def test_section_tortuosity():
sec_a = load_neuron(StringIO(u"""
((CellBody) (0 0 0 2))
((Dendrite)
(0 0 0 2)
(1 0 0 2)
(2 0 0 2)
(3 0 0 2))"""),
reader='asc').sections[1]
sec_b = load_neuron(StringIO(u"""
((CellBody) (0 0 0 2))
((Dendrite)
(0 0 0 2)
(1 0 0 2)
(1 2 0 2)
(0 2 0 2))"""),
reader='asc').sections[1]
nt.eq_(_sf.section_tortuosity(sec_a), 1.0)
nt.eq_(_sf.section_tortuosity(sec_b), 4.0 / 2.0)
for s in _nf.iter_sections(NRN):
nt.eq_(
_sf.section_tortuosity(s),
mmth.section_length(s.points) /
mmth.point_dist(s.points[0], s.points[-1]))
def test_section_tortuosity():
sec_a = load_neuron(StringIO(u"""
((CellBody) (0 0 0 2))
((Dendrite)
(0 0 0 2)
(1 0 0 2)
(2 0 0 2)
(3 0 0 2))"""),
reader='asc').sections[SECTION_ID]
sec_b = load_neuron(StringIO(u"""
((CellBody) (0 0 0 2))
((Dendrite)
(0 0 0 2)
(1 0 0 2)
(1 2 0 2)
(0 2 0 2))"""),
reader='asc').sections[SECTION_ID]
assert _sf.section_tortuosity(sec_a) == 1.0
assert _sf.section_tortuosity(sec_b) == 4.0 / 2.0
for s in _nf.iter_sections(NRN):
assert (_sf.section_tortuosity(s) == mmth.section_length(s.points) /
mmth.point_dist(s.points[0], s.points[-1]))
def test_section_tortuosity_looping_section():
sec = load_neuron(StringIO(u"""
((CellBody) (0 0 0 2))
((Dendrite)
(0 0 0 2)
(1 0 0 2)
(1 2 0 2)
(0 2 0 2)
(0 0 0 2))"""), reader='asc').sections[SECTION_ID]
with warnings.catch_warnings(record=True):
nt.eq_(_sf.section_tortuosity(sec), np.inf)
def test_setion_tortuosity_single_point():
sec = load_neuron(StringIO(u"""((CellBody) (0 0 0 2))
((Dendrite)
(1 2 3 2))"""), reader='asc').sections[SECTION_ID]
nt.eq_(_sf.section_tortuosity(sec), 1.0)