def test_neuron():
soma = neuron.make_soma(SOMA_A_PTS)
nrn = neuron.Neuron(soma, ['foo', 'bar'])
nt.assert_equal(nrn.soma.center, (11, 22, 33))
nt.assert_equal(nrn.neurites, ['foo', 'bar'])
nt.assert_equal(nrn.name, 'Neuron')
nrn = neuron.Neuron(soma, ['foo', 'bar'], 'test')
nt.assert_equal(nrn.name, 'test')
def test_bounding_box():
soma = neuron.make_soma([[0, 0, 0, 1, 1, 1, -1]])
nrn = neuron.Neuron(soma, [TREE])
ref1 = ((-1, -1, -1), (4.0, 6.0, 3.0))
for a, b in izip(nrn.bounding_box(), ref1):
nt.assert_true(np.allclose(a, b))
soma = neuron.make_soma(SOMA_A_PTS)
nrn = neuron.Neuron(soma, [TREE])
ref2 = ((-33, -22, -11), (55, 66, 77))
for a, b in izip(nrn.bounding_box(), ref2):
nt.assert_true(np.allclose(a, b))
def test_i_neurites_filter():
soma = neuron.make_soma(SOMA_A_PTS)
nrn = neuron.Neuron(soma, ['foo', 'bar', 'baz'])
ref = 'barbaz'
for i, j in izip(ref,
nrn.i_neurites(iter,
tree_filter=lambda s: s.startswith('b'))):
nt.assert_equal(i, j)
def test_i_neurites_chains():
soma = neuron.make_soma(SOMA_A_PTS)
nrn = neuron.Neuron(soma, ['foo', 'bar', 'baz'])
s = 'foobarbaz'
for i, j in izip(s, nrn.i_neurites(iter)):
nt.assert_equal(i, j)
rd = load_data(filename)
init_seg_ids = get_initial_segment_ids(rd)
trees = [make_tree(rd, sg) for sg in init_seg_ids]
soma = neuron.make_soma([rd.get_row(si) for si in get_soma_ids(rd)])
for tr in trees:
for p in point_iter(tree.ipreorder(tr)):
print p
print 'Initial segment IDs:', init_seg_ids
nrn = neuron.Neuron(soma, trees)
print 'Neuron soma raw data', [r for r in nrn.soma.iter()]
print 'Neuron soma points', [as_point(p) for p in nrn.soma.iter()]
print 'Neuron tree init points, types'
for tt in nrn.neurites:
print tt.value[COLS.ID], tt.value[COLS.TYPE]
print 'Making neuron 2'
nrn2 = make_neuron(rd)
print 'Neuron 2 soma points', [r for r in nrn2.soma.iter()]
print 'Neuron 2 soma points', [as_point(p) for p in nrn2.soma.iter()]
print 'Neuron 2 tree init points, types'
for tt in nrn2.neurites:
print tt.value[COLS.ID], tt.value[COLS.TYPE]