bftools EXCEPTION with BIG .AIM

[alexander.dejaco]

Hello!

I am currently working with some colleagues on big .AIM datasets.
Usually we load .AIM using the ij plugin or ./bfconvert of the bftools.

But we are having trouble with that on bigger datasets. (As far as I can tell all >2gb dont work.)
What we get is this exception

Exception in thread "main" 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:274)
at loci.formats.MetadataTools.populateMetadata(MetadataTools.java:236)
at loci.formats.MetadataTools.populatePixels(MetadataTools.java:138)
at loci.formats.MetadataTools.populatePixels(MetadataTools.java:101)
at loci.formats.in.AIMReader.initFile(AIMReader.java:168)
...

I searched your forums fruitlessly, I hope there is not already another topic about this that I have overseen.
What I already tried was different versions of the tools (trunk, daily, older...).
No success, yet.

Any help would be highly appreciated.
Thanks in advance and best wishes from Vienna.
Alexander.

[mlinkert]

Hi Alexander,

Thank you for the bug report; unfortunately, none of the .aim files that we have reproduce the problem. Would you be willing send an example file that causes this exception? I have sent instructions on sending files to the OME team in a private message.

Regards,
-Melissa

[mlinkert]

Hi Alexander,

Thank you for uploading sample files.

I have opened a ticket for this problem on our issue tracking system:

http://trac.openmicroscopy.org.uk/ome/ticket/11287

If you would like to receive an automated email each time that ticket is updated, please let me know and I will CC you.

Regards,
-Melissa

[alexander.dejaco]

Hi!
Thanks for your effort.
Im curious to find out where the issue resides.

Best wishes from Vienna.