def compute_zline_distance(repo, molecule_list, timepoints, z_line_spacing):
all_median_profiles = []
for molecule in molecule_list:
for timepoint in timepoints:
image_set = ImageSet(repo, [f"{'mrna'}/{molecule}/{timepoint}/"])
if image_set.__sizeof__() < 5:
logger.warning("Image set is small for {}", molecule)
total_profile = image_set.compute_zline_distance(z_line_spacing)
all_median_profiles.append(np.median(total_profile, axis=0))
return all_median_profiles
def test_compute_zline_distance(self):
image_set = ImageSet(self.repo, path_list=['mrna/actn2/immature/'])
result = image_set.compute_zline_distance(20)
test = [[0.24374599, 0.03463759, 0.0365619, 0.0436177, 0.03207184,
0.02758178, 0.0365619, 0.03207184, 0.03014753, 0.02694035,
0.02309173, 0.01860167, 0.02180885, 0.02758178, 0.01988454,
0.0, 0.0, 0.0, 0.0, 0.0],
[0.38974359, 0.01230769, 0.01025641, 0.02871795, 0.02153846,
0.02461538, 0.01948718, 0.02666667, 0.03076923, 0.01333333,
0.0225641, 0.01025641, 0.01538462, 0.01333333, 0.00923077,
0.0, 0.0, 0.0, 0.0, 0.0]]
self.assertEqual(len(result), len(test))
self.assertAlmostEqual(np.sum(result), np.sum(test), places=5)