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JEP integration for SciJava

This project aims to check the ability to use JEP backed by Maven and usable either the OS or Python environment to use with SciJava.

Requirements

  • Installing jep via pip
pip install jep
  • For Linux users : export the variable LD_PRELOAD with the path of the libpython.so file in your terminal
    • It will let JEP to enable the Numpy support
    • Normally on the release of JEP 4.1 (~Autumn 2022), this step will be useless
export LD_PRELOAD=/path/to/python/libpython3.x.so
# i.e. with a Python interpreter but it can be also from Conda or Venv
export LD_PRELOAD=/usr/bin/libpython3.10.so.1.0
  • No need to set a LD_LIBRARY_PATH environment variable
  • No need to set a PYTHONHOME environment variable

How to use

mvn -Pexec

Note: Maven eats the Python-side output. To see that as well, you can do:

mvn package dependency:copy-dependencies
java -cp target/jep-integration-0.1.0-SNAPSHOT.jar:target/dependency/'*' net.imagej.jep.Main

Then set the path to your Python executable folder :

  • For Python interpreter,
    • Commonly /usr/bin for Linux
    • C:\Program Files\Python3<x> or C:\Users\<username>\AppData\Local\Programs\Python3<x> for Windows
  • For Conda and consort environment,
    • /home/<username>/.conda/envs/<env_name>/bin for Linux
    • C:\Users\<username>\.conda\envs\<env_name>\bin for Windows
    • It is not necessary to activate the environment
  • For Venv environment : The full path to the bin directory
    • It is not necessary to activate the environment

Available scenarios

Basic JEP example

  • Simple JEP execution
  • Send and retrieve data from Python
  • Calling Java class in Python as a usual Python import
  • Check if JEP can import Numpy

Examples with ImageJ

  • Get ImageJ version from Python
  • Open an image
  • More to come

Examples with ScyJava

  • Use jimport function
    • Available only if you have a development version of ScyJava containing the JEP implementation

Misc

  • Example of a custom function in Python to import classes/objects from a package path
    • This case is created to know how JEP could be integrated in the jimport function of SciJava