lipase/tests/test0001.py

"""This script is supposed to be launched from fiji's jython interpreter
"""
# # note: fiji's jython doesn't support encoding keyword

#https://imagej.net/Scripting_Headless
#@String lipase_src_root_path
#@String raw_images_root_path

# String(label="Please enter your name",description="Name field") name
# OUTPUT String greeting
import sys
print('python version %s' % sys.version)  # prints python version

sys.path.append(lipase_src_root_path)  # necessary if run from fiji as script otherwise jython fails to find lipase's modules such as catalog

from ij import IJ
# from lipase import Lipase, ImageLogger
from catalog import ImageCatalog
from preprocessing import WhiteEstimator
from preprocessing import test_preprocessing

def run_script():
    test_preprocessing(raw_images_root_path) # eg '/Users/graffy/ownCloud/ipr/lipase/raw-images'

# note : when launched from fiji, __name__ doesn't have the value "__main__", as when launched from python
run_script()