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[fix] TestDetermineZPosition in z_localization_test.py #3408

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Merged
tepals merged 1 commit into from
Apr 13, 2026
Merged

[fix] TestDetermineZPosition in z_localization_test.py #3408

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31 changes: 16 additions & 15 deletions src/odemis/acq/align/test/z_localization_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,8 +52,10 @@
'z_calibration_range': [-9.418563712742548e-07, 8.781436287257452e-07],
}

z_stack_step_size = 50*10-9 # m
z_stack_step_size = 50e-9 # m
PRECISION = z_stack_step_size * 0.45 # Precision should be better than the step within a z stack
IMG_PATH = os.path.join(os.path.dirname(__file__), "images")


class TestDetermineZPosition(unittest.TestCase):
@classmethod
Expand All @@ -72,48 +74,48 @@ def test_determine_z_position(self):
Test for known data the outcome of the function determine_z_position
"""
# Test on an image below focus
image = read_data("images/super_z_single_beed_aprox_500nm_under_focus.tif")[0]
expected_outcome_image_1 = -592.5e-9 # Value determined using the function determine_z_position
image = read_data(os.path.join(IMG_PATH, "super_z_single_beed_aprox_500nm_under_focus.tif"))[0]
expected_outcome_image_1 = 592.5e-9 # Value determined using the function determine_z_position
z, warning = determine_z_position(image, CALIB_DATA)
self.assertEqual(warning, None)
self.assertAlmostEqual(expected_outcome_image_1, z, delta=PRECISION)

# Test on an image which is roughly in focus/point of least confusion
image = read_data("images/super_z_single_beed_semi_in_focus.tif")[0]
expected_outcome_image_2 = -62.8e-9 # Value determined using the function determine_z_position
image = read_data(os.path.join(IMG_PATH, "super_z_single_beed_semi_in_focus.tif"))[0]
expected_outcome_image_2 = 62.8e-9 # Value determined using the function determine_z_position
z, warning = determine_z_position(image, CALIB_DATA)
self.assertEqual(warning, None)
self.assertAlmostEqual(expected_outcome_image_2, z, delta=PRECISION)

# Test on an image which is above focus
image = read_data("images/super_z_single_beed_aprox_500nm_above_focus.tif")[0]
expected_outcome_image_3 = 420.6e-9 # Value determined using the function determine_z_position
image = read_data(os.path.join(IMG_PATH, "super_z_single_beed_aprox_500nm_above_focus.tif"))[0]
expected_outcome_image_3 = -420.6e-9 # Value determined using the function determine_z_position
z, warning = determine_z_position(image, CALIB_DATA)
self.assertEqual(warning, None)
self.assertAlmostEqual(expected_outcome_image_3, z, delta=PRECISION)

# Test on an image where no feature visible because it is just white noise
image = read_data("images/super_z_no_beed_just_noise.tif")[0]
image = read_data(os.path.join(IMG_PATH, "super_z_no_beed_just_noise.tif"))[0]
_, warning = determine_z_position(image, CALIB_DATA)
self.assertEqual(warning, 5) # Since the entire image is noise the warning raised should be 5

# Test on an image where no feature visible because it is entirely white
image = read_data("images/super_z_no_beed_just_white.tif")[0]
image = read_data(os.path.join(IMG_PATH, "super_z_no_beed_just_white.tif"))[0]
_, warning = determine_z_position(image, CALIB_DATA)
self.assertEqual(warning, 6) # Since the entire image is white the warning raised should be 5
self.assertEqual(warning, 6) # Since the entire image is white the warning raised should be 6

# Change the range so warning 6 is raised with an image which is just above focus
calib_data_limited_range = CALIB_DATA.copy()
calib_data_limited_range["z_calibration_range"] = (-1e-10, 1e-10)
image = read_data("images/super_z_single_beed_aprox_500nm_above_focus.tif")[0]
expected_outcome_image_3 = 420.6e-9 # Value determined using the function determine_z_position
image = read_data(os.path.join(IMG_PATH, "super_z_single_beed_aprox_500nm_above_focus.tif"))[0]
expected_outcome_image_3 = -420.6e-9 # Value determined using the function determine_z_position
z, warning = determine_z_position(image, calib_data_limited_range)
# Since the range is set to small the detected feature is to big and warning raised should be 4
self.assertEqual(warning, 4)
self.assertAlmostEqual(expected_outcome_image_3, z, delta=PRECISION)

def test_key_error(self):
image = read_data("images/super_z_single_beed_semi_in_focus.tif")[0]
image = read_data(os.path.join(IMG_PATH, "super_z_single_beed_semi_in_focus.tif"))[0]

# Check if the key error is raised when the key 'x' is missing
calib_data_missing_key = CALIB_DATA.copy()
Expand All @@ -130,7 +132,7 @@ def test_key_error(self):
# TODO Add a test to find that indeed the module not found error is raised when a module is missing.
# Maybe use something with MOCK?
# def test_module_not_found_error(self):
# image = read_data("images/super_z_single_beed_semi_in_focus.tif")[0]
# image = read_data(os.path.join(IMG_PATH, "super_z_single_beed_semi_in_focus.tif"))[0]
#
# with self.assertRaises(ModuleNotFoundError):
# _, _ = determine_z_position(image, CALIB_DATA)
Expand Down Expand Up @@ -197,7 +199,6 @@ def test_measure_z_multi_targets(self):
fiducial_size=self.fiducial_size, fiducials=self.fiducials)
f.result(30)


def test_measure_z_multi_targets_pos_shifted(self):
"""
Test measure_z_multi_targets with a pos within the FoV, but not in the center
Expand Down
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