def test_consolidate():
skel = Skeleton(
vertices=np.array([
(0, 0, 0),
(1, 0, 0),
(2, 0, 0),
(0, 0, 0),
(2, 1, 0),
(2, 2, 0),
(2, 2, 1),
(2, 2, 2),
],
dtype=np.float32),
edges=np.array([
[0, 1],
[1, 2],
[2, 3],
[3, 4],
[4, 5],
[5, 6],
[6, 7],
],
dtype=np.uint32),
radii=np.array([0, 1, 2, 3, 4, 5, 6, 7], dtype=np.float32),
vertex_types=np.array([0, 1, 2, 3, 4, 5, 6, 7], dtype=np.uint8),
)
correct_skel = Skeleton(
vertices=np.array([
(0, 0, 0),
(1, 0, 0),
(2, 0, 0),
(2, 1, 0),
(2, 2, 0),
(2, 2, 1),
(2, 2, 2),
],
dtype=np.float32),
edges=np.array([
[0, 1],
[0, 2],
[0, 3],
[1, 2],
[3, 4],
[4, 5],
[5, 6],
],
dtype=np.uint32),
radii=np.array([0, 1, 2, 4, 5, 6, 7], dtype=np.float32),
vertex_types=np.array([0, 1, 2, 4, 5, 6, 7], dtype=np.uint8),
)
consolidated = skel.consolidate()
assert np.all(consolidated.vertices == correct_skel.vertices)
assert np.all(consolidated.edges == correct_skel.edges)
assert np.all(consolidated.radii == correct_skel.radii)
assert np.all(consolidated.vertex_types == correct_skel.vertex_types)
def test_read_swc():
# From http://research.mssm.edu/cnic/swc.html
test_file = """# ORIGINAL_SOURCE NeuronStudio 0.8.80
# CREATURE
# REGION
# FIELD/LAYER
# TYPE
# CONTRIBUTOR
# REFERENCE
# RAW
# EXTRAS
# SOMA_AREA
# SHINKAGE_CORRECTION 1.0 1.0 1.0
# VERSION_NUMBER 1.0
# VERSION_DATE 2007-07-24
# SCALE 1.0 1.0 1.0
1 1 14.566132 34.873772 7.857000 0.717830 -1
2 0 16.022520 33.760513 7.047000 0.463378 1
3 5 17.542000 32.604973 6.885001 0.638007 2
4 0 19.163984 32.022469 5.913000 0.602284 3
5 0 20.448090 30.822802 4.860000 0.436025 4
6 6 21.897903 28.881084 3.402000 0.471886 5
7 0 18.461960 30.289471 8.586000 0.447463 3
8 6 19.420759 28.730757 9.558000 0.496217 7"""
skel = Skeleton.from_swc(test_file)
assert skel.vertices.shape[0] == 8
assert skel.edges.shape[0] == 7
skel_gt = Skeleton(
vertices=[[14.566132, 34.873772, 7.857000],
[16.022520, 33.760513, 7.047000],
[17.542000, 32.604973, 6.885001],
[19.163984, 32.022469, 5.913000],
[20.448090, 30.822802, 4.860000],
[21.897903, 28.881084, 3.402000],
[18.461960, 30.289471, 8.586000],
[19.420759, 28.730757, 9.558000]],
edges=[(0, 1), (1, 2), (2, 3), (3, 4), (4, 5), (2, 6), (7, 6)],
radii=[
0.717830, 0.463378, 0.638007, 0.602284, 0.436025, 0.471886,
0.447463, 0.496217
],
vertex_types=[1, 0, 5, 0, 0, 6, 0, 6],
)
assert Skeleton.equivalent(skel, skel_gt)
skel = Skeleton.from_swc(skel.to_swc())
assert np.all(np.abs(skel.vertices - skel_gt.vertices) < 0.00001)
# sorts edges
skel = skel.consolidate()
skel_gt = skel_gt.consolidate()
assert np.all(skel.edges == skel_gt.edges)
assert np.all(np.abs(skel.radii - skel_gt.radii) < 0.00001)
Nv = skel.vertices.shape[0]
Ne = skel.edges.shape[0]
for _ in range(10):
skel = Skeleton.from_swc(skel.to_swc())
assert skel.vertices.shape[0] == Nv
assert skel.edges.shape[0] == Ne