File handle not released when loading h5 data fails

[k-dominik]

Problem

When investigating #167 I found that Fiji seems to keep the file handle to an hdf5 file open if loading the data is not successful. Obviously the handle should be closed when an error occurs. Not sure this is in the hands of this library or somwhere deep in fiji/imagej. This happens with the Open Multiple Images and Labels and Open Image and Labels.

To reproduce

• Use the h5 file from this zip cr.zip
• In Fiji Plugins -> MoBiE -> Open Multiple Images and Labels
• add this file as the first image and open
• it fails 🐛
• lsof | grep cr.h5 to confirm file is still opened in Fiji

traceback

[ERROR] Command errored: Open Multiple Images and Labels...
java.lang.RuntimeException: java.lang.IllegalArgumentException: provided axes doesn't match dimensionality of image
	at org.embl.mobie.io.imagedata.IlastikImageData.open(IlastikImageData.java:141)
	at org.embl.mobie.io.imagedata.IlastikImageData.getMetadata(IlastikImageData.java:106)
	at org.embl.mobie.lib.data.ImageGridSources.setMetadata(ImageGridSources.java:188)
	at org.embl.mobie.lib.data.ImageGridSources.<init>(ImageGridSources.java:91)
	at org.embl.mobie.lib.data.GridSourcesFromPathsCreator.<init>(GridSourcesFromPathsCreator.java:51)
	at org.embl.mobie.MoBIE.<init>(MoBIE.java:169)
	at org.embl.mobie.command.open.OpenMultipleImagesAndLabelsCommand.run(OpenMultipleImagesAndLabelsCommand.java:103)
	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:750)
Caused by: java.lang.IllegalArgumentException: provided axes doesn't match dimensionality of image
	at org.embl.mobie.io.imagedata.IlastikImageData.splitIntoChannels(IlastikImageData.java:201)
	at org.embl.mobie.io.imagedata.IlastikImageData.open(IlastikImageData.java:134)
	... 15 more