Sage is a wonderful system: a big set of mathematical languages and libraries glued with Python. This is quite remarquable, but i use frequently Java for my image processing and analysis applications. In particular, the ImageJ framework allows to write plugins, making easy the application distribution. The aim is thus to easily access a Java library from a Python code. The complete method is described in this post, allowing to use ImageJ from a Sage notebook.
As Sage rely on Python, the key is to find a way to call Java code from Python. I found several solutions (excluding do-it-yourself stuff with RMI):
- Javaclass : can’t make it work. However, seems to need work in order to pass data between Java and Python worlds.
- JCC : a little bit clumsy, it particular it needs to add very large options when launching Python.
- JPype : the simplest. A Python module with an easy usage.
JPype installation
It is quite regular:
unzip JPype-0.5.4.1.zip
cd JPype-0.5.4.1
sage -python setup.py build
Here a bug usually appears. JPype rely on the sets module, which is neither included in recent Python. There is not a lot of modification. You can download a modified version here. Beware, you must still follow the README to provide the path to your JDK installation. If the compilation is OK (you can send me a mail if not), the module is installed with:
sage -python setup.py install
Now we can work inside a Sage notebook (downloadable here).
JPype use
Quite simple:
- import the module,
- launch a java virtual machine,
- import one or more Java packages.
The first parameter given to startJVM() is the path to the dynamical library of the JVM. To find it, you can do:
locate libjvm.so
The second parameter allows to extend the classpath in order to add libraries, here Image.
At this point, all the methods of Java-package ij are available, directly. We can by example load an image and display it in the notebook:
), very easily. Thus a Python object is constructed from a Java one, all the methods available:
To display side by side Lena and its edges, i need to get the pixel array of each ImageProcessor, by calling getIntArrray():
This object is Python indexable, as a regular array. I can give it directly to the Python functions that display images. Here, the implicit conversion between primitive types is realized by JPype:
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