feat: Add DICOM SEG support and MPR, referenceLines and StackSync and more #3015

sedghi · 2022-11-11T03:03:02Z

This PR adds support for DICOM SEG read and various other features. Here is the summary

DICOM SEG read is now added in the longitudinal mode (though you can add it to your own mode as well, just add the extension as dependency and sopClassHandler).

ohif-v3-rc-seg.mp4

MPR support is added via click of a button in the toolbar. If the displaySet is reconstructable it can go MPR (SEG currently load as volume so it is possible to view SEG in MPR)

ohif-v3-rc-mpr.mp4

New Side panels. Previously you had to close a panel to open another one, but the new design adds a better user experience for switching panels

New Reference Line Tools

ohif-v3-rc-reference-lines.mp4

New Stack Synchronization tool across studies

Blocked by dcmjs-org/dicomweb-client#62

Thanks to

@swederik for great architectural suggestions and discussions
@dan-rukas for great inspiring UI and UX
@wayfarer3130 and @dsmith1547 for awesome static-wado support
@pieper for great expert opinions as always
@JamesAPetts for great initial segmentation work

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Georift · 2022-11-11T06:01:12Z

Woah man this is exciting 🙂 I'll definitely be cracking open this branch when I get a spare second.

swederik

LGTM with some minor comments

extensions/cornerstone-dicom-seg/LICENSE

extensions/cornerstone-dicom-seg/package.json

extensions/cornerstone-dicom-seg/src/getSopClassHandlerModule.js

extensions/cornerstone/src/utils/transitions.ts

swederik · 2022-11-13T18:52:56Z

extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts

+      // if the below formula is not correct, on a viewport reset
+      // it will jump to a different slice than the middle one which
+      // was the initial slice, and we have some tools such as Crosshairs
+      // which rely on a relative camera modifications and those will break.


Not sure I see why this should break crosshairs. Lets discuss

extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts

extensions/cornerstone/src/commandsModule.ts

swederik · 2022-11-13T19:04:56Z

extensions/cornerstone/src/commandsModule.ts

+    },
+    toggleStackImageSync: ({ toggledState }) => {
+      if (!toggledState) {
+        STACK_IMAGE_SYNC_GROUPS_INFO.forEach(syncGroupInfo => {


Commands module is getting pretty big, maybe it should be split into multiple files. Kind of ugly to start putting global variables at the top of the file like STACK_IMAGE_SYNC_GROUPS_INFO

Yeah, I don't like the STACK_IMAGE_SYNC_GROUPS_INFO either, but this is a kind of a global thing that we need, where else do you think I should put it?

swederik · 2022-11-13T19:07:15Z

extensions/cornerstone/src/services/CornerstoneCacheService/CornerstoneCacheService.ts

+    return viewportData;
+  }
+
+  public async invalidateViewportData(


What is this used for? Not sure I get it

When displaySet gets invalidated (patient weight change)

codecov · 2022-11-14T21:09:29Z

Codecov Report

Merging #3015 (c96c01a) into v3-stable (9f1e813) will increase coverage by 13.11%.
The diff coverage is n/a.

@@              Coverage Diff               @@
##           v3-stable    #3015       +/-   ##
==============================================
+ Coverage      25.15%   38.27%   +13.11%     
==============================================
  Files            119       98       -21     
  Lines           2862     2098      -764     
  Branches         555      432      -123     
==============================================
+ Hits             720      803       +83     
+ Misses          1856     1060      -796     
+ Partials         286      235       -51

Impacted Files	Coverage Δ
...tform/core/src/services/CineService/CineService.js	`12.50% <0.00%> (-6.25%)`	⬇️
.../services/MeasurementService/MeasurementService.js	`47.23% <0.00%> (-1.96%)`	⬇️
platform/core/src/classes/CommandsManager.js	`90.69% <0.00%> (-1.14%)`	⬇️
platform/core/src/classes/MetadataProvider.js	`4.54% <0.00%> (-0.72%)`	⬇️
...core/src/services/ToolBarService/ToolBarService.js	`1.21% <0.00%> (-0.28%)`	⬇️
platform/viewer/src/index.js	`0.00% <0.00%> (ø)`
platform/viewer/src/appInit.js	`0.00% <0.00%> (ø)`
platform/core/src/utils/index.js	`100.00% <0.00%> (ø)`
platform/core/src/utils/isImage.js	`100.00% <0.00%> (ø)`
platform/core/src/services/ServicesManager.js	`100.00% <0.00%> (ø)`
... and 48 more

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cypress · 2022-11-14T21:14:41Z

Test summary

20 • 0 • 0 • 0

Run details


Project	Viewers
Status	Passed
Commit	`c96c01a`
Started	Nov 16, 2022 9:00 AM
Ended	Nov 16, 2022 9:01 AM
Duration	01:46 💡
OS	Linux Debian - 11.3
Browser	Chrome 103

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JamesAPetts · 2022-11-15T06:19:09Z

Great work!

