Compare commits

...
Author SHA1 Message Date
ohif-bot 5f4c4ab5e7 chore(release): publish [skip ci]
- @ohif/extension-cornerstone@2.6.1
 - @ohif/extension-vtk@1.4.1
 - @ohif/core@2.8.1
 - @ohif/viewer@3.10.1
2020-04-23 10:04:47 +00:00
James Petts 71205618ec fix: 🐛 Multiframe fix (#1661) 2020-04-23 12:02:51 +02:00
ohif-bot 5014ba864b chore(release): publish [skip ci]
- @ohif/extension-cornerstone@2.6.0
 - @ohif/extension-dicom-p10-downloader@0.1.0
 - @ohif/extension-vtk@1.4.0
 - @ohif/core@2.8.0
 - @ohif/viewer@3.10.0
2020-04-23 02:06:44 +00:00
James Pettsanddannyrb e96205de35 feat: configuration to hook into XHR Error handling
* Error handling.

* Fix error handling, add redirect example.

* remove debugger

* docs: whitelabeling and httpErrorHandler

* bump dicomweb-client version

* bump cornerstone-wado-image-loader version

* Add more documentation around httpErrorHandler callback

* test: add errorHandler as an expected top level export

Co-authored-by: dannyrb <danny.ri.brown@gmail.com>
2020-04-22 22:01:34 -04:00
ohif-bot 273f31ad56 chore(release): publish [skip ci]
- @ohif/extension-vtk@1.3.14
 - @ohif/core@2.7.1
 - @ohif/viewer@3.9.2
2020-04-22 20:19:12 +00:00
Danny Brown 2093a00365 fix: whiteLabeling should support component creation by passing React to defined fn (#1659) 2020-04-22 16:16:53 -04:00
dependabot[bot] b1dad6b61b chore(deps): bump https-proxy-agent from 2.2.1 to 2.2.4 in /docs/latest (#1641)
Bumps [https-proxy-agent](https://github.com/TooTallNate/node-https-proxy-agent) from 2.2.1 to 2.2.4.
- [Release notes](https://github.com/TooTallNate/node-https-proxy-agent/releases)
- [Commits](https://github.com/TooTallNate/node-https-proxy-agent/compare/2.2.1...2.2.4)

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2020-04-18 22:05:44 -04:00
ohif-bot 3a587f4e4b chore(release): publish [skip ci]
- @ohif/viewer@3.9.1
2020-04-17 16:28:57 +00:00
Danny Brown d9fc7bbb0e fix: showStudyList config (#1647)
* fix: `showStudyList` config

* showStudyList should default to true if not defined
2020-04-17 12:26:09 -04:00
ohif-bot b0cfc45f83 chore(release): publish [skip ci]
- @ohif/extension-vtk@1.3.13
 - @ohif/core@2.7.0
 - @ohif/viewer@3.9.0
2020-04-17 14:16:04 +00:00
Danny Brown 450c80b9d5 feat: set the authorization header for DICOMWeb requests if provided in query string (#1646) 2020-04-17 10:14:13 -04:00
ohif-bot d3eefb50f5 chore(release): publish [skip ci]
- @ohif/extension-dicom-p10-downloader@0.0.2
 - @ohif/extension-vtk@1.3.12
 - @ohif/core@2.6.11
 - @ohif/viewer@3.8.21
2020-04-15 17:00:38 +00:00
Emanuel Fiuza de OliveiraandJames Petts 29d4955980 Feat #1130 [WIP] Adding support for downloading and zipping files (#1501)
* Feat #1130 Adding support for downloading and zipping files

@ This is a combination of 12 commits.
 - Feat #1130 Initial Commit
 - Feat #1130 Adding support for hierachical lists
 - Feat #1130 [WIP] Adding support for downloading and zipping files
 - Feat #1130 Adding support for hierarchical folder structure study, series, instances on generated zip file
 - Feat #1130 Adding unit tests and addressing code review feedbacks
 - Feat #1130 POC (adding module to support on progress handling)
 - Feat #1130 Improving logic from progress tracking utils
 - Feat #1130 Renaming module with progress tracking utils
 - Feat #1130 Beta version of Progress Tracking utils
 - Feat #1130 Adding unit tests for Progress Tracking Utils
 - Feat #1130 Documenting public methods from progress tracking utils module
 - Feat #1130 Adding support for download and zip progress reporting

* Feat #1130 Addressing code review feedback

* Feat #1130 Preventing multiple downloads from executing at once

* Feat #1130 Improving error message for concurrent downloads

* Remove downloadAndZipSeriesOnViewports

Co-authored-by: James Petts <jamesapetts@gmail.com>
2020-04-15 18:57:57 +02:00
Nisal Upendra 2412c08595 docs: Embedding in existing react App (#1626)
Added how to embed OHIF viewer in an existing React application
2020-04-10 08:28:37 -04:00
ohif-bot d769e5c296 chore(release): publish [skip ci]
- @ohif/extension-vtk@1.3.11
 - @ohif/core@2.6.10
 - @ohif/viewer@3.8.20
2020-04-09 11:08:07 +00:00
Danny Brown d21af3f133 fix: Revert "refactor: Reduce bundle size (#1575)" (#1622)
This reverts commit 81dcbe294d.
2020-04-09 07:06:41 -04:00
ohif-bot 70672ed663 chore(release): publish [skip ci]
- @ohif/extension-cornerstone@2.5.2
 - @ohif/extension-dicom-rt@0.0.2
 - @ohif/extension-dicom-segmentation@0.1.2
 - @ohif/extension-vtk@1.3.10
 - @ohif/core@2.6.9
 - @ohif/ui@1.4.3
 - @ohif/viewer@3.8.19
2020-04-09 10:25:11 +00:00
858484f250 Support of RTSTRUCT visualization (#1524)
* Filter segs and fetch correct metadata.

* Initiate seg loading logic on series load into viewport. Need to write.

* Automatic consumption of SEG functional.

* Pull in master.

* Fix issues after pulling in master.

* Clean up old segmentation handlers.

* WIP

* WIP

* Poppulate viewport with metadata.

* Show hide/segmentation in react-vtkjs-viewport.

* feat: 🎸 View segmentations in vtkjs viewport

* Filter segs and fetch correct metadata.

* Initiate seg loading logic on series load into viewport. Need to write.

* Automatic consumption of SEG functional.

* Pull in master.

* Fix issues after pulling in master.

* Clean up old segmentation handlers.

* WIP

* WIP

* Poppulate viewport with metadata.

* Show hide/segmentation in react-vtkjs-viewport.

* feat: 🎸 View segmentations in vtkjs viewport

* Rebase on master.

* format format format

* add basic extension parts

* Updated yarn lock

* Fetch derived/referenced displaysets in sidepanel

* Add buttons, expose seriesDescription, write notes for Danny.

* Add growcut tool extention. -> Move to a seperate repo.

* Change some text fields.

* expose dialog provider

* hide draggable area

* No pointer events for now; need to revisit

* Don't filter seg from the outset for now

* fiddling about

* fix path to series data

* fix logic to determine next available labelmapindex

* Ability to swtich between labelmaps

* Return a promise so we can make sure our labelmap is loaded before pulling metadata

* Better UI to toggle labelmaps

* Fix accidental untoggle of active labelmap for ui

* Remove brush tool from cornerstone extension

* Add cstools in preInit for seg extension

* Add buttons for seg magic

* Hide the measurements panel for now

* Slightly better seg/scissor icons

* Add eraser

* ability to switch segments

* seg color / switcher

* Fix vtk labelmap cache.

* sidepanel should scroll if there's overflow

* Use a fancier range slider

* Slightly prettier buttons

* Push in progress

* A bit more reactive; handle no-meta

* Update to vtk.js 11.14.0 and react-vtkjs-viewport 0.6.0

* chore: kickstart preview

* Fix conflict issues

* Refactor panel

* Isolate increment functions

* Wip segment table

* Hide selector and add scroll to segmentation

* Increase width of segment description

* Hide not used items

* Add new select for segmentations

* Align ui

* Fix default segmentation

* Fix broken import test

* Get measurements panel back and add spacing to grouped buttons

* Hide brush and selector and refresh when switching segmentations

* Add pointer events back and fix broken tests for measurement table

* Update segment list when switching humbnails

* CR Update: Minor UI adjustments

* CR Update: Set active segment

* Move components to components folder

* Add new settings ui

* Integrate configuration

* Improve styles

* Float numbers

* Improve css

* Refresh settings menu if side panel changed

* Fix settings rendering logic and remove comments

* Extract components

* Remove not used tools

* Remove non used extension

* Use style variables and remove comments

* Remove non used dep from lock

* Remove tools

* Remove segmentation from toolbar

* Add todo and brushradius from config

* Fix packagejson growcut import

* Remove webpack config already defined in parent

* Update package json description

* Change component name to british english to us

* Improve prop types

* Rename cornerstone label map event

* Scope css

* Extract and add doc to helper

* Update jsdocs for getDerivedDatasets

* Add proptypes and cr updates

* Update tablistitem proptypes

* config is readonly, rollback destructuring

* Remove event for side panel

* Add jsdocs for util

* Extract getimageid to studymetada

* Use ohif log instead of console

* Remove specific style from side panel

* Fix default props for brush radius

* Descructure configuration props from settings component to avoid invalid props

* Update proptypes to be required (settings)

* Update readme

* Remove commandsmodule

* Get configuration module inside the component

* Set selected segment

* Rename extension and use modality to filter

* Fix for failing tests (#1423)

* hello world

* Finish rebase for Igor.

* Re-fix cornerstoneTools version that got messed up in merge.

* Fix reactivity of isDisabled, write implementation for the SEG panel.

* Nuke yarn.lock to stack CST to 4.12.0

* Remove debugger statements.

* WIP consume RTSTRUCT

* Doc API and add endpoints.

* Rebase on SEG PR.

* Update DICOM Keyword variables.

* Fix metadata vars format

* Add basic RT panel along with configuration

* Wire up configuration with settings component

* Mock structure set tables

* Improve design of settings

* Integrate list of contours

* Extract panel section

* Filter by seriesuid

* Fix slow settings

* Add jump to image

* Fix expandable items

* Improvements and CR update

* CR Update: Remove google config

* CR Update: Remove erase tool test

* CR Update: Remove instance

* CR Update: Fix issue with undefined prop

* CR Update: Update yarn lock

* Hide actions of structure item

Co-authored-by: James A. Petts <jamesapetts@gmail.com>
Co-authored-by: dannyrb <danny.ri.brown@gmail.com>
Co-authored-by: igoroctaviano] <igoroctaviano@users.noreply.github.com>
Co-authored-by: Mirna Silva <mirna.silva@radicalimaging.com>
2020-04-09 12:21:43 +02:00
ohif-bot 83f9478977 chore(release): publish [skip ci]
- @ohif/i18n@0.52.8
 - @ohif/viewer@3.8.18
2020-04-07 08:33:40 +00:00
Erik Ziegler b5b851ac7c chore(i18n): Pull latest translations from Locize to obtain French translation (thanks @salimkanoun!) (#1613)
* Pull latest translations from Locize to obtain French translation

* Fix newlines
2020-04-07 10:32:20 +02:00
ohif-bot e5175bf3e6 chore(release): publish [skip ci]
- @ohif/extension-vtk@1.3.9
 - @ohif/core@2.6.8
 - @ohif/ui@1.4.2
 - @ohif/viewer@3.8.17
2020-04-06 08:45:46 +00:00
8c8f69accb Add option for setting maximum concurrent metadata requests (@ckedar), show series in panel before their metadata is retrieved (#1576)
* Show series in Study Browser before their metadata is retrieved

* Switch to decreasing for loop after code review (thanks @ckedar!)

* feat: Limit concurrent series metadata requests (#1581)

* Limit concurrent series metadata requests

* Switch to decreasing for loop after code review (thanks @ckedar!)

* Set default maxConcurrentMetadataRequests to unlimited and add explaination of setting in config

Co-authored-by: kedar.netelixir <kedar.choudhary@netelixir.com>
Co-authored-by: Erik Ziegler <erik.sweed@gmail.com>

* Address comments from code review

* Comment out misbehaving test

Co-authored-by: Kedar <ckedar@gmail.com>
Co-authored-by: kedar.netelixir <kedar.choudhary@netelixir.com>
2020-04-06 10:43:35 +02:00
ohif-bot f9037f831d chore(release): publish [skip ci]
- @ohif/extension-vtk@1.3.8
 - @ohif/core@2.6.7
 - @ohif/viewer@3.8.16
2020-04-02 17:58:41 +00:00
James PettsandDanny Brown 9e0bd52c6a fix: 🐛 Fix multiframe images (#1595)
Co-authored-by: Danny Brown <danny.ri.brown@gmail.com>
2020-04-02 13:56:53 -04:00
ohif-bot f1b017dc08 chore(release): publish [skip ci]
- @ohif/extension-vtk@1.3.7
 - @ohif/core@2.6.6
 - @ohif/viewer@3.8.15
2020-04-02 17:32:56 +00:00
81dcbe294d refactor: Reduce bundle size (#1575)
* async load cornerstoneWADOImageLoader chunk

* Lazy initializing of CornerstoneWADIImageLoader - delayed till Viewer creation

* Async loading of react-vtkjs-viewport

* withCornerstone HOC to wrap routes requiring CornerstoneWADOImageLoader initiazation

* removed dead code in comments

* initWeWorkers is no more. Remove al its references.

Co-authored-by: kedar.netelixir <kedar.choudhary@netelixir.com>
Co-authored-by: Danny Brown <danny.ri.brown@gmail.com>
2020-04-02 13:31:14 -04:00
Pierre-Antoine Ganaye e09a3d2e93 docs: Remove dead links in docs and improve SOP Class Handler docs (#1593)
* fix docs dead links

* add examples to SOP handler docs
2020-04-02 09:24:49 -04:00
ohif-bot 978a86bf12 chore(release): publish [skip ci]
- @ohif/extension-cornerstone@2.5.1
 - @ohif/extension-dicom-html@1.1.2
 - @ohif/extension-dicom-microscopy@0.50.9
 - @ohif/extension-dicom-pdf@1.0.3
 - @ohif/viewer@3.8.14
2020-04-02 07:01:58 +00:00
0139a32213 chore: Switch asyncComponent to React Lazy/Suspense (Closes #1577) (#1582)
* Attempted Lazy load for OHIFCornerStoneViewport

* Converted dicom-(html, microscopy, pdf) & cornerstone extensions to React Lazy components

* Fixed incorrect import from OHIFDicomPDFSopClassHandler to ConnectedOHIFDicomPDFViewer

Co-authored-by: Ankit Mohan <ankit.mohan@live.in>
Co-authored-by: Erik Ziegler <erik.sweed@gmail.com>
2020-04-02 08:59:17 +02:00
ohif-bot d57158b59d chore(release): publish [skip ci]
- @ohif/extension-dicom-segmentation@0.1.1
 - @ohif/extension-vtk@1.3.6
 - @ohif/core@2.6.5
 - @ohif/viewer@3.8.13
2020-04-01 03:55:23 +00:00
Igor Octaviano 4a7ce1c093 fix: segmentation not loading (#1566)
* Fix bug

* Refactor the state of the component RTPanel
2020-03-31 23:54:02 -04:00
168 changed files with 7962 additions and 3341 deletions

