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feat: cornerstone3D stack and volume viewports (#2787)

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* 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>
This commit is contained in:
Erik ZieglerAlirezaBill Wallace
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platform/docs/versioned_docs/version-3.0/configuration/dataSources/_category_.json
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{
"label": "Data Sources",
"position": 2
}
platform/docs/versioned_docs/version-3.0/configuration/dataSources/dicom-json.md
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---
sidebar_position: 3
sidebar_label: DICOM JSON
---
# DICOM JSON
You can launch the OHIF Viewer with a JSON file which points to a DICOMWeb
server as well as a list of study and series instance UIDs along with metadata.
An example would look like
`https://v3-demo.ohif.org/viewer/dicomjson?url=https://ohif-dicom-json-example.s3.amazonaws.com/LIDC-IDRI-0001.json`
As you can see the url to the location of the JSON file is passed in the query
after the `dicomjson` string, which is
`https://ohif-dicom-json-example.s3.amazonaws.com/LIDC-IDRI-0001.json` (this
json file has been generated by OHIF team and stored in an amazon s3 bucket for
the purpose of the guide).
## DICOM JSON sample
Here we are using the LIDC-IDRI-0001 case which is a sample of the LIDC-IDRI
dataset. Let's have a look at the JSON file:
### Metadata
JSON file stores the metadata for the study level, series level and instance
level. A JSON launch file should follow the same structure as the one below.
Note that at the instance level metadata we are storing both the `metadata` and
also the `url` for the dicom file on the dicom server. In this case we are
referring to
`dicomweb:https://ohif-dicom-json-example.s3.amazonaws.com/LIDC-IDRI-0001/01-01-2000-30178/3000566.000000-03192/1-001.dcm`
which is stored in another directory in our s3. (You can actually try
downloading the dicom file by opening the url in your browser).
```json
{
"studies": [
// first study metadata
{
"StudyInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178",
"StudyDate": "20000101",
"StudyTime": "",
"PatientName": "",
"PatientID": "LIDC-IDRI-0001",
"AccessionNumber": "",
"PatientAge": "",
"PatientSex": "",
"series": [
// first series metadata
{
"SeriesInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192",
"SeriesNumber": 3000566,
"Modality": "CT",
"SliceThickness": 2.5,
"instances": [
// first instance metadata
{
"metadata": {
"Columns": 512,
"Rows": 512,
"InstanceNumber": 1,
"SOPClassUID": "1.2.840.10008.5.1.4.1.1.2",
"PhotometricInterpretation": "MONOCHROME2",
"BitsAllocated": 16,
"BitsStored": 16,
"PixelRepresentation": 1,
"SamplesPerPixel": 1,
"PixelSpacing": [0.703125, 0.703125],
"HighBit": 15,
"ImageOrientationPatient": [1, 0, 0, 0, 1, 0],
"ImagePositionPatient": [-166, -171.699997, -10],
"FrameOfReferenceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.229925374658226729607867499499",
"ImageType": ["ORIGINAL", "PRIMARY", "AXIAL"],
"Modality": "CT",
"SOPInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.262721256650280657946440242654",
"SeriesInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192",
"StudyInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178",
"WindowCenter": -600,
"WindowWidth": 1600,
"SeriesDate": "20000101"
},
"url": "dicomweb:https://ohif-dicom-json-example.s3.amazonaws.com/LIDC-IDRI-0001/01-01-2000-30178/3000566.000000-03192/1-001.dcm"
},
// second instance metadata
{
"metadata": {
"Columns": 512,
"Rows": 512,
"InstanceNumber": 2,
"SOPClassUID": "1.2.840.10008.5.1.4.1.1.2",
"PhotometricInterpretation": "MONOCHROME2",
"BitsAllocated": 16,
"BitsStored": 16,
"PixelRepresentation": 1,
"SamplesPerPixel": 1,
"PixelSpacing": [0.703125, 0.703125],
"HighBit": 15,
"ImageOrientationPatient": [1, 0, 0, 0, 1, 0],
"ImagePositionPatient": [-166, -171.699997, -12.5],
"FrameOfReferenceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.229925374658226729607867499499",
"ImageType": ["ORIGINAL", "PRIMARY", "AXIAL"],
"Modality": "CT",
"SOPInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.512235483218154065970649917292",
"SeriesInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192",
"StudyInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178",
"WindowCenter": -600,
"WindowWidth": 1600,
"SeriesDate": "20000101"
},
"url": "dicomweb:https://ohif-dicom-json-example.s3.amazonaws.com/LIDC-IDRI-0001/01-01-2000-30178/3000566.000000-03192/1-002.dcm"
}
// ..... other instances metadata
]
}
// ... other series metadata
],
"NumInstances": 133,
"Modalities": "CT"
}
// second study metadata
]
}
```
![](../../assets/img/dicom-json.png)
### Local Demo
You can run OHIF with a JSON data source against you local datasets (given that
their JSON metadata is extracted).
First you need to put the JSON file and the folder containing the dicom files
inside your `public` folder. Since files are served from your local server the
`url` for the JSON file will be `http://localhost:3000/LIDC-IDRI-0001.json` and
the dicom files will be
`dicomweb:http://localhost:3000/LIDC-IDRI-0001/01-01-2000-30178/3000566.000000-03192/1-001.dcm`.
After `yarn install` and running `yarn dev` and opening the browser at
`http://localhost:3000/viewer/dicomjson?url=http://localhost:3000/LIDC-IDRI-0001.json`
will display the viewer.
Download JSON file from
[here](https://www.dropbox.com/sh/zvkv6mrhpdze67x/AADLGK46WuforD2LopP99gFXa?dl=0)
Sample DICOM files can be downloaded from
[TCIA](https://wiki.cancerimagingarchive.net/display/Public/LIDC-IDRI) or
directly from
[here](https://www.dropbox.com/sh/zvkv6mrhpdze67x/AADLGK46WuforD2LopP99gFXa?dl=0)
Your public folder should look like this:
![](../../assets/img/dicom-json-public.png)
platform/docs/versioned_docs/version-3.0/configuration/dataSources/dicom-web.md
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---
sidebar_position: 1
sidebar_label: DICOMweb
---
# DICOMweb
## Set up a local DICOM server
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: '@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](../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&amp;autopause=0&amp;player_id=0&amp;app_id=58479" frameBorder="0" allow="autoplay; fullscreen; picture-in-picture" allowFullScreen style= {{ position:"absolute",top:0,left:0,width:"100%",height:"100%"}} title="measurement-report"></iframe>
</div>
[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
platform/docs/versioned_docs/version-3.0/configuration/dataSources/static-files.md
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---
sidebar_position: 2
sidebar_label: Static Files
---
# Static Files
There is a binary DICOM to static file generator, which provides easily served
binary files. The files are all compressed in order to reduce space
significantly, and are pre-computed for the files required for OHIF, so that the
performance of serving the files is just the read from disk/write to http stream
time, without any extra processing time.
The project for the static wado files is located here: [static-wado]:
https://github.com/wayfarer3130/static-wado
It can be compiled with Java and Gradle, and then run against a set of dicom, in
the example located in /dicom/study1 outputting to /dicomweb, and then a server
run against that data, like this:
```
git clone https://github.com/wayfarer3130/static-wado.git
cd static-wado
./gradlew installDist
StaticWado/build/install/StaticWado/bin/StaticWado -d /dicomweb /dicom/study1
cd /dicomweb
npx http-server -p 5000 --cors -g
```
There is then a dev environment in the platform/viewer directory which can be
run against those files, like this:
```
cd platform/viewer
yarn dev:static
```
Additional studies can be added to the dicomweb by re-running the StaticWado
command. It will create a single studies.gz index file (JSON DICOM file,
compressed) containing an index of all studies created. There is then a small
extension to OHIF which performs client side indexing.
The StaticWado command also knows how to deploy a client and dicomweb directory
to Amazon s3, which can then server files up directly. There is another build
setup build:aws in the viewer package.json to create such a deployment.