[ome-devel] decreasing #planes twice

[Melissa Linkert]

Hi Heinrich,

> 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.

That is expected - the fix has not yet been included in the trunk/daily
builds.  When the status of this changes from "open" to "closed":

https://github.com/openmicroscopy/bioformats/pull/27

...then the fix will have been included.

Regards,
-Melissa

On Fri, Mar 02, 2012 at 03:13:28PM +0000, Grabmayr, Heinrich wrote:
> 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