[ome-users] Bioformats opening ND2 error

[Curtis Rueden]

Hi Christian,

Nice detective work. Would you care to file a pull request with the fix?

Regards,
Curtis
On Dec 5, 2014 8:41 AM, "Christian Carsten Sachs" <c.sachs at fz-juelich.de>
wrote:

> Hello,
>
> as I'm no bioformats developer, I cannot push a fix for it, but I've
> debugged it and I might provide a hint towards a solution to the problem:
>
> The metadata parser of the ND2 reader plugin chokes at some string value
> in the
> SLxPictureMetadata.sPicturePlanes.sSampleSetting.a0.pCameraSetting dict
> of the ImageMetadataSeqLV|0 block.
> (And, not finding the true end of a string, starts to read the wrong
> data, tries to interpret it, and tries to jump to some location at
> around 140 TB (from the beginning of the file ;)), where it gets stuck
> infinitely.)
>
> I do not see why such a complex implementation for reading a string was
> choosen (RandomAccessInputStream.findString). A quick replacement of the
>
> case (8): // String
> ...
> break;
>
> block (within with NativeND2Reader.iterateIn method) e.g.
>
> char c = 0;
> StringBuilder sb = new StringBuilder();
> while((c = in.readChar()) != 0)
>   sb.append(c);
> value = sb.toString();
>
> Makes the file readily openable (with apparent metadata O.K.).
> It should be remarked that strings within nd2 files are just wide
> strings, and do not need complex parsing.
>
> Long technical text short:
>
> The file/modus operandi is ok, it looks like a bug in bioformats.
>
> Best Regards,
> Christian Sachs
>
> On 12/05/2014 01:57 PM, Peter Saxon wrote:
>
>> Hi all,
>>
>> A recent experiment has yielded a set of ND2 files which bioformats seem
>> to be struggling with. They open fine in Nikons own software ('NIS
>> viewer') which leads me to believe the files are valid and intact.
>> Samples provided below
>>
>> http://qa.openmicroscopy.org.uk/qa/feedback/10380/?token=
>> 21549ddad4b975eb1917b005f9299de4
>> or
>> https://www.dropbox.com/s/6bok66l3y5xpn7w/271120.nd2?dl=0
>>
>> The image should be a single frame, 4 x 12bit colour channels, 1392x1040
>> pixels. I've tried opening it with both the matlab tools (Bioformats
>> 5.0.6) and icy (also with 5.0.6), using Windows, Java 1.7.0_21. It
>> causes both to hang, last message displayed is
>> Parsing block 'ImageCalibra' 0%
>>
>> Am I doing something stupid, and/or does anyone know what is causing
>> these errors?
>>
>> Best wishes,
>>
>> Peter Saxon
>>
>
>
> ------------------------------------------------------------
> ------------------------------------
> ------------------------------------------------------------
> ------------------------------------
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
> ------------------------------------------------------------
> ------------------------------------
> ------------------------------------------------------------
> ------------------------------------
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20141205/caaf5354/attachment.html>