def test_downsample():
skel = PrecomputedSkeleton([
(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 PrecomputedSkeleton.equivalent(dskel, skel)
assert dskel.id == skel.id
assert dskel.id == 1337
dskel = skel.downsample(2)
dskel_gt = PrecomputedSkeleton(
[ (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 PrecomputedSkeleton.equivalent(dskel, dskel_gt)
dskel = skel.downsample(3)
dskel_gt = PrecomputedSkeleton(
[ (0,0,0), (1,1,3), (2,2,3) ], edges=[ (1,0), (1,2) ],
radii=[1,4,6], vertex_types=[1,4,6],
)
assert PrecomputedSkeleton.equivalent(dskel, dskel_gt)
skel = PrecomputedSkeleton([
(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 = PrecomputedSkeleton(
[ (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 PrecomputedSkeleton.equivalent(dskel, dskel_gt)
def test_equivalent():
assert PrecomputedSkeleton.equivalent(PrecomputedSkeleton(),
PrecomputedSkeleton())
identity = PrecomputedSkeleton([(0, 0, 0), (1, 0, 0)], [(0, 1)])
assert PrecomputedSkeleton.equivalent(identity, identity)
diffvertex = PrecomputedSkeleton([(0, 0, 0), (0, 1, 0)], [(0, 1)])
assert not PrecomputedSkeleton.equivalent(identity, diffvertex)
single1 = PrecomputedSkeleton([(0, 0, 0), (1, 0, 0)], edges=[(1, 0)])
single2 = PrecomputedSkeleton([(0, 0, 0), (1, 0, 0)], edges=[(0, 1)])
assert PrecomputedSkeleton.equivalent(single1, single2)
double1 = PrecomputedSkeleton([(0, 0, 0), (1, 0, 0)], edges=[(1, 0)])
double2 = PrecomputedSkeleton([(0, 0, 0), (1, 0, 0)], edges=[(0, 1)])
assert PrecomputedSkeleton.equivalent(double1, double2)
double1 = PrecomputedSkeleton([(0, 0, 0), (1, 0, 0), (1, 1, 0)],
edges=[(1, 0), (1, 2)])
double2 = PrecomputedSkeleton([(0, 0, 0), (1, 0, 0), (1, 1, 0)],
edges=[(2, 1), (0, 1)])
assert PrecomputedSkeleton.equivalent(double1, double2)
double1 = PrecomputedSkeleton([(0, 0, 0), (1, 0, 0), (1, 1, 0), (1, 1, 3)],
edges=[(1, 0), (1, 2), (1, 3)])
double2 = PrecomputedSkeleton([(0, 0, 0), (1, 0, 0), (1, 1, 0), (1, 1, 3)],
edges=[(3, 1), (2, 1), (0, 1)])
assert PrecomputedSkeleton.equivalent(double1, double2)
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 = PrecomputedSkeleton.from_swc(test_file)
assert skel.vertices.shape[0] == 8
assert skel.edges.shape[0] == 7
skel_gt = PrecomputedSkeleton(
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 PrecomputedSkeleton.equivalent(skel, skel_gt)
def test_downsample_joints():
skel = PrecomputedSkeleton([
(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 = PrecomputedSkeleton([
(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 PrecomputedSkeleton.equivalent(ds_skel, ds_skel_gt)
