def test_components():
skel = Skeleton(
[
(0, 0, 0),
(1, 0, 0),
(2, 0, 0),
(0, 1, 0),
(0, 2, 0),
(0, 3, 0),
],
edges=[(0, 1), (1, 2), (3, 4), (4, 5), (3, 5)],
segid=666,
)
components = skel.components()
assert len(components) == 2
assert components[0].vertices.shape[0] == 3
assert components[1].vertices.shape[0] == 3
assert components[0].edges.shape[0] == 2
assert components[1].edges.shape[0] == 3
skel1_gt = Skeleton([(0, 0, 0), (1, 0, 0), (2, 0, 0)], [(0, 1), (1, 2)])
skel2_gt = Skeleton([(0, 1, 0), (0, 2, 0), (0, 3, 0)], [(0, 1), (0, 2),
(1, 2)])
assert Skeleton.equivalent(components[0], skel1_gt)
assert Skeleton.equivalent(components[1], skel2_gt)
def test_downsample():
skel = Skeleton(
[(0, 0, 0), (1, 0, 0), (1, 1, 0), (1, 1, 3), (2, 1, 3), (2, 2, 3)],
edges=[(1, 0), (1, 2), (2, 3), (3, 4), (5, 4)],
radii=[1, 2, 3, 4, 5, 6],
vertex_types=[1, 2, 3, 4, 5, 6],
segid=1337,
)
def should_error(x):
try:
skel.downsample(x)
assert False
except ValueError:
pass
should_error(-1)
should_error(0)
should_error(.5)
should_error(2.00000000000001)
dskel = skel.downsample(1)
assert Skeleton.equivalent(dskel, skel)
assert dskel.id == skel.id
assert dskel.id == 1337
dskel = skel.downsample(2)
dskel_gt = Skeleton([(0, 0, 0), (1, 1, 0), (2, 1, 3), (2, 2, 3)],
edges=[(1, 0), (1, 2), (2, 3)],
radii=[1, 3, 5, 6],
vertex_types=[1, 3, 5, 6])
assert Skeleton.equivalent(dskel, dskel_gt)
dskel = skel.downsample(3)
dskel_gt = Skeleton(
[(0, 0, 0), (1, 1, 3), (2, 2, 3)],
edges=[(1, 0), (1, 2)],
radii=[1, 4, 6],
vertex_types=[1, 4, 6],
)
assert Skeleton.equivalent(dskel, dskel_gt)
skel = Skeleton([(0, 0, 0), (1, 0, 0), (1, 1, 0), (1, 1, 3), (2, 1, 3),
(2, 2, 3)],
edges=[(1, 0), (1, 2), (3, 4), (5, 4)],
radii=[1, 2, 3, 4, 5, 6],
vertex_types=[1, 2, 3, 4, 5, 6])
dskel = skel.downsample(2)
dskel_gt = Skeleton([(0, 0, 0), (1, 1, 0), (1, 1, 3), (2, 2, 3)],
edges=[(1, 0), (2, 3)],
radii=[1, 3, 4, 6],
vertex_types=[1, 3, 4, 6])
assert Skeleton.equivalent(dskel, dskel_gt)
def test_read_duplicate_vertex_swc():
test_file = """
1 0 -18.458370 23.227150 -84.035016 1.000000 -1
2 0 -18.159709 22.925778 -82.984344 1.000000 1
3 0 -17.861047 22.624407 -82.984344 1.000000 2
4 0 -17.562385 22.624407 -82.984344 1.000000 3
5 0 -16.965061 22.021663 -82.984344 1.000000 4
6 0 -16.965061 21.720292 -82.984344 1.000000 5
7 0 -16.069075 21.720292 -82.984344 1.000000 6
8 0 -16.069075 21.117548 -80.883000 1.000000 7
9 0 -15.770414 20.816176 -80.883000 1.000000 8
10 0 -15.770414 20.514805 -80.883000 1.000000 9
11 0 -15.770414 20.816176 -80.883000 1.000000 10
