[ome-devel] decreasing #planes twice

[Grabmayr, Heinrich]

Hi Melissa,

sorry I get back to you for this so late. I only now managed to check the resolution of the bug #7869.
I downloaded today's version of loci_tools.jar and put it into the ImageJ folder.
Then started ImageJ and took the steps described below - and again, I got the error message, independent of which two Dimensions I split.
The sample Image I used is the multi-channel-4D-series from http://www.openmicroscopy.org/site/support/file-formats/downloads/ome-tiff/ome-tiff-data

Is there anything I still need to take care of?
I checked for any other remaining loci-formats or maybe bio-formats jars in the ImageJ plugins folder, but there were none. I also restarted the computer in case the old loci-tools somehow was still opened in java or something.

Best
   Heinrich



-----Ursprüngliche Nachricht-----
Von: Melissa Linkert [mailto:melissa.linkert at gmail.com] Im Auftrag von Melissa Linkert
Gesendet: Samstag, 21. Januar 2012 02:20
An: Grabmayr, Heinrich
Cc: ome-devel Development
Betreff: Re: [ome-devel] decreasing #planes twice

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
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel