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_normalized_quadrant_densities_protein(self):
image_set = ImageSet(self.repo, path_list=['protein/arhgdia/3h/'])
result1 = image_set.compute_normalised_quadrant_densities(quadrants_num=8)
num_images = image_set.__sizeof__()
self.assertEqual(num_images, image_set.__sizeof__())
self.assertAlmostEqual(result1[result1[:, 1] == 1][:, 0].sum() / num_images,
1.098770606, places=5) # MTOC quadrant density
self.assertAlmostEqual(result1[result1[:, 1] == 0][:, 0].sum() / (num_images * 7),
0.865466580, places=5) # non MTOC quadtant density
result2 = image_set.compute_normalised_quadrant_densities(quadrants_num=8, stripes=3, stripes_flag=True)
self.assertAlmostEqual(result2[result2[:, 1] == 1][:, 0].sum() / (3 * num_images),
0.9803183396, places=5) # MTOC quadrant density
self.assertAlmostEqual(result2[result2[:, 1] == 0][:, 0].sum() / (num_images * 7 * 3),
0.6801687989, places=5) # non MTOC quadtant density
result3 = image_set.compute_normalised_quadrant_densities(quadrants_num=8, peripheral_flag=True,
stripes=3, stripes_flag=True)
self.assertAlmostEqual(result3[result3[:, 1] == 1][:, 0].sum() / (3 * num_images),
0.126123087, places=5) # MTOC quadrant density
self.assertAlmostEqual(result3[result3[:, 1] == 0][:, 0].sum() / (num_images * 7 * 3),
0.011356787, places=5) # non MTOC quadtant density
def test_compute_normalized_quadrant_densities_mrna(self):
image_set = ImageSet(self.repo, path_list=['mrna/arhgdia/2h/'])
result1 = image_set.compute_normalised_quadrant_densities(quadrants_num=8)
num_images = image_set.__sizeof__()
self.assertEqual(num_images, image_set.__sizeof__())
self.assertAlmostEqual(result1[result1[:, 1] == 1][:, 0].sum() / num_images,
1.0780173273, places=5) # MTOC quadrant density
self.assertAlmostEqual(result1[result1[:, 1] == 0][:, 0].sum() / (num_images * 7),
1.1263246459, places=5) # non MTOC quadrant density
result2 = image_set.compute_normalised_quadrant_densities(quadrants_num=8, stripes=3, stripes_flag=True)
self.assertAlmostEqual(result2[result2[:, 1] == 1][:, 0].sum() / (3 * num_images),
1.0225376792, places=5) # MTOC quadrant density
self.assertAlmostEqual(result2[result2[:, 1] == 0][:, 0].sum() / (num_images * 7 * 3),
1.08160649427, places=5) # non MTOC quadrant density
result3 = image_set.compute_normalised_quadrant_densities(quadrants_num=8, peripheral_flag=True,
stripes=3, stripes_flag=True)
self.assertAlmostEqual(result3[result3[:, 1] == 1][:, 0].sum() / (3 * num_images),
0.79154809935, places=5) # MTOC quadrant density
self.assertAlmostEqual(result3[result3[:, 1] == 0][:, 0].sum() / (num_images * 7 * 3),
0.59408432134, places=5) # non MTOC quadrant density
