[ome-devel] decreasing #planes twice

[Melissa Linkert]

Hi Heinrich,

> I just encountered a problem:
> Take an ometiff with several channels and several frames.
> Use the loci-channel splitter to split frames and export one of them as an ometiff.
> Open that (now, #T=1, #C=n) and split channels, save one of them.
> Try to open that. Here I got an error message: 
> 
> java.lang.IllegalArgumentException: Invalid C index: -1/1
> 	at loci.formats.FormatTools.getIndex(FormatTools.java:304)
> 	at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:449)
> 	at loci.formats.FormatReader.setId(FormatReader.java:1058)
> 	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:475)
> 	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:138)
> 	at loci.plugins.in.Importer.showDialogs(Importer.java:125)
> 	at loci.plugins.in.Importer.run(Importer.java:77)
> 	at loci.plugins.LociImporter.run(LociImporter.java:77)
> 	at ij.IJ.runUserPlugIn(IJ.java:183)
> 	at ij.IJ.runPlugIn(IJ.java:150)
> 	at ij.IJ.runPlugIn(IJ.java:139)
> 	at loci.plugins.shortcut.ShortcutPanel$1.run(ShortcutPanel.java:189)
> 
> I had this problem also when running my own matlab scripts that change dimension sizes. What is the problem there?

Thanks for reporting this.  I was able to duplicate the problem, and have filed
a ticket accordingly:

http://trac.openmicroscopy.org.uk/ome/ticket/7869

And, as usual, you have been CC'd on the ticket.  In general, this sort
of problem is caused by the number of channels in the metadata not
matching the number of actual channel images.  It's just a matter of
tracking down precisely where it is that the channel count is not being
set correctly.

Regards,
-Melissa

On Fri, Jan 20, 2012 at 04:38:36PM +0000, Grabmayr, Heinrich wrote:
> Hi everybody,
> 
> I just encountered a problem:
> Take an ometiff with several channels and several frames.
> Use the loci-channel splitter to split frames and export one of them as an ometiff.
> Open that (now, #T=1, #C=n) and split channels, save one of them.
> Try to open that. Here I got an error message: 
> 
> java.lang.IllegalArgumentException: Invalid C index: -1/1
> 	at loci.formats.FormatTools.getIndex(FormatTools.java:304)
> 	at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:449)
> 	at loci.formats.FormatReader.setId(FormatReader.java:1058)
> 	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:475)
> 	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:138)
> 	at loci.plugins.in.Importer.showDialogs(Importer.java:125)
> 	at loci.plugins.in.Importer.run(Importer.java:77)
> 	at loci.plugins.LociImporter.run(LociImporter.java:77)
> 	at ij.IJ.runUserPlugIn(IJ.java:183)
> 	at ij.IJ.runPlugIn(IJ.java:150)
> 	at ij.IJ.runPlugIn(IJ.java:139)
> 	at loci.plugins.shortcut.ShortcutPanel$1.run(ShortcutPanel.java:189)
> 
> I had this problem also when running my own matlab scripts that change dimension sizes. What is the problem there?
> 
> --Heinrich
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