Crash Opening .SLD file

[Rebecca Keller]

Dear Imagers,

I have some 8-10 GB time lapse series in one wavelength which give the
folowing error after a LONG wait: Anyone know what's going on here?

JPK


(Fiji Is Just) ImageJ 2.0.0-rc-9/1.49d; Java 1.6.0_24 [64-bit]; Windows 7
6.1; 52MB of 24465MB (<1%)

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.OME.getImage(OME.java:647)
at
ome.xml.meta.OMEXMLMetadataImpl.getImageName(OMEXMLMetadataImpl.java:2232)
at loci.plugins.in.ImportProcess.computeSeriesLabels(ImportProcess.java:718)
at loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:536)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:148)
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:202)
at ij.IJ.runPlugIn(IJ.java:166)
at ij.IJ.runPlugIn(IJ.java:155)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:421)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
at ij.IJ.runUserPlugIn(IJ.java:202)
at ij.IJ.runPlugIn(IJ.java:166)
at ij.IJ.runPlugIn(IJ.java:155)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:460)
at ij.io.Opener.openImage(Opener.java:315)
at ij.io.Opener.openImage(Opener.java:338)
at ij.io.Opener.open(Opener.java:145)
at ij.io.Opener.open(Opener.java:72)
at ij.plugin.Commands.run(Commands.java:27)
at ij.IJ.runPlugIn(IJ.java:172)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:662)

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[ctrueden]

Hi Rebecca,

> 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.OME.getImage(OME.java:647)

Looks like a bug in the Bio-Formats plugin [1], which is what handles the
SLD file format. SlideBook is one of the toughest formats for the OME team
to support. I suggest reporting the problem on the ome-users list [2],
which is the best place to discuss Bio-Formats issues.

Regards,
Curtis

P.S. You can also try the very latest version of Bio-Formats to see whether
it fixes the problem; see http://fiji.sc/Bio-Formats#Daily_builds

[1] http://fiji.sc/Bio-Formats
[2] http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/


On Tue, Jul 22, 2014 at 11:26 PM, Rebecca Keller <[hidden email]>
wrote:

> Dear Imagers,
>
> I have some 8-10 GB time lapse series in one wavelength which give the
> folowing error after a LONG wait: Anyone know what's going on here?
>
> JPK
>
>
> (Fiji Is Just) ImageJ 2.0.0-rc-9/1.49d; Java 1.6.0_24 [64-bit]; Windows 7
> 6.1; 52MB of 24465MB (<1%)
>
> 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.OME.getImage(OME.java:647)
> at
> ome.xml.meta.OMEXMLMetadataImpl.getImageName(OMEXMLMetadataImpl.java:2232)
> at
> loci.plugins.in.ImportProcess.computeSeriesLabels(ImportProcess.java:718)
> at loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:536)
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:148)
> 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:202)
> at ij.IJ.runPlugIn(IJ.java:166)
> at ij.IJ.runPlugIn(IJ.java:155)
> at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:421)
> at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
> at ij.IJ.runUserPlugIn(IJ.java:202)
> at ij.IJ.runPlugIn(IJ.java:166)
> at ij.IJ.runPlugIn(IJ.java:155)
> at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:460)
> at ij.io.Opener.openImage(Opener.java:315)
> at ij.io.Opener.openImage(Opener.java:338)
> at ij.io.Opener.open(Opener.java:145)
> at ij.io.Opener.open(Opener.java:72)
> at ij.plugin.Commands.run(Commands.java:27)
> at ij.IJ.runPlugIn(IJ.java:172)
> at ij.Executer.runCommand(Executer.java:131)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:662)
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html