[ome-users] Apparent Bug in reading large Leica lei files

[Melissa Linkert]

Hi Joel,

> I have been having trouble reading a Leica *lei file which is over 400MB on
> a PC running Win7, 64 bit.  There is no problem if I use a 32bit machine
> that is running Win7, oddly enough.  When I try to open the file, I get the
> following error message.  BTW, Wayne took a look at the situation and
> duplicated it, and then suggested I send this to you.
> 
> ImageJ 1.49b11; Java 1.6.0_43 [64-bit]; Mac OS X 10.6.8; 209MB of 4000MB

Thank you very much for reporting this problem.

Could you please let us know which version of Bio-Formats you have
installed on the working and non-working machines?  "Help > About
Plugins > Bio-Formats Plugins" (or "Help > About Plugins > LOCI Plugins"
if an older version is installed) should show the version number and
date.

If the working machine has a newer version than the non-working one, then
upgrading should solve the problem.  If the working machine has an older
version, though, then it would be very helpful if you could send the dataset
in question by uploading to:

http://qa.openmicroscopy.org.uk/qa/upload/

You may wish to put the dataset in a Zip file before uploading; if that
doesn't work, please let us know.

Regards,
-Melissa

On Wed, May 28, 2014 at 12:10:28AM -0400, JOEL B. SHEFFIELD wrote:
> I have been having trouble reading a Leica *lei file which is over 400MB on
> a PC running Win7, 64 bit.  There is no problem if I use a 32bit machine
> that is running Win7, oddly enough.  When I try to open the file, I get the
> following error message.  BTW, Wayne took a look at the situation and
> duplicated it, and then suggested I send this to you.
> 
> ImageJ 1.49b11; Java 1.6.0_43 [64-bit]; Mac OS X 10.6.8; 209MB of 4000MB
> (5%)
> 
> java.lang.
> IndexOutOfBoundsException: Index: 1, Size: 1
>         at java.util.ArrayList.RangeCheck(ArrayList.java:547)
>         at java.util.ArrayList.get(ArrayList.java:322)
>         at ome.xml.model.Pixels.getChannel(Pixels.java:573)
>         at
> ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9728)
>         at
> ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1686)
>         at
> loci.formats.in.LeicaReader.parseInstrumentData(LeicaReader.java:1427)
>         at loci.formats.in.LeicaReader.initFile(LeicaReader.java:698)
>         at loci.formats.FormatReader.setId(FormatReader.java:1315)
>         at
> loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
>         at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
>         at loci.plugins.in.Importer.showDialogs(Importer.java:141)
>         at loci.plugins.in.Importer.run(Importer.java:79)
>         at loci.plugins.LociImporter.run(LociImporter.java:81)
>         at ij.IJ.runUserPlugIn(IJ.java:201)
>         at ij.IJ.runPlugIn(IJ.java:165)
>         at ij.Executer.runCommand(Executer.java:131)
>         at ij.Executer.run(Executer.java:64)
>         at java.lang.Thread.run(Thread.java:680)
> 
> Joel B. Sheffield, Ph.D
> Department of Biology
> Temple University
> Philadelphia, PA 19122
> Voice: 215 204 8839
> e-mail: jbs at temple.edu
> URL:  http://astro.temple.edu/~jbs

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