12 0 -16.069075 21.117548 -80.883000 1.000000 11
13 0 -16.069075 21.418920 -80.883000 1.000000 12
14 0 -16.069075 20.816176 -78.781655 1.000000 13
15 0 -15.471752 20.213433 -76.680311 1.000000 14
16 0 -15.471752 19.309318 -76.680311 1.000000 15
17 0 -15.471752 19.007946 -75.629639 1.000000 16
18 0 -15.173090 18.706574 -74.578966 1.000000 17
19 0 -14.874428 18.706574 -74.578966 1.000000 18
20 0 -14.575766 18.405202 -74.578966 1.000000 19
"""
skel = Skeleton.from_swc(test_file)
assert skel.vertices.shape[0] == 20
skel2 = Skeleton.from_swc(skel.to_swc())
assert skel2.vertices.shape[0] == 20
assert Skeleton.equivalent(skel, skel2)
def test_equivalent():
assert Skeleton.equivalent(Skeleton(), Skeleton())
identity = Skeleton([(0, 0, 0), (1, 0, 0)], [(0, 1)])
assert Skeleton.equivalent(identity, identity)
diffvertex = Skeleton([(0, 0, 0), (0, 1, 0)], [(0, 1)])
assert not Skeleton.equivalent(identity, diffvertex)
single1 = Skeleton([(0, 0, 0), (1, 0, 0)], edges=[(1, 0)])
single2 = Skeleton([(0, 0, 0), (1, 0, 0)], edges=[(0, 1)])
assert Skeleton.equivalent(single1, single2)
double1 = Skeleton([(0, 0, 0), (1, 0, 0)], edges=[(1, 0)])
double2 = Skeleton([(0, 0, 0), (1, 0, 0)], edges=[(0, 1)])
assert Skeleton.equivalent(double1, double2)
double1 = Skeleton([(0, 0, 0), (1, 0, 0), (1, 1, 0)],
edges=[(1, 0), (1, 2)])
double2 = Skeleton([(0, 0, 0), (1, 0, 0), (1, 1, 0)],
edges=[(2, 1), (0, 1)])
assert Skeleton.equivalent(double1, double2)
double1 = Skeleton([(0, 0, 0), (1, 0, 0), (1, 1, 0), (1, 1, 3)],
edges=[(1, 0), (1, 2), (1, 3)])
double2 = Skeleton([(0, 0, 0), (1, 0, 0), (1, 1, 0), (1, 1, 3)],
edges=[(3, 1), (2, 1), (0, 1)])
assert Skeleton.equivalent(double1, double2)
def test_downsample_joints():
skel = Skeleton(
[
(2, 3, 0), # 0
(2, 2, 0), # 1
(2, 1, 0), # 2
(0, 0, 0),
(1, 0, 0),
(2, 0, 0),
(3, 0, 0),
(4, 0, 0), # 3, 4, 5, 6, 7
(2, -1, 0), # 8
(2, -2, 0), # 9
(2, -3, 0), # 10
],
edges=[(0, 1), (1, 2), (2, 5), (3, 4), (4, 5), (5, 6), (6, 7), (5, 8),
(8, 9), (9, 10)],
radii=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
vertex_types=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
segid=1337,
)
ds_skel = skel.downsample(2)
ds_skel_gt = Skeleton(
[
(2, 3, 0), # 0
(2, 2, 0), # 1
(0, 0, 0),
(2, 0, 0),
(4, 0, 0), # 2, 3, 4
(2, -2, 0), # 5
(2, -3, 0), # 6
],
edges=[(0, 1), (1, 3), (2, 3), (3, 4), (3, 5), (5, 6)],
radii=[0, 1, 3, 5, 7, 9, 10],
vertex_types=[0, 1, 3, 5, 7, 9, 10],
segid=1337,
)
assert Skeleton.equivalent(ds_skel, ds_skel_gt)
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