[ome-devel] ScanR

Rubén Muñoz ruben.munoz at embl.de
Mon Nov 2 19:47:11 GMT 2009 

I do get the 'screen' dialog. I can add a new one and at the end I get  
the screen symbol to the left followed by (0) because is empty. The  
images are in the database however.


--
Rubén Muñoz
European Molecular Biology Laboratory



On Nov 2, 2009, at 8:08 PM, josh.moore at gmx.de wrote:

>
> Ruben,
>
> Do you also not get a screen when clicking on the directory for
> import? My guess is that the OMERO.importer detection of a screen is
> causing the problem.
>
> ~J.
>
> Rubén Muñoz writes:
>> Hi Josh, forgive my fuzzy bug report.
>>
>> With the new ScanR importer I am getting an empty screen(0) but all
>> the images appear in the "today" list. They seem OK but not grouped
>> in rows and columns under the new screen.
>>
>> No error message or exception so far.
>>
>> Is this a OMERO o bioformats issue?
>>
>> El 02/11/2009, a las 19:41, "Josh Moore" <josh at glencoesoftware.com>
>> escribió:
>>
>>>
>>> Does this mean you can get things up and running now, Ruben? Or are
>>> there any other blockers?
>>>
>>> ~J.
>>>
>>> Rubén Muñoz writes:
>>>> Hi Melissa,
>>>> while now the bfconvert always generates an output file. Ive been
>>>> testing to directly import the folder into OMERO.importer. For  
>>>> that:
>>>>
>>>> - Replaced the bio-formats.jar into the importer folder
>>>> - Inserted 'Scanr' and 'Companion/Scanr' new records in the Omero
>>>> Posgres DB at table 'formats'.
>>>>
>>>> The result is:
>>>>
>>>> - Was promoted for Screening name and Proceeded with 'Add to  
>>>> queue'.
>>>> - Import process ended without Errors.
>>>> - Screen in Omero appears empty at the end of the smooth process  
>>>> (no
>>>> wells in the screen).
>>>> - At recent images some of the images 'could not be displayed  
>>>> because
>>>> are invalid images'
>>>>
>>>> I believe that youre very near to the Scanr importer, and wish to
>>>> provide you with more detailed test. But as a hint I tried to  
>>>> convert
>>>> our current Data Set to OME.tif with bfconvert and then to OME.tif
>>>> again with OME.tif. Didnt work for me.
>>>>
>>>> Is the order of the images in the output the correct? The sizes of
>>>> the
>>>> Data Set and output file do correspond. Also the Dimensions are  
>>>> well
>>>> taken (Ive checked). Only the Timepoint aré calculated based on the
>>>> other dimensions and the number of files...
>>>>
>>>> My sincere gratitude,
>>>> Ruben
>>>>
>>>> El 30/10/2009, a las 17:17, Melissa Linkert
>>>> <melissa at glencoesoftware.com> escribió:
>>>>
>>>>> Hi Ruben,
>>>>>
>>>>>> I believe you use -bigtiff flag but Im getting trouble with the  
>>>>>> big
>>>>>> datasets. Can you see if I miss something:
>>>>>>
>>>>>> ./bfconvert -bigtiff
>>>>>> /Users/gonzales/Images/161009test2/151009_001/data/--W00001--
>>>>>> P00001--Z00000--T00000--Cherry.tif test.ome.tif
>>>>>
>>>>> This is the correct command; however, there was a bug that caused
>>>>> the
>>>>> '-bigtiff' flag to be ignored.  This command should work as  
>>>>> expected
>>>>> if you update to the latest trunk build of Bio-Formats.
>>>>>
>>>>>> While you improve the ScanR,  Josh suggested that we provide you
>>>>>> Leica
>>>>>> "ome.tif" that are not really compliant. If theres place in the  
>>>>>> FTP
>>>>>> I do it
>>>>>> right away with name Leica.tar.bz2
>>>>>
>>>>> Feel free to upload, unless Leica.tar.bz2 is larger than 6 GB.
>>>>>
>>>>> Regards,
>>>>> -Melissa
>>>>>
>>>>> On Thu, Oct 29, 2009 at 4:47 PM, Rubén Muñoz <ruben.munoz at embl.d
>>>>> e> w
>>>>> rote:
>>>>>> On Oct 29, 2009, at 5:12 PM, Melissa Linkert wrote:
>>>>>>
>>>>>>> Hi Ruben,
>>>>>>
>>>>>> Hi Melissa,
>>>>>>
>>>>>>>
>>>>>>> I'm moving this discussion to the ome-devel list, as it may be  
>>>>>>> of
>>>>>>> interest to others.
>>>>>>>
>>>>>>>> Please consider my ScanrReader.java as possible help.
>>>>>>>
>>>>>>> Thank you very much for the patch.  I've committed a modified
>>>>>>> version
>>>>>>> of it to the LOCI SVN repository; you can view the changes here:
>>>>>>
>>>>>> Thats so kind of you, glad to hear that.
>>>>>>
>>>>>>>
>>>>>>> https://skyking.microscopy.wisc.edu/trac/java/changeset/5652
>>>>>>
>>>>>> I believe you use -bigtiff flag but Im getting trouble with the  
>>>>>> big
>>>>>> datasets. Can you see if I miss something:
>>>>>>
>>>>>> ./bfconvert -bigtiff
>>>>>> /Users/gonzales/Images/161009test2/151009_001/data/--W00001--
>>>>>> P00001--Z00000--T00000--Cherry.tif
>>>>>> test.ome.tif
