IMPORTANT NOTE Currently no working PyJNIus conda package for Windows available. I do need help maintaining the conda packages for operating systems that I am not familiar with or have limited access to, e.g. Windows and maybe OSX. See #6 and http://forum.imagej.net/t/imglyb-and-pyjnius-conda-package-maintainers-needed-for-windows-and-osx/11420

imglib2-imglyb aims at connecting two worlds that have been seperated for too long:

• Python with numpy
• Java with imglib2

imglib2-imglyb uses PyJNIus to access numpy arrays and expose them to ImgLib2. This means shared memory between numpy and ImgLib2, i.e. any ImgLib2 algorithm can run on numpy arrays without creating copies of the data! For example, Python users can now make use of the BigDataViewer to visualize dense volumetric data. If you are interested in using imglib2-imglyb, have a look at the imglyb-examples repository and extend the examples as needed! In addition to that, multiple notebooks demonstrate the general use.

imglib2-imlgyb is available on conda for Linux, OSX, and Windows:

conda install -c hanslovsky imglib2-imglyb

Re-activate the environment after installation to correctly set the environment variables. If this does not work for you, please follow the build instructions below.

• Python 2 or 3
• Java 8
• Apache Maven
• Apache Ant
• imglib2-unsafe
• Currently: imglib2-unsafe-0.0.1-SNAPSHOT.jar in local maven repository (see instructions below)
• pyjnius.jar (see instructions below)
• Cython

Clone (or download) the PyJNIus repository:

# get PyJNIus
git clone https://github.com/kivy/pyjnius
cd pyjnius

In order to build pyjnius.jar and install the pyjnius python package, run on Linux or OSX:

make # creates build/pyjnius.jar
export JAVA_HOME=/path/to/jdk  # optional
make tests # optional
python setup.py install

On Windows:

ant all
python setup.py build_ext --inplace -f
python setup.py install

All other instructions should work independent of the operating system.

# get imglib2-unsafe-0.0.1-SNAPSHOT
git clone https://github.com/imglib/imglib2-unsafe
cd imglib2-unsafe
mvn clean install

cd /path/to/imglib2-imglyb
mvn clean package
python setup.py install

• PyJNIus
• Java 8
• numpy

If you do not use conda you need to set your environment before using imglib2-imglyb:

export JAVA_HOME=/path/to/JAVA_HOME # not necessary if using conda
export PYJNIUS_JAR=/path/to/pyjnius/build/pyjnius.jar # not necessary if using conda
export IMGLYB_JAR=/path/to/imglib2-imglyb/target/imglib2-imglyb-<VERSION>.jar # not necessary if using conda

Note that, in your python files, the line

import imglyb

needs to come before any of

from imglyb import util
import jnius
from jnius import *

It is best to follow and extend the imglyb-examples according to your needs.

AWT, PyJNIus, and Cocoa do not get along perfectly. In general, the Cocoa event loop needs to be started before the JVM is loaded. (Thanks to @tpietzsch for figuring this out!) This requires some OS X specific code, written using PyObjC, to properly start up and shut down the Cocoa application and start the Java/Python code within it.

The OSXAWTwrapper.py script included in the imglyb library provides an example of Cocoa code and can be used to run the imglyb-examples. Two packages from PyObjC are required for this wrapper (pyobjc-core and pyobjc-framework-cocoa), and they should be installed with imglib2-imglyb on OS X.

When running the wrapper, one can either provide the name of the target module (as if using python -m) or the full path to the target script. So using the module name, the command to run the "butterfly" script in imglyb-examples looks like this: python imglyb/OSXAWTwrapper.py imglyb-examples.butterfly

Running OSXAWTwrapper.py via python -m does not work at this time.