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+1 -1
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@@ -48,7 +48,7 @@ Check out these helpful links:
-->
<!-- prettier-ignore-start -->
[ohif-org]: https://www.ohif.org
[ohif-org]: http://www.ohif.org
[dicom-web]: https://en.wikipedia.org/wiki/DICOMweb
[gh-issues]: https://github.com/OHIF/Viewers/issues
<!-- prettier-ignore-end -->
+1
View File
@@ -5,6 +5,7 @@
- [Getting Started](development/getting-started.md)
- [Contributing](development/contributing.md)
- [Continuous Integration](development/continous-integration.md)
- [Testing](development/testing.md)
- [Configuring](configuring/index.md)
- [Data Source](configuring/data-source.md)
+5 -10
View File
@@ -13,7 +13,6 @@ architected, and the role each of it's dependent libraries plays.
- [Overview](#overview)
- [Business Logic](#business-logic)
- [Component Library](#react-component-library)
- [Internationalization](#internationalization-i18n)
- [Extensions & Configuration](#extensions--configuration)
- [Common Questions](#common-questions)
@@ -74,10 +73,10 @@ This diagram is a conceptual illustration of how the Viewer is architected.
The [`@ohif/core`][core-github] project offers pre-packaged solutions for
features common to Web-based medical imaging viewers. For example:
- [Hotkeys](#)
- Hotkeys
- DICOM Web requests
- Hanging Protocols
- [Managing a study's measurements](../services/default/measurements.md)
- Managing a study's measurements
- Managing a study's DICOM metadata
- [A flexible pattern for extensions](../extensions/index.md)
- And many others
@@ -99,10 +98,6 @@ application.
[Check out our component library!](https://react.ohif.org/)
## Internationalization (i18n)
...
## Extensions & Configuration
While OHIF maintains several high value and commonly requested features in its
@@ -120,7 +115,7 @@ the viewer. Some common use cases include:
We expose common integration points via [extensions](../extensions/index.md) to
make this possible. The viewer and many of our own extensions also offer
[configuration][configuration]. For a list of extensions maintained by OHIF,
[check out this helpful table](../extensions/index.mdl#maintained-extensions).
[check out this helpful table](../extensions/index.md#maintained-extensions).
If you find yourself thinking "I wish the Viewer could do X", and you can't
accomplish it with an extension today, create a GitHub issue! We're actively
@@ -147,12 +142,12 @@ you would need to recreate.
-->
<!-- prettier-ignore-start -->
[monorepo]: #
[monorepo]: https://github.com/OHIF/Viewers/issues/768
[viewers-project]: https://github.com/OHIF/Viewers
[viewer-npm]: https://www.npmjs.com/package/@ohif/viewer
[pwa]: https://developers.google.com/web/progressive-web-apps/
[configuration]: ../configuring/index.md
[extensions]: ../extensions/index.md
[core-github]: https://github.com/OHIF/viewers/platform/core
[ui-github]: https://github.com/OHIF/Viewers/platform/ui
[ui-github]: https://github.com/OHIF/Viewers/tree/master/platform/ui
<!-- prettier-ignore-end -->
+7 -7
View File
@@ -123,7 +123,7 @@ There are two important steps to making sure this setup works:
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](deployment/recipes/nginx--image-archive.md).
[Nginx + Image Archive Deployment Recipe](./recipes/nginx--image-archive.md).
#### What if my archive doesn't support DicomWeb?
@@ -166,7 +166,7 @@ window.config = {
```
You can find an example of this setup in our
[User Account Control Deployment Recipe](deployment/recipes/user-account-control.md).
[User Account Control Deployment Recipe](./recipes/user-account-control.md).
#### Choosing a Flow for the Viewer
@@ -183,12 +183,12 @@ many possible configurations, so please don't feel limited to these setups.
Please feel free to suggest or contribute your own recipes.
- Script Include
- [Embedding the Viewer](deployment/recipes/embedded-viewer.md)
- [Embedding the Viewer](./recipes/embedded-viewer.md)
- Stand-Alone
- [Build for Production](deployment/recipes/build-for-production.md)
- [Static](deployment/recipes/static-assets.md)
- [Nginx + Image Archive](deployment/recipes/nginx--image-archive.md)
- [User Account Control](deployment/recipes/user-account-control.md)
- [Build for Production](./recipes/build-for-production.md)
- [Static](./recipes/static-assets.md)
- [Nginx + Image Archive](./recipes/nginx--image-archive.md)
- [User Account Control](./recipes/user-account-control.md)
<!--
Links
@@ -50,7 +50,7 @@ window.config = {
```
To learn more about how you can configure the OHIF Viewer, check out our
[Configuration Guide](./index.md).
[Configuration Guide](../../configuring/index.md).
<ol start="3"><li>
Render the viewer in the web page's target <code>div</code>
@@ -126,12 +126,39 @@ globally defined styles/scripts.
> We're trying to embed the OHIF Viewer into an existing React App, but seeing
> react-dom and react conflicts. What can we do?
If you are installing OHIF viewer inside another react app, you may use `installViewer` as follows:
```
import { installViewer } from '@ohif/viewer'
const ohifViewerConfig = window.config // or set it here
const containerId = 'ohif'
const componentRenderedOrUpdatedCallback = function() {
console.log('OHIF Viewer rendered/updated');
};
componentDidMount() {
installViewer(
ohifViewerConfig,
containerId,
componentRenderedOrUpdatedCallback
);
}
render () {
...
//you can render in any element you wish
<AnyTag id={containerId}/>
}
```
`installViewer` is a convenience method that pulls in some dependencies that may
not be compatible with existing `react` apps. `@ohif/viewer` also exports `App`
which is a react component that takes the `configuration` outlined above as
props. You can use it as a reusable component, and to avoid `react` version
conflict issues.
<!--
LINKS
-->
@@ -49,9 +49,7 @@ We can solve this one of two ways:
1. Have our Image Archive located at the same domain as our Web App
2. Add appropriate `Access-Control-Allow-*` HTTP headers
This solution uses the first approach, but you can see an example of the second
in the `docker-compose` bundled with this project for local development:
[HERE](https://github.com/OHIF/Viewers/blob/master/platform/viewer/.recipes/Nginx-Orthanc/docker-compose.yml)
**This solution uses the first approach.**
You can read more about CORS in this Medium article: [Understanding
CORS][understanding-cors]
@@ -121,7 +119,10 @@ likely want to update:
#### OHIF Viewer
The OHIF Viewer's configuration is imported from a static `.js` file. The configuration we use is set to a specific file when we build the viewer, and determined by the env variable: `APP_CONFIG`. You can see where we set its value in the `dockerfile` for this solution:
The OHIF Viewer's configuration is imported from a static `.js` file. The
configuration we use is set to a specific file when we build the viewer, and
determined by the env variable: `APP_CONFIG`. You can see where we set its value
in the `dockerfile` for this solution:
`ENV APP_CONFIG=config/docker_openresty-orthanc.js`
@@ -138,11 +139,11 @@ Viewer's configuration, you can run:
All other files are found in: `/docker/OpenResty-Orthanc/`
| Service | Configuration | Docs |
| ----------------- | ---------------------------------------------- | ------------------------------------------- |
| OHIF Viewer | [dockerfile][dockerfile] / [config.js][config] | You're reading them now! |
| OpenResty (Nginx) | [`/nginx.conf`][config-nginx] | [lua-resty-openidc][lua-resty-openidc-docs] |
| Orthanc | [`/orthanc.json`][config-orthanc] | [Here][orthanc-docs] |
| Service | Configuration | Docs |
| ----------------- | --------------------------------- | ------------------------------------------- |
| OHIF Viewer | [dockerfile][dockerfile] | You're reading them now! |
| OpenResty (Nginx) | [`/nginx.conf`][config-nginx] | [lua-resty-openidc][lua-resty-openidc-docs] |
| Orthanc | [`/orthanc.json`][config-orthanc] | [Here][orthanc-docs] |
## Next Steps
@@ -218,10 +219,11 @@ following resources helpful:
- [OpenResty Guide](http://www.staticshin.com/programming/definitely-an-open-resty-guide/)
- [Lua Ngx API](https://openresty-reference.readthedocs.io/en/latest/Lua_Nginx_API/)
For a different take on this setup, check out the repository one of our
community members put together:
For a different take on this setup, check out the repositories our community
members put together:
- [mjstealey/ohif-orthanc-dimse-docker](https://github.com/mjstealey/ohif-orthanc-dimse-docker)
- [trypag/ohif-orthanc-postgres-docker](https://github.com/trypag/ohif-orthanc-postgres-docker)
<!--
Links
@@ -234,8 +236,7 @@ community members put together:
[orthanc-docs]: http://book.orthanc-server.com/users/configuration.html#configuration
[lua-resty-openidc-docs]: https://github.com/zmartzone/lua-resty-openidc
<!-- SRC -->
[config]: #
[dockerfile]: #
[config-nginx]: #
[config-orthanc]: #
[dockerfile]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/.recipes/OpenResty-Orthanc/dockerfile
[config-nginx]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/.recipes/OpenResty-Orthanc/config/nginx.conf
[config-orthanc]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/.recipes/OpenResty-Orthanc/config/orthanc.json
<!-- prettier-ignore-end -->
@@ -122,7 +122,10 @@ likely want to update:
#### OHIF Viewer
The OHIF Viewer's configuration is imported from a static `.js` file. The configuration we use is set to a specific file when we build the viewer, and determined by the env variable: `APP_CONFIG`. You can see where we set its value in the `dockerfile` for this solution:
The OHIF Viewer's configuration is imported from a static `.js` file. The
configuration we use is set to a specific file when we build the viewer, and
determined by the env variable: `APP_CONFIG`. You can see where we set its value
in the `dockerfile` for this solution:
`ENV APP_CONFIG=config/docker_openresty-orthanc-keycloak.js`
@@ -146,8 +149,8 @@ All other files are found in: `/docker/OpenResty-Orthanc-Keycloak/`
| Orthanc | [`/orthanc.json`][config-orthanc] | [Here][orthanc-docs] |
| Keycloak | [`/ohif-keycloak-realm.json`][config-keycloak]\* | |
- \* These are the seed values for Keycloak. They can be manually updated at
`http://127.0.0.1/auth/admin`
\* These are the seed values for Keycloak. They can be manually updated at
`http://127.0.0.1/auth/admin`
#### Keycloak Themeing
@@ -261,12 +264,12 @@ for OAuth:
- [Diagrams of OpenID Connect Flows](https://medium.com/@darutk/diagrams-of-all-the-openid-connect-flows-6968e3990660)
- [KeyCloak: OpenID Connect Flows](https://www.keycloak.org/docs/latest/securing_apps/index.html#authorization-code)
- [Good description on SSO Protocols](https://www.keycloak.org/docs/2.5/server_admin/topics/sso-protocols/oidc.html)
For a different take on this setup, check out the repository one of our
community members put together:
For a different take on this setup, check out the repositories our community
members put together:
- [mjstealey/ohif-orthanc-dimse-docker](https://github.com/mjstealey/ohif-orthanc-dimse-docker)
- [trypag/ohif-orthanc-postgres-docker](https://github.com/trypag/ohif-orthanc-postgres-docker)
<!--
Links
@@ -278,8 +281,8 @@ community members put together:
[lua-resty-openidc-docs]: https://github.com/zmartzone/lua-resty-openidc
<!-- SRC -->
[config]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/src/config.js
[dockerfile]: https://github.com/OHIF/Viewers/tree/master/platform/viewer/.recipes
[config-nginx]: https://github.com/OHIF/Viewers/tree/master/platform/viewer/.recipes
[config-orthanc]: https://github.com/OHIF/Viewers/tree/master/platform/viewer/.recipes
[config-keycloak]: https://github.com/OHIF/Viewers/tree/master/platform/viewer/.recipes
[dockerfile]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/.recipes/OpenResty-Orthanc-Keycloak/dockerfile
[config-nginx]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/.recipes/OpenResty-Orthanc-Keycloak/config/nginx.conf
[config-orthanc]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/.recipes/OpenResty-Orthanc-Keycloak/config/orthanc.json
[config-keycloak]: https://github.com/OHIF/Viewers/blob/master/platform/viewer/.recipes/OpenResty-Orthanc-Keycloak/config/ohif-keycloak-realm.json
<!-- prettier-ignore-end -->
+2 -2
View File
@@ -114,8 +114,8 @@ the tips above will help ensure your changes are reviewed.
## Testing contribution pull requests
OHIF uses [netlify](netlify.com) so that pull requests are autogenerated and
available for testing.
OHIF uses [netlify](https://www.netlify.com/) so that pull requests are
autogenerated and available for testing.
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.
+1 -1
View File
@@ -132,7 +132,7 @@ feature `X` or scenario `Y`? Open an issue and let's discuss.
[flow-org]: https://flow.org/
<!-- Talks -->
[assert-js-talks]: https://www.youtube.com/playlist?list=PLZ66c9_z3umNSrKSb5cmpxdXZcIPNvKGw
[kent-talk]: https://www.youtube.com/watch?list=PLV5CVI1eNcJgNqzNwcs4UKrlJdhfDjshf
[kent-talk]: https://www.youtube.com/watch?v=Fha2bVoC8SE
[gleb-talk]: https://www.youtube.com/watch?v=5FnalKRjpZk
[kent-blog]: https://kentcdodds.com/blog/unit-vs-integration-vs-e2e-tests
<!-- Images -->
@@ -31,6 +31,7 @@
</td>
<td>Viewport, Toolbar</td>
</tr>
<!-- dicom-html -->
<tr>
<td>
<a href="https://www.npmjs.com/package/@ohif/extension-dicom-html">DICOM HTML</a>
@@ -40,6 +41,7 @@
</td>
<td>Viewport, SopClassHandler</td>
</tr>
<!-- dicom-pdf -->
<tr>
<td>
<a href="https://www.npmjs.com/package/@ohif/extension-dicom-pdf">DICOM PDF</a>
@@ -49,6 +51,7 @@
</td>
<td>Viewport, SopClassHandler</td>
</tr>
<!-- dicom-microscopy -->
<tr>
<td>
<a href="https://www.npmjs.com/package/@ohif/extension-dicom-microscopy">DICOM Microscopy</a>
@@ -58,5 +61,15 @@
</td>
<td>Viewport, SopClassHandler</td>
</tr>
<!-- dicom-segmentation -->
<tr>
<td>
<a href="https://www.npmjs.com/package/@ohif/extension-dicom-segmentation">DICOM Segmentation</a>
</td>
<td>
Renders segmentation images for a <a href="https://github.com/OHIF/Viewers/blob/master/extensions/dicom-segmentation/src/OHIFDicomSegSopClassHandler.js#L5-L7">specific SopClassUID</a>.
</td>
<td>Panel, Toolbar</td>
</tr>
</tbody>
</table>
+11 -9
View File
@@ -74,7 +74,8 @@ export default {
### Registering an Extension
There are two different ways to register and configure extensions: At
[runtime](#runtime-extensions) and at [build time](#bundled-extensions).
[runtime](#registering-at-runtime) and at
[build time](#registering-at-build-time).
You can leverage one or both strategies. Which one(s) you choose depend on your
application's requirements. Each [module](#modules) defined by the extension
@@ -82,9 +83,9 @@ becomes available to the core application via the `ExtensionManager`.
#### Registering at Runtime
The `@ohif/viewer` uses a [configuration file](#) at startup. The schema for
that file includes an `Extensions` key that supports an array of extensions to
register.
The `@ohif/viewer` uses a [configuration file](../viewer/configuration.md) at
startup. The schema for that file includes an `Extensions` key that supports an
array of extensions to register.
```js
// prettier-ignore
@@ -193,8 +194,8 @@ today, create a GitHub issue!
The `ExtensionManager` is a class made available to us via the `@ohif/core`
project (platform/core). Our application instantiates a single instance of it,
and provides a `ServicesManager` and `CommandsManager` along with the application's
configuration through the appConfig key (optional).
and provides a `ServicesManager` and `CommandsManager` along with the
application's configuration through the appConfig key (optional).
```js
const commandsManager = new CommandsManager();
@@ -202,7 +203,7 @@ const servicesManager = new ServicesManager();
const extensionManager = new ExtensionManager({
commandsManager,
servicesManager,
appConfig
appConfig,
});
```
@@ -212,8 +213,9 @@ The `ExtensionManager` only has a few public members:
- `registerExtensions` - Registers an array of extensions
- `modules` - An object containing registered extensions by `MODULE_TYPE`
During registration, lifecycle hooks and modules have access to the extension's config,
the application's config and `ExtensionManager`'s `ServicesManager` and `CommandsManager` instances.
During registration, lifecycle hooks and modules have access to the extension's
config, the application's config and `ExtensionManager`'s `ServicesManager` and
`CommandsManager` instances.
Our `@ohif/viewer` uses the `modules` member to access registered extensions at
appropriate places in our application.
@@ -1,9 +1,9 @@
# Module: SOP Class Handler
An extension can register a SOP Class Handler Module by defining a
`getSopClassHandlerModule` method. The SOP Class Handler is a bit different from
the other modules, as it doesn't provide a `1:1` schema for UI or provide it's
own components. It instead defines:
An extension can register a [SOP Class][sop-class-link] Handler Module by
defining a `getSopClassHandlerModule` method. The [SOP Class][sop-class-link]
Handler is a bit different from the other modules, as it doesn't provide a `1:1`
schema for UI or provide it's own components. It instead defines:
- `sopClassUIDs`: an array of string SOP Class UIDs that the
`getDisplaySetFromSeries` method should be applied to.
@@ -76,6 +76,13 @@ getSopClassHandlerModule({ servicesManager, commandsManager }) {
};
```
### More examples :
- [Dicom-HTML SOP][dicom-html-sop]
- [Dicom-PDF SOP][dicom-pdf-sop]
- [Dicom-Microscopy SOP][dicom-micro-sop]
- [Dicom-Segmentation SOP][dicom-seg-sop]
## `@ohif/viewer` usage
We use the `sopClassHandlerModule`s in three different places:
@@ -88,3 +95,11 @@ Each time, it is used to map study and series data to `displaySets`. It does
this by working alongside the `StudyMetadataManager` in `@ohif/core`. That
manager has the method `createDisplaySets` that takes an array of
`sopClassHandlerModules`.
<!-- prettier-ignore-start -->
[sop-class-link]: http://dicom.nema.org/dicom/2013/output/chtml/part04/sect_B.5.html
[dicom-html-sop]: https://github.com/OHIF/Viewers/blob/master/extensions/dicom-html/src/OHIFDicomHtmlSopClassHandler.js#L4-L12
[dicom-pdf-sop]: https://github.com/OHIF/Viewers/blob/master/extensions/dicom-pdf/src/OHIFDicomPDFSopClassHandler.js#L4-L6
[dicom-micro-sop]: https://github.com/OHIF/Viewers/blob/master/extensions/dicom-microscopy/src/DicomMicroscopySopClassHandler.js#L5-L7
[dicom-seg-sop]: https://github.com/OHIF/Viewers/blob/master/extensions/dicom-segmentation/src/OHIFDicomSegSopClassHandler.js#L5-L7
<!-- prettier-ignore-end -->
+2 -2
View File
@@ -75,7 +75,7 @@ items to our ["Active Development" GitHub Project Board][gh-board]. Items on
this project board are either in active development by Core Team members, or
queued up for development as in-progress items are completed.
> :pencil: Want to contribute but not sure where to start? Check out [Up for
> 🖋 Want to contribute but not sure where to start? Check out [Up for
> grabs][label-grabs] issues and our [Contributing
> documentation][contributing-docs]
@@ -156,5 +156,5 @@ addressed and a Stable version is released.
[ohif-prod]: https://viewer.ohif.org
[gh-board]: https://github.com/OHIF/Viewers/projects/4
[label-grabs]: https://github.com/OHIF/Viewers/issues?q=is%3Aissue+is%3Aopen+label%3A%22Up+For+Grabs+%3Araising_hand_woman%3A%22
[contributing-docs]: https://docs.ohif.org/contributing/
[contributing-docs]: ./development/contributing.md
<!-- prettier-ignore-end -->
+1 -1
View File
@@ -62,7 +62,7 @@ able to fail or be removed. Related patterns that may reduce coupling include:
-->
<!-- prettier-ignore-start -->
[commands]: #/
[commands]: ../extensions/modules/commands.md
[core-services]: https://github.com/OHIF/Viewers/tree/master/platform/core/src/services
[services-manager]: https://github.com/OHIF/Viewers/blob/master/platform/core/src/services/ServicesManager.js
[cross-cutting-concerns]: https://en.wikipedia.org/wiki/Cross-cutting_concern
+2 -2
View File
@@ -2,8 +2,8 @@
- [Overview](#overview)
- [Example](#example)
- [Tips & Tricks](#/)
- [Maintained Services](#/)
- [Tips & Tricks](#tips--tricks)
- [Maintained Services](#maintained-services)
## Overview
+53 -1
View File
@@ -11,7 +11,59 @@ are:
```js
window.config = {
routerBasename: '/',
whiteLabelling: {},
/**
* "White Labeling" is used to change the branding, look, and feel of the OHIF
* Viewer. These settings, and the color variables that are used by our components,
* are the easiest way to rebrand the application.
*
* More extensive changes are made possible through swapping out the UI library,
* Viewer project, or extensions.
*/
whiteLabeling: {
/* Optional: Should return a React component to be rendered in the "Logo" section of the application's Top Navigation bar */
createLogoComponentFn: function(React) {
return React.createElement('a', {
target: '_self',
rel: 'noopener noreferrer',
className: 'header-brand',
href: '/',
style: {
display: 'block',
textIndent: '-9999px',
background: 'url(/svg-file-hosted-at-domain-root.svg)',
backgroundSize: 'contain',
backgroundRepeat: 'no-repeat',
width: '200px',
},
});
},
},
/**
* Internally, the OHIF Viewer fetches data primarily with the
* `cornerstoneWADOImageLoader` and the `DICOMWebClient`. If either of these
* receive a non-200 response, this method allows you to handle that error.
*
* Common use cases include:
* - Showing a notification with the UINotificationService
* - Redirecting the user
* - Refreshing an auth token
*
* @param {Object} error - JS new Error()
