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

[Stéphane Dallongeville]

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 If your version of bio-formats/loci-tools is outdated, I suggest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(OMEXMLMe
>> tadataImpl.java:9731)
>>      at
>> loci.formats.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetad
>> 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/
>>
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>
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