* feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: cs3d tools and toolGroups (#20) * add more tools to work with cs3d mode * fix hotkeys * add stack manager usage for stach viewports * add image scrollbar * wip viewport overlay * fix toAnnotation schema for tools * fix the unnecessary size change that triggered resize * hanging protocol improvement to allow unmatched errors * study description matching for hanging protocol * fix the displaysetOptions to work * fix handle the active tool when a new viewport is added * fix separate toolGroups for mode * apply review comments * apply review comments * yarn lock * feat: overlay component (#21) * fix default displayset options * add viewport overlay * apply review comments * feat: loading and orientation indicators (#22) * add loading indicator * add orientation marker initial work * apply review comments * fix: orientation markers (#23) * finished the orientation markers * fix various broken cypress tests * apply review comments * update yarn lock * feat: re-working measurement tracking mode with cornerstone3d (#2805) * feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: Add Measurement tracking mode with cs3D (#2789) * feat: first render for cornerstone3d tracked viewport * make tool active work * wip for SR extension * renamed dicom sr to cornerstone dicom sr * remove cornerstone from dicom pdf and video * move dicom sr logic to sr extension * feat: Add hydration for the length tool * fix SR display tool for length using cs3d * fix default config * fix: various bugs with sr viewport and tracking * fix promptying to continue tracking for when SR is created * feat: add keep trackign of unique identifiers * fix hydration for same imageIds * feat: Add SR toolGroup creation on modeEnter * feat: remove the need for separate mapper for SR hydration * add SR display for ellipse * handle hydration of elliptical ROI tool * remove cornerstone extension * add arrow mapping * feat: Add ArrowAnnotate SR display and hydration * apply review comments * apply review comments * move viewport labels to the viewportData * apply review comments * fix: integration cypress tests with cornerstone3D and add CINE tool (#2795) * fix: integration cypress tests with cornerstone3D * revert to addOrUpdate as it makes more sense * fix local drag and drop * fix tests * move dicomLoaderService to cornerstone extension * fix various import bugs * fix bug for local PT series * fix various unit tests * bump cs3d versions * add angle and magnify tool * bump dependencies to avoid broken peerDeps * feat: add initial work for capture using cs3d * feat: show annotations on the image capture * feat: add svg layer export * feat: Add CINE Tool * feat: remove unnecessary viewport rendering for cine state changes Co-authored-by: Erik Ziegler <erik.sweed@gmail.com> * docs: modify and improve documentation (#2800) * cleanup docs versionings * feat: Add all version explanations * version docs for 3.0 * wip for changing docs * wip for updated docs * add utility module documentation * fix demo with nohoisting of history * add slides and video to resources * apply review comments * fix: drag and drop SR into SR viewport (#2803) * update yarn lock Co-authored-by: Erik <erik.sweed@gmail.com> * update pathnames to match v3-stable * update the e2e pathname * fix: various bugs with regard to tracking workflow (#2811) * fix: various issues with measurement panel * fix: update default tool style for annotations * fix: annotatoin label getting removed * feat: Add backward compatibility for SR hydration with legacy cornerstone * fix: cursors and ellipse ROI max style * fix: ArrowAnnotate SRDisplay * apply review comments * bump package versions * fix: bugin rehydration of SR * fix: e2e tests * fix active viewport thickness and arrowTool ui * add readme for measurement tracking * use uploaded image for readme * add back images * try to fix e2e test * fix: window level presets hotkeys * Update README.md * update yarn lock * feat: volume api and TMTV mode (#2817) * feat: volumeAPI and TMTV mode * feat: use cs3d cache service to obtain viewportData * wip for volume api * wip: fusion viewport * feat: add blend mode option * wip for image scrollbar * fix drag and drop thumbnail * wip for image scrollbar for voluems * fix: element mismatch bug for scroll * feat: Add image scrollbar to volumes * feat: add syncGroups to volume api * feat: add tmtv mode initial setup * feat: add initial image options for the stack viewports * feat: Add custom load strategy for volume viewports via HP * apply review comments fix: Jump presets cs3d (#2812) * feat: Add JumpPreset to OHIF for Cornerstone3D * fix: accessing viewport service from servicesManager feat: volume API and TMTV mode (#2814) * fix: do not display overlays