[ome-devel] Bioformats Exporter

[Melissa Linkert]

Hi Rubén,

Thanks for mentioning this problem.  Updating to the latest trunk
build (r6459) should fix OME-TIFF export from ImageJ, but please let
me know if you continue to see an error message.

Regards,
-Melissa

On Thu, May 27, 2010 at 4:53 AM, Rubén Muñoz <ruben.munoz at embl.de> wrote:
> Hi Melissa,
>
> I suspect that the latest updates of loci-plugins have an additional problem different to the number of Series.
>
> ImageJ Bio-Formats Exporter is broken for imported ScanR images in newest releases. One can reproduce this using Plugins->LOCI->Bio-Formats Exporter (test.ome.tif)
>
> I have asked my colleagues if the images are represented in Big Endian. That's the case but some ArrayList seems empty now.
>
> The problem is not reproducible before r6200 and the stack trace prompts from  right before the compression algorithm selection:
>
> java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
>        at java.util.ArrayList.RangeCheck(ArrayList.java:547)
>        at java.util.ArrayList.get(ArrayList.java:322)
>        at ome.xml.r201004.Pixels.getBinData(Pixels.java:504)
>        at loci.formats.ome.OMEXMLMetadataImpl.getPixelsBinDataBigEndian(OMEXMLMetadataImpl.java:639)
>        at loci.plugins.out.Exporter.run(Exporter.java:287)
>        at loci.plugins.LociExporter.run(LociExporter.java:73)
>        at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:247)
>        at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:102)
>        at ij.IJ.runUserPlugIn(IJ.java:185)
>        at ij.IJ.runPlugIn(IJ.java:150)
>        at ij.Executer.runCommand(Executer.java:145)
>        at ij.Executer.run(Executer.java:76)
>        at java.lang.Thread.run(Thread.java:637)
>
>