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Update to pom-scijava 44#128

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Update to pom-scijava 44#128
ctrueden wants to merge 4 commits into
juglab:masterfrom
ctrueden:psj44

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@ctrueden

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This updates the project to extend pom-scijava 44.0.0. It also adds missing directly-used dependencies and makes some other minor fixes to the project POM.

I noticed the following errors and warnings in the console, although all tests pass on my system:

[INFO] Running sc.fiji.labkit.ui.InitialLabelingTest
Error, labeling file is empty: /tmp/labkit-InitialLabelingTest-3687977385678443139.czi.labeling

[INFO] Running sc.fiji.labkit.ui.utils.sparse.HDF5SaverTest
The RandomAccessible net.imglib2.view.fluent.RandomAccessibleView$$Lambda$712/709502635@53d4376d is only be supported through the fall-back implementation of PrimitiveBlocks. 
All View dimensions must map to a dimension of the underlying NativeImg. That is Views.addDimension(...) is not allowed.

The second one in particular may need adjustments to account for newer ImgLib2 behavior.

@ctrueden

ctrueden commented Jun 15, 2026

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Note that even after this PR is merged, labkit-ui will need further adjustment to support n5 v4, which will be part of pom-scijava 45. Current test failures with n5 v4 include:

[ERROR] Errors: 
[ERROR]   HDF5SaverTest.testPartitionedWriting:73 » NoSuchMethod 'void org.janelia.saalfeldlab.n5.DatasetAttributes.<init>(long[], int[], org.janelia.saalfeldlab  .n5.DataType, org.janelia.saalfeldlab.n5.Compression)'
[ERROR]   HDF5SaverTest.testPartitionedWriting2:86 » NoSuchMethod 'void org.janelia.saalfeldlab.n5.DatasetAttributes.<init>(long[], int[], org.janelia.saalfeldla  b.n5.DataType, org.janelia.saalfeldlab.n5.Compression)'
[ERROR]   HDF5SaverTest.testSave2d:62 » NoSuchMethod 'void org.janelia.saalfeldlab.n5.DatasetAttributes.<init>(long[], int[], org.janelia.saalfeldlab.n5.DataType  , org.janelia.saalfeldlab.n5.Compression)'
[ERROR]   HDF5SaverTest.testSave4d:53 » NoSuchMethod 'void org.janelia.saalfeldlab.n5.DatasetAttributes.<init>(long[], int[], org.janelia.saalfeldlab.n5.DataType  , org.janelia.saalfeldlab.n5.Compression)'

CC @maarzt @bogovicj

Edit: Or: the fix may be needed in a BDV component:

java.lang.NoSuchMethodError: 'void org.janelia.saalfeldlab.n5.DatasetAttributes.<init>(long[], int[], org.janelia.saalfeldlab.n5.DataType, org.janelia.saalfeldla
ompression)'
  at bdv.export.WriteSequenceToHdf5$HDF5DatasetIO.createDataset(WriteSequenceToHdf5.java:519)
  at bdv.export.WriteSequenceToHdf5$HDF5DatasetIO.createDataset(WriteSequenceToHdf5.java:489)
  at bdv.export.ExportScalePyramid.writeScalePyramid(ExportScalePyramid.java:289)
  at bdv.export.WriteSequenceToHdf5.writeViewToHdf5PartitionFile(WriteSequenceToHdf5.java:647)
  at bdv.export.WriteSequenceToHdf5.writeViewToHdf5PartitionFile(WriteSequenceToHdf5.java:558)
  at bdv.export.WriteSequenceToHdf5.writeHdf5PartitionFile(WriteSequenceToHdf5.java:440)
  at bdv.export.WriteSequenceToHdf5.writeHdf5File(WriteSequenceToHdf5.java:159)
  at sc.fiji.labkit.ui.utils.HDF5Saver.writeHDF5Block(HDF5Saver.java:244)

CC @tpietzsch

Edit 2: OK, I see @bogovicj already did it with bigdataviewer/bigdataviewer-core@d06c7f9, and @tpietzsch released 10.6.11. I will try it.

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