[ome-devel] Re: [ome-users] importing multiples pixel sets ?

[Zachary Pincus]

Is this something that VisBio can help with? Maybe just in terms of  
opening up all of the individual images and stitching them together  
into an OME-TIFF or OME-XML file, or even perhaps using VisBio to  
actually send the data to the OME server?

Of course, the custom importer/perl route is best if this needs to be  
automated, but -- and this is out of my own curiosity -- is all the  
groundwork there in VisBio to do this sort of task?

Zach



On Jan 11, 2006, at 2:03 PM, Josiah Johnston wrote:

> I think your best bet will be a custom importer or a perl script.  
> The API for creating module executions, and tying inputs and  
> outputs to them is readily available to perl scripts. The relevant  
> functions are in OME/src/perl2/OME/Tasks/ModuleExecutionManager.pm
>
> The steps to the scripts roughly are:
> 	write a placeholder module to describe each transformation. You  
> can base this off a combination of
> OME/src/xml/OME/Annotations/AnnotationModule.ome and OME/src/xml/ 
> OME/Analysis/Filters/HighPassFilter.ome
> 	write a script that, given an original image file and a derived  
> image, will
> i) import the original image into OME,
> ii) use OME::Tasks::ModuleExecutionManager->createMEX(...) to  
> initiate an 'execution' of your placeholder module against your  
> newly imported image
> iii) use OME::Tasks::ModuleExecutionManager->addActualInput(...) to  
> register the image's pixels as inputs to your new MEX
> iv) use OME::Tasks::PixelsManager->createPixels(...) to start a new  
> set of pixels that will store your derived image
> v) use the returned $pixels_data object to write the derived  
> image's binary data to the image server
> vi) use OME::Tasks::PixelsManager->finishPixels(...) to finalize  
> the pixels
> vii) register the mex as finished by calling $MEX->status 
> ( 'FINISHED' );
> viii) commit the database transaction (e.g. $session- 
> >commitTransaction() )
>
> Ideally, you would also set the timing information for the MEX, but  
> that's somewhat optional.
>
> The alternative is to write module wrappers for your  
> transformations, and execute a chain on the original images. If  
> your transformations can be executed on the command line, then I  
> will fix the command line handler to execute one of your functions.  
> I have been contemplating fixing it for a while, but lack a use case.
>
> -Josiah
>
> On Jan 11, 2006, at 4:31 PM, kristian kvilekval wrote:
>
>>
>> We have several related images that could possible
>> be stored as pixel sets.  These include
>> Z-series, projections, normalized images
>> and color equalized images.
>>
>> These are currently stored in different files.
>> Is there an easy way to import these as several
>> pixel sets of the same image or will a custom importer need
>> to be written.
>>
>> In a similar vein, we would like capture the relationship
>> between the pixel sets using something similar to a module
>> execution identifier.  Is this supported?
>>
>> Thanks,
>> kris
>>
>> -- 
>> Kristian Kvilekval
>> kris at cs.ucsb.edu  http://www.cs.ucsb.edu/~kris w:805-893-2526 h: 
>> 504-9756
>>
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>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>
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