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.imageengine import IImageEngine, PixelType, Aabb  # pylint: disable=import-error
from lipase.imagej.ijimageengine import IJImageEngine, IJImage  # pylint: disable=import-error
from lipase.preprocessing import WhiteEstimator, correct_non_uniform_lighting  # pylint: disable=import-error
from lipase.maxima_finder import MaximaFinder  # pylint: disable=import-error
from lipase.template_matcher import TemplateMatcher  # pylint: disable=import-error
from lipase.traps_detector import TrapsDetector  # pylint: disable=import-error
from lipase.catalog import ImageCatalog, Sequence  # pylint: disable=import-error

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 test_uniform_lighting_correction(self):
        non_uniform_sequence = self.catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0']
        uniform_sequence = correct_non_uniform_lighting(non_uniform_sequence, 'DM300_nofilter_vis', white_estimator=WhiteEstimator(open_size=75, close_size=75, average_size=75))

    def test_traps_detector(self):
        # the typical value of peaks is -500 and the value between peaks is below -2500
        threshold = -1500.0
        tolerance = 1500
        maxima_finder = MaximaFinder(threshold, tolerance)
        template_matcher = TemplateMatcher(maxima_finder)
        traps_detector = TrapsDetector(template_matcher)
        sequence = self.catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0']
        x_min = 423
        x_max = 553
        y_min = 419
        y_max = 533
        trap_aabb = Aabb(x_min, y_min, x_max, y_max)
        matches = traps_detector.compute_traps_mask(sequence, 'DM300_nofilter_vis', trap_aabb)

        num_traps = len(matches)
        print("number of traps found : %d" % num_traps)
        num_expected_traps = 13  # 13 traps are completely visible in the 
        self.assertAlmostEqual(len(matches), num_expected_traps, delta=1.0)

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()