[ome-users] Saving as Quicktime fails after latest Fiji update

[Melissa Linkert]

Hi Matt,

> After a recent update by Fiji, the Loci Bio-formats Exporter Quicktime
> functionality fails.  This has worked well in the past.
> 
> I am running Mac OS X 10.6.8.
> ImageJ: 1.47i
> Java: 1.6.0_37 (64 bit)
> Loci Plugins for ImageJ, revision d58fa88, built 31 Jan 2013
> Release: 4.5-DEV
> 
> "Update Fiji" indicates Fiji is up to date.
> 
> Steps to reproduce error:
> 1) File -> New... -> Image.  400x400 pix, 3 stacks
> 2) Plugins -> LOCI -> BioFormats Exporter.
> 3) Save as: foo.mov, Quicktime Format.
> 4) None of the "Write each..." boxes checked.
> 
> I get the following exception:

Thank you for the detailed bug report.  We have just now fixed this
problem, and so the next version of Bio-Formats should work as before
(see: https://github.com/openmicroscopy/bioformats/pull/373).

In the meantime, checking one of the "Write ... to a separate file" boxes should
allow you to save QuickTime files.

Regards,
-Melissa

On Mon, Feb 11, 2013 at 08:20:17AM -0600, Matt Wyczalkowski wrote:
> Hi,
> 
> After a recent update by Fiji, the Loci Bio-formats Exporter Quicktime
> functionality fails.  This has worked well in the past.
> 
> I am running Mac OS X 10.6.8.
> ImageJ: 1.47i
> Java: 1.6.0_37 (64 bit)
> Loci Plugins for ImageJ, revision d58fa88, built 31 Jan 2013
> Release: 4.5-DEV
> 
> "Update Fiji" indicates Fiji is up to date.
> 
> Steps to reproduce error:
> 1) File -> New... -> Image.  400x400 pix, 3 stacks
> 2) Plugins -> LOCI -> BioFormats Exporter.
> 3) Save as: foo.mov, Quicktime Format.
> 4) None of the "Write each..." boxes checked.
> 
> I get the following exception:
> 
> java.lang.reflect.InvocationTargetException
>     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>     at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>     at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>     at java.lang.reflect.Method.invoke(Method.java:597)
>     at ij.Command.runPlugIn(Command.java:148)
>     at ij.Command.runCommand(Command.java:97)
>     at ij.Executer.run(Executer.java:64)
>     at java.lang.Thread.run(Thread.java:680)
> Caused by: java.lang.IllegalArgumentException: Invalid Z size: 0
>     at loci.formats.FormatTools.getZCTCoords(FormatTools.java:403)
>     at loci.plugins.out.Exporter.run(Exporter.java:545)
>     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:187)
>     at ij.IJ.runPlugIn(IJ.java:152)
>     ... 8 more
> 
> Any help would be appreciated.
> 
> Regards,
> 
> Matt
> 
> ---
> Matthew A. Wyczalkowski, Ph.D.
> NIH NRSA Postdoctoral Fellow
> Taber Lab, Department of Biomedical Engineering
> Washington University in St. Louis
> http://taberlab.seas.wustl.edu
> wyczalkowskim at wustl.edu

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