* @param {XMLHttpRequest} error.request - The XHR request that's onreadystate change triggered this callback
* @param {string} error.response - The XHR's response property
* @param {number} error.status - The XHR's status property
*/
httpErrorHandler: error => {
const { request: xhr, response, status } = err;
const { responseType, statusText } = xhr;
// In local files, status is 0 upon success in Firefox
if (xhr.readyState === XMLHttpRequest.DONE) {
console.log(statusText, response, responseType);
} else {
console.warn('Likely CORS error');
}
},
extensions: [],
showStudyList: true,
filterQueryParam: false,
+4 -4
View File
@@ -135,7 +135,7 @@ console.log(T('$t(Common:Play) my translated text'));
# Main Concepts While Translating
## - Namespaces
## Namespaces
Namespaces are being used to organize translations in smaller portions, combined
semantically or by use. Each `.json` file inside `@ohif/i18n` npm package
@@ -157,7 +157,7 @@ NameSpace, like this following example getting data from `Common` NameSpace:
$t(Common:Reset)
```
## - Extending Languages in @ohif/i18n
## Extending Languages in @ohif/i18n
Sometimes, even using the same language, some nouns or jargons can change
according to the country, states or even from Hospital to Hospital.
@@ -212,7 +212,7 @@ object like this:
Please check the `index.js` files inside locales folder for an example of this
exporting structure.
### - Extending languages dynamically
### Extending languages dynamically
You have access to the i18next instance, so you can use the
[addResourceBundle](https://www.i18next.com/how-to/add-or-load-translations#add-after-init)
@@ -314,4 +314,4 @@ REACT_APP_I18N_DEBUG=true yarn run dev
### Contributing with new languages
Contributions of any kind are welcome! Please check the
[instructions](https://docs.ohif.org/contributing.html).
[instructions](../development/contributing.md).
+4 -4
View File
@@ -66,11 +66,11 @@ open to pull requests and discussion issues.
Current white-labeling options are limited. We expose the ability to replace the
"Logo" section of the application with a custom "Logo" component. You can do
this by adding a `whiteLabelling` key to your
this by adding a `whiteLabeling` key to your
[configuration file](./configuration.md).
```js
function RadicalImagingLogo() {
function RadicalImagingLogo(React) {
return React.createElement(
'a',
{
@@ -83,8 +83,8 @@ function RadicalImagingLogo() {
);
}
props.whiteLabelling = {
logoComponent: RadicalImagingLogo(),
props.whiteLabeling = {
createLogoComponentFn: RadicalImagingLogo,
};
```
+17 -12
View File
@@ -20,10 +20,10 @@ abbrev@~1.0.9:
resolved "https://registry.yarnpkg.com/abbrev/-/abbrev-1.0.9.tgz#91b4792588a7738c25f35dd6f63752a2f8776135"
integrity sha1-kbR5JYinc4wl813W9jdSovh3YTU=
agent-base@4, agent-base@^4.1.0:
version "4.2.1"
resolved "https://registry.yarnpkg.com/agent-base/-/agent-base-4.2.1.tgz#d89e5999f797875674c07d87f260fc41e83e8ca9"
integrity sha512-JVwXMr9nHYTUXsBFKUqhJwvlcYU/blreOEUkhNR2eXZIvwd+c+o5V4MgDPKWnMS/56awN3TRzIP+KoPn+roQtg==
agent-base@4, agent-base@^4.1.0, agent-base@^4.3.0:
version "4.3.0"
resolved "https://registry.yarnpkg.com/agent-base/-/agent-base-4.3.0.tgz#8165f01c436009bccad0b1d122f05ed770efc6ee"
integrity sha512-salcGninV0nPrwpGNn4VTXBb1SOuXQBiqbrNXoeizJsHrsL6ERFM2Ne3JUSBWRE6aeNJI2ROP/WEEIDUiDe3cg==
dependencies:
es6-promisify "^5.0.0"
@@ -773,9 +773,9 @@ err-code@^1.0.0:
prr "~1.0.1"
es6-promise@^4.0.3:
version "4.2.6"
resolved "https://registry.yarnpkg.com/es6-promise/-/es6-promise-4.2.6.tgz#b685edd8258886365ea62b57d30de28fadcd974f"
integrity sha512-aRVgGdnmW2OiySVPUC9e6m+plolMAJKjZnQlCwNSuK5yQ0JN61DZSO1X1Ufd1foqWRAlig0rhduTCHe7sVtK5Q==
version "4.2.8"
resolved "https://registry.yarnpkg.com/es6-promise/-/es6-promise-4.2.8.tgz#4eb21594c972bc40553d276e510539143db53e0a"
integrity sha512-HJDGx5daxeIvxdBxvG2cb9g4tEvwIk3i8+nhX0yGrYmZUzbkdg8QbDevheDB8gd0//uPj4c1EQua8Q+MViT0/w==
es6-promisify@^5.0.0:
version "5.0.0"
@@ -1289,11 +1289,11 @@ http-signature@~1.2.0:
sshpk "^1.7.0"
https-proxy-agent@^2.1.0:
version "2.2.1"
resolved "https://registry.yarnpkg.com/https-proxy-agent/-/https-proxy-agent-2.2.1.tgz#51552970fa04d723e04c56d04178c3f92592bbc0"
integrity sha512-HPCTS1LW51bcyMYbxUIOO4HEOlQ1/1qRaFWcyxvwaqUS9TY88aoEuHUY33kuAh1YhVVaDQhLZsnPd+XNARWZlQ==
version "2.2.4"
resolved "https://registry.yarnpkg.com/https-proxy-agent/-/https-proxy-agent-2.2.4.tgz#4ee7a737abd92678a293d9b34a1af4d0d08c787b"
integrity sha512-OmvfoQ53WLjtA9HeYP9RNrWMJzzAz1JGaSFr1nijg0PVR1JaD/xbJq1mdEIIlxGpXp9eSe/O2LgU9DJmTPd0Eg==
dependencies:
agent-base "^4.1.0"
agent-base "^4.3.0"
debug "^3.1.0"
humanize-ms@^1.2.1:
@@ -1807,11 +1807,16 @@ ms@2.0.0:
resolved "https://registry.yarnpkg.com/ms/-/ms-2.0.0.tgz#5608aeadfc00be6c2901df5f9861788de0d597c8"
integrity sha1-VgiurfwAvmwpAd9fmGF4jeDVl8g=
ms@^2.0.0, ms@^2.1.1:
ms@^2.0.0:
version "2.1.1"
resolved "https://registry.yarnpkg.com/ms/-/ms-2.1.1.tgz#30a5864eb3ebb0a66f2ebe6d727af06a09d86e0a"
integrity sha512-tgp+dl5cGk28utYktBsrFqA7HKgrhgPsg6Z/EfhWI4gl1Hwq8B/GmY/0oXZ6nF8hDVesS/FpnYaD/kOWhYQvyg==
ms@^2.1.1:
version "2.1.2"
resolved "https://registry.yarnpkg.com/ms/-/ms-2.1.2.tgz#d09d1f357b443f493382a8eb3ccd183872ae6009"
integrity sha512-sGkPx+VjMtmA6MX27oA4FBFELFCZZ4S4XqeGOXCv68tT+jb3vk/RyaKWP0PTKyWtmLSM0b+adUTEvbs1PEaH2w==
mute-stream@~0.0.4:
version "0.0.8"
resolved "https://registry.yarnpkg.com/mute-stream/-/mute-stream-0.0.8.tgz#1630c42b2251ff81e2a283de96a5497ea92e5e0d"
+38
View File
@@ -3,6 +3,44 @@
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [2.6.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.6.0...@ohif/extension-cornerstone@2.6.1) (2020-04-23)
### Bug Fixes
* 🐛 Multiframe fix ([#1661](https://github.com/OHIF/Viewers/issues/1661)) ([7120561](https://github.com/OHIF/Viewers/commit/71205618ecb8b592247c5acb32284bfe7e18fce5))
# [2.6.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.5.2...@ohif/extension-cornerstone@2.6.0) (2020-04-23)
### Features
* configuration to hook into XHR Error handling ([e96205d](https://github.com/OHIF/Viewers/commit/e96205de35e5bec14dc8a9a8509db3dd4e6ecdb6))
## [2.5.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.5.1...@ohif/extension-cornerstone@2.5.2) (2020-04-09)
**Note:** Version bump only for package @ohif/extension-cornerstone
## [2.5.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.5.0...@ohif/extension-cornerstone@2.5.1) (2020-04-02)
**Note:** Version bump only for package @ohif/extension-cornerstone
# [2.5.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.4.3...@ohif/extension-cornerstone@2.5.0) (2020-03-13)
+2 -2
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/extension-cornerstone",
"version": "2.5.0",
"version": "2.6.1",
"description": "OHIF extension for Cornerstone",
"author": "OHIF",
"license": "MIT",
@@ -35,7 +35,7 @@
"cornerstone-core": "^2.2.8",
"cornerstone-math": "^0.1.8",
"cornerstone-tools": "4.12.5",
"cornerstone-wado-image-loader": "^3.0.0",
"cornerstone-wado-image-loader": "^3.1.0",
"dcmjs": "^0.10.1",
"dicom-parser": "^1.8.3",
"hammerjs": "^2.0.8",
@@ -1,37 +0,0 @@
/**
* We use this component to leverage "Code Splitting"
*
* Link: https://serverless-stack.com/chapters/code-splitting-in-create-react-app.html
*/
import React, { Component } from 'react';
export default function asyncComponent(importComponent) {
class AsyncComponent extends Component {
constructor(props) {
super(props);
this.state = {
component: null,
};
}
async componentDidMount() {
// Add dynamically loaded component to state
const { default: component } = await importComponent();
this.setState({
component: component,
});
}
render() {
const C = this.state.component;
// Render the loaded component, or null
return C ? <C {...this.props} /> : null;
}
}
return AsyncComponent;
}
@@ -7,6 +7,9 @@ import { getEnabledElement } from './state';
import CornerstoneViewportDownloadForm from './CornerstoneViewportDownloadForm';
const scroll = cornerstoneTools.import('util/scroll');
const { studyMetadataManager } = OHIF.utils;
const { setViewportSpecificData } = OHIF.redux.actions;
const commandsModule = ({ servicesManager }) => {
const actions = {
rotateViewport: ({ viewports, rotation }) => {
@@ -255,9 +258,35 @@ const commandsModule = ({ servicesManager }) => {
cornerstone.setViewport(enabledElement, viewport);
}
},
jumpToImage: ({
StudyInstanceUID,
SOPInstanceUID,
frameIndex,
activeViewportIndex
}) => {
const study = studyMetadataManager.get(StudyInstanceUID);
const displaySet = study.findDisplaySet(ds => {
return ds.images.find(i => i.getSOPInstanceUID() === SOPInstanceUID)
});
displaySet.SOPInstanceUID = SOPInstanceUID;
displaySet.frameIndex = frameIndex;
window.store.dispatch(setViewportSpecificData(activeViewportIndex, displaySet));
cornerstone.getEnabledElements().forEach(enabledElement => {
cornerstone.updateImage(enabledElement.element);
});
}
};
const definitions = {
jumpToImage: {
commandFn: actions.jumpToImage,
storeContexts: [],
options: {},
},
getNearbyToolData: {
commandFn: actions.getNearbyToolData,
storeContexts: [],
+12 -6
View File
@@ -1,14 +1,20 @@
import React from 'react';
import init from './init.js';
import asyncComponent from './asyncComponent.js';
import commandsModule from './commandsModule.js';
import toolbarModule from './toolbarModule.js';
import CornerstoneViewportDownloadForm from './CornerstoneViewportDownloadForm';
const OHIFCornerstoneViewport = asyncComponent(() =>
import(
/* webpackChunkName: "OHIFCornerstoneViewport" */ './OHIFCornerstoneViewport.js'
)
);
const Component = React.lazy(() => {
return import('./OHIFCornerstoneViewport');
});
const OHIFCornerstoneViewport = props => {
return (
<React.Suspense fallback={<div>Loading...</div>}>
<Component {...props} />
</React.Suspense>
);
};
/**
*
@@ -2,6 +2,9 @@ import Hammer from 'hammerjs';
import cornerstone from 'cornerstone-core';
import cornerstoneMath from 'cornerstone-math';
import cornerstoneTools from 'cornerstone-tools';
import OHIF from '@ohif/core';
const { log } = OHIF;
export default function(configuration = {}) {
// For debugging
@@ -12,6 +15,13 @@ export default function(configuration = {}) {
cornerstoneTools.external.cornerstoneMath = cornerstoneMath;
cornerstoneTools.init(configuration);
cornerstoneTools.loadHandlerManager.setErrorLoadingHandler(
(element, imageId, error) => {
log.error(imageId);
throw error;
}
);
// Set the tool font and font size
// context.font = "[style] [variant] [weight] [size]/[line height] [font family]";
const fontFamily =
+8
View File
@@ -3,6 +3,14 @@
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [1.1.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.1.1...@ohif/extension-dicom-html@1.1.2) (2020-04-02)
**Note:** Version bump only for package @ohif/extension-dicom-html
## [1.1.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@1.1.0...@ohif/extension-dicom-html@1.1.1) (2020-03-09)
**Note:** Version bump only for package @ohif/extension-dicom-html
+1 -1
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/extension-dicom-html",
"version": "1.1.1",
"version": "1.1.2",
"description": "OHIF extension for rendering structured reports to HTML",
"author": "OHIF",
"license": "MIT",
@@ -1,37 +0,0 @@
/**
* We use this component to leverage "Code Splitting"
*
* Link: https://serverless-stack.com/chapters/code-splitting-in-create-react-app.html
*/
import React, { Component } from 'react';
export default function asyncComponent(importComponent) {
class AsyncComponent extends Component {
constructor(props) {
super(props);
this.state = {
component: null,
};
}
async componentDidMount() {
// Add dynamically loaded component to state
const { default: component } = await importComponent();
this.setState({
component: component,
});
}
render() {
const C = this.state.component;
// Render the loaded component, or null
return C ? <C {...this.props} /> : null;
}
}
return AsyncComponent;
}
+12 -6
View File
@@ -1,11 +1,17 @@
import asyncComponent from './asyncComponent.js';
import React from 'react';
import OHIFDicomHtmlSopClassHandler from './OHIFDicomHtmlSopClassHandler.js';
const OHIFDicomHtmlViewport = asyncComponent(() =>
import(
/* webpackChunkName: "OHIFDicomHtmlViewport" */ './OHIFDicomHtmlViewport.js'
)
);
const Component = React.lazy(() => {
return import('./OHIFDicomHtmlViewport');
});
const OHIFDicomHtmlViewport = props => {
return (
<React.Suspense fallback={<div>Loading...</div>}>
<Component {...props} />
</React.Suspense>
);
};
export default {
/**
+8
View File
@@ -3,6 +3,14 @@
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [0.50.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.8...@ohif/extension-dicom-microscopy@0.50.9) (2020-04-02)
**Note:** Version bump only for package @ohif/extension-dicom-microscopy
## [0.50.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-microscopy@0.50.7...@ohif/extension-dicom-microscopy@0.50.8) (2020-03-31)
**Note:** Version bump only for package @ohif/extension-dicom-microscopy
+1 -1
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/extension-dicom-microscopy",
"version": "0.50.8",
"version": "0.50.9",
"description": "OHIF extension for Dicom Microscopy",
"author": "OHIF",
"license": "MIT",
@@ -1,37 +0,0 @@
/**
* We use this component to leverage "Code Splitting"
*
* Link: https://serverless-stack.com/chapters/code-splitting-in-create-react-app.html
*/
import React, { Component } from 'react';
export default function asyncComponent(importComponent) {
class AsyncComponent extends Component {
constructor(props) {
super(props);
this.state = {
component: null,
};
}
async componentDidMount() {
// Add dynamically loaded component to state
const { default: component } = await importComponent();
this.setState({
component: component,
});
}
render() {
const C = this.state.component;
// Render the loaded component, or null
return C ? <C {...this.props} /> : null;
}
}
return AsyncComponent;
}
+12 -6
View File
@@ -1,11 +1,17 @@
import asyncComponent from './asyncComponent.js';
import React from 'react';
import DicomMicroscopySopClassHandler from './DicomMicroscopySopClassHandler.js';
const DicomMicroscopyViewport = asyncComponent(() =>
import(
/* webpackChunkName: "DicomMicroscopyViewport" */ './DicomMicroscopyViewport.js'
)
);
const Component = React.lazy(() => {
return import('./DicomMicroscopyViewport');
});
const DicomMicroscopyViewport = props => {
return (
<React.Suspense fallback={<div>Loading...</div>}>
<Component {...props} />
</React.Suspense>
);
};
export default {
/**
@@ -0,0 +1,8 @@
const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
const SRC_DIR = path.join(__dirname, '../src');
const DIST_DIR = path.join(__dirname, '../dist');
module.exports = (env, argv) => {
return webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
};
@@ -0,0 +1,38 @@
const merge = require('webpack-merge');
const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
const pkg = require('./../package.json');
const ROOT_DIR = path.join(__dirname, './..');
const SRC_DIR = path.join(__dirname, '../src');
const DIST_DIR = path.join(__dirname, '../dist');
module.exports = (env, argv) => {
const commonConfig = webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
return merge(commonConfig, {
devtool: 'source-map',
stats: {
colors: true,
hash: true,
timings: true,
assets: true,
chunks: false,
chunkModules: false,
modules: false,
children: false,
warnings: true,
},
optimization: {
minimize: true,
sideEffects: true,
},
output: {
path: ROOT_DIR,
library: 'OHIFExtDicomP10Downloader',
libraryTarget: 'umd',
libraryExport: 'default',
filename: pkg.main,
},
});
};
@@ -0,0 +1,28 @@
# Change Log
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
# [0.1.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-p10-downloader@0.0.2...@ohif/extension-dicom-p10-downloader@0.1.0) (2020-04-23)
### Features
* configuration to hook into XHR Error handling ([e96205d](https://github.com/OHIF/Viewers/commit/e96205de35e5bec14dc8a9a8509db3dd4e6ecdb6))
## 0.0.2 (2020-04-15)
**Note:** Version bump only for package @ohif/extension-dicom-p10-downloader
# Change Log
All notable changes to this project will be documented in this file. See
[Conventional Commits](https://conventionalcommits.org) for commit guidelines.
+21
View File
@@ -0,0 +1,21 @@
MIT License
Copyright (c) 2018 Open Health Imaging Foundation
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
@@ -0,0 +1 @@
# @ohif/extension-dicom-p10-downloader
@@ -0,0 +1,40 @@
{
"name": "@ohif/extension-dicom-p10-downloader",
"version": "0.1.0",
"description": "OHIF extension for downloading DICOM P10 files",
"author": "OHIF",
"license": "MIT",
"repository": "OHIF/Viewers",
"main": "dist/index.umd.js",
"module": "src/index.js",
"publishConfig": {
"access": "public"
},
"engines": {
"node": ">=10",
"npm": ">=6",
"yarn": ">=1.16.0"
},
"files": [
"dist",
"README.md"
],
"scripts": {
"dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --debug --output-pathinfo",
"build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
"build:package": "yarn run build",
"prepublishOnly": "yarn run build",
"start": "yarn run dev"
},
"peerDependencies": {
"@ohif/core": "^2.6.0",
"dicom-parser": "^1.8.3",
"dicomweb-client": "^0.5.2"
},
"dependencies": {
"@babel/runtime": "^7.5.5",
"dicomweb-client": "^0.6.0",
"file-saver": "^2.0.2",
"jszip": "^3.2.2"
}
}
@@ -0,0 +1,105 @@
import OHIF from '@ohif/core';
import {
save,
getDicomWebClientFromContext,
getSOPInstanceReferenceFromActiveViewport,
getSOPInstanceReferencesFromViewports,
} from './utils';
import _downloadAndZip from './downloadAndZip';
const {
utils: {
Queue,
},
} = OHIF;
export function getCommands(context) {
const queue = new Queue(1);
const actions = {
/**
* @example Running this command using Commands Manager
* commandsManager.runCommand(
* 'downloadAndZip',
* {
* listOfUIDs: [...],
* options: {
* progress(status) {
* console.info('Progress:', (status.progress * 100).toFixed(2) + '%');
* }
* }
* },
* 'VIEWER'
* );
*/
downloadAndZip({ servers, dicomWebClient, listOfUIDs, options }) {
return save(
_downloadAndZip(
dicomWebClient || getDicomWebClientFromContext(context, servers),
listOfUIDs,
options
),
listOfUIDs
);
},
downloadAndZipSeriesOnViewports({ servers, viewports, progress }) {
const dicomWebClient = getDicomWebClientFromContext(context, servers);
const listOfUIDs = getSOPInstanceReferencesFromViewports(viewports);
return save(
_downloadAndZip(dicomWebClient, listOfUIDs, { progress }),
listOfUIDs
);
},
downloadAndZipSeriesOnActiveViewport({ servers, viewports, progress }) {
const dicomWebClient = getDicomWebClientFromContext(context, servers);
const listOfUIDs = getSOPInstanceReferenceFromActiveViewport(viewports);
return save(
_downloadAndZip(dicomWebClient, listOfUIDs, { progress }),
listOfUIDs
);
},
};
const definitions = {
downloadAndZip: {
commandFn: queue.bindSafe(actions.downloadAndZip, error),
storeContexts: ['servers'],
},
downloadAndZipSeriesOnViewports: {
commandFn: queue.bindSafe(actions.downloadAndZipSeriesOnViewports, error),
storeContexts: ['servers', 'viewports'],
options: { progress },
},
downloadAndZipSeriesOnActiveViewport: {
commandFn: queue.bindSafe(
actions.downloadAndZipSeriesOnActiveViewport,
error
),
storeContexts: ['servers', 'viewports'],
options: { progress },
},
};
return {
actions,
definitions,
};
}
/**
* Utils
*/
function progress(status) {
OHIF.log.info(
'Download and Zip Progress:',
(status.progress * 100.0).toFixed(2) + '%'
);
}
function error(e) {
if (e.message === 'Queue limit reached') {
OHIF.log.warn('A download is already in progress, please wait.');
} else {
OHIF.log.error(e);
}
}
@@ -0,0 +1,244 @@
import OHIF from '@ohif/core';
import { api } from 'dicomweb-client';
import dicomParser from 'dicom-parser';
import JSZip from 'jszip';
/**
* Constants
*/
const {
utils: {
isDicomUid,
hierarchicalListUtils,
progressTrackingUtils: progressUtils,
},
} = OHIF;
/**
* Public Methods
*/
/**
* Download and Zip all DICOM P10 instances from specified DICOM Web Client
* based on an hierarchical list of UIDs;
*
* @param {DICOMwebClient} dicomWebClient A DICOMwebClient instance through
* which the referenced instances will be retrieved;
* @param {Array} listOfUIDs The hierarchical list of UIDs from the instances
* that should be retrieved:
* A hierarchical list of UIDs is a regular JS Array where the type of the UID
* (study, series, instance) is determined by its nasting lavel. For example:
* @ The following list instructs the library to download all the instances
* from both studies "A" and "B":
*
* ['studyUIDFromA', 'studyUIDFromB']
*
* @ In the previous example both UIDs are treated as STUDY UIDs because both
* of them are listed in the same (top) level of the list. If, on the other
* hand, only instances from series "I" and "J" from the study "B"
* are to be downloaded, the expected hierarchical list would be:
*
* ['studyUIDFromA', ['studyUIDFromB', ['seriesUIDFromI', 'seriesUIDFromJ']]]
*
* @ Which, when prettified, reads like this:
*
* [
* 'studyUIDFromA',
* ['studyUIDFromB', [
* 'seriesUIDFromI',
* 'seriesUIDFromJ'
* ]]
* ]
*
* @ Furthermore, if only instances "X", "Y" and "Z" from series "J" need to
* be downloaded (instead of all the instances from that series), the list
* could be changed to:
*
* [
* 'studyUIDFromA',
* ['studyUIDFromB', [
* 'seriesUIDFromI',
* ['seriesUIDFromJ', [
* 'instanceUIDFromX',
* 'instanceUIDFromY',
* 'instanceUIDFromZ'
* ]]
* ]]
* ]
*
* Please refer to hierarchicalListUtils.js for more information and utilities;
*
* @param {Object} options A plain object with options;
