def test_get_section_radial_distances(self):
_close(_nrt.section_radial_distances(self.sec_nrn),
get('section_radial_distances', self.ref_nrn))
for t in NeuriteType:
_close(_nrt.section_radial_distances(self.sec_nrn, neurite_type=t),
get('section_radial_distances', self.ref_nrn, neurite_type=t))
def test_principal_direction_extents():
# test with a realistic neuron
nrn = nm.load_neuron(os.path.join(H5_PATH, 'bio_neuron-000.h5'))
p_ref = [1672.9694359427331, 142.43704397865031, 226.45895382204986,
415.50612748523838, 429.83008974193206, 165.95410536922873,
346.83281498399697]
p = _nf.principal_direction_extents(nrn)
_close(np.array(p), np.array(p_ref))
def test_principal_direction_extents():
principal_dir = list(_nf.principal_direction_extents(SIMPLE))
assert_allclose(principal_dir, (14.736052694538641, 12.105102672688004))
# test with a realistic neuron
nrn = nm.load_neuron(os.path.join(H5_PATH, 'bio_neuron-000.h5'))
p_ref = [
1672.9694359427331, 142.43704397865031, 226.45895382204986,
415.50612748523838, 429.83008974193206, 165.95410536922873,
346.83281498399697
]
p = _nf.principal_direction_extents(nrn)
_close(np.array(p), np.array(p_ref))
def test_get_section_path_distances(self):
_close(_nrt.section_path_lengths(self.sec_nrn), get('section_path_distances', self.ref_nrn))
for t in NeuriteType:
_close(_nrt.section_path_lengths(self.sec_nrn, neurite_type=t),
get('section_path_distances', self.ref_nrn, neurite_type=t))
pl = [_sec.section_path_length(s) for s in i_chain2(self.sec_nrn_trees)]
_close(pl, get('section_path_distances', self.ref_nrn))
def test_get_section_path_distances(self):
_close(_nrt.section_path_lengths(self.sec_nrn), get('section_path_distances', self.ref_nrn))
for t in NeuriteType:
_close(_nrt.section_path_lengths(self.sec_nrn, neurite_type=t),
get('section_path_distances', self.ref_nrn, neurite_type=t))
pl = [_sec.section_path_length(s) for s in i_chain2(self.sec_nrn_trees)]
_close(pl, get('section_path_distances', self.ref_nrn))
def test_get_remote_bifurcation_angles(self):
_close(_nrt.remote_bifurcation_angles(self.sec_nrn),
get('remote_bifurcation_angles', self.ref_nrn))
for t in NeuriteType:
_close(_nrt.remote_bifurcation_angles(self.sec_nrn, neurite_type=t),
get('remote_bifurcation_angles', self.ref_nrn, neurite_type=t))
ba = [_bf.remote_bifurcation_angle(b)
for b in i_chain2(self.sec_nrn_trees, iterator_type=Section.ibifurcation_point)]
_close(ba, get('remote_bifurcation_angles', self.ref_nrn))
def test_get_remote_bifurcation_angles(self):
_close(_nrt.remote_bifurcation_angles(self.sec_nrn),
get('remote_bifurcation_angles', self.ref_nrn))
for t in NeuriteType:
_close(_nrt.remote_bifurcation_angles(self.sec_nrn, neurite_type=t),
get('remote_bifurcation_angles', self.ref_nrn, neurite_type=t))
ba = [_bf.remote_bifurcation_angle(b)
for b in i_chain2(self.sec_nrn_trees, iterator_type=Tree.ibifurcation_point)]
_close(ba, get('remote_bifurcation_angles', self.ref_nrn))
def test_get_trunk_section_lengths(self):
_close(_nrn.trunk_section_lengths(self.sec_nrn),
get('trunk_section_lengths', self.ref_nrn))
for t in NeuriteType:
_close(_nrn.trunk_section_lengths(self.sec_nrn, neurite_type=t),
get('trunk_section_lengths', self.ref_nrn, neurite_type=t))
def test_get_trunk_section_lengths(self):
_close(_nrn.trunk_section_lengths(self.sec_nrn), get('trunk_section_lengths', self.ref_nrn))
for t in NeuriteType:
_close(_nrn.trunk_section_lengths(self.sec_nrn, neurite_type=t),
get('trunk_section_lengths', self.ref_nrn, neurite_type=t))
