[ome-devel] Calling matlab code from OME frontend

[Josiah Johnston]

The way we tie matlab code to OME is through the analysis engine. This 
abstracts the handling of the matlab code.
Instructions are available online:
http://openmicroscopy.org/api/xml/AML/matlab.html
Examples of modules & chains are available in the source tree under 
OME/src/xml/OME/Tests/

A slightly lower level interface is given by the perl package 
OME::Matlab, which is in OME/src/perl2/OME/Matlab/Matlab.pm

It sounds like you are attempting a different method of running the 
matlab script from OME. I've never seen the error you refer to. When we 
initiate non-interactive execution of matlab analysis chains via the 
web frontend, we have to deal with issues of running matlab under the 
apache user. This requires switching the license manager, and adding 
the library path to /etc/ld.so.conf (on Fedora systems anyways).

Hope this helps.

-Josiah

On Mar 18, 2006, at 12:47 PM, Sumanth Jagannath wrote:

> Hi,
>
> I have a matlab function that is to be called from the OME frontend. 
> The
> script works fine when I call it from the command line. But fails with 
> the
> an error when I run it from the frontend ( cgi script ).
>
> I checked in the groups page for matlab and the suggestion is to use
> "-desktop" option when we want to run matlab without a controlling
> terminal. I have tried this, but it didn't work.
>
> I am sure that there is some code in OME, that abstracts this handling 
> of
> matlab code. Would be grateful if you can give me pointers to the 
> code, or
> suggestions on how to call matlab without a controlling terminal.
>
> ( I know this problem is not OME specific, but am hoping that you would
> have experienced this problem before ).
>
> (Details of the matlab error:
> Internal error 2: Could not determine the path of the
>                    MATLAB root directory.
>
>                    original command path = /home/matlab/bin/matlab
>                    current  command path = /home/matlab/bin/matlab
>
> )
> Versions of matlab Version 7.0.4.352 (R14)
>
>
> thanks in advance,
> --Sumanth
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