[ome-devel] OME and matlab - trouble connecting

[Ilya Goldberg]

On Jul 28, 2006, at 7:45 PM, Arpun Nagaraja wrote:
>
> You may have to reinstall OME at this point, to make sure it's using
> this copy of the MatlabHandler.  For reasons I haven't been able to
> discern, it sometimes doesn't use your modified version of the
> Handler.

I noticed this kind of behavior, and it appears to be specific to OS  
X.  Basically, you can't use 'apachectl restart' to re-load shared  
libraries or code-fragments into the apache process.  You have to  
shut it down completely and start it back up (apachectl stop/ 
apachectl start).  This doesn't appear to be the case with Linux.   
The OME installer uses restart, so even re-installing OME isn't  
enough to force reloading of shared libs and code-fragments/bundles  
on OS X.

-I


>
> I'm not certain this will work on Linux.  One of the reasons we
> haven't committed this stuff is because we didn't get a chance to
> test it on non-Mac systems.  Looks like you'll be our guinea pig.
>
> Let us know how things turn out.  Good luck!
>
> -Arpun
>
> On Jul 28, 2006, at 6:30 PM, debartolomeo at ece.ucsb.edu wrote:
>
>> Hi,
>>
>> I'm trying to get Matlab working with ome and am running into
>> problems.
>>
>> When I try to use the UI to run the analysis chain, I get the
>> following
>> error in the UI:
>> "Cannot open a connection to Matlab! at /usr/share/perl/5.8/CGI/
>> Carp.pm
>> line 314"
>>
>> But, when I try this from the command line:
>> ome execute -d "MyDataset" -a "Matlab Test Chain", I get the  
>> following
>> error in the UI:
>> "ERROR saving pixels to omeis w/ command:
>> 	ome_output_9_PixelsArray_pix =
>> setPixels(openConnectionOMEIS('http://claw/cgi-bin/omeis'), 686,
>> ome_output_9_PixelsArray);
>>>> ??? Invalid MEX-file
>> '/home/omedev/OME/src/matlab/OMEIS/setPixels.mexglx':
>> /home/matlab/bin/glnx86/../../sys/os/glnx86/libgcc_s.so.1: version
>> `GCC_3.3' not found (required by /usr/lib/libstdc++.so.6)."
>>
>> Again, running "Histogram Equalization Preprocessing Chain" from
>> the UI, I
>> get:
>> "Cannot open a connection to Matlab! at /usr/share/perl/5.8/CGI/
>> Carp.pm
>> line 314."
>>
>> But, when I try:
>> ome execute -d "MyDataset" -a "Histogram Equalization Preprocessing
>> Chain", I get:
>> "getROI/getPixels failed for pixels 482. The returned MATLAB array  
>> has
>> dimensions (0, 0, 1, 1, 1) at
>> /usr/local/share/perl/5.8.4/OME/Analysis/Handlers/MatlabHandler.pm
>> line
>> 562,  line 1."
>>
>> I'm new at this system, so there may be something very fundamental
>> that
>> I'm not yet understanding, but any suggestions on how to proceed
>> would be
>> very appreciated.
>>
>>
>> _______________________________________________
>> ome-devel mailing list
>> ome-devel at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
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