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Issue opening jp2 in ImageJ

Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats
Please note:
Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

Issue opening jp2 in ImageJ

Postby ltracy » Fri Sep 06, 2013 8:01 pm

Hello,

I am trying to open jp2 files (sized between 1 and 5 MB) using the Bio-Formats importer on Image J and I keep receiving this error message:

java.lang.StringIndexOutOfBoundsException: String index out of range: -9532
at java.lang.AbstractStringBuilder.substring(AbstractStringBuilder.java:881)
at java.lang.StringBuffer.substring(StringBuffer.java:416)
at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:1377)
at loci.formats.FormatReader.setId(FormatReader.java:1183)
at loci.formats.DelegateReader.setId(DelegateReader.java:259)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
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:680)

I tried selecting "crop on import" and was met with the same message. Any ideas on how to fix this??

Thanks,
Lauren
ltracy
 
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Re: Issue opening jp2 in ImageJ

Postby mlinkert » Mon Sep 09, 2013 8:45 am

Hi Lauren,

Could you please confirm that you are using a recent version of Bio-Formats? If you select "Help > About Plugins > LOCI Plugins", the version number and date will be shown. 4.4.8 is the latest stable version, so if you see a version number prior to that then I would suggest upgrading.

If upgrading does not solve the problem, then could you please send one of the files that causes this error message so that we can better fix the problem? You can upload the file to:

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

Regards,
-Melissa
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mlinkert
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Location: Southwest Wisconsin


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