Python Cookbook 2Nd Edition Jun 1002005 [Electronic resources] نسخه متنی

Recipe 11.15. Implementing an ImageJ Plug-in in Jython

Credit: Ferdinand Jamitzky, Edoardo
"Dado" Marcora

Problem

You perform image processing using the
excellent free program ImageJ and need to extend it with your own
plug-ins, but you want to code those plug-ins in Jython rather than
in Java.

Solution

Jython can do all that Java can, but with Python's
elegance and high productivity. For example, here is an ImageJ
plug-in that implements a simple image inverter:

import ij
class Inverter_py(ij.plugin.filter.PlugInFilter):
def setup(self, arg, imp):
""@sig public int setup(String arg, ij.ImagePlus imp)""
return ij.plugin.filter.PlugInFilter.DOES_8G
def run(self,ip):
""@sig public void run(ij.process.ImageProcessor ip)""
pixels = ip.getPixels( )
width = ip.getWidth( )
r = ip.getRoi( )
for y in range(r.y, r.y+r.height):
for x in range(r.x, r.x+r.width):
i = y*width + x
pixels[i] = 255-pixels[i]

Discussion

To make this plug-in usable from ImageJ, all you need to do is
compile it into a Java bytecode class using the
jythonc command with the appropriate command-line
option switches. For example, I use IBM's open
source Java compiler, jikes, and I have placed it
into the C:\ImageJ directory, which also holds
the plugins and jre
subdirectories. So, in my case, the command line to use is:

# jythonc -w C:\ImageJ\plugins\Jython -C C:\ImageJ\jikes
-J "-bootclasspath C:\ImageJ\jre\lib\rt.jar -nowarn"

If you use Sun's Java SDK, or other Java
implementations, you just change the -C argument,
which indicates the path of your Java compiler and the
-J argument, which specifies the options to pass
to your Java compiler.

See Also

ImageJ is at http://rsb.info.nih.gov/ij/; Jython is at
http://www.jython.org; jikes is
at http://www-124.ibm.com/developerworks/oss/jikes/;
for more on using Jython with Imagej, http://marcora.caltech.edu/jython_imagej_howto.