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Merged
merged 6 commits into from
Aug 29, 2024
Merged

Addition of getType() API #115

merged 6 commits into from
Aug 29, 2024

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@tpietzsch
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@tpietzsch tpietzsch commented Apr 5, 2024

Changes that will be required after imglib/imglib2#312 is merged and released

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tpietzsch commented Apr 5, 2024

Bumping parent to pom-scijava-37.0.0 causes the following test failures with
IllegalArgument Invalid service: net.imagej.legacy.LegacyService

@ctrueden any idea what could be going on there and how to fix it?

[ERROR] Errors:
[ERROR]   GarbageCollectionTest.<init>:53 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   GarbageCollectionTest.<init>:53 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   InitialLabelingTest.testDoNotCrashWhenLabelingFileIsEmpty:62 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   InitialLabelingTest.testEnumeratedAxis:78 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   SegmentationUseCaseTest.test:78 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   SegmentationUseCaseTest.testMultiChannel:111 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   LabelingSerializationTest.<init>:69 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   LabelingSerializationTest.<init>:69 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   LabelingSerializationTest.<init>:69 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   LabelingSerializationTest.<init>:69 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   DefaultSegmentationModelTest.testListener:58 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   DefaultSegmentationModelTest.testLoadClassifierWithDifferentLabels:81 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   CalculateProbabilityMapWithLabkitIJ1PluginTest.test:21 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   CalculateProbabilityMapWithLabkitPluginTest.test:44 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   LabkitProbabilityMapForImagesInDirectoryPluginTest.<init>:71 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   LabkitSegmentImagesInDirectoryPluginTest.<init>:73 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   SegmentImageWithLabkitIJ1PluginTest.test:21 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   SegmentImageWithLabkitPluginTest.test:44 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   SegmentRGBImageTest.testSegmentation:61 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   SegmentRGBImageTest.testTraining:79 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   LabkitProjectFileSerializerTest.testOpen:59 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   LabkitProjectFileSerializerTest.testSave:47->exampleProject:84 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   SegmentationToolTest.<init>:51->openImage:81 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   SegmentationToolTest.<init>:51->openImage:81 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService
[ERROR]   TrainableSegmentationSegmenterTest.testClassify3DStackInSlices:59 » IllegalArgument Invalid service: net.imagej.legacy.LegacyService

@tpietzsch tpietzsch mentioned this pull request Apr 5, 2024
Merged
@tpietzsch
POM: Bump parent to pom-scijava-38.0.1
8164ffc
@tpietzsch
POM: Bump dependency versions
83eaa1e 
	imglib2 -> 7.1.0
	imglib2-realtransform -> 4.0.3
	imglib2-roi -> 0.15.0
	imglib2-cache -> 1.0.0-beta-18
	imglib2-algorithm -> 0.15.3
	bigdataviewer-core -> 10.6.0
@tpietzsch
Adapt API changes introduced by imglib/imglib2-roi#71
1db7ae7
@tpietzsch
Add missing getType() implementations
2fc86c5
@tpietzsch tpietzsch force-pushed the feature-rai-getType branch from c9a8eaa to 2fc86c5 Compare August 19, 2024 10:24
@tpietzsch tpietzsch marked this pull request as ready for review August 19, 2024 10:24
@maarzt
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maarzt commented Aug 27, 2024

@tpietzsch Thank you for the PR !!

What are the steps and timing required to get this released & deployed together with imglib2-7.1 ?

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tpietzsch commented Aug 27, 2024

It would be cool if you could make a release now. I'll ping you when the imglib2-7.1 is on the Fiji update site

maarzt added 2 commits August 29, 2024 11:57
@maarzt
Avoid using ImgLabeling.getType()
426c907 
In imglib2-7.1 the way Utils.getTypeFromInterval(...) works was changed.
Currently it triggers a NullPointerException for an ImgLabeling. This
workaround fixes the problem.
@maarzt
Bump dependency to labkit-pixel-classification version 0.1.18
32bdfb5
@maarzt maarzt merged commit 43eebfe into master Aug 29, 2024
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maarzt commented Aug 29, 2024 •
edited
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A made the releases:

  • labkit-pixel-classification 0.1.18
  • labkit-ui 0.4.0

@tpietzsch Could you please upload the labkit jars together with imglib2, I don't yet have the privileges to upload to Fiji's core update sites.

I also found a bug in imglib2-roi - imgLabeling.getType(). Even after fixing the bug Utils.getType(imgLabeling).createVariable() creates a LabelingType that behaves differently than with imglib2-6.1. Don't know why exactly. Here is the PR that hopefully fixes the bug imglib/imglib2-roi#73

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3 participants

@tpietzsch @maarzt