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Bug 669 - LOCI .mov file export failure
LOCI .mov file export failure
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Bio-Formats
unspecified
Macintosh Mac OS
: P2 critical
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-10-10 08:07 CDT by vasja_urbancic
Modified: 2014-07-14 13:07 CDT
2 users (show)

See Also:
Description vasja_urbancic 2013-10-10 08:07:40 CDT 
When trying to export an RGB image sequence (from three RGB stacks combined together) as a .mov or .avi file, the following "Exception" report comes up.

Any ideas how to solve this and export movies from Fiji would be greatly appreciated. Thank you!

Kind regards,
Vasja


(Fiji Is Just) ImageJ 1.48d; Java 1.6.0_26 [64-bit]; Mac OS X 10.6.8; 178MB of 995MB (17%)
 
java.lang.IllegalArgumentException: ZCT size vs image count mismatch (sizeZ=25, sizeC=3, sizeT=1, total=25)
	at loci.formats.FormatTools.getZCTCoords(FormatTools.java:424)
	at loci.plugins.out.Exporter.run(Exporter.java:556)
	at loci.plugins.LociExporter.run(LociExporter.java:77)
	at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:262)
	at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:111)
	at ij.IJ.runUserPlugIn(IJ.java:198)
	at ij.IJ.runPlugIn(IJ.java:160)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:680)



(Fiji Is Just) ImageJ 1.48d; Java 1.6.0_26 [64-bit]; Mac OS X 10.6.8; 893MB of 995MB (89%)
 
java.lang.IllegalArgumentException: ZCT size vs image count mismatch (sizeZ=25, sizeC=3, sizeT=1, total=25)
	at loci.formats.FormatTools.getZCTCoords(FormatTools.java:424)
	at loci.plugins.out.Exporter.run(Exporter.java:556)
	at loci.plugins.LociExporter.run(LociExporter.java:77)
	at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:262)
	at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:111)
	at ij.IJ.runUserPlugIn(IJ.java:198)
	at ij.IJ.runPlugIn(IJ.java:160)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:680)
Comment 1 Curtis Rueden 2013-10-23 14:38:19 CDT 
Thanks for the bug report. I filed a ticket for this problem in the OME Trac:
https://trac.openmicroscopy.org.uk/ome/ticket/11569
Comment 2 Curtis Rueden 2014-06-16 14:50:07 CDT 
Just quickly wanted to confirm that I can still reproduce this bug with an up-to-date Fiji running the Bio-Formats daily build. (Just try running Bio-Formats Exporter to save the Fly Brain sample as a JPEG, for example.)
Comment 3 Johannes Schindelin 2014-06-17 16:37:01 CDT 
I guess that the original poster is better served by the suggestion to use File>Export>Image... which uses SCIFIO to export the movie. That one works (but the command was not yet available when the bug was reported).
Comment 4 Curtis Rueden 2014-06-26 22:22:03 CDT 
There is now a fix for the problem under review:

https://github.com/openmicroscopy/bioformats/pull/1179

Once the fix is merged, it will be available from the Bio-Formats update site within 24 hours.
Comment 5 Curtis Rueden 2014-07-14 13:07:23 CDT 
This fix merged on June 27. So enabling the Bio-Formats update should resolve the issue. Please reopen if not.