def test_segment_meander_angles_single_section():
feat = 'segment_meander_angles'
nrn = nm.load_neuron(StringIO(u"""((CellBody) (0 0 0 0))
((Dendrite)
(0 0 0 2)
(1 0 0 2)
(1 1 0 2)
(2 1 0 2)
(2 2 0 2)))"""),
reader='asc')
nrt = nrn.neurites[0]
pop = core.Population([nrn])
ref = [math.pi / 2, math.pi / 2, math.pi / 2]
nt.eq_(ref, get_feature(feat, nrt).tolist())
nt.eq_(ref, get_feature(feat, nrn).tolist())
nt.eq_(ref, get_feature(feat, pop).tolist())
def test_segment_meander_angles_single_section():
class Mock(object):
pass
feat = 'segment_meander_angles'
sec = core.Section(
np.array([[0, 0, 0], [1, 0, 0], [1, 1, 0], [2, 1, 0], [2, 2, 0]]))
nrt = core.Neurite(sec)
nrn = Mock()
nrn.neurites = [nrt]
nrn.soma = None
pop = core.Population([nrn])
ref = [math.pi / 2, math.pi / 2, math.pi / 2]
nt.eq_(ref, fst_get(feat, nrt).tolist())
nt.eq_(ref, fst_get(feat, nrn).tolist())
nt.eq_(ref, fst_get(feat, pop).tolist())
DATA_PATH = joinp(_path, '../../../test_data')
NRN1 = load_neuron(joinp(DATA_PATH, 'swc/Neuron.swc'))
NEURONS = [
NRN1,
load_neuron(joinp(DATA_PATH, 'swc/Single_basal.swc')),
load_neuron(joinp(DATA_PATH, 'swc/Neuron_small_radius.swc')),
load_neuron(joinp(DATA_PATH, 'swc/Neuron_3_random_walker_branches.swc')),
]
TOT_NEURITES = sum(len(N.neurites) for N in NEURONS)
REVERSED_NEURITES = load_neuron(
joinp(DATA_PATH, 'swc/ordering/reversed_NRN_neurite_order.swc'))
POP = core.Population(NEURONS, name='foo')
def assert_sequence_equal(a, b):
nt.eq_(tuple(a), tuple(b))
def test_iter_neurites_default():
assert_sequence_equal(POP.neurites, [n for n in core.iter_neurites(POP)])
def test_iter_neurites_nrn_order():
assert_sequence_equal(
list(
core.iter_neurites(REVERSED_NEURITES,
neurite_order=NeuriteIter.NRN)),
