[ome-users] MetaXpress image has cropped metadata values (with fix)

[Mario Emmenlauer]

Hi Sebastien,

thanks for the pointer again. I followed the pull request on Feb. 10, but
did not check back later, and therefore missed Melissas comment from Feb 16!
I agree the issue is fully fixed on your side already, thanks for the help!

Cheers,

    Mario



On 20.03.2015 12:33, Sebastien Besson wrote:
> Dear Mario,
> 
> this looks like the same underlying issue as the one you reported a month ago in
> http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-February/005037.html
> 
> Roger had opened a Pull Request to fix this bug and this change got merged into the 5.1
> development line - see https://github.com/openmicroscopy/bioformats/pull/1584.
> 
> I retested the sample file you sent using the last development milestone of Bio-Formats 5.1.x
> http://downloads.openmicroscopy.org/bio-formats/5.1.0-m4/ and the metadata should be correctly
> read by the upcoming 5.1.0 release of Bio-Formats:
> 
> $ ./bftools/showinf -version
> Version: 5.1.0-m4
> VCS revision: 51bf71d
> Build date: 19 February 2015
> $ ./bftools/showinf b0BCDSL-T069_wG06_s6_z0_t1_cCy5_u001.tif | grep Experiment
> Experiment base name: SL-HeLa4channels
> Experiment set: SL-HeLa4channels
> 
> Best regards,
> Sebastien
> 
>> On 20 Mar 2015, at 10:55, Mario Emmenlauer <mario at emmenlauer.de> wrote:
>>
>>
>> Dear Bio-Formats developers,
>>
>> I have a small issue with MetaXpress meta data. When I read the image
>> (link below), several metadata values are missing their first character.
>> An example is 'Experiment base name' for which I expect to get
>> 'SL-HeLa4channels', instead I receive 'L-HeLa4channels'. I could identify
>> in components/formats-gpl/src/loci/formats/in/MetamorphReader.java the
>> code expects always a dummy character after the colon, however in my case
>> I think this dummy is missing. Here a proposed fix:
>>
>> -          String value = line.substring(colon + 2);
>> +          // Mario Emmenlauer, 2015.03.20: There is not always a space after
>> +          // the colon, so better use 'trim()' instead of expecting a space:
>> +          String value = line.substring(colon + 1).trim();
>>
>> I did not extensively check this fix, so maybe use it with a bit of
>> caution. The image I used is here:
>>    http://data.marssoft.de/b0BCDSL-T069_wG06_s6_z0_t1_cCy5_u001.tif
>>
>> All the best, and thanks for your great work,
>>
>>     Mario Emmenlauer
>>
>>
>>
>>
>>
>>
>> -- 
>> Mario Emmenlauer BioDataAnalysis             Mobil: +49-(0)151-68108489
>> Balanstrasse 43                    mailto: mario.emmenlauer * unibas.ch
>> D-81669 München                          http://www.marioemmenlauer.de/
>>
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-- 
A: Yes.
> Q: Are you sure?
>> A: Because it reverses the logical flow of conversation.
>>> Q: Why is top posting annoying in email?

Mario Emmenlauer BioDataAnalysis             Mobil: +49-(0)151-68108489
Balanstrasse 43                    mailto: mario.emmenlauer * unibas.ch
D-81669 München                          http://www.biodataanalysis.de/