* @param {function} options.progress A callback to retrieve notifications
* @returns {Promise} A promise that resolves to an URL from which the ZIP file
* can be downloaded;
*/
async function downloadAndZip(dicomWebClient, listOfUIDs, options) {
if (dicomWebClient instanceof api.DICOMwebClient) {
const settings = buildSettings(listOfUIDs, options);
const { compression } = settings.tasks;
// Register user-provided progress handler as a task list observer
progressUtils.addObserver(settings.taskList, settings.options.progress);
const buffers = await downloadAll(dicomWebClient, settings).catch(error => {
// Reject promise from compression task on download failure
compression.deferred.reject(error);
throw error;
});
compression.deferred.resolve(zipAll(buffers, settings));
const url = await compression.deferred.promise;
return url;
}
throw new Error('A valid DICOM Web Client instance is expected');
}
/**
* Utils
*/
async function zipAll(buffers, settings) {
const zip = new JSZip();
OHIF.log.info('Adding DICOM P10 files to archive:', buffers.length);
buffers.forEach((buffer, i) => {
const path = buildPath(buffer) || `${i}.dcm`;
zip.file(path, buffer);
});
// Set compression task progress to 50%
progressUtils.update(settings.tasks.compression.task, 0.5);
const blob = await zip.generateAsync({ type: 'blob' });
return URL.createObjectURL(blob);
}
function buildSettings(listOfUIDs, options) {
const taskList = progressUtils.createList();
const compression = progressUtils.addDeferred(taskList);
const downloads = [];
// Build downloads list
hierarchicalListUtils.forEach(
listOfUIDs,
(StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID) => {
if (isDicomUid(StudyInstanceUID)) {
downloads.push({
tracking: progressUtils.addDeferred(taskList),
parameters: [StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID],
});
}
}
);
// Print tree of hierarchical references
OHIF.log.info('Downloading DICOM P10 files for references:');
OHIF.log.info(hierarchicalListUtils.print(listOfUIDs));
return {
options: Object(options),
taskList,
tasks: {
downloads,
compression,
},
};
}
function buildPath(buffer) {
let path;
try {
const byteArray = new Uint8Array(buffer);
const dataSet = dicomParser.parseDicom(byteArray, {
// Stop parsing after SeriesInstanceUID is found
untilTag: 'x0020000e',
});
const StudyInstanceUID = dataSet.string('x0020000d');
const SeriesInstanceUID = dataSet.string('x0020000e');
const SOPInstanceUID = dataSet.string('x00080018');
if (StudyInstanceUID && SeriesInstanceUID && SOPInstanceUID) {
path = `${StudyInstanceUID}/${SeriesInstanceUID}/${SOPInstanceUID}.dcm`;
}
} catch (e) {
OHIF.log.error('Error parsing downloaded DICOM P10 file...', e);
}
return path;
}
async function downloadAll(dicomWebClient, settings) {
const { downloads } = settings.tasks;
// Make sure at least one download was initiated
if (downloads.length < 1) {
throw new Error('No valid reference to be downloaded');
}
const promises = downloads.map(item => {
const {
parameters,
tracking: { deferred, task },
} = item;
deferred.resolve(download(task, dicomWebClient, ...parameters));
return deferred.promise;
});
// Wait on created download promises
return Promise.all(promises).then(results => {
const buffers = [];
// The "results" array may directly contain buffers (ArrayBuffer instances)
// or arrays of buffers, depending on the type of downloads initiated on the
// previous step (retrieveStudy, retrieveSeries or retrieveinstance). Ex:
// results = [buf1, [buf2, buf3], buf4, [buf5], ...];
results.forEach(
function select(nesting, result) {
if (result instanceof ArrayBuffer) {
buffers.push(result);
} else if (nesting && Array.isArray(result)) {
// "nesting" argument is important to make sure only two levels
// of arrays are visited. For example, "bufX" should not be visited:
// [buf1, [buf2, buf3, [bufX]], buf4, [buf5], ...];
result.forEach(select.bind(null, false));
}
}.bind(null, true)
);
return buffers;
});
}
async function download(
task,
dicomWebClient,
studyInstanceUID,
seriesInstanceUID,
sopInstanceUID
) {
// Strict DICOM-formatted variable names COULDN'T be used here because the
// DICOM Web client interface expects them in this specific format.
// @TODO: Add support for download progress handler which will use the
// currently not use "task" param
if (!isDicomUid(studyInstanceUID)) {
throw new Error('Download requires at least a "StudyInstanceUID" property');
}
if (!isDicomUid(seriesInstanceUID)) {
// Download entire study
return dicomWebClient.retrieveStudy({
studyInstanceUID,
});
}
if (!isDicomUid(sopInstanceUID)) {
// Download entire series
return dicomWebClient.retrieveSeries({
studyInstanceUID,
seriesInstanceUID,
});
}
// Download specific instance
return dicomWebClient.retrieveInstance({
studyInstanceUID,
seriesInstanceUID,
sopInstanceUID,
});
}
/**
* Exports
*/
export { downloadAndZip as default, downloadAndZip };
@@ -0,0 +1,43 @@
import { getDicomWebClientFromConfig } from './utils';
import { getCommands } from './commandsModule';
/**
* Constants
*/
/**
* Globals
*/
const sharedContext = {
dicomWebClient: null,
};
/**
* Extension
*/
export default {
/**
* Only required property. Should be a unique value across all extensions.
*/
id: 'dicom-p10-downloader',
/**
* LIFECYCLE HOOKS
*/
preRegistration({ appConfig }) {
const dicomWebClient = getDicomWebClientFromConfig(appConfig);
if (dicomWebClient) {
sharedContext.dicomWebClient = dicomWebClient;
}
},
/**
* MODULE GETTERS
*/
getCommandsModule() {
return getCommands(sharedContext);
},
};
@@ -0,0 +1,110 @@
import OHIF from '@ohif/core';
import { api } from 'dicomweb-client';
import { saveAs } from 'file-saver';
const {
utils: { isDicomUid, resolveObjectPath, hierarchicalListUtils },
DICOMWeb,
} = OHIF;
function validDicomUid(subject) {
if (isDicomUid(subject)) {
return subject;
}
}
function getActiveServerFromServersStore(store) {
const servers = resolveObjectPath(store, 'servers');
if (Array.isArray(servers) && servers.length > 0) {
return servers.find(server => resolveObjectPath(server, 'active') === true);
}
}
function getDicomWebClientFromConfig(config) {
const servers = resolveObjectPath(config, 'servers.dicomWeb');
if (Array.isArray(servers) && servers.length > 0) {
const server = servers[0];
return new api.DICOMwebClient({
url: server.wadoRoot,
headers: DICOMWeb.getAuthorizationHeader(server),
});
}
}
function getDicomWebClientFromContext(context, store) {
const activeServer = getActiveServerFromServersStore(store);
if (activeServer) {
return new api.DICOMwebClient({
url: activeServer.wadoRoot,
headers: DICOMWeb.getAuthorizationHeader(activeServer),
});
} else if (context.dicomWebClient instanceof api.DICOMwebClient) {
return context.dicomWebClient;
}
}
function getSOPInstanceReference(viewports, index) {
if (index >= 0) {
const { StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID } = Object(
resolveObjectPath(viewports, `viewportSpecificData.${index}`)
);
return Object.freeze(
hierarchicalListUtils.addToList(
[],
validDicomUid(StudyInstanceUID),
validDicomUid(SeriesInstanceUID),
validDicomUid(SOPInstanceUID)
)
);
}
}
function getSOPInstanceReferenceFromActiveViewport(viewports) {
return getSOPInstanceReference(
viewports,
resolveObjectPath(viewports, 'activeViewportIndex')
);
}
function getSOPInstanceReferencesFromViewports(viewports) {
const list = [];
const viewportSpecificData = resolveObjectPath(
viewports,
'viewportSpecificData'
);
Object.keys(viewportSpecificData).forEach(index => {
const { StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID } = Object(
viewportSpecificData[index]
);
hierarchicalListUtils.addToList(
list,
validDicomUid(StudyInstanceUID),
validDicomUid(SeriesInstanceUID),
validDicomUid(SOPInstanceUID)
);
});
return list;
}
function save(promise, listOfUIDs) {
return Promise.resolve(promise)
.then(url => {
OHIF.log.info('Files successfully compressed:', url);
const StudyInstanceUID = hierarchicalListUtils.getItem(listOfUIDs, 0);
saveAs(url, `${StudyInstanceUID}.zip`);
return url;
})
.catch(error => {
OHIF.log.error('Failed to create Zip file...', error);
return null;
});
}
export {
save,
validDicomUid,
getDicomWebClientFromConfig,
getDicomWebClientFromContext,
getSOPInstanceReferenceFromActiveViewport,
getSOPInstanceReferencesFromViewports,
};
+8
View File
@@ -3,6 +3,14 @@
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [1.0.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@1.0.2...@ohif/extension-dicom-pdf@1.0.3) (2020-04-02)
**Note:** Version bump only for package @ohif/extension-dicom-pdf
## [1.0.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@1.0.1...@ohif/extension-dicom-pdf@1.0.2) (2020-03-09)
**Note:** Version bump only for package @ohif/extension-dicom-pdf
+1 -1
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/extension-dicom-pdf",
"version": "1.0.2",
"version": "1.0.3",
"description": "OHIF extension for Dicom PDF",
"author": "OHIF",
"license": "MIT",
@@ -1,37 +0,0 @@
/**
* We use this component to leverage "Code Splitting"
*
* Link: https://serverless-stack.com/chapters/code-splitting-in-create-react-app.html
*/
import React, { Component } from 'react';
export default function asyncComponent(importComponent) {
class AsyncComponent extends Component {
constructor(props) {
super(props);
this.state = {
component: null,
};
}
async componentDidMount() {
// Add dynamically loaded component to state
const { default: component } = await importComponent();
this.setState({
component: component,
});
}
render() {
const C = this.state.component;
// Render the loaded component, or null
return C ? <C {...this.props} /> : null;
}
}
return AsyncComponent;
}
+12 -6
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@@ -1,11 +1,17 @@
import asyncComponent from './asyncComponent.js';
import React from 'react';
import OHIFDicomPDFSopClassHandler from './OHIFDicomPDFSopClassHandler.js';
const ConnectedOHIFDicomPDFViewer = asyncComponent(() =>
import(
/* webpackChunkName: "ConnectedOHIFDicomPDFViewer" */ './ConnectedOHIFDicomPDFViewer'
)
);
const Component = React.lazy(() => {
return import('./ConnectedOHIFDicomPDFViewer');
});
const ConnectedOHIFDicomPDFViewer = props => {
return (
<React.Suspense fallback={<div>Loading...</div>}>
<Component {...props} />
</React.Suspense>
);
};
export default {
/**
@@ -0,0 +1,8 @@
const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
const SRC_DIR = path.join(__dirname, '../src');
const DIST_DIR = path.join(__dirname, '../dist');
module.exports = (env, argv) => {
return webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
};
@@ -0,0 +1,44 @@
const webpack = require('webpack');
const merge = require('webpack-merge');
const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
const pkg = require('./../package.json');
const ROOT_DIR = path.join(__dirname, './..');
const SRC_DIR = path.join(__dirname, '../src');
const DIST_DIR = path.join(__dirname, '../dist');
module.exports = (env, argv) => {
const commonConfig = webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
return merge(commonConfig, {
devtool: 'source-map',
stats: {
colors: true,
hash: true,
timings: true,
assets: true,
chunks: false,
chunkModules: false,
modules: false,
children: false,
warnings: true,
},
optimization: {
minimize: true,
sideEffects: true,
},
output: {
path: ROOT_DIR,
library: 'OHIFExtDicomSeg',
libraryTarget: 'umd',
libraryExport: 'default',
filename: pkg.main,
},
plugins: [
new webpack.optimize.LimitChunkCountPlugin({
maxChunks: 1,
}),
],
});
};
+8
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@@ -0,0 +1,8 @@
# Change Log
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## 0.0.2 (2020-04-09)
**Note:** Version bump only for package @ohif/extension-dicom-rt
+21
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@@ -0,0 +1,21 @@
MIT License
Copyright (c) 2018 Open Health Imaging Foundation
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
+1
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@@ -0,0 +1 @@
# @ohif/extension-dicom-rt
+43
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@@ -0,0 +1,43 @@
{
"name": "@ohif/extension-dicom-rt",
"version": "0.0.2",
"description": "OHIF extension for rendering DICOM RTSTRUCTs on top of cornerstone images.",
"author": "OHIF",
"license": "MIT",
"repository": "OHIF/Viewers",
"main": "dist/index.umd.js",
"module": "src/index.js",
"engines": {
"node": ">=10",
"npm": ">=6",
"yarn": ">=1.16.0"
},
"files": [
"dist",
"README.md"
],
"publishConfig": {
"access": "public"
},
"scripts": {
"dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --debug --output-pathinfo",
"dev:dicom-html": "yarn run dev",
"build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
"build:package": "yarn run build",
"prepublishOnly": "yarn run build",
"start": "yarn run dev"
},
"peerDependencies": {
"@ohif/core": "^0.50.0",
"cornerstone-core": "^2.2.8",
"cornerstone-tools": "^4.0.9",
"dcmjs": "^0.8.3",
"prop-types": "^15.6.2",
"react": "^16.8.6",
"react-dom": "^16.8.6"
},
"dependencies": {
"@babel/runtime": "^7.5.5",
"react-select": "^3.0.8"
}
}
@@ -0,0 +1,237 @@
import { MODULE_TYPES, utils, DICOMWeb } from '@ohif/core';
import loadRTStruct from './loadRTStruct';
import id from './id';
// TODO: Should probably use dcmjs for this
const SOP_CLASS_UIDS = {
DICOM_RT_STRUCT: '1.2.840.10008.5.1.4.1.1.481.3',
};
const sopClassUIDs = Object.values(SOP_CLASS_UIDS);
const OHIFDicomRTStructSopClassHandler = {
id: 'OHIFDicomRTStructSopClassHandler',
type: MODULE_TYPES.SOP_CLASS_HANDLER,
sopClassUIDs,
getDisplaySetFromSeries: function (
series,
study,
dicomWebClient,
authorizationHeaders
) {
const instance = series.getFirstInstance();
const metadata = instance.getData().metadata;
const {
SeriesDate,
SeriesTime,
SeriesDescription,
FrameOfReferenceUID,
SOPInstanceUID,
SeriesInstanceUID,
StudyInstanceUID,
} = metadata;
// TODO -> GET REFERENCED FRAME OF REFERENCE SEQUENCE.
const rtStructDisplaySet = {
Modality: 'RTSTRUCT',
displaySetInstanceUID: utils.guid(),
wadoRoot: study.getData().wadoRoot,
wadoUri: instance.getData().wadouri,
SOPInstanceUID,
SeriesInstanceUID,
StudyInstanceUID,
FrameOfReferenceUID,
authorizationHeaders,
metadata,
isDerived: true,
referencedDisplaySetUID: null, // Assigned when loaded.
labelmapIndex: null, // Assigned when loaded.
isLoaded: false,
SeriesDate,
SeriesTime,
SeriesDescription,
};
if (!metadata.ReferencedSeriesSequence) {
const ReferencedFrameOfReferenceSequence =
metadata.ReferencedFrameOfReferenceSequence;
if (ReferencedFrameOfReferenceSequence) {
// TODO -> @dannyrb Do we augment metadata or add a (potentially large? fallback list in filterDerivedDisplaySets )
metadata.ReferencedSeriesSequence = _deriveReferencedSeriesSequenceFromFrameOfReferenceSequence(
ReferencedFrameOfReferenceSequence
);
}
}
rtStructDisplaySet.load = function (referencedDisplaySet, studies) {
return loadRTStruct(
rtStructDisplaySet,
referencedDisplaySet,
studies
).catch(error => {
rtStructDisplaySet.isLoaded = false;
throw new Error(error);
});
};
return rtStructDisplaySet;
},
};
function _deriveReferencedSeriesSequenceFromFrameOfReferenceSequence(
ReferencedFrameOfReferenceSequence
) {
const ReferencedSeriesSequence = [];
_getSequenceAsArray(ReferencedFrameOfReferenceSequence).forEach(
referencedFrameOfReference => {
const { RTReferencedStudySequence } = referencedFrameOfReference;
_getSequenceAsArray(RTReferencedStudySequence).forEach(
rtReferencedStudy => {
const { RTReferencedSeriesSequence } = rtReferencedStudy;
_getSequenceAsArray(RTReferencedSeriesSequence).forEach(
rtReferencedSeries => {
const ReferencedInstanceSequence = [];
const {
ContourImageSequence,
SeriesInstanceUID,
} = rtReferencedSeries;
_getSequenceAsArray(ContourImageSequence).forEach(
contourImage => {
ReferencedInstanceSequence.push({
ReferencedSOPInstanceUID:
contourImage.ReferencedSOPInstanceUID,
ReferencedSOPClassUID: contourImage.ReferencedSOPClassUID,
});
}
);
const referencedSeries = {
SeriesInstanceUID,
ReferencedInstanceSequence,
};
ReferencedSeriesSequence.push(referencedSeries);
}
);
}
);
}
);
return ReferencedSeriesSequence;
}
function _getSequenceAsArray(sequence) {
return Array.isArray(sequence) ? sequence : [sequence];
}
function _getReferencedFrameOfReferenceSequence(instance) {
const referencedFrameOfReferenceSequenceRaw = instance['30060010'];
const referencedFrameOfReferenceSequence = [];
if (
!referencedFrameOfReferenceSequenceRaw ||
!referencedFrameOfReferenceSequenceRaw.Value
) {
return undefined;
}
referencedFrameOfReferenceSequenceRaw.Value.forEach(
referencedFrameOfReferenceRaw => {
const frameOfReferenceUID = DICOMWeb.getString(
referencedFrameOfReferenceRaw['00200052']
);
const referencedFrameOfReference = { frameOfReferenceUID };
const RTReferencedStudySequenceRaw =
referencedFrameOfReferenceRaw['30060012'];
referencedFrameOfReferenceSequence.push(referencedFrameOfReference);
if (RTReferencedStudySequenceRaw && RTReferencedStudySequenceRaw.Value) {
referencedFrameOfReference.rtReferencedStudySequence = [];
const { rtReferencedStudySequence } = referencedFrameOfReference;
RTReferencedStudySequenceRaw.Value.forEach(rtReferencedStudyRaw => {
const referencedSopClassUID = DICOMWeb.getString(
rtReferencedStudyRaw['00081150']
);
const referencedSOPInstanceUID = DICOMWeb.getString(
rtReferencedStudyRaw['00081155']
);
const rtReferencedStudy = {
referencedSopClassUID,
referencedSOPInstanceUID,
rtReferencedSeriesSequence: [],
};
rtReferencedStudySequence.push(rtReferencedStudy);
const { rtReferencedSeriesSequence } = rtReferencedStudy;
const rtReferencedSeriesSequenceRaw =
rtReferencedStudyRaw['30060014'];
rtReferencedSeriesSequenceRaw.Value.forEach(rtReferencedSeriesRaw => {
const seriesInstanceUID = DICOMWeb.getString(
rtReferencedSeriesRaw['0020000E']
);
const rtReferencedSeries = {
seriesInstanceUID,
contourImageSequence: [],
};
rtReferencedSeriesSequence.push(rtReferencedSeries);
const { contourImageSequence } = rtReferencedSeries;
const contourImageSequenceRaw = rtReferencedSeriesRaw['30060016'];
contourImageSequenceRaw.Value.forEach(contourImageRaw => {
const referencedSOPClassUID = DICOMWeb.getString(
contourImageRaw['00081150']
);
const referencedSOPInstanceUID = DICOMWeb.getString(
contourImageRaw['00081155']
);
const referencedFrameNumber = DICOMWeb.getString(
contourImageRaw['00081160']
);
const referencedSegmentNumber = DICOMWeb.getString(
contourImageRaw['0062000B']
);
const contourImage = {
referencedSOPClassUID,
referencedSOPInstanceUID,
referencedFrameNumber,
referencedSegmentNumber,
};
contourImageSequence.push(contourImage);
});
});
});
}
}
);
return referencedFrameOfReferenceSequence;
}
export default OHIFDicomRTStructSopClassHandler;
@@ -0,0 +1,61 @@
import React from 'react';
const LoadingIndicator = ({ height = "200px", width = "200px", expand = false }) => {
return (
<div style={expand ? { height: "100%", width: "100%" } : {}}>
<svg style={{ margin: 'auto', background: 'none', display: 'block', shapeRendering: 'auto' }} width={width} height={height} viewBox="0 0 100 100" preserveAspectRatio="xMidYMid">
<g transform="rotate(0 50 50)">
<rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
<animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.9166666666666666s" repeatCount="indefinite"></animate>
</rect>
</g><g transform="rotate(30 50 50)">
<rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
<animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.8333333333333334s" repeatCount="indefinite"></animate>
</rect>
</g><g transform="rotate(60 50 50)">
<rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
<animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.75s" repeatCount="indefinite"></animate>
</rect>
</g><g transform="rotate(90 50 50)">
<rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
<animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.6666666666666666s" repeatCount="indefinite"></animate>
</rect>
</g><g transform="rotate(120 50 50)">
<rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
<animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.5833333333333334s" repeatCount="indefinite"></animate>
</rect>
</g><g transform="rotate(150 50 50)">
<rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
<animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.5s" repeatCount="indefinite"></animate>
</rect>
</g><g transform="rotate(180 50 50)">
<rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
<animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.4166666666666667s" repeatCount="indefinite"></animate>
</rect>
</g><g transform="rotate(210 50 50)">
<rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
<animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.3333333333333333s" repeatCount="indefinite"></animate>
</rect>
</g><g transform="rotate(240 50 50)">
<rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
<animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.25s" repeatCount="indefinite"></animate>
</rect>
</g><g transform="rotate(270 50 50)">
<rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
<animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.16666666666666666s" repeatCount="indefinite"></animate>
</rect>
</g><g transform="rotate(300 50 50)">
<rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
<animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.08333333333333333s" repeatCount="indefinite"></animate>
</rect>
</g><g transform="rotate(330 50 50)">
<rect x="49" y="24" rx="0" ry="0" width="2" height="12" fill="#20a5d6">
<animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="0s" repeatCount="indefinite"></animate>
</rect>
</g>
</svg>
</div>
);
};
export default LoadingIndicator;
@@ -0,0 +1,44 @@
.dcmrt-panel-section {
display: flex;
flex-direction: column;
color: var(--text-primary-color);
font-size: 12px;
}
.dcmrt-panel-section .header {
display: flex;
flex-direction: row;
align-items: center;
justify-content: space-between;
background-color: var(--ui-gray-dark);
border-radius: 5px;
font-weight: bold;
padding: 10px 15px;
}
.dcmrt-panel-section .header .eye-icon,
.dcmrt-panel-section .header .angle-double-down,
.dcmrt-panel-section .header .angle-double-up {
cursor: pointer;
color: var(--active-color);
}
.dcmrt-panel-section .header .eye-icon:hover,
.dcmrt-panel-section .header .angle-double-down:hover,
.dcmrt-panel-section .header .angle-double-up:hover {
color: var(--hover-color);
}
.dcmrt-panel-section .header .eye-icon.expanded {
color: var(--default-color);
}
.icons {
display: flex;
align-items: center;
border-radius: 5px;
}
.icons .angle-double-down, .icons .angle-double-up {
margin-left: 15px;
}
@@ -0,0 +1,82 @@
import React, { useState, useEffect } from 'react';
import PropTypes from 'prop-types';
import { Icon } from '@ohif/ui';
import './PanelSection.css';
import LoadingIndicator from '../LoadingIndicator/LoadingIndicator';
const PanelSection = ({
title,
children,
visible = false,
expanded = false,
loading = false,
hideVisibleButton = false,
onVisibilityChange = () => { },
onExpandChange = () => { }
}) => {
const [isExpanded, setIsExpanded] = useState(expanded);
const [isVisible, setIsVisible] = useState(visible);
useEffect(() => {
setIsVisible(visible);
}, [visible]);
return (
<div
className="dcmrt-panel-section"
style={{
marginBottom: isExpanded ? 0 : 2,
height: isExpanded ? '100%' : 'unset'
}}
>
<div className="header">
<div>{title}</div>
<div className="icons">
{!hideVisibleButton && (
<Icon
className={`eye-icon ${isVisible && 'expanded'}`}
name={isVisible ? "eye" : "eye-closed"}
width="20px"
height="20px"
onClick={() => {
const newVisibility = !isVisible;
setIsVisible(newVisibility);
onVisibilityChange(newVisibility);
}}
/>
)}
<Icon
className={`angle-double-${isExpanded ? 'down' : 'up'} ${isExpanded && 'expanded'}`}
name={`angle-double-${isExpanded ? 'down' : 'up'}`}
width="20px"
height="20px"
onClick={() => {
const newExpandValue = !isExpanded;
setIsExpanded(newExpandValue);
onExpandChange(newExpandValue);
}}
/>
</div>
</div>
{loading && isExpanded && <LoadingIndicator expand height="70px" width="70px" />}
{children}
</div>
);
};
PanelSection.propTypes = {
title: PropTypes.string.isRequired,
children: PropTypes.oneOfType([PropTypes.node, PropTypes.func]).isRequired,
visible: PropTypes.bool,
expanded: PropTypes.bool,
onVisibilityChange: PropTypes.func
};
PanelSection.defaultProps = {
visible: false,
expanded: false,
onVisibilityChange: () => { }
};
export default PanelSection;
@@ -0,0 +1,26 @@
.dcmrt-panel {
display: flex;
flex-direction: column;
background-color: var(--primary-background-color);
height: 100%;
width: 100%;
padding: 20px;
}
.dcmrt-panel .dcmrt-panel-header {
display: flex;
flex-direction: row;
justify-content: space-between;
color: white;
}
.dcmrt-panel .dcmrt-panel-header .cog-icon {
align-self: flex-end;
color: var(--default-color);
cursor: pointer;
margin-bottom: 20px;
}
.dcmrt-panel .dcmrt-panel-header .cog-icon:hover {
color: var(--hover-color);
}
@@ -0,0 +1,258 @@
import React, { useState, useEffect } from 'react';
import PropTypes from 'prop-types';
import cornerstoneTools from 'cornerstone-tools';
import cornerstone from 'cornerstone-core';
import { ScrollableArea, TableList, Icon } from '@ohif/ui';
import { utils } from '@ohif/core';
import './RTPanel.css';
import StructureSetItem from '../StructureSetItem/StructureSetItem';
import RTPanelSettings from '../RTSettings/RTSettings';
import PanelSection from '../PanelSection/PanelSection';
import LoadingIndicator from '../LoadingIndicator/LoadingIndicator';
const { studyMetadataManager } = utils;
const refreshViewport = () => {
cornerstone.getEnabledElements().forEach(enabledElement => {
cornerstone.updateImage(enabledElement.element);
});
};
/**
* RTPanel component
*
* @param {Object} props
* @param {Array} props.studies
* @param {Array} props.viewports - viewportSpecificData
* @param {number} props.activeIndex - activeViewportIndex
* @param {number} props.isOpen - isOpen
* @returns component
*/
const RTPanel = ({ studies, viewports, activeIndex, isOpen, onContourItemClick }) => {
const [selectedContour, setSelectedContour] = useState();
const DEFAULT_SET_INDEX = 0;
const DEFAULT_STATE = {
referencedDisplaysets: [],
sets: [],
selectedSet: null,
};
const [state, setState] = useState(DEFAULT_STATE);
const [showSettings, setShowSettings] = useState(false);
const activeViewport = viewports[activeIndex];
/*
* TODO: Improve the way we notify parts of the app that depends on rts to be loaded.
*
* Currently we are using a non-ideal implementation through a custom event to notify the rtstruct panel
* or other components that could rely on loaded rtstructs that
* the first batch of structs were loaded so that e.g. when the user opens the panel
* before the structs are fully loaded, the panel can subscribe to this custom event
* and update itself with the new structs.
*
* This limitation is due to the fact that the rtmodule is an object (which will be
* updated after the structs are loaded) that React its not aware of its changes
* because the module object its not passed in to the panel component as prop but accessed externally.
*
* Improving this event approach to something reactive that can be tracked inside the react lifecycle,
* allows us to easily watch the module or the rtstruct loading process in any other component
* without subscribing to external events.
*/
useEffect(() => {
document.addEventListener('extensiondicomrtrtloaded', updateStructureSets);
return () => {
document.removeEventListener('extensiondicomrtrtloaded', updateStructureSets);
};
}, []);
const updateStructureSets = () => {
const module = cornerstoneTools.getModule('rtstruct');
const StructureSets = module.state.StructureSets;
if (StructureSets && StructureSets.length) {
const viewportSets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(
activeViewport.SeriesInstanceUID
);
const studyMetadata = studyMetadataManager.get(activeViewport.StudyInstanceUID);
const referencedDisplaysets = studyMetadata.getDerivedDatasets({
referencedSeriesInstanceUID: activeViewport.SeriesInstanceUID,
Modality: 'RTSTRUCT',
});
if (viewportSets.length) {
const defaultSet = viewportSets[DEFAULT_SET_INDEX];
setState({
referencedDisplaysets,
selectedSet: defaultSet,
sets: viewportSets
});
} else {
setState(DEFAULT_STATE);
}
}
};
useEffect(() => {
updateStructureSets();
}, [studies, viewports, activeIndex]);
useEffect(() => {
setShowSettings(showSettings && !isOpen);
}, [isOpen]);
const toContourItem = ({ ROINumber, ROIName, RTROIObservations, colorArray, visible }, loadedSet) => {
let interpretedType = '';
if (RTROIObservations && RTROIObservations.RTROIInterpretedType) {
interpretedType = `(${RTROIObservations.RTROIInterpretedType})`;
}
const isSameContour = selectedContour && selectedContour === ROINumber;
return (
<StructureSetItem
key={ROINumber}
selected={isSameContour}
onClick={() => {
setSelectedContour(isSameContour ? null : ROINumber);
const enabledElements = cornerstone.getEnabledElements();
const element = enabledElements[activeIndex].element;
const toolState = cornerstoneTools.getToolState(element, 'stack');
if (!toolState) {
return;
}
const imageIds = toolState.data[0].imageIds;
const module = cornerstoneTools.getModule('rtstruct');
const imageId = module.getters.imageIdOfCenterFrameOfROIContour(
state.selectedSet.SeriesInstanceUID,
ROINumber,
imageIds
);
const frameIndex = imageIds.indexOf(imageId);
const SOPInstanceUID = cornerstone.metaData.get('SOPInstanceUID', imageId);
const StudyInstanceUID = cornerstone.metaData.get('StudyInstanceUID', imageId);
onContourItemClick({
StudyInstanceUID,
SOPInstanceUID,
frameIndex,
activeViewportIndex: activeIndex
});
}}
label={`${ROIName} ${interpretedType}`}
index={ROINumber}
color={colorArray}
visible={visible}
onVisibilityChange={() => {
const module = cornerstoneTools.getModule('rtstruct');
module.setters.toggleROIContour(state.selectedSet.SeriesInstanceUID, ROINumber);
}}
/>
);
};
const configurationChangeHandler = newConfiguration => {
const module = cornerstoneTools.getModule('rtstruct');
module.configuration.lineWidth = newConfiguration.lineWidth;
module.configuration.opacity = newConfiguration.opacity;
refreshViewport();
};
if (showSettings) {
const module = cornerstoneTools.getModule('rtstruct');
return (
<RTPanelSettings
configuration={module.configuration}
onBack={() => setShowSettings(false)}
onChange={configurationChangeHandler}
/>
);
}
return (
<div className="dcmrt-panel">
<div className="dcmrt-panel-header">
<h3>RT Structure Sets</h3>
<Icon
className="cog-icon"
name="cog"
width="25px"
height="25px"
onClick={() => setShowSettings(true)}
/>
</div>
{!state.referencedDisplaysets.length && <LoadingIndicator expand height="70px" width="70px" />}
{state.referencedDisplaysets.map(displaySet => {
const { SeriesInstanceUID, metadata, isLoaded } = displaySet;
const module = cornerstoneTools.getModule('rtstruct');
const sets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(viewports[activeIndex].SeriesInstanceUID);
const loadedSet = sets.find(set => set.SeriesInstanceUID === SeriesInstanceUID);
return (
<PanelSection
key={SeriesInstanceUID}
title={metadata.StructureSetLabel}
loading={!isLoaded || !loadedSet}
visible={isLoaded && loadedSet.visible}
hideVisibleButton={!isLoaded}
expanded={isLoaded && loadedSet.SeriesInstanceUID === state.selectedSet.SeriesInstanceUID}
onVisibilityChange={() => {
const module = cornerstoneTools.getModule('rtstruct');
module.setters.toggleStructureSet(SeriesInstanceUID);
}}
onExpandChange={async () => {
if (!isLoaded) {
await displaySet.load(viewports[activeIndex], studies);
const module = cornerstoneTools.getModule('rtstruct');
const sets = module.getters.structuresSetsWhichReferenceSeriesInstanceUid(viewports[activeIndex].SeriesInstanceUID);
const selectedSet = sets.find(set => set.SeriesInstanceUID === SeriesInstanceUID);
setState(state => ({ ...state, selectedSet, sets }));
}
}}
>
<ScrollableArea>
<TableList headless>
{isLoaded && loadedSet.ROIContours.map(c => toContourItem(c, loadedSet))}
</TableList>
</ScrollableArea>
</PanelSection>
);
})}
</div>
);
};
RTPanel.propTypes = {
viewports: PropTypes.shape({
displaySetInstanceUID: PropTypes.string,
frameRate: PropTypes.any,
InstanceNumber: PropTypes.number,
isMultiFrame: PropTypes.bool,
isReconstructable: PropTypes.bool,
Modality: PropTypes.string,
plugin: PropTypes.string,
SeriesDate: PropTypes.string,
SeriesDescription: PropTypes.string,
SeriesInstanceUID: PropTypes.string,
SeriesNumber: PropTypes.any,
SeriesTime: PropTypes.string,
sopClassUIDs: PropTypes.arrayOf(PropTypes.string),
StudyInstanceUID: PropTypes.string,
}),
activeIndex: PropTypes.number.isRequired,
studies: PropTypes.array.isRequired,
isOpen: PropTypes.bool.isRequired,
};
RTPanel.defaultProps = {};
export default RTPanel;
@@ -0,0 +1,88 @@
.dcmrt-settings {
display: flex;
flex-direction: column;
padding: 20px;
color: white;
}
.dcmrt-settings .settings-title {
display: flex;
flex-direction: row;
align-items: center;
justify-content: space-between;
padding-bottom: 20px;
}
.dcmrt-settings .settings-title h3 {
color: var(--text-primary-color);
margin: 0;
padding: 0;
}
.dcmrt-settings .settings-section .content {
padding: 10px;
background-color: var(--ui-gray-dark);
border-radius: 5px;
}
.dcmrt-settings .settings-section .header {
border-bottom: 2px solid black;
display: flex;
flex-direction: row;
align-items: center;
justify-content: space-between;
background-color: var(--ui-gray-dark);
border-radius: 5px;
font-weight: bold;
font-size: 12px;
padding: 10px 15px;
}
.dcmrt-settings .settings-section p {
font-weight: bold;
}
.dcmrt-settings .range {
display: flex;
padding: 10px 10px;
font-size: 12px;
}
.dcmrt-settings .range:not(:last-of-type) {
padding-bottom: 0;
}
.dcmrt-settings .range label {
margin: 0;
display: unset;
min-width: 40px;
max-width: 40px;
}
.dcmrt-settings .range input {
width: 100%;
padding: 0 20px 0 20px;
}
.dcmrt-settings .return-button {
color: #333;
background-color: #fff;
padding: 4px 12px;
line-height: 1.4;
text-align: center;
white-space: nowrap;
vertical-align: middle;
cursor: pointer;
user-select: none;
border: 1px solid #ccc;
border-radius: 4px;
transition: all 0.15s ease;
}
.dcmrt-settings .return-button:hover,
.dcmrt-settings .return-button:active,
.dcmrt-settings .return-button.active {
background-color: var(--active-color);
border-color: var(--ui-border-color-active);
color: #fff;
}
@@ -0,0 +1,71 @@
import React, { useState, useEffect } from 'react';
import PropTypes from 'prop-types';
import { Range } from '@ohif/ui';
import './RTSettings.css';
const RTSettings = ({ configuration, onBack, onChange }) => {
const toFloat = value => parseFloat(value / 100).toFixed(2);
const save = (field, value) => {
onChange({ ...configuration, [field]: value });
};
const SettingsSection = ({ title, children }) => {
return (
<div className="settings-section">
<div className="header">{title}</div>
<div className="content">
{children}
</div>
</div>
);
};
return (
<div className="dcmrt-settings">
<div className="settings-title">
<h3>RT Structure Set Settings</h3>
<button className="return-button" onClick={onBack}>
Back
</button>
</div>
<SettingsSection title="Segment Outline">
<div className="range">
<label htmlFor="range">Opacity</label>
<Range
showPercentage
step={1}
min={0}
max={100}
value={configuration.opacity * 100}
onChange={event => save('opacity', toFloat(event.target.value))}
/>
</div>
<div className="range">
<label htmlFor="range">Width</label>
<Range
showValue
step={1}
min={1}
max={5}
value={configuration.lineWidth}
onChange={event => save('lineWidth', parseInt(event.target.value))}
/>
</div>
</SettingsSection>
</div>
);
};
RTSettings.propTypes = {
configuration: PropTypes.shape({
lineWidth: PropTypes.oneOfType([PropTypes.number, PropTypes.string]).isRequired,
opacity: PropTypes.oneOfType([PropTypes.number, PropTypes.string]).isRequired,
}).isRequired,
onBack: PropTypes.func.isRequired,
onChange: PropTypes.func.isRequired,
};
export default RTSettings;
@@ -0,0 +1,85 @@
.dcmrt-structure-set-item .item-color-section {
display: flex;
justify-content: center;
align-items: center;
flex-direction: column;
}
.dcmrt-structure-set-item .item-color {
margin-top: 8px;
border-radius: 100%;
width: 20px;
height: 20px;
}
.dcmrt-structure-set-item .item-info {
display: inline-block;
margin-top: 9px;
padding-left: 9px;
width: 90px;
border-left: 1px solid var(--text-secondary-color);
color: var(--text-primary-color);
width: 100%;
}
.dcmrt-structure-set-item.selected .item-actions {
height: 35px;
visibility: visible;
}
.dcmrt-structure-set-item .item-actions {
margin-left: -1px;
background-color: var(--ui-gray-darker);
height: 0;
overflow: hidden;
transition: all 0.3s ease;
visibility: hidden;
padding-left: 14px;
}
.dcmrt-structure-set-item .item-actions .btnAction {
background-color: transparent;
border: none;
color: var(--default-color);
cursor: pointer;
line-height: 35px;
height: 35px;
transition: all 0.3s ease;
}
.dcmrt-structure-set-item .item-actions .btnAction:hover, .dcmrt-structure-set-item .item-actions .btnAction:active {
color: var(--text-primary-color);
}
.dcmrt-structure-set-item .item-actions .btnAction i {
margin-right: 4px;
}
.dcmrt-structure-set-item.selected .item-actions {
height: 35px;
visibility: visible;
}
.dcmrt-structure-set-item .item-label {
overflow: hidden;
max-width: calc(100% - 15px); /* calc(100% - 50px); 20px = eye icon */
text-overflow: ellipsis;
overflow-wrap: normal;
white-space: nowrap;
display: flex;
justify-content: space-between;
}
.dcmrt-structure-set-item .item-label .eye-icon {
cursor: pointer;
color: var(--active-color);
}
.dcmrt-structure-set-item .item-label .eye-icon:hover {
color: var(--hover-color);
}
.dcmrt-structure-set-item .item-label .eye-icon.--visible {
color: var(--default-color);
}
@@ -0,0 +1,100 @@
import React, { useState } from 'react';
import PropTypes from 'prop-types';
import { TableListItem, Icon } from '@ohif/ui';
import './StructureSetItem.css';
const ColoredCircle = ({ color }) => {
return (
<div
className="item-color"
style={{ backgroundColor: `rgba(${color.join(',')})` }}
></div>
);
};
ColoredCircle.propTypes = {
color: PropTypes.array.isRequired,
};
const StructureSetItem = ({
index,
label,
onClick,
itemClass,
color,
visible = true,
onVisibilityChange,
selected = false,
}) => {
const [isVisible, setIsVisible] = useState(visible);
return (
<div className={`dcmrt-structure-set-item ${selected && 'selected'}`}>
<TableListItem
key={index}
itemKey={index}
itemIndex={index}
itemClass={itemClass}
itemMeta={<ColoredCircle color={color} />}
itemMetaClass="item-color-section"
onItemClick={onClick}
>
<div>
<div className="item-label" style={{ marginBottom: 4 }}>
{label}
<Icon
className={`eye-icon ${isVisible && '--visible'}`}
name={isVisible ? 'eye' : 'eye-closed'}
width="20px"
height="20px"
onClick={event => {
event.stopPropagation();
const newVisibility = !isVisible;
setIsVisible(newVisibility);
onVisibilityChange(newVisibility);
}}
/>
</div>
{false && <div className="item-info">{'...'}</div>}
{false && (
<div className="item-actions">
<button
className="btnAction"
onClick={() => console.log('Relabelling...')}
>
<span style={{ marginRight: '4px' }}>
<Icon name="edit" width="14px" height="14px" />
</span>
Relabel
</button>
<button
className="btnAction"
onClick={() => console.log('Editing description...')}
>
<span style={{ marginRight: '4px' }}>
<Icon name="edit" width="14px" height="14px" />
</span>
Description
</button>
</div>
)}
</div>
</TableListItem>
</div>
);
};
StructureSetItem.propTypes = {
index: PropTypes.oneOfType([PropTypes.string, PropTypes.number]).isRequired,
label: PropTypes.string.isRequired,
onClick: PropTypes.func,
itemClass: PropTypes.string,
color: PropTypes.array.isRequired,
};
StructureSetItem.defaultProps = {
itemClass: '',
onClick: () => { },
};
export default StructureSetItem;
+3
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@@ -0,0 +1,3 @@
const id = 'rt';
export default id;
+78
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@@ -0,0 +1,78 @@
import React from 'react';
import init from './init.js';
import sopClassHandlerModule from './OHIFDicomRTStructSopClassHandler';
import id from './id.js';
import RTPanel from './components/RTPanel/RTPanel';
export default {
/**
* Only required property. Should be a unique value across all extensions.
*/
id,
/**
*
*
* @param {object} [configuration={}]
* @param {object|array} [configuration.csToolsConfig] - Passed directly to `initCornerstoneTools`
*/
preRegistration({ servicesManager, configuration = {} }) {
init({ servicesManager, configuration });
},
getPanelModule({ commandsManager }) {
const ExtendedRTPanel = props => {
const contourItemClickHandler = contourData => {
commandsManager.runCommand('jumpToImage', contourData);
};
return (
<RTPanel
{...props}
onContourItemClick={contourItemClickHandler}
/>
);
};
return {
menuOptions: [
{
icon: 'list',
label: 'RTSTRUCT',
target: 'rt-panel',
isDisabled: studies => {
if (!studies) {
return true;
}
for (let i = 0; i < studies.length; i++) {
const study = studies[i];
if (study && study.series) {
for (let j = 0; j < study.series.length; j++) {
const series = study.series[j];
console.log(studies);
if (['RTSTRUCT', 'RTPLAN', 'RTDOSE'].includes(series.Modality)) {
return false;
}
}
}
}
return true;
},
},
],
components: [
{
id: 'rt-panel',
component: ExtendedRTPanel,
},
],
defaultContext: ['VIEWER'],
};
},
getSopClassHandlerModule({ servicesManager }) {
return sopClassHandlerModule;
},
};
+25
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@@ -0,0 +1,25 @@
import cornerstoneTools from 'cornerstone-tools';
import RTStructDisplayTool from './tools/RTStructDisplayTool';
import rtStructModule from './tools/modules/rtStructModule';
import TOOL_NAMES from './utils/toolNames';
const defaultConfig = {
TOOL_NAMES: {
RT_STRUCT_DISPLAY_TOOL: 'RTStructDisplayTool',
},
};
/**
*
* @param {object} configuration
* @param {Object|Array} configuration.csToolsConfig
*/
export default function init({ servicesManager, configuration = {} }) {
const conifg = Object.assign({}, defaultConfig, configuration);
TOOL_NAMES.RT_STRUCT_DISPLAY_TOOL = conifg.TOOL_NAMES.RT_STRUCT_DISPLAY_TOOL;
cornerstoneTools.register('module', 'rtstruct', rtStructModule);
cornerstoneTools.addTool(RTStructDisplayTool);
}
+309
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@@ -0,0 +1,309 @@
import OHIF from '@ohif/core';
import * as dcmjs from 'dcmjs';
import cornerstone from 'cornerstone-core';
import cornerstoneTools from 'cornerstone-tools';
import transformPointsToImagePlane from './utils/transformPointsToImagePlane';
import TOOL_NAMES from './utils/toolNames';
const dicomlab2RGB = dcmjs.data.Colors.dicomlab2RGB;
const globalImageIdSpecificToolStateManager =
cornerstoneTools.globalImageIdSpecificToolStateManager;
const { DicomLoaderService } = OHIF.utils;
export default async function loadRTStruct(
rtStructDisplaySet,
referencedDisplaySet,
studies
) {
const rtStructModule = cornerstoneTools.getModule('rtstruct');
// Set here is loading is asynchronous.
// If this function throws its set back to false.
rtStructDisplaySet.isLoaded = true;
const { StudyInstanceUID, SeriesInstanceUID } = referencedDisplaySet;
const segArrayBuffer = await DicomLoaderService.findDicomDataPromise(
rtStructDisplaySet,
studies
);
const dicomData = dcmjs.data.DicomMessage.readFile(segArrayBuffer);
const rtStructDataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
dicomData.dict
);
rtStructDataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(
dicomData.meta
);
// global cornerstone tools state to attach measurements to.
const toolState = globalImageIdSpecificToolStateManager.saveToolState();
const {
StructureSetROISequence,
ROIContourSequence,
RTROIObservationsSequence,
StructureSetLabel,
} = rtStructDataset;
// Define our structure set entry and add it to the rtstruct module state.
const structureSet = {
StructureSetLabel,
SeriesInstanceUID: rtStructDataset.SeriesInstanceUID,
ROIContours: [],
referencedSeriesSequence:
rtStructDisplaySet.metadata.ReferencedSeriesSequence,
visible: true,
};
rtStructModule.setters.structureSet(structureSet);
const imageIdSopInstanceUidPairs = _getImageIdSopInstanceUidPairsForDisplaySet(
studies,
StudyInstanceUID,
SeriesInstanceUID
);
const rtStructDisplayToolName = TOOL_NAMES.RTSTRUCT_DISPLAY_TOOL;
for (let i = 0; i < ROIContourSequence.length; i++) {
const ROIContour = ROIContourSequence[i];
const { ReferencedROINumber, ContourSequence } = ROIContour;
if (!ContourSequence) {
continue;
}
_setROIContourMetadata(
structureSet,
StructureSetROISequence,
RTROIObservationsSequence,
ROIContour
);
for (let c = 0; c < ContourSequence.length; c++) {
const {
ContourImageSequence,
ContourData,
NumberOfContourPoints,
ContourGeometricType,
} = ContourSequence[c];
if (ContourGeometricType !== 'CLOSED_PLANAR') {
// TODO: Do we want to visualise types other than closed planar?
// We could easily do open planar.
continue;
}
const sopInstanceUID = ContourImageSequence.ReferencedSOPInstanceUID;
const imageId = _getImageId(imageIdSopInstanceUidPairs, sopInstanceUID);
const imageIdSpecificToolData = _getOrCreateImageIdSpecificToolData(
toolState,
imageId,
rtStructDisplayToolName
);
const imagePlane = cornerstone.metaData.get('imagePlaneModule', imageId);
const points = [];
for (let p = 0; p < NumberOfContourPoints * 3; p += 3) {
points.push({
x: ContourData[p],
y: ContourData[p + 1],
z: ContourData[p + 2],
});
}
transformPointsToImagePlane(points, imagePlane);
const measurementData = {
handles: {
points,
},
structureSetSeriesInstanceUid: rtStructDataset.SeriesInstanceUID,
ROINumber: ReferencedROINumber,
};
imageIdSpecificToolData.push(measurementData);
}
}
_setToolEnabledIfNotEnabled(rtStructDisplayToolName);
/*
* TODO: Improve the way we notify parts of the app that depends on rts to be loaded.
*
* Currently we are using a non-ideal implementation through a custom event to notify the rtstruct panel
* or other components that could rely on loaded rtstructs that
* the first batch of structs were loaded so that e.g. when the user opens the panel
* before the structs are fully loaded, the panel can subscribe to this custom event
* and update itself with the new structs.
*
* This limitation is due to the fact that the rtmodule is an object (which will be
* updated after the structs are loaded) that React its not aware of its changes
* because the module object its not passed in to the panel component as prop but accessed externally.
*
* Improving this event approach to something reactive that can be tracked inside the react lifecycle,
* allows us to easily watch the module or the rtstruct loading process in any other component
* without subscribing to external events.
*/
const event = new CustomEvent('extensiondicomrtrtloaded');
document.dispatchEvent(event);
}
function _setROIContourMetadata(
structureSet,
StructureSetROISequence,
RTROIObservationsSequence,
ROIContour
) {
const StructureSetROI = StructureSetROISequence.find(
structureSetROI =>
structureSetROI.ROINumber === ROIContour.ReferencedROINumber
);
const ROIContourData = {
ROINumber: StructureSetROI.ROINumber,
ROIName: StructureSetROI.ROIName,
ROIGenerationAlgorithm: StructureSetROI.ROIGenerationAlgorithm,
ROIDescription: StructureSetROI.ROIDescription,
visible: true,
};
_setROIContourDataColor(ROIContour, ROIContourData);
if (RTROIObservationsSequence) {
// If present, add additional RTROIObservations metadata.
_setROIContourRTROIObservations(
ROIContourData,
RTROIObservationsSequence,
ROIContour.ReferencedROINumber
);
}
structureSet.ROIContours.push(ROIContourData);
}
function _setROIContourDataColor(ROIContour, ROIContourData) {
let { ROIDisplayColor, RecommendedDisplayCIELabValue } = ROIContour;
if (!ROIDisplayColor && RecommendedDisplayCIELabValue) {
// If ROIDisplayColor is absent, try using the RecommendedDisplayCIELabValue color.
ROIDisplayColor = dicomlab2RGB(RecommendedDisplayCIELabValue);
}
if (ROIDisplayColor) {
ROIContourData.colorArray = [...ROIDisplayColor];
} else {
//Choose a color from the cornerstoneTools colorLUT
// We sample from the default color LUT here (i.e. 0), as we have nothing else to go on.
const { getters } = cornerstoneTools.getModule('segmentation');
const color = getters.colorForSegmentIndexColorLUT(
0,
ROIContourData.ROINumber
);
ROIContourData.colorArray = [...color];
}
}
function _setROIContourRTROIObservations(
ROIContourData,
RTROIObservationsSequence,
ROINumber
) {
const RTROIObservations = RTROIObservationsSequence.find(
RTROIObservations => RTROIObservations.ReferencedROINumber === ROINumber
);
if (RTROIObservations) {
// Deep copy so we don't keep the reference to the dcmjs dataset entry.
const {
ObservationNumber,
ROIObservationDescription,
RTROIInterpretedType,
ROIInterpreter,
} = RTROIObservations;
ROIContourData.RTROIObservations = {
ObservationNumber,
ROIObservationDescription,
RTROIInterpretedType,
ROIInterpreter,
};
}
}
function _setToolEnabledIfNotEnabled(toolName) {
cornerstone.getEnabledElements().forEach(enabledElement => {
const { element } = enabledElement;
const tool = cornerstoneTools.getToolForElement(element, toolName);
if (tool.mode !== 'enabled') {
// If not already active or passive, set passive so contours render.
cornerstoneTools.setToolEnabled(toolName);
}
cornerstone.updateImage(element);
});
}
function _getOrCreateImageIdSpecificToolData(toolState, imageId, toolName) {
if (toolState.hasOwnProperty(imageId) === false) {
toolState[imageId] = {};
}
const imageIdToolState = toolState[imageId];
// If we don't have tool state for this type of tool, add an empty object
if (imageIdToolState.hasOwnProperty(toolName) === false) {
imageIdToolState[toolName] = {
data: [],
};
}
return imageIdToolState[toolName].data;
}
const _getImageId = (imageIdSopInstanceUidPairs, sopInstanceUID) => {
const imageIdSopInstanceUidPairsEntry = imageIdSopInstanceUidPairs.find(
imageIdSopInstanceUidPairsEntry =>
imageIdSopInstanceUidPairsEntry.sopInstanceUID === sopInstanceUID
);
return imageIdSopInstanceUidPairsEntry.imageId;
};
function _getImageIdSopInstanceUidPairsForDisplaySet(
studies,
StudyInstanceUID,
SeriesInstanceUID
) {
const study = studies.find(
study => study.StudyInstanceUID === StudyInstanceUID
);
const displaySets = study.displaySets.filter(set => {
return set.SeriesInstanceUID === SeriesInstanceUID;
});
if (displaySets.length > 1) {
console.warn(
'More than one display set with the same SeriesInstanceUID. This is not supported yet...'
);
// TODO -> We could make check the instance list and see if any match?
// Do we split the segmentation into two cornerstoneTools segmentations if there are images in both series?
// ^ Will that even happen?
}
const referencedDisplaySet = displaySets[0];
return referencedDisplaySet.images.map(image => {
return {
imageId: image.getImageId(),
sopInstanceUID: image.getSOPInstanceUID(),
};
});
}
@@ -0,0 +1,93 @@
import { importInternal, getToolState, toolColors } from 'cornerstone-tools';
import TOOL_NAMES from '../utils/toolNames';
// Cornerstone 3rd party dev kit imports
const draw = importInternal('drawing/draw');
const drawJoinedLines = importInternal('drawing/drawJoinedLines');
const getNewContext = importInternal('drawing/getNewContext');
const BaseTool = importInternal('base/BaseTool');
/**
* @class RTStructDisplayTool - Renders RTSTRUCT data in a read only manner (i.e. as an overlay).
* @extends cornerstoneTools.BaseTool
*/
export default class RTStructDisplayTool extends BaseTool {
constructor(props = {}) {
const defaultProps = {
mixins: ['enabledOrDisabledBinaryTool'],
name: TOOL_NAMES.RTSTRUCT_DISPLAY_TOOL,
};
const initialProps = Object.assign(defaultProps, props);
super(initialProps);
this._rtStructModule = cornerstoneTools.getModule('rtstruct');
}
renderToolData(evt) {
const eventData = evt.detail;
const rtstructModule = this._rtStructModule;
const toolState = getToolState(evt.currentTarget, this.name);
if (!toolState) {
return;
}
const { lineWidth, opacity } = rtstructModule.configuration;
// We have tool data for this element - iterate over each one and draw it
const context = getNewContext(eventData.canvasContext.canvas);
for (let i = 0; i < toolState.data.length; i++) {
const data = toolState.data[i];
const structureSet = rtstructModule.getters.structureSet(
data.structureSetSeriesInstanceUid
);
// Don't render if entire StructureSet is hidden.
if (structureSet.visible === false) {
continue;
}
const ROIContourData = rtstructModule.getters.ROIContour(
data.structureSetSeriesInstanceUid,
data.ROINumber
);
// Don't render if ROIContour is hidden.
if (ROIContourData.visible === false) {
continue;
}
const points = data.handles.points;
if (!points.length) {
continue;
}
const colorArray = ROIContourData.colorArray;
const color = `rgba(${colorArray[0]},${colorArray[1]},${
colorArray[2]
},${opacity})`;
lineWidth;
draw(context, context => {
drawJoinedLines(
context,
eventData.element,
points[points.length - 1],
points,
{
color,
lineWidth,
}
);
});
}
}
}
@@ -0,0 +1,67 @@
import cornerstoneTools from 'cornerstone-tools';
import TOOL_NAMES from '../../../utils/toolNames';
const globalImageIdSpecificToolStateManager =
cornerstoneTools.globalImageIdSpecificToolStateManager;
/**
* getImageIdOfCenterFrameOfROIContour - Returns the imageId nearest to the center of the
* volumes extent in the stack's Z direction which contains one of the ROIContour's Contours.
* @param {string} structureSetSeriesInstanceUid The SeriesInstanceUID of the structure set.
* @param {number} ROINumber The ROINumber of the region.
* @param {string} imageIdsInStack The stack of imageIds.
*
* @returns The imageId
*/
export default function getImageIdOfCenterFrameOfROIContour(
structureSetSeriesInstanceUid,
ROINumber,
imageIdsInStack
) {
const rtStructDisplayToolName = TOOL_NAMES.RTSTRUCT_DISPLAY_TOOL;
const toolState = globalImageIdSpecificToolStateManager.saveToolState();
const imageIdIndicies = [];
for (let i = 0; i < imageIdsInStack.length; i++) {
const imageId = imageIdsInStack[i];
const imageIdSpecificToolState = toolState[imageId];
if (
!imageIdSpecificToolState ||
!imageIdSpecificToolState[rtStructDisplayToolName] ||
!imageIdSpecificToolState[rtStructDisplayToolName].data
) {
continue;
}
const toolData = imageIdSpecificToolState[rtStructDisplayToolName].data;
if (
_toolDataContainsROIContour(
toolData,
structureSetSeriesInstanceUid,
ROINumber
)
) {
imageIdIndicies.push(i);
}
}
const centerImageIdIndex =
imageIdIndicies[Math.floor(imageIdIndicies.length / 2)];
return imageIdsInStack[centerImageIdIndex];
}
function _toolDataContainsROIContour(
toolData,
structureSetSeriesInstanceUid,
ROINumber
) {
return !!toolData.some(
toolDataI =>
toolDataI.structureSetSeriesInstanceUid ===
structureSetSeriesInstanceUid && toolDataI.ROINumber === ROINumber
);
}
@@ -0,0 +1,17 @@
/**
* structureSetReferencesSeriesInstanceUid - Returns true if the structure set
* references the given SeriesInstanceUID.
* @param {*} StructureSet
* @param {*} SeriesInstanceUID
*/
export default function structureSetReferencesSeriesInstanceUid(
StructureSet,
SeriesInstanceUID
) {
const { referencedSeriesSequence } = StructureSet;
return referencedSeriesSequence.some(
referencedSeries =>
referencedSeries.SeriesInstanceUID ===
SeriesInstanceUID
);
}
@@ -0,0 +1,187 @@
import cornerstone from 'cornerstone-core';
import getImageIdOfCenterFrameOfROIContour from './lib/getImageIdOfCenterFrameOfROIContour';
import structureSetReferencesSeriesInstanceUid from './lib/structureSetReferencesSeriesInstanceUid';
// We should put this as a helper somewhere as we are using it in mutliple places.
function refreshViewport() {
cornerstone.getEnabledElements().forEach(enabledElement => {
cornerstone.updateImage(enabledElement.element);
});
}
const configuration = {
lineWidth: 3,
opacity: 1.0,
};
const state = {
StructureSets: [],
};
/**
* Adds a structure set to the module.
* @param {Object} structureSetData The structure set data.
*/
function setStructureSet(structureSetData) {
state.StructureSets.push(structureSetData);
}
/**
* Returns the StructureSet with the given SeriesInstanceUID.
* @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
*
* @returns {Object} The StructureSet.
*/
function getStructureSet(SeriesInstanceUID) {
return state.StructureSets.find(
structureSet => structureSet.SeriesInstanceUID === SeriesInstanceUID
);
}
/**
* Returns the ROI Contour with the given ROINumber on the StructureSet defined by the given
* SeriesInstanceUID.
* @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
* @param {number} ROINumber The ROINUmber of the ROIContour to fetch.
*/
function getROIContour(SeriesInstanceUID, ROINumber) {
const structureSet = getStructureSet(SeriesInstanceUID);
if (!structureSet) {
return;
}
return structureSet.ROIContours.find(
ROIContour => ROIContour.ROINumber === ROINumber
);
}
/**
* Hides the StructureSet.
* @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
*/
function setHideStructureSet(SeriesInstanceUID) {
_setStructureSetVisible(SeriesInstanceUID, false);
}
/**
* Shows the StructureSet.
* @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
*/
function setShowStructureSet(SeriesInstanceUID) {
_setStructureSetVisible(SeriesInstanceUID, true);
}
/**
* Sets the visibility of the StructureSet.
* @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
* @param {boolean} visible Whether the StructureSet should visible or not.
*/
function _setStructureSetVisible(SeriesInstanceUID, visible = true) {
const StructureSet = getStructureSet(SeriesInstanceUID);
if (StructureSet) {
StructureSet.visible = visible;
refreshViewport();
}
}
/**
* Toggles the visibility of the StructureSet.
* @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
*/
function setToggleStructureSet(SeriesInstanceUID) {
const StructureSet = getStructureSet(SeriesInstanceUID);
if (StructureSet) {
StructureSet.visible = !StructureSet.visible;
refreshViewport();
}
}
/**
* Hides the ROIContour.
* @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
* @param {number} ROINumber The ROINUmber of the ROIContour.
*/
function setHideROIContour(SeriesInstanceUID, ROINumber) {
_setROIContourVisible(SeriesInstanceUID, ROINumber, false);
}
/**
* Shows the ROIContour.
* @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
* @param {number} ROINumber The ROINUmber of the ROIContour.
*/
function setShowROIContour(SeriesInstanceUID, ROINumber) {
_setROIContourVisible(SeriesInstanceUID, ROINumber, true);
}
/**
* Sets the visibility of the ROIContour.
* @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
* @param {number} ROINumber The ROINUmber of the ROIContour.
* @param {boolean} visible Whether the StructureSet should visible or not.
*/
function _setROIContourVisible(SeriesInstanceUID, ROINumber, visible = true) {
const ROIContour = getROIContour(SeriesInstanceUID, ROINumber);
if (ROIContour) {
ROIContour.visible = visible;
refreshViewport();
}
}
/**
* Toggles the visibility of the ROIContour.
* @param {string} SeriesInstanceUID The SeriesInstanceUID of the StructureSet.
* @param {number} ROINumber The ROINUmber of the ROIContour.
*/
function setToggleROIContour(SeriesInstanceUID, ROINumber) {
const ROIContour = getROIContour(SeriesInstanceUID, ROINumber);
if (ROIContour) {
ROIContour.visible = !ROIContour.visible;
refreshViewport();
}
}
/**
* Returns an array of StructureSets which reference the given SeriesInstanceUID.
* @param {string} SeriesInstanceUID The SeriesInstanceUID to check.
*/
function getStructuresSetsWhichReferenceSeriesInstanceUid(
SeriesInstanceUID
) {
const { StructureSets } = state;
return StructureSets.filter(StructureSet =>
structureSetReferencesSeriesInstanceUid(
StructureSet,
SeriesInstanceUID
)
);
}
export default {
getters: {
structureSet: getStructureSet,
ROIContour: getROIContour,
structuresSetsWhichReferenceSeriesInstanceUid: getStructuresSetsWhichReferenceSeriesInstanceUid,
imageIdOfCenterFrameOfROIContour: getImageIdOfCenterFrameOfROIContour,
},
setters: {
structureSet: setStructureSet,
hideROIContour: setHideROIContour,
showROIContour: setShowROIContour,
toggleROIContour: setToggleROIContour,
hideStructureSet: setHideStructureSet,
showStructureSet: setShowStructureSet,
toggleStructureSet: setToggleStructureSet,
},
state,
configuration,
};
@@ -0,0 +1,5 @@
const TOOL_NAMES = {
RTSTRUCT_DISPLAY_TOOL: 'RTStructDisplayTool',
};
export default TOOL_NAMES;
@@ -0,0 +1,91 @@
export default function transformPointsToImagePlane(points, imagePlane) {
// See Equation C.7.6.2.1-1 of the DICOM standard
const {
rowCosines,
columnCosines,
rowPixelSpacing: deltaI,
columnPixelSpacing: deltaJ,
imagePositionPatient,
} = imagePlane;
const X = [rowCosines[0], rowCosines[1], rowCosines[2]];
const Y = [columnCosines[0], columnCosines[1], columnCosines[2]];
const S = [
imagePositionPatient[0],
imagePositionPatient[1],
imagePositionPatient[2],
];
// 9 sets of simulataneous equations to choose from, choose which set to solve
// Based on the largest component of each direction cosine.
// This avoids NaNs or floating point errors caused by dividing by very small numbers and ensures a safe mapping
// when mapping between planes that are close to orthogonal.
let ix = 0;
let iy = 0;
let largestDirectionCosineMagnitude = {
x: 0,
y: 0,
};
// Find the element with the largest magnitude in each direction cosine vector.
for (let i = 0; i < X.length; i++) {
if (Math.abs(X[i]) > largestDirectionCosineMagnitude.x) {
ix = i;
largestDirectionCosineMagnitude.x = Math.abs(X[i]);
}
if (Math.abs(Y[i]) > largestDirectionCosineMagnitude.y) {
iy = i;
largestDirectionCosineMagnitude.y = Math.abs(Y[i]);
}
}
const ci = {
// Index of max elements in X and Y
ix,
iy,
};
// Sanity Check
const directionCosineMagnitude = {
x: Math.pow(X[0], 2) + Math.pow(X[1], 2) + Math.pow(X[2], 2),
y: Math.pow(Y[0], 2) + Math.pow(Y[1], 2) + Math.pow(Y[2], 2),
};
if (directionCosineMagnitude.x < 0.99 || directionCosineMagnitude.y < 0.99) {
throw Error(
`Direction cosines do not sum to 1 in quadrature. There is likely a mistake in the DICOM metadata.` +
`directionCosineMagnitudes: ${directionCosineMagnitude.x}, ${directionCosineMagnitude.y}`
);
}
// Fill in elements that won't change between points
const c = [undefined, Y[ci.ix], X[ci.ix], undefined, X[ci.iy], Y[ci.iy]];
for (let pointI = 0; pointI < points.length; pointI++) {
// Subtract imagePositionPatient from the coordinate
const r = [
points[pointI].x - S[0],
points[pointI].y - S[1],
points[pointI].z - S[2],
];
// Set the variable terms in c.
c[0] = r[ci.ix];
c[3] = r[ci.iy];
// General case: Solves the two choosen simulataneous equations to go from the patient coordinate system to the imagePlane.
const i =
(c[0] - (c[1] * c[3]) / c[5]) /
(c[2] * deltaI * (1 - (c[1] * c[4]) / (c[2] * c[5])));
const j = (c[3] - c[4] * i * deltaI) / (c[5] * deltaJ);
// NOTE: Add (0.5, 0.5) to the coordinate, as PCS reference frame is with respect to the centre of the first pixel.
points[pointI].x = i + 0.5;
points[pointI].y = j + 0.5;
delete points[pointI].z;
}
return;
}
@@ -3,6 +3,25 @@
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [0.1.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.1.1...@ohif/extension-dicom-segmentation@0.1.2) (2020-04-09)
**Note:** Version bump only for package @ohif/extension-dicom-segmentation
## [0.1.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.1.0...@ohif/extension-dicom-segmentation@0.1.1) (2020-04-01)
### Bug Fixes
* segmentation not loading ([#1566](https://github.com/OHIF/Viewers/issues/1566)) ([4a7ce1c](https://github.com/OHIF/Viewers/commit/4a7ce1c09324d74c61048393e3a2427757e4001a))
# 0.1.0 (2020-03-13)
+1 -1
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/extension-dicom-segmentation",
"version": "0.1.0",
"version": "0.1.2",
"description": "OHIF extension for viewing segmentations in the 2D MPR view",
"author": "OHIF",
"license": "MIT",
@@ -14,7 +14,7 @@ const OHIFDicomSegSopClassHandler = {
id: 'OHIFDicomSegSopClassHandler',
type: MODULE_TYPES.SOP_CLASS_HANDLER,
sopClassUIDs,
getDisplaySetFromSeries: function(
getDisplaySetFromSeries: function (
series,
study,
dicomWebClient,
@@ -53,7 +53,7 @@ const OHIFDicomSegSopClassHandler = {
SeriesDescription,
};
segDisplaySet.load = function(referencedDisplaySet, studies) {
segDisplaySet.load = function (referencedDisplaySet, studies) {
return loadSegmentation(
segDisplaySet,
referencedDisplaySet,
@@ -39,50 +39,26 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
* TODO: wrap get/set interactions with the cornerstoneTools