ILyAHA · 2022-11-15T11:58:53Z

extensions/cornerstone-dicom-seg/src/getSopClassHandlerModule.js

+  const segments = {};
+
+  dataset.SegmentSequence.forEach(segment => {
+    const cielab = segment.RecommendedDisplayCIELabValue;


Here can be crashed. RecommendedDisplayCIELabValue is optional in dicom

Thanks I will fix it later

manoocher · 2022-11-16T13:45:17Z

Hi team,
This PR contains exciting features and improvement, I immediately deployed it all features are the our long waited ones. Though in PT/SR studies the Fusion is not listed in the study browser? I tried the same study with an old version (older then stable) and it works. What could be the cause?

sedghi added 30 commits November 9, 2022 12:58

feat: add initial sop class handler for SEG

00398ce

feat: move segmentation service

b0a83e5

update segmentation service methods

923f258

fix: viewport data structure

3741873

feat: Add initial render for the DICOM SEG for each displaySet

61a4657

fix: various wrong architectural dependencies between services

b424f43

feat: initial separate SEG display in each viewport

9fbf0f6

feat: refactore viewport action bar

57ba012

initial work for SEG hydration

1c2fff0

fix: various bugs regarding drag and dropping different viewports

152ece3

fix: rendering issues for multiple seg displaysets

83d6073

fix: bugs for thumbnail and hydration

22e46a3

feat: fix the initial segment color

bb3f8d8

update after rebase

aaccf2f

feat: initial design for the segmentation group table

603efbb

feat: initial new design for the segmentation panel

f6ee1f7

feat: segmentation panel

d3fbc36

feat: make segmentation appear on all related viewports

bab9b25

fix: segmentation load bug based on functional groups

49f989a

initial work for segmentation crosshairs

e96d6d0

fix: various stylings and functionality

62dfba2

fix: various stylings for the seg panel

7909144

fix: overflow styles

7f67621

feat: add more ui components

9027c10

feat: added segmentation config

5c959cc

feat: add jump to segment

f7474a4

feat: add jump to segment for DICOM SEG viewport

45595c7

fix: bugs after rebase

670b9f1

feat: jump in segmentation viewport

9f3ffaa

fix: mpr support for seg

3a77010

sedghi added 2 commits November 10, 2022 20:01

feat: make showing loading indicator configurable and add docs

4b6130c

bump versions and add more docs

50aa81d

sedghi requested review from swederik and wayfarer3130 November 11, 2022 03:03

fix demo

f9f9f0f

swederik approved these changes Nov 13, 2022

View reviewed changes

ahlaughland mentioned this pull request Nov 14, 2022

How do we access the labelmaps2D? cornerstonejs/cornerstone3D#276

Closed

sedghi added 5 commits November 14, 2022 15:16

update cornerstone versions

d8ace73

apply review comments

2ff82ff

feat: add reference lines

c3be517

fix build

caa4099

fix unit tests

19fd336

sedghi added 2 commits November 14, 2022 17:37

add reference lines icon

d2b3c2f

fix: e2e tests

f4c5718

sedghi changed the title ~~Feat/dicom seg~~ feat: Add DICOM SEG support and MPR, referenceLines and StackSync and more Nov 15, 2022

sedghi added 2 commits November 14, 2022 21:32

fix static wado config

7ed97be

docs: add segmentation service docs

9fb47a3

ILyAHA suggested changes Nov 15, 2022

View reviewed changes

sedghi and others added 3 commits November 15, 2022 11:22

fix: docker build

97496aa

fix: keep camera and bump versions

206577a

Try re-enabling minification to fix deploy previews

c96c01a

sedghi merged commit 83ea228 into v3-stable Nov 16, 2022

sedghi deleted the feat/dicom-seg branch January 22, 2025 16:13

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feat: Add DICOM SEG support and MPR, referenceLines and StackSync and more #3015

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feat: Add DICOM SEG support and MPR, referenceLines and StackSync and more #3015

feat: Add DICOM SEG support and MPR, referenceLines and StackSync and more #3015

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sedghi commented Nov 11, 2022 • edited Loading

Blocked by dcmjs-org/dicomweb-client#62

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