[ome-users] nd2 files: IndexOutOfBoundsException

[Melissa Linkert]

Hi Guilhem,

Thank you again for offering to send a file - FTP details have now been
sent to you via private email.  We will continue to investigate once a file
is uploaded.

Regards,
-Melissa


On Mon, Nov 26, 2018 at 6:11 AM David Gault (Staff) <d.gault at dundee.ac.uk>
wrote:

> Hi,
>
> Thank you for raising this bug. If you have any smaller files (< 2GB) that
> reproduce the same behaviour you can upload them to
> https://www.openmicroscopy.org/qa2/qa/upload/, otherwise we will arrange
> FTP details for you to transfer the larger original file for testing.
> I have opened a Bio-Formats Trello card to track this issue:
> https://trello.com/c/dDcSZtur/296-indexoutofboundsexception
>
> With Thanks,
> David Gault
>
> On 23 Nov 2018, at 18:05, Guilhem Chenon <guilhem.chenon at espci.fr> wrote:
>
> Hello,
>
> I am having trouble with several random .nd2 files which will  not open
> with Bio-Formats plugin either in ImageJ or Matlab. When I call bfGetReader
> on the file, I get this error message:
>
> Error using bfGetReader (line 85)
> Java exception occurred:
> 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:689)
>
>     at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:1348)
>
>     at loci.formats.FormatReader.setId(FormatReader.java:1401)
>
>     at loci.formats.DelegateReader.setId(DelegateReader.java:291)
>
>     at loci.formats.ImageReader.setId(ImageReader.java:835)
>
>     at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
>
>     at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
>
>     at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
>
>     at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289)
>
> The original file is quite big (10Gb), so I can only upload it through
> FTP. When I crop the file in NIS, interestingly, it works, so for now my
> workaround is to crop the image itself because apparently NIS  re-encodes
> channels and timepoints during cropping so I can open it with Bio-Formats.
>
> Moreover, these problematic files open fine with the ImageJ ND2 Reader
> plugin (https://imagej.nih.gov/ij/plugins/nd2-reader.html).
>
> Thank you for your time.
>
> Best regards,
> --
> Guilhem CHENON
> LCMD - ESPCI Paris
>
>
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