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_looping_section():
sec = Section([(0, 0, 0), (1, 0, 0), (1, 2, 0), (0, 2, 0), (0, 0, 0)])
# is infinity
nt.eq_(_sf.section_tortuosity(sec), np.inf)
nt.ok_(math.isinf(_sf.section_tortuosity(sec)))
nt.ok_(np.isinf(_sf.section_tortuosity(sec)))
# is not NaN
nt.ok_(not math.isnan(_sf.section_tortuosity(sec)))
nt.ok_(not np.isnan(_sf.section_tortuosity(sec)))
def test_section_tortuosity():
sec_a = Section([(0, 0, 0), (1, 0, 0), (2, 0, 0), (3, 0, 0)])
sec_b = Section([(0, 0, 0), (1, 0, 0), (1, 2, 0), (0, 2, 0)])
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_looping_section():
sec = Section([(0, 0, 0), (1, 0, 0), (1, 2, 0), (0, 2, 0), (0, 0, 0)])
# is infinity
nt.eq_(_sf.section_tortuosity(sec), np.inf)
nt.ok_(math.isinf(_sf.section_tortuosity(sec)))
nt.ok_(np.isinf(_sf.section_tortuosity(sec)))
# is not NaN
nt.ok_(not math.isnan(_sf.section_tortuosity(sec)))
nt.ok_(not np.isnan(_sf.section_tortuosity(sec)))
def test_section_tortuosity():
sec_a = Section([(0, 0, 0), (1, 0, 0), (2, 0, 0), (3, 0, 0)])
sec_b = Section([(0, 0, 0), (1, 0, 0), (1, 2, 0), (0, 2, 0)])
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_looping_section():
sec = Section([
(0, 0, 0), (1, 0, 0), (1, 2, 0), (0, 2, 0), (0, 0, 0)
])
with warnings.catch_warnings(record=True):
nt.eq_(_sf.section_tortuosity(sec), np.inf)
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[1]
with warnings.catch_warnings(record=True):
nt.eq_(_sf.section_tortuosity(sec), np.inf)
def test_setion_tortuosity_empty_section():
sec = Section([])
nt.eq_(_sf.section_tortuosity(sec), 1.0)
def test_setion_tortuosity_single_point():
sec = Section([(1, 2, 3)])
nt.eq_(_sf.section_tortuosity(sec), 1.0)
def test_setion_tortuosity_empty_section():
sec = Section([])
nt.eq_(_sf.section_tortuosity(sec), 1.0)
def test_setion_tortuosity_single_point():
sec = Section([(1, 2, 3)])
nt.eq_(_sf.section_tortuosity(sec), 1.0)
