How to use Pyimagej on Python

[chautuankien]

I am having a java code that receive input of xml file and return an ImagePlus object (ImagePlus is an object in imageJ). But I am developing a python project. Instead of convert java code to python code, I want to execute that java code on python, and analysize that ImagePlus object (I want to use pyimagej)

Does anybody know how to do it?

[ctrueden]

@chautuankien Sure, PyImageJ is intended to help with use cases like this.

Your Python code would look something like this:

import imagej
import scyjava.config
from scyjava import jimport

# Add your Java code to the classpath before Java initializes.
# This assumes your code is bundled at /path/to/my-imageplus-loader.jar.
# For more about how to configure Java's class path, see:
# - https://docs.oracle.com/javase/8/docs/technotes/tools/findingclasses.html#userclass
# - https://stackoverflow.com/q/2396493/1207769
scyjava.config.add_classpath("/path/to/my-imageplus-loader.jar")

# Initialize the ImageJ2 gateway
ij = imagej.init()

# Import my Java class.
# This assumes the class is called ImagePlusLoader and resides in package imagefromxml.
# Change it to the fully qualified class name of the Java code you want to call.
ImagePlusLoader = jimport("imagefromxml.ImagePlusLoader")
imp = ImagePlusLoader().load("/path/to/the-data.xml")

# Convert the ImagePlus into an xarray (a NumPy ndarray with metadata)
narr = ij.py.from_java(imp)

# Now you can work with the ndarray as usual with Python functions
print(narr.shape)

For more details on how to use PyImageJ, check out the tutorial notebooks.