[ome-devel] Automatically attach txt files during upload

[Kai Schleicher]

OK, great!

Thanks a lot,
Kai

On 08.06.2015 10:48, William Moore wrote:
> 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 
> <mailto: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:
>>
>>  1. 20150601_Beadswell4_4ch_1516_SI_001.dv
>>  2. 20150601_Beadswell4_4ch_1516_SI_001.log
>>  3. 20150601_Beadswell4_4ch_1516_SI_001_SIR.dv
>>  4. 20150601_Beadswell4_4ch_1516_SI_001_SIR_ALX.dv
>>  5. 20150601_Beadswell4_4ch_1516_SI_001_SIR_ALX_log.txt
>>  6. 20150601_Beadswell4_4ch_1516_SI_001_SIR_log.txt
>>  7. 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 
>>> <mailto: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 
>>>> <mailto: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 
>> <mailto: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

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