on mip viewports * feat: add optional disableCommands for toggle buttons * fix: toggleCrossharis * feat: config the crosshairs * feat: add PetSUV Panel for changing metadata * feat: initial work for the rectangleROIThreshold panel * wip: measurement service * roi threshold working * feat: Add displayText to segmentations * feat: add remove segmentation * feat: add csv export * feat: add RT export for annotations in tmtv mode * fix: fusion to use pt in tmtv mode and measuremet mappings * fix: various bugs * apply review comments * apply review comments * feat: add fusion color maps * add readme to tmtv mode * Update README.md * fix: try to fix build * fix unit tests * Update README.md * feat: add about to the panel * fix: changing strategy in roi panel * apply review comments * update package versions * wip for stackPrefetch * fix: cornerstone3d hydration and renaming (#2818) * update readme * renamed cornerstone extension * wip for renaming cornerstone3D variables * wip for renaming cornerstone3D variables * wip for fixing bugs for SR viewport * fix: jumpToMeasurement and initial label after hydration * fix: fileName capitalization * feat: use the new prefetch stack in the cs3d (#2820) * feat: use the new prefetch stack in the cs3d * use viewport scroll api for stack viewport * fix cine stop when scrollbar changes * feat: use new prefetch events * fix loading state to not show repeatedly * fix: various bugs for tmtv mode thresholding and new icons (#2823) * feat: make tmtv mode available in worklist * feat: add new icons for tmtv mode * feat: add fusion color icon * fix: parallel scale calculation * fix: bump Cornerstone to get large image support working * fix: Fix issues with CPU viewport flipping, including config files * fix: bump cornerstone to fix magnify tool * fix: Bump Cornerstone version to fix resetCamera issue in StackViewport * ci: Add _headers file to enable CORS headers for Netlify Drag/Drop deploys * fix: WADO-URI was not working. PET Metadata was coming from the wrong place. Fixed some minor React errors * feat(OHIF):Allow modes and extensions to be added after commpile time. (#2838) Also works with the compile time add that the existing cli uses, so that both build types work. Eric and I agreed this doesn't change existing functionality, but is almost entirely build issues/fixes. * bump: dependency versions to fix hydration bugs (#2848) * bump: dcmjs version to fix hydration bugs * try to fix tests * bump dependency versions Co-authored-by: Alireza <ar.sedghi@gmail.com> Co-authored-by: Bill Wallace <wayfarer3130@gmail.com>
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DICOMweb
Set up a local DICOM server
ATTENTION! Already have a remote or local server? Skip to the configuration section 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.
- Choose and install an Image Archive
- Upload data to your archive (e.g. with DCMTK's [storescu][storescu] or your archive's web interface)
- Keep the server running
For our purposes, we will be using Orthanc, but you can see a list of
other Open Source options below.
Requirements
Not sure if you have docker installed already? Try running docker --version
in command prompt or terminal
If you are using
Docker Toolboxyou 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 | W/ Docker |
| Orthanc | W/ Docker |
| DICOMcloud (DICOM Web only) | Installation |
| OsiriX (Mac OSX only) | Desktop Client |
| 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:
# Runs orthanc so long as window remains open
yarn run orthanc:up
Upload your first Study:
- Navigate to
Orthanc's web interface at
http://localhost:8042/app/explorer.htmlin a web browser. - In the top right corner, click "Upload"
- Click "Select files to upload..." and select one or more DICOM files
- 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.
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:
# 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 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:
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-envsets three environment variables- PROXY_TARGET:
/dicom-web - PROXY_DOMAIN:
http://localhost:8042 - APP_CONFIG:
config/docker_nginx-orthanc.js
- PROXY_TARGET:
webpack-dev-serverruns using the.webpack/webpack.pwa.jsconfiguration 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:
window.config = {
routerBasename: '/',
extensions: [],
modes: [],
showStudyList: true,
dataSources: [
{
friendlyName: 'dcmjs DICOMWeb Server',
namespace: '@ohif/extension-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.
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
DCM4chee installation is out of scope for these tutorials and can be found here
An overview of steps for running OHIF Viewer using a local DCM4CHEE is shown below: