feat: volume API and TMTV mode #2814

sedghi · 2022-05-26T02:10:02Z

Adds petSUV panel which shows the metadata for the matched PT and also makes them editable
Adds metadata invalidation and force re-loading the data when the metadata is changed
Adds feature to be able to set tool configurations on the tool
Adds automatic slabThickness calculation for the volume viewport
Fix UI discrepancy between v3-stable and tmtv mode

codecov · 2022-05-26T02:12:42Z

Codecov Report

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@@                  Coverage Diff                   @@
##             feat/volumeAPI-base    #2814   +/-   ##
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  Coverage                       ?   30.89%           
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  Files                          ?      103           
  Lines                          ?     2269           
  Branches                       ?      447           
======================================================
  Hits                           ?      701           
  Misses                         ?     1288           
  Partials                       ?      280

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cypress · 2022-05-26T02:17:27Z

Test summary

0 • 6 • 0 • 14

Run details


Project	Viewers
Status	Failed
Commit	`ea2938f`
Started	May 31, 2022 7:55 PM
Ended	May 31, 2022 7:56 PM
Duration	01:06 💡
OS	Linux Debian - 10.9
Browser	Chrome 88

View run in Cypress Dashboard ➡️

Failures

	OHIFPdfDisplay.spec.js	1
1	OHIF PDF Display > checks if series thumbnails are being displayed
	OHIFVideoDisplay.spec.js	1
1	OHIF Video Display > checks if series thumbnails are being displayed
	measurement-tracking/OHIFCornerstoneHotkeys.spec.js	1
1	OHIF Cornerstone Hotkeys > checks if hotkeys "R" and "L" can rotate the image
	measurement-tracking/OHIFCornerstoneToolbar.spec.js	1
1	OHIF Cornerstone Toolbar > checks if all primary buttons are being displayed
	measurement-tracking/OHIFStudyViewer.spec.js	1
1	OHIF Study Viewer Page > checks if series thumbnails are being displayed
	study-list/OHIFStudyList.spec.js	1
1	OHIF Study List > Desktop resolution > Displays several studies initially

This comment has been generated by cypress-bot as a result of this project's GitHub integration settings. You can manage this integration in this project's settings in the Cypress Dashboard

JamesAPetts

My review is limited as I cant get the actual mode to work. I get blank viewports and the following react error: The prop viewportDatais marked as required inCornerstoneImageScrollbar, but its value is null.

This happens with both the current published cornerstone3D versions, and the linked versions from your most recent PR.

Otherwise, some comments in line.

extensions/cornerstone-3d/src/Viewport/OHIFCornerstone3DViewport.tsx

extensions/cornerstone-3d/src/commandsModule.js

extensions/cornerstone-3d/src/services/ViewportService/Cornerstone3DViewportService.ts

extensions/measurement-tracking/src/panels/PanelStudyBrowserTracking/index.tsx

extensions/tmtv/src/getHangingProtocolModule.js

extensions/tmtv/src/utils/getStudiesForPatientByStudyInstanceUID.js

JamesAPetts · 2022-05-26T09:15:01Z

extensions/tmtv/src/index.tsx

@@ -1,5 +1,6 @@
 import { id } from './id';
 import getHangingProtocolModule from './getHangingProtocolModule';
+import getPanelModule from './getPanelModule';


I wonder if this should just be a generic pet-suv module rather than named the tmtv extension? The hanging protocol and side panel could be re-used in other modes, no?

Yes I agree, pet-suv will be more understood and get a better audiance than tmtv.

JamesAPetts

A bunch of comments in line, but lets discuss tomorrow as well.

extensions/cornerstone-3d/src/Viewport/Overlays/ViewportOverlay.tsx

extensions/cornerstone-3d/src/commandsModule.js

extensions/cornerstone-3d/src/initMeasurementService.js

extensions/tmtv/src/utils/measurementServiceMappings/measurementServiceMappingsFactory.js

extensions/tmtv/src/utils/measurementServiceMappings/utils/getSOPInstanceAttributes.js

JamesAPetts

LGTM, minor comments.

...ornerstone-3d/src/utils/measurementServiceMappings/measurementServiceMappingsFactory.test.js

extensions/default/src/commandsModule.js

extensions/tmtv/src/Panels/PanelROIThresholdSegmentation/PanelROIThresholdSegmentation.tsx

modes/tmtv/README.md

* feat: use cs3d cache service to obtain viewportData * wip for volume api * wip: fusion viewport * feat: add blend mode option * wip for image scrollbar * fix drag and drop thumbnail * wip for image scrollbar for voluems * fix: element mismatch bug for scroll * feat: Add image scrollbar to volumes * feat: add syncGroups to volume api * feat: add tmtv mode initial setup * feat: add initial image options for the stack viewports * feat: Add custom load strategy for volume viewports via HP * apply review comments fix: Jump presets cs3d (#2812) * feat: Add JumpPreset to OHIF for Cornerstone3D * fix: accessing viewport service from servicesManager feat: volume API and TMTV mode (#2814) * fix: do not display overlays on mip viewports * feat: add optional disableCommands for toggle buttons * fix: toggleCrossharis * feat: config the crosshairs * feat: add PetSUV Panel for changing metadata * feat: initial work for the rectangleROIThreshold panel * wip: measurement service * roi threshold working * feat: Add displayText to segmentations * feat: add remove segmentation * feat: add csv export * feat: add RT export for annotations in tmtv mode * fix: fusion to use pt in tmtv mode and measuremet mappings * fix: various bugs * apply review comments * apply review comments * feat: add fusion color maps * add readme to tmtv mode * Update README.md * fix: try to fix build * fix unit tests * Update README.md * feat: add about to the panel * fix: changing strategy in roi panel * apply review comments

* feat: volumeAPI and TMTV mode * feat: use cs3d cache service to obtain viewportData * wip for volume api * wip: fusion viewport * feat: add blend mode option * wip for image scrollbar * fix drag and drop thumbnail * wip for image scrollbar for voluems * fix: element mismatch bug for scroll * feat: Add image scrollbar to volumes * feat: add syncGroups to volume api * feat: add tmtv mode initial setup * feat: add initial image options for the stack viewports * feat: Add custom load strategy for volume viewports via HP * apply review comments fix: Jump presets cs3d (#2812) * feat: Add JumpPreset to OHIF for Cornerstone3D * fix: accessing viewport service from servicesManager feat: volume API and TMTV mode (#2814) * fix: do not display overlays on mip viewports * feat: add optional disableCommands for toggle buttons * fix: toggleCrossharis * feat: config the crosshairs * feat: add PetSUV Panel for changing metadata * feat: initial work for the rectangleROIThreshold panel * wip: measurement service * roi threshold working * feat: Add displayText to segmentations * feat: add remove segmentation * feat: add csv export * feat: add RT export for annotations in tmtv mode * fix: fusion to use pt in tmtv mode and measuremet mappings * fix: various bugs * apply review comments * apply review comments * feat: add fusion color maps * add readme to tmtv mode * Update README.md * fix: try to fix build * fix unit tests * Update README.md * feat: add about to the panel * fix: changing strategy in roi panel * apply review comments * update package versions * wip for stackPrefetch

* feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <[email protected]> * feat: cs3d tools and toolGroups (#20) * add more tools to work with cs3d mode * fix hotkeys * add stack manager usage for stach viewports * add image scrollbar * wip viewport overlay * fix toAnnotation schema for tools * fix the unnecessary size change that triggered resize * hanging protocol improvement to allow unmatched errors * study description matching for hanging protocol * fix the displaysetOptions to work * fix handle the active tool when a new viewport is added * fix separate toolGroups for mode * apply review comments * apply review comments * yarn lock * feat: overlay component (#21) * fix default displayset options * add viewport overlay * apply review comments * feat: loading and orientation indicators (#22) * add loading indicator * add orientation marker initial work * apply review comments * fix: orientation markers (#23) * finished the orientation markers * fix various broken cypress tests * apply review comments * update yarn lock * feat: re-working measurement tracking mode with cornerstone3d (#2805) * feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <[email protected]> * feat: Add Measurement tracking mode with cs3D (#2789) * feat: first render for cornerstone3d tracked viewport * make tool active work * wip for SR extension * renamed dicom sr to cornerstone dicom sr * remove cornerstone from dicom pdf and video * move dicom sr logic to sr extension * feat: Add hydration for the length tool * fix SR display tool for length using cs3d * fix default config * fix: various bugs with sr viewport and tracking * fix promptying to continue tracking for when SR is created * feat: add keep trackign of unique identifiers * fix hydration for same imageIds * feat: Add SR toolGroup creation on modeEnter * feat: remove the need for separate mapper for SR hydration * add SR display for ellipse * handle hydration of elliptical ROI tool * remove cornerstone extension * add arrow mapping * feat: Add ArrowAnnotate SR display and hydration * apply review comments * apply review comments * move viewport labels to the viewportData * apply review comments * fix: integration cypress tests with cornerstone3D and add CINE tool (#2795) * fix: integration cypress tests with cornerstone3D * revert to addOrUpdate as it makes more sense * fix local drag and drop * fix tests * move dicomLoaderService to cornerstone extension * fix various import bugs * fix bug for local PT series * fix various unit tests * bump cs3d versions * add angle and magnify tool * bump dependencies to avoid broken peerDeps * feat: add initial work for capture using cs3d * feat: show annotations on the image capture * feat: add svg layer export * feat: Add CINE Tool * feat: remove unnecessary viewport rendering for cine state changes Co-authored-by: Erik Ziegler <[email protected]> * docs: modify and improve documentation (#2800) * cleanup docs versionings * feat: Add all version explanations * version docs for 3.0 * wip for changing docs * wip for updated docs * add utility module documentation * fix demo with nohoisting of history * add slides and video to resources * apply review comments * fix: drag and drop SR into SR viewport (#2803) * update yarn lock Co-authored-by: Erik <[email protected]> * update pathnames to match v3-stable * update the e2e pathname * fix: various bugs with regard to tracking workflow (#2811) * fix: various issues with measurement panel * fix: update default tool style for annotations * fix: annotatoin label getting removed * feat: Add backward compatibility for SR hydration with legacy cornerstone * fix: cursors and ellipse ROI max style * fix: ArrowAnnotate SRDisplay * apply review comments * bump package versions * fix: bugin rehydration of SR * fix: e2e tests * fix active viewport thickness and arrowTool ui * add readme for measurement tracking * use uploaded image for readme * add back images * try to fix e2e test * fix: window level presets hotkeys * Update README.md * update yarn lock * feat: volume api and TMTV mode (#2817) * feat: volumeAPI and TMTV mode * feat: use cs3d cache service to obtain viewportData * wip for volume api * wip: fusion viewport * feat: add blend mode option * wip for image scrollbar * fix drag and drop thumbnail * wip for image scrollbar for voluems * fix: element mismatch bug for scroll * feat: Add image scrollbar to volumes * feat: add syncGroups to volume api * feat: add tmtv mode initial setup * feat: add initial image options for the stack viewports * feat: Add custom load strategy for volume viewports via HP * apply review comments fix: Jump presets cs3d (#2812) * feat: Add JumpPreset to OHIF for Cornerstone3D * fix: accessing viewport service from servicesManager feat: volume API and TMTV mode (#2814) * fix: do not display overlays on mip viewports * feat: add optional disableCommands for toggle buttons * fix: toggleCrossharis * feat: config the crosshairs * feat: add PetSUV Panel for changing metadata * feat: initial work for the rectangleROIThreshold panel * wip: measurement service * roi threshold working * feat: Add displayText to segmentations * feat: add remove segmentation * feat: add csv export * feat: add RT export for annotations in tmtv mode * fix: fusion to use pt in tmtv mode and measuremet mappings * fix: various bugs * apply review comments * apply review comments * feat: add fusion color maps * add readme to tmtv mode * Update README.md * fix: try to fix build * fix unit tests * Update README.md * feat: add about to the panel * fix: changing strategy in roi panel * apply review comments * update package versions * wip for stackPrefetch * fix: cornerstone3d hydration and renaming (#2818) * update readme * renamed cornerstone extension * wip for renaming cornerstone3D variables * wip for renaming cornerstone3D variables * wip for fixing bugs for SR viewport * fix: jumpToMeasurement and initial label after hydration * fix: fileName capitalization * feat: use the new prefetch stack in the cs3d (#2820) * feat: use the new prefetch stack in the cs3d * use viewport scroll api for stack viewport * fix cine stop when scrollbar changes * feat: use new prefetch events * fix loading state to not show repeatedly * fix: various bugs for tmtv mode thresholding and new icons (#2823) * feat: make tmtv mode available in worklist * feat: add new icons for tmtv mode * feat: add fusion color icon * fix: parallel scale calculation * fix: bump Cornerstone to get large image support working * fix: Fix issues with CPU viewport flipping, including config files * fix: bump cornerstone to fix magnify tool * fix: Bump Cornerstone version to fix resetCamera issue in StackViewport * ci: Add _headers file to enable CORS headers for Netlify Drag/Drop deploys * fix: WADO-URI was not working. PET Metadata was coming from the wrong place. Fixed some minor React errors * feat(OHIF):Allow modes and extensions to be added after commpile time. (#2838) Also works with the compile time add that the existing cli uses, so that both build types work. Eric and I agreed this doesn't change existing functionality, but is almost entirely build issues/fixes. * bump: dependency versions to fix hydration bugs (#2848) * bump: dcmjs version to fix hydration bugs * try to fix tests * bump dependency versions Co-authored-by: Alireza <[email protected]> Co-authored-by: Bill Wallace <[email protected]>

sedghi added 5 commits May 24, 2022 17:17

fix: do not display overlays on mip viewports

a4ac2c9

feat: add optional disableCommands for toggle buttons

9abc82e

fix: toggleCrossharis

2f89718

feat: config the crosshairs

1e3c7d0

feat: add PetSUV Panel for changing metadata

32c2ba3

sedghi requested a review from JamesAPetts May 26, 2022 02:41

JamesAPetts reviewed May 26, 2022

View reviewed changes

sedghi added 9 commits May 26, 2022 17:10

feat: initial work for the rectangleROIThreshold panel

7837c0b

wip: measurement service

046de43

roi threshold working

dab70ba

feat: Add displayText to segmentations

4775807

feat: add remove segmentation

def346e

feat: add csv export

56e9bc5

feat: add RT export for annotations in tmtv mode

96d38db

fix: fusion to use pt in tmtv mode and measuremet mappings

533eb97

fix: various bugs

906014e

sedghi changed the title ~~feat: TMTV mode~~ feat: volume API and TMTV mode May 29, 2022

JamesAPetts reviewed May 29, 2022

View reviewed changes

sedghi added 7 commits May 30, 2022 12:50

apply review comments

329a5f3

apply review comments

e02311c

feat: add fusion color maps

e30eca1

add readme to tmtv mode

a65c860

Update README.md

a2d5f91

fix: try to fix build

221a80e

fix unit tests

714bdf0

JamesAPetts approved these changes May 31, 2022

View reviewed changes

sedghi added 2 commits May 31, 2022 14:12

Update README.md

abd36cf

feat: add about to the panel

af5b44f

sedghi added 2 commits May 31, 2022 15:27

fix: changing strategy in roi panel

5a5a180

apply review comments

ea2938f

sedghi merged commit 4983078 into feat/volumeAPI-base May 31, 2022

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feat: volume API and TMTV mode #2814

feat: volume API and TMTV mode #2814

sedghi commented May 26, 2022 •

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cypress bot commented May 26, 2022 •

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JamesAPetts May 26, 2022

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feat: volume API and TMTV mode #2814

feat: volume API and TMTV mode #2814

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sedghi commented May 26, 2022 •

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