[ome-users] bug in Bio-Formats with LEI file

[Balaji Ramalingam]

Hi,

Thank you for the files (spotted and tested them locally).
I was able to reproduce the bug and extract the stack-trace as well.

Created a ticket on this regard,
https://trac.openmicroscopy.org.uk/ome/ticket/12098

Will get looked into, soon.

Best,
Balaji

On 18/03/2014 11:23, "Stéphane Dallongeville"
<stephane.dallongeville at pasteur.fr> wrote:

>Hi,
>
>I tested both on 4.4.8 and 5 version (and for this one i tested beta and
>rc2) and the bug happen every time.
>The FTP i was referring is the Bio-Format test FTP where you can upload
>some problematic dataset.
>I'm almost certain that is just a specific metadata issue as i was able
>to open other LEI dataset without any problem.
>
>Best,
>
>- Stephane
>
>
>Le 18/03/2014 12:04, Balaji Ramalingam a écrit :
>> Hi,
>>
>> Could you please let us know the version of bio-formats/Loci-tools you
>>are
>> using?
>> I couldn¹t get access to the files that you had uploaded (More details
>>of
>> the FTP site?).
>>
>> But I tested a few Œ.lei' uploads via insight(latest release version,
>> which uses bio-formats 5) and opened them as well.
>> If your version of bio-formats/loci-tools is outdated, I suggest
>> downloading the latest version from our downloads page,
>>
>> For Bio-formats,
>> http://downloads.openmicroscopy.org/bio-formats/5.0.0/
>>
>> And for OMERO clients,
>> http://downloads.openmicroscopy.org/omero/5.0.0/
>>
>> This should hopefully solve the problem.
>> If you still see the issue in the latest version as well (highly
>> unlikely), please do let us know.
>>
>> Best,
>> Balaji
>>
>> On 18/03/2014 08:47, "Stéphane Dallongeville"
>> <stephane.dallongeville at pasteur.fr> wrote:
>>
>>> Hi,
>>>
>>> Just wanted to report this problem : trying to opening a multi serie
>>>LEI
>>> file with LOCI i obtained the following error message :
>>>
>>> java.lang.IndexOutOfBoundsException: Index: 1, Size: 1
>>>      at java.util.ArrayList.RangeCheck(ArrayList.java:547)
>>>      at java.util.ArrayList.get(ArrayList.java:322)
>>>      at ome.xml.model.Pixels.getChannel(Pixels.java:573)
>>>      at
>>>
>>>loci.formats.ome.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXML
>>>Me
>>> tadataImpl.java:9731)
>>>      at
>>>
>>>loci.formats.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMet
>>>ad
>>> ata.java:1686)
>>>      at
>>> loci.formats.in.LeicaReader.parseInstrumentData(LeicaReader.java:1410)
>>>      at loci.formats.in.LeicaReader.initFile(LeicaReader.java:695)
>>>      at loci.formats.FormatReader.setId(FormatReader.java:1360)
>>>
>>> The same dataset converted to LIF does open correctly so i guess it is
>>> just a problem with metadata retrieving from the LEI reader.
>>> I uploaded the sample to the FTP, it's named "3c x40 correct.zip", it's
>>> an archive containing both the LEI and LIF file.
>>> Thanks.
>>>
>>> --
>>> Stephane Dallongeville
>>> Unité d'Analyse d'Images Biologiques
>>> CNRS URA 2582
>>> Institut Pasteur
>>> 25 rue du Dr Roux - 75015 Paris - France
>>>
>>> Tel: +33 (0)1 45 68 86 90
>>> Fax: +33 (0)1 40 61 33 30
>>>
>>> http://www.bioimageanalysis.org/
>>>
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>
>


The University of Dundee is a registered Scottish Charity, No: SC015096