Open hedjour opened 1 year ago
watching
This is not related to #3 but to #5 Sorry I make a mistake...
(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```
So you can reproduce the error @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
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:
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>
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
The XML BasePath is not correct.
With a good absolute path I can open the atlas image. But not run Abba pluggin, any idea @NicoKiaru
I can not open a file here are the exception file, output of your demand. Exception.txt