Yup - please ask me for details. We are also integrating ImageJ into
subimager.
There are two big obstacles to running a JVM inside Python:
* Threading model - it's very difficult to convince the JVM to shut down
if it believes it has started a user interface and it's very difficult
to convince the JVM to shut down its threads. You can't start the JVM on
a daemon thread or convince Windows that a thread is a daemon thread.
Python hangs on exit, waiting for JVM threads to terminate.
* AWT - as Curtis says, the AWT and Python windowing toolkits battle
over the UI thread under Mac OS X.
Our JavaBridge solution is perhaps the best solution for executing a JVM
within Python. It lets you instantiate any Java object with Python
garbage collection of the object when it goes out of scope and you can
run any Java method and pass in any primitive or object type. There are
helper methods for reflection and for wrapping Java objects. But see above.
I have used Python and Corba to connect Python to C# in a previous life
(I've forgotten the libraries I used). That's somewhat hairy and
involved and not a general solution (you have to rebuild both sides of
everything when interfaces change). IMHO, a lightweight,
application-specific protocol is best and a transport protocol such as
TCP, HTTP or SOAP is your best shot at getting the data sent back and
forth in a platform-neutral manner.
--Lee
On 4/4/2012 10:55 AM, Curtis Rueden wrote:
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
<mailto: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
I think Sean Arms at Unidata was looking at JCC at one point.
Don
On 4/4/12 7:38 AM, stephen.pascoe@xxxxxxxxxx
<mailto: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
<tel:%2B44%20%280%291235%20445980> Centre of Environmental Data
Archival STFC Rutherford Appleton Laboratory, Harwell Oxford,
Didcot
OX11 0QX, UK
-----Original Message----- From: Robert Casey
[mailto:rob@xxxxxxxxxxxxxxxxxxx
<mailto:rob@xxxxxxxxxxxxxxxxxxx>] Sent: 04 April 2012 14:31 To:
Pascoe, Stephen (STFC,RAL,RALSP); John Caron Cc:
netcdf-java@xxxxxxxxxxxxxxxx
<mailto:netcdf-java@xxxxxxxxxxxxxxxx>;
thredds@xxxxxxxxxxxxxxxx <mailto: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
-Rob
On Apr 4, 2012, at 1:02 AM,<stephen.pascoe@xxxxxxxxxx
<mailto:stephen.pascoe@xxxxxxxxxx>> wrote:
Hi John,
Direct experience beyond playing, no; but I've come across
several
options:
* 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
<tel:%2B44%20%280%291235%20445980> Centre of Environmental
Data
Archival STFC Rutherford Appleton Laboratory, Harwell Oxford,
Didcot OX11 0QX, UK
-----Original Message----- From:
thredds-bounces@xxxxxxxxxxxxxxxx
<mailto:thredds-bounces@xxxxxxxxxxxxxxxx>
[mailto:thredds-bounces@xxxxxxxxxxxxxxxx
<mailto: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
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list thredds@xxxxxxxxxxxxxxxx
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unsubscribe, visit:
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Scanned by iCritical.
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mailing
list thredds@xxxxxxxxxxxxxxxx
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Don Murray
NOAA/ESRL/PSD and CIRES
303-497-3596 <tel:303-497-3596>
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