Abba pluggin and new Fiji version atlas disappear

[hedjour]

I can not open a file here are the exception file, output of your demand.
Exception.txt

[mkitti]

watching

[mkitti]

Error location:
https://sissource.ethz.ch/sispub/jhdf5/-/blob/master/source/java/ch/systemsx/cisd/hdf5/HDF5BaseReader.java#L221

[NicoKiaru]

Related: #3

[hedjour]

This is not related to #3 but to #5 Sorry I make a mistake...

[mkitti]

(Fiji Is Just) ImageJ 2.9.0/1.53t; Java 1.8.0_322 [64-bit]; Linux 5.19.0-35-generic; 315MB of 40867MB (<1%)
 
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:308)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:166)
	at ij.IJ.runPlugIn(IJ.java)
	at ij.Executer.runCommand(Executer.java:152)
	at ij.Executer.run(Executer.java:70)
	at java.lang.Thread.run(Thread.java:750)
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:304)
	... 5 more
Caused by: java.lang.RuntimeException: Module threw exception
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	... 1 more
Caused by: java.lang.RuntimeException: ch.systemsx.cisd.hdf5.exceptions.HDF5FileNotFoundException: Path does not exit. (/home/jelongueville/.abba/abba_atlases/WHS_SD_rat_atlas_v4_b.xml/..\WHS_SD_rat_atlas_v4.h5)
	at bdv.ij.BigDataViewerPlugIn.run(BigDataViewerPlugIn.java:139)
	at org.scijava.command.CommandModule.run(CommandModule.java:196)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
	... 6 more
Caused by: ch.systemsx.cisd.hdf5.exceptions.HDF5FileNotFoundException: Path does not exit. (/home/jelongueville/.abba/abba_atlases/WHS_SD_rat_atlas_v4_b.xml/..\WHS_SD_rat_atlas_v4.h5)
	at ch.systemsx.cisd.hdf5.HDF5BaseReader.openFile(HDF5BaseReader.java:221)
	at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:177)
	at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:155)
	at ch.systemsx.cisd.hdf5.HDF5ReaderConfigurator.reader(HDF5ReaderConfigurator.java:81)
	at ch.systemsx.cisd.hdf5.HDF5FactoryProvider$HDF5Factory.openForReading(HDF5FactoryProvider.java:55)
	at ch.systemsx.cisd.hdf5.HDF5Factory.openForReading(HDF5Factory.java:54)
	at bdv.img.hdf5.Hdf5ImageLoader.open(Hdf5ImageLoader.java:183)
	at bdv.img.hdf5.Hdf5ImageLoader.getSetupImgLoader(Hdf5ImageLoader.java:389)
	at bdv.img.hdf5.Hdf5ImageLoader.getSetupImgLoader(Hdf5ImageLoader.java:79)
	at bdv.BigDataViewer.initSetupNumericType(BigDataViewer.java:279)
	at bdv.BigDataViewer.initSetups(BigDataViewer.java:311)
	at bdv.BigDataViewer.open(BigDataViewer.java:532)
	at bdv.BigDataViewer.open(BigDataViewer.java:550)
	at bdv.ij.BigDataViewerPlugIn.run(BigDataViewerPlugIn.java:135)
	... 9 more```

[NicoKiaru]

So you can reproduce the error @mkitti ?

[mkitti]

I have not tried. I was just trying to figure out what generates this URL with the ..\ /home/jelongueville/.abba/abba_atlases/WHS_SD_rat_atlas_v4_b.xml/..\WHS_SD_rat_atlas_v4.h5

[NicoKiaru]

The xml and hdf5 files are here:

https://zenodo.org/record/7492551#.ZCL3svZBxD8

As far I understood, to reproduce the error (with @hedjour configuration), you simply need to download these two files, put them in the same folder, and then in Fiji, run Plugins>BigDataViewer>Open Xml/Hdf5

For the path 'parsing', the xml deserialization happens here:

https://github.com/bigdataviewer/bigdataviewer-core/blob/60e1c2639c7d3b5d4e1b48e4ee80efedc689addf/src/main/java/bdv/img/hdf5/XmlIoHdf5ImageLoader.java#L64-L71

The xml file contains these lines that specify the path and the image loader:

<ImageLoader format="bdv.hdf5">
      <hdf5 type="relative">ccf2017-mod65000-border-centered-mm-bc.h5</hdf5>
</ImageLoader>

[NicoKiaru]

Oh, actually the xml hdf5 is this one:

https://zenodo.org/record/5644162#.ZCL46vZBxD8

Not sure it changes anything, but this dataset is much smaller

[mkitti]

The XML BasePath is not correct.

[hedjour]

With a good absolute path I can open the atlas image.
But not run Abba pluggin, any idea @NicoKiaru