[ome-users] importing multiples pixel sets ?

[Josiah Johnston]

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
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>