[ome-devel] Bioformats Exporter

[Rubén Muñoz]

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)