Opening CZI in Fiji causes an ArrayIndexOutOfBoundsException

[hornm]

Hi all,

I'm not sure who I should address with this issue, so I just ask here:

Opening this czi-image with Fiji (bioformats 5...) causes an AIOOBE:

java.lang.ArrayIndexOutOfBoundsException: 1
at loci.formats.in.ZeissCZIReader.translateExperiment(ZeissCZIReader.java:2190)
at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1214)
at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:699)
at loci.formats.FormatReader.setId(FormatReader.java:1315)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
at loci.plugins.in.Importer.showDialogs(Importer.java:141)
at loci.plugins.in.Importer.run(Importer.java:79)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:201)
at ij.IJ.runPlugIn(IJ.java:165)
at ij.IJ.runPlugIn(IJ.java:154)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:421)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
at ij.IJ.runUserPlugIn(IJ.java:201)
at ij.IJ.runPlugIn(IJ.java:165)
at ij.IJ.runPlugIn(IJ.java:154)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:454)
at ij.io.Opener.openImage(Opener.java:311)
at ij.io.Opener.openImage(Opener.java:334)
at ij.io.Opener.open(Opener.java:144)
at ij.io.Opener.open(Opener.java:71)
at ij.plugin.Commands.run(Commands.java:27)
at ij.IJ.runPlugIn(IJ.java:171)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:662)

Any ideas?

Thank you very much in advance!

Best,
Martin

[melissalinkert]

Thanks Martin - I can reproduce this with 5.0.2. Do you happen to know which version of Zen was used to acquire this file?

[melissalinkert]

See also http://fiji.sc/bugzilla/show_bug.cgi?id=760

[sebi06]

Both file are identical since we reported the problem 1st to the KNIME guys. And I was not aware, that they already filed a bug entry ti Fiji. So I created a duplicate. Sorry for this...

In case of Fiji bug ID= 760 it was the latest ZEN version 2012 SP2 with Hotfix 6. I am currently not aware of any changes some did inside the CZI, but the strange thing is that some CZI files work, while the reported ones do not. And the fact that it used to work for both test files.

Cheers, Sebi

[melissalinkert]

The fix for this problem is in #1153