[ome-users] Issue with Bio-Formats Importer

[Melissa Linkert]

Hi Hallie,

Thank you for uploading a file, and apologies for the delay.

> I am trying to convert .nd2 files to .tiff using the Bio-Formats plugin. When I select the importer options and submit I get this exception error message:
> 
> (Fiji Is Just) ImageJ 2.0.0-rc-45/1.50g; Java 1.8.0_66 [64-bit]; Mac OS X 10.11.2; 95MB of 5433MB (1%) java.lang.IndexOutOfBoundsException: Index: 0, Size: 0 at java.util.ArrayList.rangeCheck(ArrayList.java:653) at java.util.ArrayList.get(ArrayList.java:429) at loci.formats.FormatReader.getSizeC(FormatReader.java:719) at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:1342) at loci.formats.FormatReader.setId(FormatReader.java:1426) at loci.formats.DelegateReader.setId(DelegateReader.java:290) at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505) at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143) at loci.plugins.in.Importer.showDialogs(Importer.java:140) at loci.plugins.in.Importer.run(Importer.java:76) at loci.plugins.LociImporter.run(LociImporter.java:78) at ij.IJ.runUserPlugIn(IJ.java:212) at ij.IJ.runPlugIn(IJ.java:176) at ij.Executer.runCommand(Executer.java:137) at ij.Executer.run(Executer.java:66) at java.lang.Thread.run(Thread.java:745)

We were able to duplicate this problem, and are currently testing a fix:

https://github.com/openmicroscopy/bioformats/pull/2284

The fix is currently expected to be included in the upcoming 5.2.0
release of Bio-Formats.

Regards,
-Melissa

On Tue, Mar 01, 2016 at 03:40:54PM +0000, Balaji Ramalingam (Staff) wrote:
> Hi,
> 
> Thank you for the bug report.  Yes, we will need to see the original
> larger .nd2 file.  As it's too large for our QA system (>2GB), we will be sending the FTP server credentials in a
> private mail.
> 
> It would be great if you could send a screenshot of your import options as well, this would help us troubleshoot your issue in better detail.
> 
> Best,
> Balaji
> 
> 
> 
> __________________
> 
> Mr Balaji Ramalingam
> 
> Software Developer
> 
> OME Team
> 
> College of Life Sciences
> 
> University of Dundee
> 
> From: Hallie Comfort <halliecomfort at gmail.com<mailto:halliecomfort at gmail.com>>
> Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
> Date: Monday, 29 February 2016 21:44
> To: "ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>" <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
> Subject: [ome-users] Issue with Bio-Formats Importer
> 
> Hello,
> 
> I am trying to convert .nd2 files to .tiff using the Bio-Formats plugin. When I select the importer options and submit I get this exception error message:
> 
> (Fiji Is Just) ImageJ 2.0.0-rc-45/1.50g; Java 1.8.0_66 [64-bit]; Mac OS X 10.11.2; 95MB of 5433MB (1%) java.lang.IndexOutOfBoundsException: Index: 0, Size: 0 at java.util.ArrayList.rangeCheck(ArrayList.java:653) at java.util.ArrayList.get(ArrayList.java:429) at loci.formats.FormatReader.getSizeC(FormatReader.java:719) at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:1342) at loci.formats.FormatReader.setId(FormatReader.java:1426) at loci.formats.DelegateReader.setId(DelegateReader.java:290) at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505) at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143) at loci.plugins.in.Importer.showDialogs(Importer.java:140) at loci.plugins.in.Importer.run(Importer.java:76) at loci.plugins.LociImporter.run(LociImporter.java:78) at ij.IJ.runUserPlugIn(IJ.java:212) at ij.IJ.runPlugIn(IJ.java:176) at ij.Executer.runCommand(Executer.java:137) at ij.Executer.run(Executer.java:66) at java.lang.Thread.run(Thread.java:745)
> 
> I have successfully converted similar files but am having problems with a specific one. Can I send you the file to try and figure out what is wrong? It is over 2gb.
> 
> Thanks for the help,
> Hallie Comfort
> 
> The University of Dundee is a registered Scottish Charity, No: SC015096

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