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Hi John & everyone, Depending on your application you could also wire Java and Python > together using inter-process communication. There is a plethora of > RPC libraries out there with good Python and Java support. E.g. > protocol buffers. > We faced the same problem trying to integrate Bio-Formats (a Java library; http://github.com/openmicroscopy/bioformats) and into CellProfiler (a Python application; http://github.com/CellProfiler). The first solution was in-process. However, there are some difficulties with launching and managing a JVM from native code: * You may not know a priori how much memory to assign to the Java max heap, and it cannot be changed after the JVM has launched. * Java never returns RAM to the system; the garbage collector just frees it internally for Java to reuse. * AFAIK, you cannot only ever start one JVM; even if it terminates, you cannot start a second one. * Unless you are very careful, Mac OS X has threading issues with Java AWT. Hence, the CellProfiler team developed a second solution, inter-process this time, called subimager: https://github.com/CellProfiler/subimager Subimager is a lightweight HTTP server that can be queried from Python, which avoids most of the pitfalls mentioned above (though you still have to decide on a max heap size, of course). Lastly, CellProfiler abstracts the integration mechanism into a class that supports both in-process and inter-process, depending on the circumstances: https://github.com/CellProfiler/CellProfiler/blob/master/imagej/ijbridge.py It is now working very well! Maybe you can pursue a similar approach. For further reading, check out my "Interfacing from non-Java code" page: http://loci.wisc.edu/bio-formats/interfacing-non-java-code It is part of the Bio-Formats developer documentation but would be totally applicable to netCDF Java or any other Java library, too. Regards, Curtis On Wed, Apr 4, 2012 at 9:18 AM, Don Murray <don.murray@xxxxxxxx> wrote: > I think John is looking for something that would allow C Python to call > into the netCDF-Java libraries. For that, the two options seem to be: > > JPype > JCC > > or using interprocess communication. Here's a good presentation on > different approaches that I found on the web: > > http://www.slideshare.net/**onyame/mixing-python-and-java<http://www.slideshare.net/onyame/mixing-python-and-java> > > I think Sean Arms at Unidata was looking at JCC at one point. > > Don > > > On 4/4/12 7:38 AM, stephen.pascoe@xxxxxxxxxx wrote: > >> The important question is why you need Python. If it's to access >> some C library with python bindings (e.g. numpy or netCDF4-python) >> then Jython isn't appropriate and you'll need one of those >> Python<->bridges JPype or Jepp. >> >> If you need the very latest Python features (particularly Python 3) >> you'll also find Jython is a bit behind CPython. Many standard >> Python frameworks now work with Jython (e.g. Django, SQLAlchemy) but >> you'd have to check the compatibility of each dependency. >> >> Otherwise Jython is the most popular and well maintained choice. >> >> Depending on your application you could also wire Java and Python >> together using inter-process communication. There is a plethora of >> RPC libraries out there with good Python and Java support. E.g. >> protocol buffers. >> >> Stephen. >> >> --- Stephen Pascoe +44 (0)1235 445980 Centre of Environmental Data >> Archival STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot >> OX11 0QX, UK >> >> >> -----Original Message----- From: Robert Casey >> [mailto:rob@iris.washington.**edu <rob@xxxxxxxxxxxxxxxxxxx>] Sent: 04 >> April 2012 14:31 To: >> Pascoe, Stephen (STFC,RAL,RALSP); John Caron Cc: >> netcdf-java@xxxxxxxxxxxxxxxx; thredds@xxxxxxxxxxxxxxxx Subject: Re: >> [thredds] Java to Python tools >> >> >> Hi John- >> >> If you use Jython, it looks to be pretty seamless. I am just >> starting to develop in Jython, so I can't claim experience in this >> department yet. The first section of this page details Java within >> Jython. >> >> http://www.jython.org/**jythonbook/en/1.0/**JythonAndJavaIntegration.html<http://www.jython.org/jythonbook/en/1.0/JythonAndJavaIntegration.html> >> >> -Rob >> >> >> On Apr 4, 2012, at 1:02 AM,<stephen.pascoe@xxxxxxxxxx> wrote: >> >> Hi John, >>> >>> Direct experience beyond playing, no; but I've come across several >>> options: >>> >>> * Jpype : >>> http://sourceforge.net/**project/jpype<http://sourceforge.net/project/jpype>-- >>> embeds a JVM in >>> Python * Jepp : http://jepp.soureforge.net -- embeds Python >>> interpreter in Java * Jython : http://www.jython.org -- A Python >>> implementation in the JVM. >>> >>> I expect you want Jpype as in your case Python is doing the >>> wrapping. I tested it out once and it worked for me. The project >>> seems isn't exactly active but it still appears to be in use. >>> >>> Cheers, Stephen. >>> >>> --- Stephen Pascoe +44 (0)1235 445980 Centre of Environmental Data >>> Archival STFC Rutherford Appleton Laboratory, Harwell Oxford, >>> Didcot OX11 0QX, UK >>> >>> >>> -----Original Message----- From: >>> thredds-bounces@xxxxxxxxxxxx.**edu<thredds-bounces@xxxxxxxxxxxxxxxx> >>> [mailto:thredds-bounces@**unidata.ucar.edu<thredds-bounces@xxxxxxxxxxxxxxxx>] >>> On Behalf Of John Caron >>> Sent: 04 April 2012 00:20 To: Java NetCDF; THREDDS community >>> Subject: [thredds] Java to Python tools >>> >>> >>> Hi all: >>> >>> Anyone have experience with ways to wrap java in Python? We are >>> thinking about how to solve this issue again. >>> >>> John >>> >>> ______________________________**_________________ thredds mailing >>> list thredds@xxxxxxxxxxxxxxxx For list information or to >>> unsubscribe, visit: >>> http://www.unidata.ucar.edu/**mailing_lists/<http://www.unidata.ucar.edu/mailing_lists/>-- >>> Scanned by iCritical. >>> >>> ______________________________**_________________ thredds mailing >>> list thredds@xxxxxxxxxxxxxxxx For list information or to >>> unsubscribe, visit: >>> http://www.unidata.ucar.edu/**mailing_lists/<http://www.unidata.ucar.edu/mailing_lists/> >>> >> >> > -- > Don Murray > NOAA/ESRL/PSD and CIRES > 303-497-3596 > http://www.esrl.noaa.gov/psd/**people/don.murray/<http://www.esrl.noaa.gov/psd/people/don.murray/> > > > ______________________________**_________________ > netcdf-java mailing list > netcdf-java@xxxxxxxxxxxxxxxx > For list information or to unsubscribe, visit: > http://www.unidata.ucar.edu/**mailing_lists/<http://www.unidata.ucar.edu/mailing_lists/> >
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