def test_compute_focus_error():
image = np.random.normal(loc=0.0, scale=1.0, size=10000)
image = np.reshape(image, (100, 100))
# error: sequence 'neighborhood_size' too short
with pytest.raises(ValueError):
_ = stack.compute_focus(image, neighborhood_size=[11])
# error: sequence 'neighborhood_size' too long
with pytest.raises(ValueError):
_ = stack.compute_focus(image, neighborhood_size=(5, 11, 31))
def test_in_focus_selection(dtype):
x = x_3d_out_focus.astype(dtype)
expected_y = x_3d.astype(dtype)
focus = stack.compute_focus(x_3d_out_focus, neighborhood_size=31)
y = stack.in_focus_selection(x, focus, proportion=3)
assert_array_equal(y, expected_y)
assert y.dtype == dtype
def test_compute_focus_format(dtype, neighborhood_size):
# 2D input
image = np.random.normal(loc=0.0, scale=1.0, size=10000)
image = np.reshape(image, (100, 100)).astype(dtype)
focus = stack.compute_focus(image, neighborhood_size=neighborhood_size)
assert focus.dtype == np.float64
assert focus.shape == image.shape
assert focus.min() >= 1
# 3D input
image = np.random.normal(loc=0.0, scale=1.0, size=100000)
image = np.reshape(image, (10, 100, 100)).astype(dtype)
focus = stack.compute_focus(image, neighborhood_size=neighborhood_size)
assert focus.dtype == np.float64
assert focus.shape == image.shape
assert focus.min() >= 1
def test_get_in_focus_indices():
focus = stack.compute_focus(x_3d_out_focus, neighborhood_size=31)
# number of slices to keep
indices_to_keep = stack.get_in_focus_indices(focus, proportion=3)
assert isinstance(indices_to_keep, list)
assert len(indices_to_keep) == 3
assert indices_to_keep[0] == 1
assert indices_to_keep[1] == 3
assert indices_to_keep[2] == 4
# proportion of slices to keep
indices_to_keep = stack.get_in_focus_indices(focus, proportion=0.5)
assert isinstance(indices_to_keep, list)
assert len(indices_to_keep) == 3
assert indices_to_keep[0] == 1
assert indices_to_keep[1] == 3
assert indices_to_keep[2] == 4
# 0 slice
indices_to_keep = stack.get_in_focus_indices(focus, proportion=0)
assert isinstance(indices_to_keep, list)
assert len(indices_to_keep) == 0
# error: float > 1
with pytest.raises(ValueError):
_ = stack.get_in_focus_indices(focus, proportion=3.)
# error: 'proportion' < 0
with pytest.raises(ValueError):
_ = stack.get_in_focus_indices(focus, proportion=-3)
def test_compute_focus():
focus = stack.compute_focus(x_out_focus, neighborhood_size=31)
average_focus = focus.mean(axis=(1, 2))
assert round(average_focus[0], 5) == 1.
assert round(average_focus[1], 5) > 1.
assert round(average_focus[2], 5) == 1.
assert round(average_focus[3], 5) > 1.
assert round(average_focus[4], 5) > 1.
assert round(average_focus[5], 5) == 1.