ohif-viewer/platform/docs/versioned_docs/version-3.0/deployment/index.md
Erik Ziegler bd1c38c00c
feat: cornerstone3D stack and volume viewports (#2787)
* 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>
2022-07-27 12:39:04 -04:00

13 KiB

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1 Overview

Deployment

The OHIF Viewer can be embedded in other web applications via it's packaged script source, or served up as a stand-alone PWA (progressive web application) 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

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 and modes 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
  • 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, 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.

Part 2 - Host Your App

There are a lot of benefits to hosting 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

Easy

Advanced

Data

The OHIF Viewer is able to connect to any data source that implements the DICOM Web Standard. 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.

What if I don't have an imaging archive?

We provide some guidance on configuring a local image archive in our Data Source Essentials guide. Hosting an archive remotely is a little trickier. You can check out some of our advanced 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 its 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

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.

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:

e.g. 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

Sample JSON format:

{
  "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": [11.6, -92.5, 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

Implementation Notes:

  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.

CORS Issues (Cross-Origin Resource Sharing)

If you host a JSON API or Images on a different domain from 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:

Let's 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

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.