[ome-devel] Automatically attach txt files during upload

[William Moore]

Hi Kai,

 The files you have there will not be recognised by Bio-Formats as they are not all
included in the known "companion files" extensions in the DeltavisionReader - 
see https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/DeltavisionReader.java#L122

I've created a ticket with the information you've provided https://trac.openmicroscopy.org/ome/ticket/12913
and we'll be in touch if we need any more info.

 Many thanks,

  Will.



On 5 Jun 2015, at 16:58, Kai Schleicher <kai.schleicher at unibas.ch> wrote:

> Hi Will,
> 
> thanks so much for your quick response!
> 
> The files are beeing created on a DeltaVision OMX Blaze in SI mode for super resolution using the OMX software on a windows machine. 
> 
> Using Softworx, the super-resolution image is reconstructed from the raw data and then the different channels are aligned.
> 
> With this procedure, I end up with several files, for example:
> 20150601_Beadswell4_4ch_1516_SI_001.dv
> 20150601_Beadswell4_4ch_1516_SI_001.log
> 20150601_Beadswell4_4ch_1516_SI_001_SIR.dv
> 20150601_Beadswell4_4ch_1516_SI_001_SIR_ALX.dv
> 20150601_Beadswell4_4ch_1516_SI_001_SIR_ALX_log.txt
> 20150601_Beadswell4_4ch_1516_SI_001_SIR_log.txt
> 20150601_Beadswell4_4ch_1516_SI_001_task.sh.joblog
> here, SIR = reconstructed image, and
> ALX= camera alignment done
> 
> If there is anything else you need, don't hesitate to ask.
> 
> Cheers,
> Kai
> 
> 
> 
> On 02.06.2015 09:05, William Moore wrote:
>> Hi Kai,
>> 
>> In order for additional files to be included as part of an image import, they need to be recognised by Bio-Formats as "companion files" that are associated with that image.
>> 
>> In the case of Deltavision images, Bio-Formats should automatically recognise any acquisition and deconvolution log files that are generated by Softworx.
>> If you're finding that this is not happening for you, please let us know the names of the files and how they are being created.
>> 
>>  Regards,
>> 
>>    Will.
>> 
>> 
>> On 2 Jun 2015, at 07:48, Kai Schleicher <kai.schleicher at unibas.ch> wrote:
>> 
>>> Hi,
>>> 
>>> Is it possible to automatically attach a *.txt file of the same name as the image file to the image during upload?
>>> This *.txt file could for example be a log file that's automatically generated during aquisition when using Softworx.
>>> 
>>> Thanks and cheers,
>>> Kai
>>>  -- 
>>> Kai Schleicher, PhD | Postdoctoral Fellow in Light Microscopy | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel
>>> Phone: +41 61 267 22 50 | kai.schleicher at unibas.ch | www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch
>>> _______________________________________________
>>> ome-devel mailing list
>>> ome-devel at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>> 
> 
> -- 
> Kai Schleicher, PhD | Postdoctoral Fellow in Light Microscopy | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel
> Phone: +41 61 267 22 50 | kai.schleicher at unibas.ch | www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel

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