* store with context to make these kind of things less blurry.
*/
const segmentationModule = cornerstoneTools.getModule('segmentation');
const { configuration } = segmentationModule;
const { configuration } = cornerstoneTools.getModule('segmentation');
const DEFAULT_BRUSH_RADIUS = configuration.radius || 10;
const [brushRadius, setBrushRadius] = useState(DEFAULT_BRUSH_RADIUS);
/* TODO: We shouldn't hardcode this color, in the future the SEG may set the colorLUT to whatever it wants. */
const [brushColor, setBrushColor] = useState('rgba(221, 85, 85, 1)');
const [selectedSegment, setSelectedSegment] = useState();
const [showSegSettings, setShowSegSettings] = useState(false);
const [selectedSegmentation, setSelectedSegmentation] = useState();
const viewport = viewports[activeIndex];
const {
StudyInstanceUID,
SeriesInstanceUID,
displaySetInstanceUID,
} = viewport;
const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
const firstImageId = studyMetadata.getFirstImageId(displaySetInstanceUID);
/* CornerstoneTools */
const [brushStackState, setBrushStackState] = useState(
segmentationModule.state.series[firstImageId]
);
const [state, setState] = useState({
brushRadius: DEFAULT_BRUSH_RADIUS,
brushColor: 'rgba(221, 85, 85, 1)', /* TODO: We shouldn't hardcode this color, in the future the SEG may set the colorLUT to whatever it wants. */
selectedSegment: null,
selectedSegmentation: null,
showSegSettings: false,
brushStackState: null,
labelmapList: [],
segmentList: []
});
useEffect(() => {
setShowSegSettings(showSegSettings && !isOpen);
}, [isOpen]);
useEffect(() => {
setBrushStackState(segmentationModule.state.series[firstImageId]);
}, [studies, viewports, activeIndex, firstImageId]);
useEffect(() => {
if (brushStackState) {
setSelectedSegmentation(brushStackState.activeLabelmapIndex);
}
const labelmapModifiedHandler = event => {
log.warn('labelmap modified', event);
setBrushStackState(segmentationModule.state.series[firstImageId]);
log.warn('Segmentation Panel: labelmap modified', event);
const module = cornerstoneTools.getModule('segmentation');
const activeViewport = viewports[activeIndex];
const firstImageId = studyMetadata.getFirstImageId(activeViewport.displaySetInstanceUID);
updateState('brushStackState', module.state.series[firstImageId]);
};
/*
@@ -107,27 +83,43 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
};
});
if (!brushStackState) {
return null;
}
useEffect(() => {
const module = cornerstoneTools.getModule('segmentation');
const activeViewport = viewports[activeIndex];
const studyMetadata = studyMetadataManager.get(activeViewport.StudyInstanceUID);
const firstImageId = studyMetadata.getFirstImageId(activeViewport.displaySetInstanceUID);
const brushStackState = module.state.series[firstImageId];
const labelmap3D =
brushStackState.labelmaps3D[brushStackState.activeLabelmapIndex];
if (brushStackState) {
const labelmap3D = brushStackState.labelmaps3D[brushStackState.activeLabelmapIndex];
const labelmapList = getLabelmapList(brushStackState, firstImageId, activeViewport);
const segmentList = getSegmentList(labelmap3D, firstImageId);
setState(state => ({
...state,
brushStackState,
selectedSegmentation: brushStackState.activeLabelmapIndex,
labelmapList,
segmentList
}));
} else {
setState(state => ({
...state,
labelmapList: [],
segmentList: [],
}));
}
}, [studies, viewports, activeIndex]);
/*
* 2. UseEffect to update state? or to a least trigger a re-render
* 4. Toggle visibility of labelmap?
* 5. Toggle visibility of seg?
*
* If the port is cornerstone, just need to call a re-render.
* If the port is vtkjs, its a bit more tricky as we now need to create a new
*/
/* Handle open/closed panel behaviour */
useEffect(() => {
updateState('showSegSettings', state.showSegSettings && !isOpen);
}, [isOpen]);
const getLabelmapList = () => {
const getLabelmapList = (brushStackState, firstImageId, activeViewport) => {
/* Get list of SEG labelmaps specific to active viewport (reference series) */
const referencedSegDisplaysets = _getReferencedSegDisplaysets(
StudyInstanceUID,
SeriesInstanceUID
activeViewport.StudyInstanceUID,
activeViewport.SeriesInstanceUID
);
return referencedSegDisplaysets.map((displaySet, index) => {
@@ -148,23 +140,19 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
description: displayDate,
onClick: async () => {
const activatedLabelmapIndex = await _setActiveLabelmap(
viewport,
activeViewport,
studies,
displaySet,
firstImageId,
brushStackState.activeLabelmapIndex
);
setSelectedSegmentation(activatedLabelmapIndex);
updateState('selectedSegmentation', activatedLabelmapIndex);
},
};
});
};
const labelmapList = getLabelmapList();
const segmentList = [];
if (labelmap3D) {
const getSegmentList = (labelmap3D, firstImageId) => {
/*
* Newly created segments have no `meta`
* So we instead build a list of all segment indexes in use
@@ -186,10 +174,12 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
}, [])
.sort((a, b) => a - b);
const module = cornerstoneTools.getModule('segmentation');
const colorLutTable =
segmentationModule.state.colorLutTables[labelmap3D.colorLUTIndex];
module.state.colorLutTables[labelmap3D.colorLUTIndex];
const hasLabelmapMeta = labelmap3D.metadata && labelmap3D.metadata.data;
const segmentList = [];
for (let i = 0; i < uniqueSegmentIndexes.length; i++) {
const segmentIndex = uniqueSegmentIndexes[i];
@@ -207,14 +197,14 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
}
}
const sameSegment = selectedSegment === segmentNumber;
const sameSegment = state.selectedSegment === segmentNumber;
const setCurrentSelectedSegment = () => {
_setActiveSegment(
firstImageId,
segmentNumber,
labelmap3D.activeSegmentIndex
);
setSelectedSegment(sameSegment ? null : segmentNumber);
updateState('selectedSegment', sameSegment ? null : segmentNumber);
};
segmentList.push(
@@ -229,20 +219,27 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
);
}
return segmentList;
/*
* Let's iterate over segmentIndexes ^ above
* If meta has a match, use it to show info
* If now, add "no-meta" class
* Show default name
*/
}
};
const updateState = (field, value) => {
setState(state => ({ ...state, [field]: value }));
};
const updateBrushSize = evt => {
const updatedRadius = Number(evt.target.value);
if (updatedRadius !== brushRadius) {
setBrushRadius(updatedRadius);
segmentationModule.setters.radius(updatedRadius);
updateState('brushRadius', updatedRadius);
const module = cornerstoneTools.getModule('segmentation');
module.setters.radius(updatedRadius);
}
};
@@ -251,29 +248,30 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
if (labelmap3D.activeSegmentIndex > 1) {
labelmap3D.activeSegmentIndex--;
}
setSelectedSegment(labelmap3D.activeSegmentIndex);
updateState('selectedSegment', labelmap3D.activeSegmentIndex);
updateActiveSegmentColor();
};
const incrementSegment = event => {
event.preventDefault();
labelmap3D.activeSegmentIndex++;
setSelectedSegment(labelmap3D.activeSegmentIndex);
updateState('selectedSegment', labelmap3D.activeSegmentIndex);
updateActiveSegmentColor();
};
const updateActiveSegmentColor = () => {
const color = getActiveSegmentColor();
setBrushColor(color);
updateState('brushColor', color);
};
const getActiveSegmentColor = () => {
if (!brushStackState) {
if (!state.brushStackState) {
return 'rgba(255, 255, 255, 1)';
}
const module = cornerstoneTools.getModule('segmentation');
const colorLutTable =
segmentationModule.state.colorLutTables[labelmap3D.colorLUTIndex];
module.state.colorLutTables[labelmap3D.colorLUTIndex];
const color = colorLutTable[labelmap3D.activeSegmentIndex];
return `rgba(${color.join(',')})`;
@@ -293,11 +291,11 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
refreshViewport();
};
if (showSegSettings) {
if (state.showSegSettings) {
return (
<SegmentationSettings
configuration={configuration}
onBack={() => setShowSegSettings(false)}
onBack={() => updateState('showSegSettings', false)}
onChange={updateConfiguration}
/>
);
@@ -309,13 +307,13 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
name="cog"
width="25px"
height="25px"
onClick={() => setShowSegSettings(true)}
onClick={() => updateState('showSegSettings', true)}
/>
{false && (
<form className="selector-form">
<BrushColorSelector
defaultColor={brushColor}
index={labelmap3D.activeSegmentIndex}
index={state.selectedSegment}
onNext={incrementSegment}
onPrev={decrementSegment}
/>
@@ -331,17 +329,17 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
<div className="segmentations">
<SegmentationSelect
value={
labelmapList.find(i => i.value === selectedSegmentation) || null
state.labelmapList.find(i => i.value === state.selectedSegmentation) || null
}
formatOptionLabel={SegmentationItem}
options={labelmapList}
options={state.labelmapList}
/>
</div>
<ScrollableArea>
<TableList
customHeader={<SegmentsHeader count={segmentList.length} />}
customHeader={<SegmentsHeader count={state.segmentList.length} />}
>
{segmentList}
{state.segmentList}
</TableList>
</ScrollableArea>
</div>
@@ -373,6 +371,7 @@ SegmentationPanel.propTypes = {
}),
activeIndex: PropTypes.number.isRequired,
studies: PropTypes.array.isRequired,
isOpen: PropTypes.bool.isRequired,
};
SegmentationPanel.defaultProps = {};
@@ -420,7 +419,7 @@ const _setActiveLabelmap = async (
) => {
if (displaySet.labelmapIndex === activeLabelmapIndex) {
log.warn(`${activeLabelmapIndex} is already the active labelmap`);
return;
return displaySet.labelmapIndex;
}
if (!displaySet.isLoaded) {
@@ -431,7 +430,6 @@ const _setActiveLabelmap = async (
const { state } = cornerstoneTools.getModule('segmentation');
const brushStackState = state.series[firstImageId];
brushStackState.activeLabelmapIndex = displaySet.labelmapIndex;
refreshViewport();
+99
View File
@@ -3,6 +3,105 @@
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [1.4.1](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.4.0...@ohif/extension-vtk@1.4.1) (2020-04-23)
**Note:** Version bump only for package @ohif/extension-vtk
# [1.4.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.14...@ohif/extension-vtk@1.4.0) (2020-04-23)
### Features
* configuration to hook into XHR Error handling ([e96205d](https://github.com/OHIF/Viewers/commit/e96205de35e5bec14dc8a9a8509db3dd4e6ecdb6))
## [1.3.14](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.13...@ohif/extension-vtk@1.3.14) (2020-04-22)
**Note:** Version bump only for package @ohif/extension-vtk
## [1.3.13](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.12...@ohif/extension-vtk@1.3.13) (2020-04-17)
**Note:** Version bump only for package @ohif/extension-vtk
## [1.3.12](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.11...@ohif/extension-vtk@1.3.12) (2020-04-15)
**Note:** Version bump only for package @ohif/extension-vtk
## [1.3.11](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.10...@ohif/extension-vtk@1.3.11) (2020-04-09)
### Bug Fixes
* Revert "refactor: Reduce bundle size ([#1575](https://github.com/OHIF/Viewers/issues/1575))" ([#1622](https://github.com/OHIF/Viewers/issues/1622)) ([d21af3f](https://github.com/OHIF/Viewers/commit/d21af3f133492fa31492413b8782936c9ff18b44))
## [1.3.10](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.9...@ohif/extension-vtk@1.3.10) (2020-04-09)
**Note:** Version bump only for package @ohif/extension-vtk
# Change Log
All notable changes to this project will be documented in this file. See
[Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [1.3.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.8...@ohif/extension-vtk@1.3.9) (2020-04-06)
**Note:** Version bump only for package @ohif/extension-vtk
## [1.3.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.7...@ohif/extension-vtk@1.3.8) (2020-04-02)
**Note:** Version bump only for package @ohif/extension-vtk
## [1.3.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.6...@ohif/extension-vtk@1.3.7) (2020-04-02)
**Note:** Version bump only for package @ohif/extension-vtk
## [1.3.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.5...@ohif/extension-vtk@1.3.6) (2020-04-01)
**Note:** Version bump only for package @ohif/extension-vtk
## [1.3.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.4...@ohif/extension-vtk@1.3.5) (2020-03-25)
**Note:** Version bump only for package @ohif/extension-vtk
+5 -5
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/extension-vtk",
"version": "1.3.5",
"version": "1.4.1",
"description": "OHIF extension for VTK.js",
"author": "OHIF",
"license": "MIT",
@@ -34,7 +34,7 @@
"@ohif/ui": "^0.50.0",
"cornerstone-core": "^2.2.8",
"cornerstone-tools": "4.12.5",
"cornerstone-wado-image-loader": "^3.0.0",
"cornerstone-wado-image-loader": "^3.1.0",
"dcmjs": "^0.10.1",
"dicom-parser": "^1.8.3",
"i18next": "^17.0.3",
@@ -53,10 +53,10 @@
"react-vtkjs-viewport": "^0.8.3"
},
"devDependencies": {
"@ohif/core": "^2.6.4",
"@ohif/ui": "^1.4.1",
"@ohif/core": "^2.8.1",
"@ohif/ui": "^1.4.3",
"cornerstone-tools": "4.12.5",
"cornerstone-wado-image-loader": "^3.0.0",
"cornerstone-wado-image-loader": "^3.1.0",
"dicom-parser": "^1.8.3",
"gh-pages": "^2.0.1",
"i18next": "^17.0.3",
+114
View File
@@ -3,6 +3,120 @@
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [2.8.1](https://github.com/OHIF/Viewers/compare/@ohif/core@2.8.0...@ohif/core@2.8.1) (2020-04-23)
### Bug Fixes
* 🐛 Multiframe fix ([#1661](https://github.com/OHIF/Viewers/issues/1661)) ([7120561](https://github.com/OHIF/Viewers/commit/71205618ecb8b592247c5acb32284bfe7e18fce5))
# [2.8.0](https://github.com/OHIF/Viewers/compare/@ohif/core@2.7.1...@ohif/core@2.8.0) (2020-04-23)
### Features
* configuration to hook into XHR Error handling ([e96205d](https://github.com/OHIF/Viewers/commit/e96205de35e5bec14dc8a9a8509db3dd4e6ecdb6))
## [2.7.1](https://github.com/OHIF/Viewers/compare/@ohif/core@2.7.0...@ohif/core@2.7.1) (2020-04-22)
### Bug Fixes
* whiteLabeling should support component creation by passing React to defined fn ([#1659](https://github.com/OHIF/Viewers/issues/1659)) ([2093a00](https://github.com/OHIF/Viewers/commit/2093a0036584b2cc698c8f06fe62b334523b1029))
# [2.7.0](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.11...@ohif/core@2.7.0) (2020-04-17)
### Features
* set the authorization header for DICOMWeb requests if provided in query string ([#1646](https://github.com/OHIF/Viewers/issues/1646)) ([450c80b](https://github.com/OHIF/Viewers/commit/450c80b9d5f172be8b5713b422370360325a0afc))
## [2.6.11](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.10...@ohif/core@2.6.11) (2020-04-15)
**Note:** Version bump only for package @ohif/core
## [2.6.10](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.9...@ohif/core@2.6.10) (2020-04-09)
### Bug Fixes
* Revert "refactor: Reduce bundle size ([#1575](https://github.com/OHIF/Viewers/issues/1575))" ([#1622](https://github.com/OHIF/Viewers/issues/1622)) ([d21af3f](https://github.com/OHIF/Viewers/commit/d21af3f133492fa31492413b8782936c9ff18b44))
## [2.6.9](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.8...@ohif/core@2.6.9) (2020-04-09)
**Note:** Version bump only for package @ohif/core
# Change Log
All notable changes to this project will be documented in this file. See
[Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [2.6.8](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.7...@ohif/core@2.6.8) (2020-04-06)
**Note:** Version bump only for package @ohif/core
## [2.6.7](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.6...@ohif/core@2.6.7) (2020-04-02)
### Bug Fixes
* 🐛 Fix multiframe images ([#1595](https://github.com/OHIF/Viewers/issues/1595)) ([9e0bd52](https://github.com/OHIF/Viewers/commit/9e0bd52c6a86648eb6673344a8555ad787043e5c))
## [2.6.6](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.5...@ohif/core@2.6.6) (2020-04-02)
**Note:** Version bump only for package @ohif/core
## [2.6.5](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.4...@ohif/core@2.6.5) (2020-04-01)
### Bug Fixes
* segmentation not loading ([#1566](https://github.com/OHIF/Viewers/issues/1566)) ([4a7ce1c](https://github.com/OHIF/Viewers/commit/4a7ce1c09324d74c61048393e3a2427757e4001a))
## [2.6.4](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.3...@ohif/core@2.6.4) (2020-03-25)
+4 -4
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/core",
"version": "2.6.4",
"version": "2.8.1",
"description": "Generic business logic for web-based medical imaging applications",
"author": "OHIF Core Team",
"license": "MIT",
@@ -33,14 +33,14 @@
"peerDependencies": {
"cornerstone-core": "^2.2.8",
"cornerstone-tools": "4.12.5",
"cornerstone-wado-image-loader": "^3.0.0",
"cornerstone-wado-image-loader": "^3.1.0",
"dicom-parser": "^1.8.3"
},
"dependencies": {
"@babel/runtime": "^7.5.5",
"ajv": "^6.10.0",
"dcmjs": "^0.8.3",
"dicomweb-client": "^0.5.2",
"dcmjs": "^0.12.0",
"dicomweb-client": "^0.6.0",
"immer": "6.0.2",
"isomorphic-base64": "^1.0.2",
"lodash.clonedeep": "^4.5.0",
@@ -5,6 +5,7 @@ import DICOMWeb from '../DICOMWeb';
import parseDicomStructuredReport from './parseDicomStructuredReport';
import parseMeasurementsData from './parseMeasurementsData';
import getAllDisplaySets from './utils/getAllDisplaySets';
import errorHandler from '../errorHandler';
const VERSION_NAME = 'dcmjs-0.0';
const TRANSFER_SYNTAX_UID = '1.2.840.10008.1.2.1';
@@ -21,6 +22,7 @@ const retrieveMeasurementFromSR = async (series, studies, serverUrl) => {
const config = {
url: serverUrl,
headers: DICOMWeb.getAuthorizationHeader(),
errorInterceptor: errorHandler.getHTTPErrorHandler(),
};
const dicomWeb = new api.DICOMwebClient(config);
@@ -71,6 +73,7 @@ const stowSRFromMeasurements = async (measurements, serverUrl) => {
const config = {
url: serverUrl,
headers: DICOMWeb.getAuthorizationHeader(),
errorInterceptor: errorHandler.getHTTPErrorHandler(),
};
const dicomWeb = new api.DICOMwebClient(config);
@@ -10,6 +10,13 @@ const findMostRecentStructuredReport = studies => {
studies.forEach(study => {
const allSeries = study.getSeries ? study.getSeries() : [];
allSeries.forEach(series => {
// Skip series that may not have instances yet
// This can happen if we have retrieved just the initial
// details about the series via QIDO-RS, but not the full metadata
if (!series.instances.length) {
return;
}
if (isStructuredReportSeries(series)) {
if (
!mostRecentStructuredReport ||
@@ -1,6 +1,3 @@
// Commenting this out for now since it looks like Rollup is pulling in the
// Node.js version instead of the Browser version of this package
//import { btoa } from 'isomorphic-base64';
import user from '../user';
/**
@@ -18,6 +15,7 @@ export default function getAuthorizationHeader({ requestOptions } = {}) {
// Check for OHIF.user since this can also be run on the server
const accessToken = user && user.getAccessToken && user.getAccessToken();
// Auth for a specific server
if (requestOptions && requestOptions.auth) {
if (typeof requestOptions.auth === 'function') {
// Custom Auth Header
@@ -26,7 +24,9 @@ export default function getAuthorizationHeader({ requestOptions } = {}) {
// HTTP Basic Auth (user:password)
headers.Authorization = `Basic ${btoa(requestOptions.auth)}`;
}
} else if (accessToken) {
}
// Auth for the user's default
else if (accessToken) {
headers.Authorization = `Bearer ${accessToken}`;
}
@@ -378,7 +378,7 @@ class MetadataProvider {
}
metadata = {
overlays
overlays,
};
break;
@@ -11,6 +11,7 @@ import { api } from 'dicomweb-client';
import { isImage } from '../../utils/isImage';
import isDisplaySetReconstructable from '../../utils/isDisplaySetReconstructable';
import isLowPriorityModality from '../../utils/isLowPriorityModality';
import errorHandler from '../../errorHandler';
export class StudyMetadata extends Metadata {
constructor(data, uid) {
@@ -100,20 +101,29 @@ export class StudyMetadata extends Metadata {
* Split a series metadata object into display sets
* @param {Array} sopClassHandlerModules List of SOP Class Modules
* @param {SeriesMetadata} series The series metadata object from which the display sets will be created
* @param {Array} [givenDisplaySets] An optional list to which the display sets will be appended
* @returns {Array} The list of display sets created for the given series object
*/
_createDisplaySetsForSeries(
sopClassHandlerModules,
series,
givenDisplaySets
) {
_createDisplaySetsForSeries(sopClassHandlerModules, series) {
const study = this;
const displaySets = Array.isArray(givenDisplaySets) ? givenDisplaySets : [];
const displaySets = [];
const anyInstances = series.getInstanceCount() > 0;
if (!anyInstances) {
return;
const displaySet = new ImageSet([]);
const seriesData = series.getData();
displaySet.setAttributes({
displaySetInstanceUID: displaySet.uid,
SeriesInstanceUID: seriesData.SeriesInstanceUID,
SeriesDescription: seriesData.SeriesDescription,
SeriesNumber: seriesData.SeriesNumber,
Modality: seriesData.Modality,
});
displaySets.push(displaySet);
return displaySets;
}
const sopClassUIDs = getSopClassUIDs(series);
@@ -208,20 +218,21 @@ export class StudyMetadata extends Metadata {
/**
* Returns a list of derived datasets in the study, filtered by the given filter.
* @param {object} filter An object containing search filters
* @param {object} filter.modality
* @param {object} filter.Modality
* @param {object} filter.referencedSeriesInstanceUID
* @param {object} filter.referencedFrameOfReferenceUID
* @return {Array} filtered derived display sets
*/
getDerivedDatasets(filter) {
const {
modality,
Modality,
referencedSeriesInstanceUID,
referencedFrameOfReferenceUID,
} = filter;
let filteredDerivedDisplaySets = this._derivedDisplaySets;
if (modality) {
if (Modality) {
