[ome-users] More matlab questions

[Tom Macura]

Hi Brian,

Sorry we haven't been able to reply to your email. I've been swamped  
trying to get a paper out. Once it's published all your MATLAB/OME  
problems will go away because everything will be revealed!

It will be best if you send me the complete XML files rather than  
posting snippets. Ideally I would like the ST, Module, and Chain XML  
files and including MATLAB scripts. This would help me give your  
better advice. Now I am forced to speculate.

Are you sure that you want two outputs BinaryPixels and BinaryTag of  
the same Semantic Type? Isn't BinaryTag basically a string?

I think the Module's Formal Outputs should look like this:

<Declaration>
	<FormalInput Name="Pixels" SemanticTypeName="Pixels" Count="!"/>
	<FormalOutput Name="BinaryPixels with Tag"  
SemanticTypeName="PixelSet" Count="!"/>
  </Declaration>

with Execution Instructions:

<FunctionInputs>
	<Input><PixelsArray FormalInput="Pixels"/></Input>
</FunctionInputs>
<FunctionOutputs>
          <Output><PixelsArray FormalOutput="BinaryPixels with Tag"  
ConvertToDatatype="uint16"/></Output>
          <Output><Scalar OutputLocation="BinaryPixels with Tag.Tag"/ 
 ></Output>
  </FunctionOutputs>

This way Tags will travel along with the Pixels.

Tom

On Feb 21, 2007, at 1:49 PM, Brian Ruttenberg wrote:

> I'm currently trying to integrate some matlab execution modules  
> into our
> OME database, and I'm running into some trouble.  Hopefully someone  
> out
> there can lend some insight...
>
> I have a matlab function that outputs pixels and a string tag.  In our
> database, we have a semantic type called a PixelSet, which is just a
> label of the different operations that we have performed on a set of
> pixels.  So ideally, I would like this matlab analysis module to  
> output
> directly into that semantic type with the pixel reference and the  
> string
> tag of the operation performed.    However, I can't seem to get the  
> two
> outputs go to the same database entry.
>
> For example, in my analysis module I have:
>
>        .....
>           <Declaration>
>             <FormalInput Name="Pixels" SemanticTypeName="Pixels"  
> Count="!"/>
>             <FormalOutput Name="BinaryPixels"
> SemanticTypeName="PixelSet" Count="!"/>
>              <FormalOutput Name="BinaryTag"  
> SemanticTypeName="PixelSet"
> Count="!"/>
>           </Declaration>
>
>                   <ExecutionInstructions ExecutionGranularity="I"
> xmlns="http://www.openmicroscopy.org/XMLschemas/MLI/IR2/MLI.xsd"
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
>             <FunctionInputs>
>                            <Input><PixelsArray
> FormalInput="Pixels"/></Input>
>             </FunctionInputs>
>             <FunctionOutputs>
>                            <Output><PixelsArray
> FormalOutput="BinaryPixels" ConvertToDatatype="uint16"/></Output>
>                            <Output><Scalar
> OutputLocation="BinaryTag.Tag"/></Output>
>             </FunctionOutputs>
>           </ExecutionInstructions>
>      ....
>
>
> Where PixelSet contains a pixel reference and a string tag.  But  
> int the
> database, it is stored as:
>
> ome=# select * from pixelset;
>  attribute_id | image_id | module_execution_id |    tag    | pixels
> --------------+----------+---------------------+-----------+--------
>         .....
>           222 |       17 |                  83 | default     |    220
>           232 |       18 |                  84 | default     |    230
>           725 |        1 |                 105 |                   
> |    722
>           726 |        1 |                 105 | Binarized |
>           730 |        2 |                 107 |                   
> |    727
>           731 |        2 |                 107 | Binarized |
>           735 |        3 |                 109 |                   
> |    732
>           736 |        3 |                 109 | Binarized |
>           740 |        4 |                 111 |                   
> |    737
>           741 |        4 |                 111 | Binarized |
>           745 |        5 |                 113 |                   
> |    742
>           746 |        5 |                 113 | Binarized |
>
> As you can see, the two outputs each have their own attribute ID's,  
> but
> I would like to combine them so the Tags and the Pixels match up in  
> the
> database.
>
> Hopefully I'm not way off on this, but any help would be greatly
> appreciated.  Thanks!
>
> Brian
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users