83 lines
4.2 KiB
Python
83 lines
4.2 KiB
Python
"""This script is supposed to be launched from fiji's jython interpreter
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"""
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# # note: fiji's jython doesn't support encoding keyword
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# https://imagej.net/Scripting_Headless
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#@ String raw_images_root_path
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import unittest # unittest2 doesn't exist in fiji
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import sys
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from lipase.imageengine import IImageEngine, PixelType, Aabb
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from lipase.imagej.ijimageengine import IJImageEngine, IJImage
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from lipase.preprocessing import WhiteEstimator, correct_non_uniform_lighting
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from lipase.maxima_finder import MaximaFinder
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from lipase.template_matcher import TemplateMatcher
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from lipase.traps_detector import TrapsDetector
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from lipase.catalog import ImageCatalog, Sequence
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class TestLipase(unittest.TestCase):
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RAW_IMAGES_ROOT_PATH = raw_images_root_path # eg '/Users/graffy/ownCloud/ipr/lipase/raw-images' pylint: disable=undefined-variable
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# we need to know if the test succeeded or not https://stackoverflow.com/questions/4414234/getting-pythons-unittest-results-in-a-teardown-method
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# CURRENT_RESULT = None # holds last result object passed to run method
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def setUp(self):
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print("initializing TestLipase instance")
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IImageEngine.set_instance(IJImageEngine())
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self.catalog = ImageCatalog(self.RAW_IMAGES_ROOT_PATH)
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def tearDown(self):
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print("uninitializing TestLipase instance")
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self.catalog = None
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def test_estimate_white(self):
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sequence = self.catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2']
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white_estimator = WhiteEstimator(open_size=75, close_size=75, average_size=75)
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white_estimate = white_estimator.estimate_white([sequence], ['DM300_327-353_fluo'])
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# find_white_reference_image(white_estimate, sequence.get_white())
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print(white_estimate)
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IImageEngine.get_instance().save_as_tiff(white_estimate, './white_estimate.tiff')
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# assert False, "hellooooo"
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print('end of test_estimate_white')
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def test_uniform_lighting_correction(self):
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non_uniform_sequence = self.catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0']
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uniform_sequence = correct_non_uniform_lighting(non_uniform_sequence, 'DM300_nofilter_vis', white_estimator=WhiteEstimator(open_size=75, close_size=75, average_size=75))
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def test_traps_detector(self):
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# the typical value of peaks is -500 and the value between peaks is below -2500
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threshold = -1500.0
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tolerance = 1500
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maxima_finder = MaximaFinder(threshold, tolerance)
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template_matcher = TemplateMatcher(maxima_finder)
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traps_detector = TrapsDetector(template_matcher)
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sequence = self.catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0']
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x_min = 423
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x_max = 553
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y_min = 419
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y_max = 533
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trap_aabb = Aabb(x_min, y_min, x_max, y_max)
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matches = traps_detector.compute_traps_mask(sequence, 'DM300_nofilter_vis', trap_aabb)
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num_traps = len(matches)
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print("number of traps found : %d" % num_traps)
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num_expected_traps = 13 # 13 traps are completely visible in the
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self.assertAlmostEqual(len(matches), num_expected_traps, delta=1.0)
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def run_script():
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# unittest.main() # this would result in : ImportError: No module named __main__
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# solution from : https://discourse.mcneel.com/t/using-unittest-in-rhino-python-not-possible/15364
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suite = unittest.TestLoader().loadTestsFromTestCase(TestLipase)
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stream = sys.stdout # by default it's sys.stderr, which doesn't appear in imagej's output
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test_result = unittest.TextTestRunner(stream=stream, verbosity=2).run(suite)
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print('test_result : %s' % test_result)
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# 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)
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with open('/tmp/test_result.txt', 'w') as f:
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f.write('%d' % {True: 0, False: 1}[test_result.wasSuccessful()])
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print('end of run_script')
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# note : when launched from fiji, __name__ doesn't have the value "__main__", as when launched from python
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run_script()
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