http://localhost:8080/dcm4chee-arc/aets/DCM4CHEE/wado>
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# 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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# DICOM Message Service Element
DIMSE Stands for [DICOM Message Service Element](http://dicom.nema.org/medical/dicom/current/output/chtml/part07/chapter_7.html) and is the standard method through which DICOM archives communicate. We support this messaging standard for the retrieval of study, series, and instance metadata because it is widely support. For certain PACS systems, it also (currently) provides faster query results than DICOMWeb.
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# Connecting to Image Archives
We support DIMSE and DICOMWeb. Which one to use is up to you and depends on your PACS system. DICOMWeb requires no setup on the PACS-side whatsoever, whereas DIMSE may require you to add the 'OHIFDCM' aeTitle to the known DICOM Modalities of your Archive. This is the case for Orthanc, for example (See https://github.com/OHIF/Viewers/wiki/Orthanc-with-DIMSE).
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# Orthanc with Docker
Depending on whether or not you want uploaded studies to persist in Orthanc after Docker has been closed, there are two different methods for starting the Docker image:
## Temporary data storage
This command will start an instance of the jodogne/orthanc-plugins Docker image. *All data will be removed when the instance is stopped!*
````
docker run --rm -p 4242:4242 -p 8042:8042 jodogne/orthanc-plugins
````
## Persistent data storage
In order to allow your data to persist after the instance is stopped, you first need to create an image and attached data volume with Docker. The steps are as follows:
1. Create a persistent data volume for Orthanc to use
````
docker create --name sampledata -v /sampledata jodogne/orthanc-plugins
````
**Note: On Windows, you need to use an absolute path for the data volume, like so:**
````
docker create --name sampledata -v '//C/Users/erik/sampledata' jodogne/orthanc-plugins
````
2. Run Orthanc from Docker with the data volume attached
````
docker run --volumes-from sampledata -p 4242:4242 -p 8042:8042 jodogne/orthanc-plugins
````
3. Upload your data and it will be persisted
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# Example: Osirix
...
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# Contributing
...
### 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?
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.
We will provide feedback on your pull requests as soon as possible. Following the tips above will help ensure your changes are reviewed.
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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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# Tool Management
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# Building for Production
**This tutorial considers the current folder as `OHIFViewer/`**.
### Dependencies
First, you need to have installed:
- [Node.js](https://nodejs.org/) and [NPM](https://www.npmjs.com/)
- [Meteor](https://www.meteor.com/)
- [MongoDB](https://www.mongodb.com/)
**MongoDB** is actually **not required** if you have a **remote MongoDB**. If your database is **local** then you need to have it running.
### Check your packages
Inside of the viewer folder make sure NPM packages are updated for production:
```bash
npm install --production
```
### Building
There are two ways of building OHIF Viewer for a specific DICOM server: **Automatically** or **Manually**.
For both, we use the `meteor build` (check it's [docs](https://guide.meteor.com/deployment.html#custom-deployment)) app and **Orthanc Dicom Web Server**.
For `meteor build` it's necessary to inform an output folder `myOutputFolder`.
**Remember to change `myOutputFolder` to your folder location.**
OHIF Viewer will be built using **Orthanc DICOM Web server** configuration file `../config/orthancDICOMWeb.json` to set `METEOR_SETTINGS` environment var.
*To run with another server, just point to the corresponding `.json` located in `config` folder or create your own.*
#### Build automatically
After this step, go directly to [Prepare to run production build](#prepare-to-run-production-build).
##### Non-windows users
```bash
METEOR_PACKAGE_DIRS="../Packages" METEOR_SETTINGS=$(cat ../config/orthancDICOMWeb.json) meteor build --directory myOutputFolder
```
##### Windows users
Since there is no `cat` command in Windows `cmd`, use Windows `PowerShell` (at least version 3.0) instead.
In `PowerShell`, open a new shell as an `admin`:
```bash
Start-Process powershell -Verb runAs
```
Then:
**Remember to change `OHIFViewerFolderLocation` to OHIFViewer's folder location.**
```bash
cd OHIFViewerFolderLocation
$settings = Get-Content ..\config\orthancDICOMWeb.json -Raw
$settings = $settings -replace "`n","" -replace "`r","" -replace " ",""
[Environment]::SetEnvironmentVariable("METEOR_SETTINGS", $settings, "Machine")
SET METEOR_PACKAGE_DIRS="../Packages"
meteor build --directory myOutputFolder
```
#### Build manually
OHIF Viewer will be built normally, but with no DICOM Server information, which needs to be added when running the build. This is described in [Manually adding DICOM Server to the Viewer](#manually-adding-dicom-server-to-the-viewer).
##### Non-windows users
```bash
METEOR_PACKAGE_DIRS="../Packages" meteor build --directory myOutputFolder
```
##### Windows users in `cmd`
```bash
SET METEOR_PACKAGE_DIRS="../Packages"
meteor build --directory myOutputFolder
```
### Prepare to run production build
If everything went ok, `meteor build` created a `bundle` folder inside `myOutputFolder`.
**Remember to change `myOutputFolder` to your folder location.**
Go to that folder:
```bash
cd myOutputFolder/bundle
```
Now install the **NPM dependencies**:
```bash
cd programs/server
npm install
```
### To run production build
Go back to the `bundle` folder:
```bash
cd ../..
```
or (**Remember to change `myOutputFolder` to your folder location.**):
```bash
cd myOutputFolder/bundle
```
3 environment variables are set before running Node.js:
- `MONGO_URL`: is the url to MongoDB. If it's **local**, you need to have it running
- `ROOT_URL`: the hostname where you can access your Viewer in the browser
- `PORT`: the port the Viewer will run
This way, the Viewer can be accessed in `http://localhost:3000`, with MongoDB running locally using 27017 port (it's default).
##### Non-windows users
```bash
MONGO_URL=mongodb://localhost:27017/myapp ROOT_URL=http://localhost PORT=3000 node main.js
```
##### Windows users in `cmd`
```bash
SET MONGO_URL=mongodb://localhost:27017/myapp
SET ROOT_URL=http://localhost
SET PORT=3000
node main.js
```
### Manually adding DICOM Server to the Viewer
If DICOM Server was configured automatically during the building process, skip this step.
Access the viewer `http://localhost:3000` and toggle the **Options** menu, located at top right corner. Select **Server Information** option.
In **Server Information** dialog click on **Add a new server** button and fill the fields accordingly to the DICOM Server to be added.
In case of doubts about any field in this dialog, use `config/orthancDICOMWeb.json` as reference.
After filling the form, click on the **Save** button and the new server will be listed. Make sure to activate it by clicking on the left most button (a checkbox button) in the **Actions** column.
Refresh the page and Viewer will be connected to the DICOM Server.
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# Security
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