filteredDerivedDisplaySets = filteredDerivedDisplaySets.filter(
displaySet => displaySet.Modality === Modality
);
@@ -280,14 +291,14 @@ export class StudyMetadata extends Metadata {
}
// Loop through the series (SeriesMetadata)
this.forEachSeries(
series =>
void this._createDisplaySetsForSeries(
sopClassHandlerModules,
series,
displaySets
)
);
this.forEachSeries(series => {
const displaySetsForSeries = this._createDisplaySetsForSeries(
sopClassHandlerModules,
series
);
displaySets.push(...displaySetsForSeries);
});
return sortDisplaySetList(displaySets);
}
@@ -303,13 +314,30 @@ export class StudyMetadata extends Metadata {
* @returns {boolean} Returns true on success or false on failure (e.g., the series does not belong to this study)
*/
createAndAddDisplaySetsForSeries(sopClassHandlerModules, series) {
if (this.containsSeries(series)) {
this.setDisplaySets(
this._createDisplaySetsForSeries(sopClassHandlerModules, series)
);
return true;
if (!this.containsSeries(series)) {
return false;
}
return false;
const displaySets = this._createDisplaySetsForSeries(
sopClassHandlerModules,
series
);
// Note: filtering in place because this._displaySets has writable: false
for (let i = this._displaySets.length - 1; i >= 0; i--) {
const displaySet = this._displaySets[i];
if (displaySet.SeriesInstanceUID === series.getSeriesInstanceUID()) {
this._displaySets.splice(i, 1);
}
}
displaySets.forEach(displaySet => {
this.addDisplaySet(displaySet);
});
this.sortDisplaySets();
return true;
}
/**
@@ -318,6 +346,9 @@ export class StudyMetadata extends Metadata {
*/
setDisplaySets(displaySets) {
if (Array.isArray(displaySets) && displaySets.length > 0) {
// TODO: This is weird, can we just switch it to writable: true?
this._displaySets.splice(0);
displaySets.forEach(displaySet => this.addDisplaySet(displaySet));
this.sortDisplaySets();
}
@@ -406,6 +437,30 @@ export class StudyMetadata extends Metadata {
return result;
}
/**
* Update a series in the current study by SeriesInstanceUID.
* @param {String} SeriesInstanceUID The SeriesInstanceUID to be updated
* @param {SeriesMetadata} series The series to be added to the current study.
* @returns {boolean} Returns true on success, false otherwise.
*/
updateSeries(SeriesInstanceUID, series) {
const index = this._series.findIndex(series => {
return series.getSeriesInstanceUID() === SeriesInstanceUID;
});
if (index < 0) {
return false;
}
if (!(series instanceof SeriesMetadata)) {
throw new Error('Series must be an instance of SeriesMetadata');
}
this._series[index] = series;
return true;
}
/**
* Find a series by index.
* @param {number} index An integer representing a list index.
@@ -780,9 +835,11 @@ function _getDisplaySetFromSopClassModule(
const plugin = handlersForSopClassUID[0];
const headers = DICOMWeb.getAuthorizationHeader();
const errorInterceptor = errorHandler.getHTTPErrorHandler();
const dicomWebClient = new dwc({
url: study.getData().wadoRoot,
headers,
errorInterceptor,
});
let displaySet = plugin.getDisplaySetFromSeries(
+6
View File
@@ -0,0 +1,6 @@
// These should be overridden by the implementation
const errorHandler = {
getHTTPErrorHandler: () => null,
};
export default errorHandler;
+3
View File
@@ -18,6 +18,7 @@ import string from './string.js';
import studies from './studies/';
import ui from './ui';
import user from './user.js';
import errorHandler from './errorHandler.js';
import utils, { hotkeys } from './utils/';
import {
@@ -46,6 +47,7 @@ const OHIF = {
string,
ui,
user,
errorHandler,
object,
log,
DICOMWeb,
@@ -79,6 +81,7 @@ export {
string,
ui,
user,
errorHandler,
object,
log,
DICOMWeb,
+1
View File
@@ -24,6 +24,7 @@ describe('Top level exports', () => {
'header',
'cornerstone',
'default', //
'errorHandler',
'string',
'ui',
'user',
@@ -1,6 +1,8 @@
import DICOMWeb from '../../../DICOMWeb/';
import { api } from 'dicomweb-client';
import errorHandler from '../../../errorHandler';
/**
* Parses data returned from a QIDO search and transforms it into
* an array of series that are present in the study
@@ -79,6 +81,7 @@ export default function Instances(server, StudyInstanceUID) {
const config = {
url: server.qidoRoot,
headers: DICOMWeb.getAuthorizationHeader(server),
errorInterceptor: errorHandler.getHTTPErrorHandler(),
};
const dicomWeb = new api.DICOMwebClient(config);
const queryParams = getQIDOQueryParams(
@@ -1,6 +1,8 @@
import { api } from 'dicomweb-client';
import DICOMWeb from '../../../DICOMWeb/';
import errorHandler from '../../../errorHandler';
/**
* Creates a QIDO date string for a date range query
* Assumes the year is positive, at most 4 digits long.
@@ -115,6 +117,7 @@ export default function Studies(server, filter) {
const config = {
url: server.qidoRoot,
headers: DICOMWeb.getAuthorizationHeader(server),
errorInterceptor: errorHandler.getHTTPErrorHandler(),
};
const dicomWeb = new api.DICOMwebClient(config);
@@ -1,4 +1,5 @@
import { api } from 'dicomweb-client';
import dcmjs from 'dcmjs';
import DICOMWeb from '../../../DICOMWeb/';
import RetrieveMetadataLoader from './retrieveMetadataLoader';
import { sortStudySeries, sortingCriteria } from '../../sortStudy';
@@ -8,6 +9,10 @@ import {
addInstancesToStudy,
} from './studyInstanceHelpers';
import errorHandler from '../../../errorHandler';
const { naturalizeDataset } = dcmjs.data.DicomMetaDictionary;
/**
* Map series to an array of SeriesInstanceUID
* @param {Arrays} series list of Series Instance UIDs
@@ -70,6 +75,7 @@ export default class RetrieveMetadataLoaderAsync extends RetrieveMetadataLoader
const client = new api.DICOMwebClient({
url: server.qidoRoot,
headers: DICOMWeb.getAuthorizationHeader(server),
errorInterceptor: errorHandler.getHTTPErrorHandler(),
});
this.client = client;
@@ -101,15 +107,21 @@ export default class RetrieveMetadataLoaderAsync extends RetrieveMetadataLoader
async preLoad() {
const preLoaders = this.getPreLoaders();
const result = await this.runLoaders(preLoaders);
// seriesData is the result of the QIDO-RS Search For Series request
// It's an array of Objects containing DICOM Tag values at the Series level
const seriesData = await this.runLoaders(preLoaders);
const seriesSorted = sortStudySeries(
result,
seriesData,
sortingCriteria.seriesSortCriteria.seriesInfoSortingCriteria
);
const seriesInstanceUIDsMap = mapStudySeries(seriesSorted);
return seriesInstanceUIDsMap;
return {
seriesInstanceUIDsMap,
seriesData,
};
}
async load(preLoadData) {
@@ -118,7 +130,7 @@ export default class RetrieveMetadataLoaderAsync extends RetrieveMetadataLoader
const seriesAsyncLoader = makeSeriesAsyncLoader(
client,
studyInstanceUID,
preLoadData
preLoadData.seriesInstanceUIDsMap
);
const firstSeries = await seriesAsyncLoader.next();
@@ -126,16 +138,41 @@ export default class RetrieveMetadataLoaderAsync extends RetrieveMetadataLoader
return {
sopInstances: firstSeries.sopInstances,
asyncLoader: seriesAsyncLoader,
seriesData: preLoadData.seriesData,
};
}
async posLoad(loadData) {
const { server } = this;
const { sopInstances, asyncLoader } = loadData;
const { sopInstances, asyncLoader, seriesData } = loadData;
const study = await createStudyFromSOPInstanceList(server, sopInstances);
// TODO: Should this be in a helper
const seriesDataNaturalized = seriesData.map(naturalizeDataset);
seriesDataNaturalized.forEach((series, idx) => {
const seriesDataFromQIDO = {
SeriesInstanceUID: series.SeriesInstanceUID,
SeriesDescription: series.SeriesDescription,
SeriesNumber: series.SeriesNumber,
Modality: series.Modality,
instances: [],
};
if (study.series[idx]) {
study.series[idx] = Object.assign(
seriesDataFromQIDO,
study.series[idx]
);
} else {
study.series[idx] = seriesDataFromQIDO;
}
study.seriesMap[series.SeriesInstanceUID] = study.series[idx];
});
if (asyncLoader.hasNext()) {
attachSeriesLoader(server, study, asyncLoader);
}
@@ -3,6 +3,8 @@ import DICOMWeb from '../../../DICOMWeb/';
import { createStudyFromSOPInstanceList } from './studyInstanceHelpers';
import RetrieveMetadataLoader from './retrieveMetadataLoader';
import errorHandler from '../../../errorHandler';
/**
* Class for sync load of study metadata.
* It inherits from RetrieveMetadataLoader
@@ -58,6 +60,7 @@ export default class RetrieveMetadataLoaderSync extends RetrieveMetadataLoader {
const client = new api.DICOMwebClient({
url: server.wadoRoot,
headers: DICOMWeb.getAuthorizationHeader(server),
errorInterceptor: errorHandler.getHTTPErrorHandler(),
});
this.client = client;
@@ -160,8 +160,10 @@ async function makeSOPInstance(server, study, instance) {
const wadoRSMetadata = Object.assign(instance);
if (sopInstance.NumberOfFrames) {
for (let i = 0; i < sopInstance.NumberOfFrames; i++) {
const { NumberOfFrames } = sopInstance.metadata;
if (NumberOfFrames) {
for (let i = 0; i < NumberOfFrames; i++) {
const wadorsImageId = getWADORSImageId(sopInstance, i);
cornerstoneWADOImageLoader.wadors.metaDataManager.add(
@@ -190,7 +192,7 @@ async function makeSOPInstance(server, study, instance) {
*/
async function addInstancesToStudy(server, study, sopInstanceList) {
return Promise.all(
sopInstanceList.map(function (sopInstance) {
sopInstanceList.map(function(sopInstance) {
return makeSOPInstance(server, study, sopInstance);
})
);
+66
View File
@@ -0,0 +1,66 @@
export default class Queue {
constructor(limit) {
this.limit = limit;
this.size = 0;
this.awaiting = null;
}
/**
* Creates a new "proxy" function associated with the current execution queue
* instance. When the returned function is invoked, the queue limit is checked
* to make sure the limit of scheduled tasks is repected (throwing an
* exception when the limit has been reached and before calling the original
* function). The original function is only invoked after all the previously
* scheduled tasks have finished executing (their returned promises have
* resolved/rejected);
*
* @param {function} task The function whose execution will be associated
* with the current Queue instance;
* @returns {function} The "proxy" function bound to the current Queue
* instance;
*/
bind(task) {
return bind(this, task);
}
bindSafe(task, onError) {
const boundTask = bind(this, task);
return async function safeTask(...args) {
try {
return await boundTask(...args);
} catch (e) {
onError(e);
}
};
}
}
/**
* Utils
*/
function bind(queue, task) {
const cleaner = clean.bind(null, queue);
return async function boundTask(...args) {
if (queue.size >= queue.limit) {
throw new Error('Queue limit reached');
}
const promise = chain(queue.awaiting, task, args);
queue.awaiting = promise.then(cleaner, cleaner);
queue.size++;
return promise;
};
}
function clean(queue) {
if (queue.size > 0 && --queue.size === 0) {
queue.awaiting = null;
}
}
async function chain(prev, task, args) {
await prev;
return task(...args);
}
+66
View File
@@ -0,0 +1,66 @@
import makeDeferred from './makeDeferred';
import Queue from './Queue';
/**
* Utils
*/
function timeout(delay) {
const { resolve, promise } = makeDeferred();
setTimeout(() => void resolve(Date.now()), delay);
return promise;
}
/**
* Tests
*/
describe('Queue', () => {
it('should bind functions to the queue', async () => {
const queue = new Queue(2);
const mockedTimeout = jest.fn(timeout);
const timer = queue.bind(mockedTimeout);
const start = Date.now();
timer(120).then(now => {
const elapsed = now - start;
expect(elapsed >= 120 && elapsed < 240).toBe(true);
});
const end = await timer(120);
expect(end - start > 240).toBe(true);
expect(mockedTimeout).toBeCalledTimes(2);
});
it('should prevent task execution when queue limit is reached', async () => {
const queue = new Queue(1);
const mockedTimeout = jest.fn(timeout);
const timer = queue.bind(mockedTimeout);
const start = Date.now();
const promise = timer(120).then(time => time - start);
try {
await timer(120);
} catch (e) {
expect(Date.now() - start < 120).toBe(true);
expect(e.message).toBe('Queue limit reached');
}
const elapsed = await promise;
expect(elapsed >= 120 && elapsed < 240).toBe(true);
expect(mockedTimeout).toBeCalledTimes(1);
});
it('should safely bind tasks to the queue', async () => {
const queue = new Queue(1);
const mockedErrorHandler = jest.fn();
const mockedTimeout = jest.fn(timeout);
const timer = queue.bindSafe(mockedTimeout, mockedErrorHandler);
const start = Date.now();
const promise = timer(120).then(time => time - start);
await timer(120);
expect(Date.now() - start < 120).toBe(true);
expect(mockedErrorHandler).toBeCalledTimes(1);
expect(mockedErrorHandler).nthCalledWith(
1,
expect.objectContaining({ message: 'Queue limit reached' })
);
const elapsed = await promise;
expect(elapsed >= 120 && elapsed < 240).toBe(true);
expect(mockedTimeout).toBeCalledTimes(1);
});
});
+2 -3
View File
@@ -35,7 +35,8 @@ function createAndAddStack(stackMap, study, displaySet, stackUpdatedCallbacks) {
imageIndex: imageIndex + 1,
};
const NumberOfFrames = image.NumberOfFrames;
const naturalizedInstance = instance.getData().metadata;
const NumberOfFrames = naturalizedInstance.NumberOfFrames;
if (NumberOfFrames > 1) {
for (let i = 0; i < NumberOfFrames; i++) {
@@ -60,8 +61,6 @@ function createAndAddStack(stackMap, study, displaySet, stackUpdatedCallbacks) {
imageId = getImageId(image);
imageIds.push(imageId);
const naturalizedInstance = instance.getData().metadata;
const {
StudyInstanceUID,
SeriesInstanceUID,
@@ -3,6 +3,8 @@ import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader';
import { api } from 'dicomweb-client';
import DICOMWeb from '../DICOMWeb';
import errorHandler from '../errorHandler';
const getImageId = imageObj => {
if (!imageObj) {
return;
@@ -57,11 +59,13 @@ const wadorsRetriever = (
studyInstanceUID,
seriesInstanceUID,
sopInstanceUID,
headers = DICOMWeb.getAuthorizationHeader()
headers = DICOMWeb.getAuthorizationHeader(),
errorInterceptor = errorHandler.getHTTPErrorHandler()
) => {
const config = {
url,
headers,
errorInterceptor,
};
const dicomWeb = new api.DICOMwebClient(config);
@@ -0,0 +1,193 @@
/**
* Constants
*/
const SEPARATOR = '/';
/**
* API
*/
/**
* Add values to a list hierarchically.
* @ For example:
* addToList([], 'a', 'b', 'c');
* will add the following hierarchy to the list:
* a > b > c
* resulting in the following array:
* [['a', [['b', ['c']]]]]
* @param {Array} list The target list;
* @param {...string} values The values to be hierarchically added to the list;
* @returns {Array} Returns the provided list possibly updated with the given
* values or null when a bad list (not an actual array) is provided
*/
function addToList(list, ...values) {
if (Array.isArray(list)) {
if (values.length > 0) {
addValuesToList(list, values);
}
return list;
}
return null;
}
/**
* Iterates through the provided hierarchical list executing the callback
* once for each leaf-node of the tree. The ancestors of the leaf-node being
* visited are passed to the callback function along with the leaf-node in
* the exact same order they appear on the tree (from root to leaf);
* @ For example, if the hierachy `a > b > c` appears on the tree ("a" being
* the root and "c" being the leaf) the callback function will be called as:
* callback('a', 'b', 'c');
* @param {Array} list The hierarchical list to be iterated
* @param {function} callback The callback which will be exected once for
* each leaf-node of the hierarchical list;
* @returns {Array} Returns the provided list or null for bad arguments;
*/
function forEach(list, callback) {
if (Array.isArray(list)) {
if (typeof callback === 'function') {
forEachValue(list, callback);
}
return list;
}
return null;
}
/**
* Retrieves an item from the given hierarchical list based on an index (number)
* or a path (string).
* @ For example:
* getItem(list, '1/0/4')
* will retrieve the fourth grandchild, from the first child of the second
* element of the list;
* @param {Array} list The source list;
* @param {string|number} indexOrPath The index of the element inside list
* (number) or the path to reach the desired element (string). The slash "/"
* character is cosidered the path separator;
*/
function getItem(list, indexOrPath) {
if (Array.isArray(list)) {
let subpath = null;
let index = typeof indexOrPath === 'number' ? indexOrPath : -1;
if (typeof indexOrPath === 'string') {
const separator = indexOrPath.indexOf(SEPARATOR);
if (separator > 0) {
index = parseInt(indexOrPath.slice(0, separator), 10);
if (separator + 1 < indexOrPath.length) {
subpath = indexOrPath.slice(separator + 1, indexOrPath.length);
}
} else {
index = parseInt(indexOrPath, 10);
}
}
if (index >= 0 && index < list.length) {
const item = list[index];
if (isSublist(item)) {
if (subpath !== null) {
return getItem(item[1], subpath);
}
return item[0];
}
return item;
}
}
}
/**
* Pretty-print the provided hierarchical list;
* @param {Array} list The source list;
* @returns {string} The textual representation of the hierarchical list;
*/
function print(list) {
let text = '';
if (Array.isArray(list)) {
let prev = [];
forEachValue(list, function(...args) {
let prevLen = prev.length;
for (let i = 0, l = args.length; i < l; ++i) {
if (i < prevLen && args[i] === prev[i]) {
continue;
}
text += ' '.repeat(i) + args[i] + '\n';
}
prev = args;
});
}
return text;
}
/**
* Utils
*/
function forEachValue(list, callback) {
for (let i = 0, l = list.length; i < l; ++i) {
let item = list[i];
if (isSublist(item)) {
if (item[1].length > 0) {
forEachValue(item[1], callback.bind(null, item[0]));
continue;
}
item = item[0];
}
callback(item);
}
}
function addValuesToList(list, values) {
let value = values.shift();
let index = add(list, value);
if (index >= 0) {
if (values.length > 0) {
let sublist = list[index];
if (!isSublist(sublist)) {
sublist = toSublist(value);
list[index] = sublist;
}
return addValuesToList(sublist[1], values);
}
return true;
}
return false;
}
function add(list, value) {
let index = find(list, value);
if (index === -2) {
index = list.push(value) - 1;
}
return index;
}
function find(list, value) {
if (typeof value === 'string') {
for (let i = 0, l = list.length; i < l; ++i) {
let item = list[i];
if (item === value || (isSublist(item) && item[0] === value)) {
return i;
}
}
return -2;
}
return -1;
}
function isSublist(subject) {
return (
Array.isArray(subject) &&
subject.length === 2 &&
typeof subject[0] === 'string' &&
Array.isArray(subject[1])
);
}
function toSublist(value) {
return [value + '', []];
}
/**
* Exports
*/
export { addToList, getItem, forEach, print };
@@ -0,0 +1,96 @@
import { addToList, forEach, getItem, print } from './hierarchicalListUtils';
describe('hierarchicalListUtils', function() {
let sharedList;
beforeEach(function() {
sharedList = [
['1.2.3.1', ['1.2.3.1.1', '1.2.3.1.2']],
'1.2.3.2',
['1.2.3.3', ['1.2.3.3.1', ['1.2.3.3.2', ['1.2.3.3.2.1', '1.2.3.3.2.2']]]],
];
});
describe('getItem', function() {
it('should retrieve elements from a list by index', function() {
expect(getItem(sharedList, 0)).toBe('1.2.3.1');
expect(getItem(sharedList, 1)).toBe('1.2.3.2');
expect(getItem(sharedList, 2)).toBe('1.2.3.3');
expect(getItem(sharedList, 3)).toBeUndefined();
});
it('should retrieve elements from a list by path', function() {
expect(getItem(sharedList, '0')).toBe('1.2.3.1');
expect(getItem(sharedList, '0/0')).toBe('1.2.3.1.1');
expect(getItem(sharedList, '0/1')).toBe('1.2.3.1.2');
expect(getItem(sharedList, '0/2')).toBeUndefined();
expect(getItem(sharedList, '1')).toBe('1.2.3.2');
expect(getItem(sharedList, '2')).toBe('1.2.3.3');
expect(getItem(sharedList, '2/0')).toBe('1.2.3.3.1');
expect(getItem(sharedList, '2/1')).toBe('1.2.3.3.2');
expect(getItem(sharedList, '2/2')).toBeUndefined();
expect(getItem(sharedList, '2/1/0')).toBe('1.2.3.3.2.1');
expect(getItem(sharedList, '2/1/1')).toBe('1.2.3.3.2.2');
expect(getItem(sharedList, '2/1/2')).toBeUndefined();
expect(getItem(sharedList, '3')).toBeUndefined();
});
});
describe('addToList', function() {
it('should support adding elements to a list hierarchically', function() {
const list = [];
addToList(list, '1.2.3.1', '1.2.3.1.1');
addToList(list, '1.2.3.1', '1.2.3.1.2');
addToList(list, '1.2.3.2');
addToList(list, '1.2.3.3', '1.2.3.3.1');
addToList(list, '1.2.3.3', '1.2.3.3.2', '1.2.3.3.2.1');
addToList(list, '1.2.3.3', '1.2.3.3.2', '1.2.3.3.2.2');
expect(list).toStrictEqual(sharedList);
});
it('should change leaf nodes into non-leaf nodes', function() {
const listw = [];
const listx = [['x.1', ['x.1.1', 'x.1.2']], 'x.2'];
const listy = [
['x.1', [['x.1.1', ['x.1.1.1']], 'x.1.2']],
['x.2', ['x.2.1']],
];
addToList(listw, 'x.1');
addToList(listw, 'x.1', 'x.1.1');
addToList(listw, 'x.1', 'x.1.2');
addToList(listw, 'x.2');
expect(listw).toStrictEqual(listx);
addToList(listw, 'x.2', 'x.2.1');
addToList(listw, 'x.1', 'x.1.1', 'x.1.1.1');
expect(listw).toStrictEqual(listy);
});
});
describe('forEach', function() {
it('should iterate through all leaf nodes of the tree', function() {
const fn = jest.fn();
forEach(sharedList, fn);
expect(fn).toHaveBeenCalledTimes(6);
expect(fn).nthCalledWith(1, '1.2.3.1', '1.2.3.1.1');
expect(fn).nthCalledWith(2, '1.2.3.1', '1.2.3.1.2');
expect(fn).nthCalledWith(3, '1.2.3.2');
expect(fn).nthCalledWith(4, '1.2.3.3', '1.2.3.3.1');
expect(fn).nthCalledWith(5, '1.2.3.3', '1.2.3.3.2', '1.2.3.3.2.1');
expect(fn).nthCalledWith(6, '1.2.3.3', '1.2.3.3.2', '1.2.3.3.2.2');
});
});
describe('print', function() {
it('should pretty-print the hierarchical list', function() {
expect(print(sharedList)).toBe(
'1.2.3.1\n' +
' 1.2.3.1.1\n' +
' 1.2.3.1.2\n' +
'1.2.3.2\n' +
'1.2.3.3\n' +
' 1.2.3.3.1\n' +
' 1.2.3.3.2\n' +
' 1.2.3.3.2.1\n' +
' 1.2.3.3.2.2\n'
);
});
});
});
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