def test_path_length_caching():
skeleton = Skeleton(skeleton3d)
t0 = process_time()
distances = skeleton.path_lengths()
t1 = process_time()
distances2 = skeleton.path_lengths()
t2 = process_time()
assert t2 - t1 < t1 - t0
assert np.all((distances > 0.99 + np.sqrt(2))
& (distances < 5.01 + 5 * np.sqrt(2)))
def test_skeleton1_topo():
skeleton = Skeleton(skeleton1)
assert skeleton.paths.shape == (4, np.sum(skeleton1) + 1)
paths_list = skeleton.paths_list()
reference_paths = [[8, 6, 1, 2, 3, 4, 5, 7, 11, 10, 13], [8, 9, 13],
[8, 12, 14], [13, 15, 16, 17]]
d0 = 1 + np.sqrt(2)
reference_distances = [5 * d0, d0, d0, 1 + d0]
for path in reference_paths:
assert path in paths_list or path[::-1] in paths_list
assert_allclose(sorted(skeleton.path_lengths()),
sorted(reference_distances))
def test_skeleton_summarize():
image = np.zeros(skeleton2.shape, dtype=float)
image[skeleton2] = 1 + np.random.random(np.sum(skeleton2))
skeleton = Skeleton(image)
summary = summarize(skeleton)
assert set(summary['skeleton-id']) == {1, 2}
assert (np.all(summary['mean-pixel-value'] < 2)
and np.all(summary['mean-pixel-value'] > 1))
def test_junction_first():
"""Ensure no self-edges exist in multi-pixel junctions.
Before commit 64047622, the skeleton class would include self-edges
within junctions in its paths list, but only when the junction was visited
before any of its adjacent branches. This turns out to be tricky to achieve
but not impossible in 2D.
"""
assert [1, 1] not in Skeleton(junction_first).paths_list()
def test_path_stdev():
image = np.zeros(skeleton1.shape, dtype=float)
image[skeleton1] = 1 + np.random.random(np.sum(skeleton1))
skeleton = Skeleton(image)
# longest_path should be 0, but could change.
longest_path = np.argmax(skeleton.path_lengths())
dev = skeleton.path_stdev()[longest_path]
assert 0.09 < dev < 0.44 # chance is < 1/10K that this will fail
# second check: first principles.
skeleton2 = Skeleton(image**2)
# (Var = StDev**2 = E(X**2) - (E(X))**2)
assert_allclose(skeleton.path_stdev()**2,
skeleton2.path_means() - skeleton.path_means()**2)
def test_tip_junction_edges():
skeleton = Skeleton(skeleton4)
reference_paths = [[1, 2], [2, 4, 5], [2, 7]]
paths_list = skeleton.paths_list()
for path in reference_paths:
assert path in paths_list or path[::-1] in paths_list
def test_skeleton_coordinates():
skeleton = Skeleton(skeleton1)
last_path_coordinates = skeleton.path_coordinates(3)
assert_allclose(last_path_coordinates, [[3, 3], [4, 4], [4, 5], [4, 6]])
def test_skeleton1_float():
image = np.zeros(skeleton1.shape, dtype=float)
image[skeleton1] = 1 + np.random.random(np.sum(skeleton1))
skeleton = Skeleton(image)
path, data = skeleton.path_with_data(0)
assert 1.0 < np.mean(data) < 2.0
def test_tiny_cycle():
skeleton = Skeleton(tinycycle)
assert skeleton.paths.shape == (1, 5)