[ome-users] Matlap trouble "mex -O"

[T. J. Macura]

Hey Valentin,

Well let me be forward and ask: are you using MATLAB or Octave?
Maybe if you have both installed but the path points to the Octave mex 
tool. The /usr/lib/octave stuff below raised my suspicions:

>   + mkoctfile -DHAVE_OCTAVE_21 -v -o newPixels.oct mex_newPixels.cc
> /usr/lib/octave/2.1.69/site/oct/i386-pc-linux-gnu/octave-
> forge/mex.o
> -I/usr/lib/octave/2.1.69/site/oct/i386-pc-linux-gnu/octave-forge -O
> -inline -I../../C/omeis-http/ -L../../C/omei

OME data such as annotations etc. (more formally: semantic type 
attributes)  is stored in the postgress DB  but the pixels data is 
stored on the OME Image Server (OMEIS).

I wrote a cURL based client library to OMEIS that allows C programs to 
get pixels from OMEIS.
I also wrote MATLAB mex bindings to the cURL client library. Info here: 
http://www.openmicroscopy.org/api/omeis/matlab-mex.html
Once the OME/MATLAB stuff is installed, you gain very easy access to 
OME images from the MATLAB command-line e.g:
im = getPixels (openConnectionOMEIS('http://localhost/cgi-bin/omeis'), 
n_id);
imshow(im);

The install fails when it is trying to compile the mex bindings to the 
OMEIS client library.

> Are you sure about the "-O" flag ?
Completely unnecessary. The -O and -inline flags are supposed to, by 
the MATLAB mex shell script, be passed directly to gcc.
This is just optimisation stuffs. If you want to change the flags, the 
relevant Makefiles are

src/matlab/OMEIS/Makefile
src/matlab/OME/Statistics/haralick/Makefile
src/matlab/OME/Statistics/zernike/Makefile

But I think you should double check that the MATLAB mex not Octave mex 
is called.

The reason we decided to use MATLAB not Octave is because MATLAB has 
more extensive libraries/optimisations that many developers require. I 
think an OME/Octave interface is a good idea but unfortunately, I don't 
have time in the near future (next two months) to work on this by 
myself. However, if you have interest in doing some work in that 
direction, I will be able to help you.

Tom
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