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 raw_images_root_path

import unittest  # unittest2 doesn't exist in fiji
import sys
from lipase.catalog import ImageCatalog, Sequence
from lipase.imageengine import IImageEngine
from lipase.imagej.ijimageengine import IJImageEngine, IJImage
from lipase.preprocessing import WhiteEstimator

class TestLipase(unittest.TestCase):

    RAW_IMAGES_ROOT_PATH = raw_images_root_path  # eg '/Users/graffy/ownCloud/ipr/lipase/raw-images' pylint: disable=undefined-variable

    # we need to know if the test succeeded or not https://stackoverflow.com/questions/4414234/getting-pythons-unittest-results-in-a-teardown-method
    # CURRENT_RESULT = None  # holds last result object passed to run method

    def setUp(self):
        print("initializing TestLipase instance")
        IImageEngine.set_instance(IJImageEngine())
        self.catalog = ImageCatalog(self.RAW_IMAGES_ROOT_PATH)

    def tearDown(self):
        print("uninitializing TestLipase instance")
        self.catalog = None

    

    def test_estimate_white(self):
        sequence = self.catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2']
        white_estimator = WhiteEstimator(open_size=75, close_size=75, average_size=75)
        white_estimate = white_estimator.estimate_white([sequence], ['DM300_327-353_fluo'])
        # find_white_reference_image(white_estimate, sequence.get_white())
        print(white_estimate)
        IImageEngine.get_instance().save_as_tiff(white_estimate, './white_estimate.tiff')
        # assert False, "hellooooo"
        print('end of test_estimate_white')


def run_script():

    # unittest.main() # this would result in : ImportError: No module named __main__
    # solution from : https://discourse.mcneel.com/t/using-unittest-in-rhino-python-not-possible/15364
    suite = unittest.TestLoader().loadTestsFromTestCase(TestLipase)
    stream = sys.stdout  # by default it's sys.stderr, which doesn't appear in imagej's output
    test_result = unittest.TextTestRunner(stream=stream, verbosity=2).run(suite)
    print('test_result : %s' % test_result)
    # store summary of the result in a file so that the caller of imagej can detect that this python script failed (imagej seems to always return error code 0, regardless the error returned by the python script it executes : even sys.exit(1) doesn't change this)
    with open('/tmp/test_result.txt', 'w') as f:
        f.write('%d' % {True: 0, False: 1}[test_result.wasSuccessful()])
    print('end of run_script')

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