[ome-devel] ScanR

[Rubén Muñoz]

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 
] ...................................................................... 
........................................................................ 
........................................................................ 
........................................................................ 
........................................................................ 
........................................................................ 
........................................................................ 
........................................................................ 
........................................................................ 
...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................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.de>  
> 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>