>>>>>> /Users/gonzales/Images/161009test2/151009_001/data/--W00001--
>>>>>> P00001--Z00000--T00000--Cherry.tif
>>>>>> [Olympus ScanR] -> test.ome.tif [OME-TIFF]
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>>>>>> ......................................................Exception  
>>>>>> in
>>>>>> thread "main" loci.formats.FormatException: File is too large;  
>>>>>> call
>>>>>> setBigTiff(true)
>>>>>>      at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java: 
>>>>>> 188)
>>>>>>      at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java: 
>>>>>> 223)
>>>>>>      at loci.formats.out.OMETiffWriter.saveBytes
>>>>>> (OMETiffWriter.java:193)
>>>>>>      at loci.formats.ImageWriter.saveBytes(ImageWriter.java:185)
>>>>>>      at
>>>>>> loci.formats.tools.ImageConverter.testConvert 
>>>>>> (ImageConverter.java:
>>>>>> 228)
>>>>>>      at loci.formats.tools.ImageConverter.main
>>>>>> (ImageConverter.java:253)
>>>>>>
>>>>>>>
>>>>>>> The only major difference between the committed changes and your
>>>>>>> patch
>>>>>>> is that the committed changes do not have hard-coded well,
>>>>>>> position,
>>>>>>> Z, T, and channel counts.  The number of wells is currently  
>>>>>>> being
>>>>>>> calculated from the well names in the "well selection table +
>>>>>>> cDNA"
>>>>>>> table.  The number of channels (core[0].sizeC) is equivalent to
>>>>>>> the
>>>>>>> number of channels defined in experiment_description.xml that  
>>>>>>> have
>>>>>>> the
>>>>>>> "idle" flag set to 0.
>>>>>>
>>>>>> So the information was there, just awaiting for someone to find  
>>>>>> the
>>>>>> way to
>>>>>> read it.
>>>>>>
>>>>>>>
>>>>>>> The latest revision of ScanrReader does correctly detect the
>>>>>>> dimensions for all of the datasets that I have.  If you continue
>>>>>>> to
>>>>>>> experience problems, though, please let me know.
>>>>>>>
>>>>>>
>>>>>> While you improve the ScanR,  Josh suggested that we provide you
>>>>>> Leica
>>>>>> "ome.tif" that are not really compliant. If theres place in the  
>>>>>> FTP
>>>>>> I do it
>>>>>> right away with name Leica.tar.bz2
>>>>>>
>>>>>>> Regards,
>>>>>>> -Melissa
>>>>>>
>>>>>> Regards,
>>>>>>
>>>>>> Ruben
>>>>>>
>>>>>>>
>>>>>>> On Fri, Oct 23, 2009 at 5:53 PM, Rubén Muñoz <ruben.munoz at embl.d
>>>>>>> e> wrote:
>>>>>>>>
>>>>>>>> Hi Melissa, thanks for your reply.
>>>>>>>>
>>>>>>>> I'd be happy to fix this, but first would like to clarify  
>>>>>>>> that an
>>>>>>>> assumption is correct.
>>>>>>>>
>>>>>>>> core[0].sizeC (the number of channels) is taken from a block  
>>>>>>>> like
>>>>>>>> this:
>>>>>>>>
>>>>>>>> <Name>multiple_channel_typedef</Name>
>>>>>>>> <Dimsize>3</Dimsize>
>>>>>>>>
>>>>>>>> Yes, but not all the channels are finally used.
>>>>>>>> While the experiment_descriptor.xml reads:
>>>>>>>> <Name>multiple_channel_typedef</Name>
>>>>>>>> <Dimsize>12</Dimsize>
>>>>>>>> The directory only has two channel Cherry and eGFP.
>>>>>>>>
>>>>>>>> My understanding is that Dimsize is used in multiple places,  
>>>>>>>> and
>>>>>>>> its
>>>>>>>> usage is determined by the value in in the "Name" element.  Is
>>>>>>>> this
>>>>>>>> correct?  If so, do you know what the correct Name values are  
>>>>>>>> for
>>>>>>>> channels and positions?
>>>>>>>>
>>>>>>>> That's how it should be...
>>>>>>>> ... but the new set only gets converted for me when I fix all  
>>>>>>>> the
>>>>>>>> next
>>>>>>>> values:
>>>>>>>> wellColumns = 2;
>>>>>>>> wellRows = 3;
>>>>>>>> core[0].sizeC = 2;
>>>>>>>> core[0].sizeT = 6;
>>>>>>>> core[0].sizeZ = 3;
>>>>>>>> Im sorry to do that now but a colleague is going to offer me
>>>>>>>> details
>>>>>>>> about
>>>>>>>> experiment_descriptor.xml.
>>>>>>>> Additionally I introduced some code to handle different  
>>>>>>>> positions
>>>>>>>> in a
>>>>>>>> well,
>>>>>>>> P00001, P00002 and so on.
>>>>>>>> Please consider my ScanrReader.java as possible help. It is
>>>>>>>> working well
>>>>>>>> for
>>>>>>>> the set and generates an OME.TIF with 1.7G that imports to  
>>>>>>>> OMERO
>>>>>>>> and
>>>>>>>> displays Z, T, and C data in the correct way
>>>>>>>> .
>>>>>>>> Regards,
>>>>>>>> Ruben
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>> <ScanrReader.java>
>>>>>>
>>>>>>
>>>> _______________________________________________
>>>> ome-devel mailing list
>>>> ome-devel at lists.openmicroscopy.org.uk
>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>> _______________________________________________
>> ome-devel mailing list
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