[ome-users] ND2 question

Melissa Linkert melissa at glencoesoftware.com
Thu Feb 14 03:29:47 GMT 2013


Hi Henry,

> I was wondering if you all are aware of the bug reading nd2 files created
> by the most recent version of Nikon Elements with loci_tools.jar 4.4.6?
> When I try to open an nd2, I get the stack trace below. Do you know if this
> is fixable/if there is some kind of workaround? I'm happy to send you a
> test file if you need.

Thank you for the bug report.

If you could send a file that demonstrates the problem, that would be
very helpful.  You can upload files here:

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

If that doesn't work, please let us know and we'll send alternate upload
instructions.

Regards,
-Melissa

P.S. For future, it is best to send questions like this to the ome-users
mailing list (in CC), as that ensures a prompt reply even if I am away.

On Wed, Feb 13, 2013 at 12:01:54PM -0800, Henry Pinkard wrote:
> Hi Melissa,
> 
> I was wondering if you all are aware of the bug reading nd2 files created
> by the most recent version of Nikon Elements with loci_tools.jar 4.4.6?
> When I try to open an nd2, I get the stack trace below. Do you know if this
> is fixable/if there is some kind of workaround? I'm happy to send you a
> test file if you need.
> 
> Best,
> Henry
> 
> 
> java.lang.IllegalArgumentException: 0 must not be null and positive.
> at ome.xml.model.primitives.PositiveInteger.<init>(PositiveInteger.java:56)
> at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:266)
> at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:240)
> at loci.formats.ChannelFiller.setId(ChannelFiller.java:267)
> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
> at loci.formats.DimensionSwapper.setId(DimensionSwapper.java:292)
> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
> at loci.plugins.in.ImportProcess.setId(ImportProcess.java:685)
> at loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:522)
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:150)
> 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:185)
> at ij.IJ.runPlugIn(IJ.java:152)
> at ij.Executer.runCommand(Executer.java:127)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:662)



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