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fiji-hpc / hpc-datastore

Server-side of the HPC DataStore project - Java API, shell scripts
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legacy BDV: convert data and send it always as gray16 #24

Open xulman opened 11 months ago

xulman commented 11 months ago

[ERROR] Command errored: Create new dataset from XML/HDF5 java.lang.NoSuchMethodError: net.imglib2.img.basictypeaccess.ArrayDataAccessFactory.get(Lnet/imglib2/type/NativeType;)Ljava/lang/Object; at bdv.export.ExportScalePyramid$BlockCreator.forType(ExportScalePyramid.java:431) at bdv.export.ExportScalePyramid.writeScalePyramid(ExportScalePyramid.java:237) at cz.it4i.fiji.datastore.rest_client.WriteSequenceToN5.writeScalePyramid(WriteSequenceToN5.java:249) at cz.it4i.fiji.datastore.rest_client.WriteSequenceToN5.writeN5File(WriteSequenceToN5.java:208) at cz.it4i.fiji.datastore.ij.ExportSPIMAsN5PlugIn.run(ExportSPIMAsN5PlugIn.java:220) at org.scijava.command.CommandModule.run(CommandModule.java:196) at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:125) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:64) at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:247) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)

xulman commented 11 months ago

this looks like mismatch between BDV and imglib2 actually

xulman commented 11 months ago

nope, the issue was that I was using G8 (instead of G16) sooo, renaming the issue to "online convert *->G16"

interesting fact: when opening export.xml directly from the drive, BDV opens well (even when the data is G8)

xulman commented 11 months ago

connected #25

xulman commented 11 months ago

the PR #26 should be the solution to this issue