[ome-users] OMERO-CellProfiler: too many open files

[Mark Woodbridge]

Hi Bram,

Many thanks. I'll try this out as soon as I get my Matlab license.

OMERO developers: would you consider merging these changes, assuming 
that they work with the trunk version of OMERO?

CellProfiler is being rewritten in Python but lots of people will be 
using the Matlab version in the meantime.

Mark.

b.gerritsen at nki.nl wrote:
> Hello Mark,
> 
> Included is a zip-file containing the requested files. They are modified versions of identically named matlab scripts from http://svn.openmicroscopy.org.uk/svn/omero/tags/omero-4.0.3/components/tools/cellprofiler/
> 
> Please note that I modified these scripts to suit the needs at my institute. There is no guarantee they will work for you, though I hope they do.
> 
> Kind regards,
> Bram
> 
> ________________________________________
> From: Mark Woodbridge [m.woodbridge at imperial.ac.uk]
> Sent: Thursday, June 11, 2009 12:29 PM
> To: ome-users at lists.openmicroscopy.org.uk
> Cc: Bram Gerritsen
> Subject: Re: [ome-users] OMERO-CellProfiler: too many open files
> 
> Hi Bram,
> 
> Would you consider sharing the changes you made to the
> OMERO/CellProfiler integration code to make it compatible with Beta4 and
> the latest CellProfiler? We're interested in getting this integration
> working, and I guess that others may be too.
> 
> I would also be interested to hear if you (or anyone else) has had any
> success compiling the OMERO/CellProfiler integration code using the
> Matlab Compiler so that it can be used on client machines without Matlab
> licenses.
> 
> Regards,
> 
> Mark.
> 
> 
> b.gerritsen at nki.nl wrote:
>> Dear all,
>>
>> When I analyze many images from the omero db in CellProfiler, the run fails after about 50 to 100 images with an Ice.SocketException. In the same error report a java.io.Exception is shown telling me there are too many open files. Closer inspection of matlab shows there are 16 files opened with every call to "createOmeroJavaService", but these files are not closed during the run, not even after a call to "session.close()". As soon as matlab tries to open more than 1024 files I get the exception.
>>
>> Here is some more information about the system I'm running Omero on:
>>
>> Red Hat Enterprise Linux 5.3
>> Omero Beta 4.0.3
>> Postgresql 8.1.4
>> ZeroC Ice 3.3.1
>> Python 2.4.3
>> Matlab 7.8.0 (R2009a)
>> CellProfiler (developer version) 1.0.5811 Branch 1.0.6027
>>
>> I had to change the OmeroLoader.m, numImages.m, and CPOMEROimread.m files to be able to analyze images from omero beta 4 in cellprofiler (apparently the matlab scripts from "http://svn.openmicroscopy.org.uk/svn/omero/tags/omero-4.0.3/" are not compatible with the beta 4 release nor with recent versions of cellprofiler).
>>
>> Thanks in advance!
>> Bram Gerritsen
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