def test_graft():
m = Morphology(os.path.join(_path, 'simple2.swc'))
new_axon = graft.find_axon(m)
neuron = Morphology(os.path.join(_path, 'simple.swc'))
graft.graft_axon(neuron, new_axon)
grafted_axon = graft.find_axon(neuron)
points = np.vstack([section.points for section in grafted_axon.iter()])
assert_array_equal(
points,
np.array([[0., 0., 0.], [1., 2., 0.], [1., 2., 0.], [3., 4.5, 0.],
[1., 2., 0.], [-5., -4., 0.], [-5., -4., 1.]],
dtype=np.float32))
def test_graft():
for rng in [np.random, np.random.default_rng(0)]:
m = Morphology(DATA / 'simple2.swc')
new_axon = graft.find_axon(m)
neuron = Morphology(DATA / 'simple.swc')
graft.graft_axon(neuron, new_axon)
grafted_axon = graft.find_axon(neuron)
points = np.vstack([section.points for section in grafted_axon.iter()])
assert_array_equal(
points,
np.array([[0., 0., 0.], [1., 2., 0.], [1., 2., 0.], [3., 4.5, 0.],
[1., 2., 0.], [-5., -4., 0.], [-5., -4., 1.]],
dtype=np.float32))
def test_self_graft():
'''Grafting a neuron with its own neuron'''
filename = os.path.join(_path, 'neuron.asc')
new_axon = graft.find_axon(ImmutMorphology(filename))
neuron = Morphology(filename)
graft.graft_axon(neuron, new_axon)
expected = Morphology(filename)
ok_(not diff(expected, neuron))
def test_self_graft():
'''Grafting a neuron with its own neuron'''
filename = DATA / 'neuron.asc'
new_axon = graft.find_axon(ImmutMorphology(filename))
neuron = Morphology(filename)
graft.graft_axon(neuron, new_axon)
expected = Morphology(filename)
assert not diff(expected, neuron)
def test_graft_axon_on_synthesized_cell():
np.random.seed(0)
# donor neuron is empty
assert_raises(NoAxonException, graft.graft_axon, SIMPLE, Morphology())
donor_neuron = Morphology(os.path.join(_path, 'simple3.asc'))
synthesized_cell = Morphology(os.path.join(_path, 'synthesized_cell.asc'))
graft.graft_axon(synthesized_cell, donor_neuron)
axon = graft.find_axon(synthesized_cell)
assert_array_almost_equal(
axon.points,
[[5.110419, 5.486378, 4.9647303], [5.110419, 1.486378, 4.9647303]])
def test_graft_axon_on_synthesized_cell():
np.random.seed(0)
# donor neuron is empty
with pytest.raises(NoAxonException):
graft.graft_axon(SIMPLE, Morphology())
donor_neuron = Morphology(DATA / 'simple3.asc')
synthesized_cell = Morphology(DATA / 'synthesized_cell.asc')
graft.graft_axon(synthesized_cell, donor_neuron)
axon = graft.find_axon(synthesized_cell)
assert_array_almost_equal(
axon.points,
[[5.1272364, 5.4825425, 4.9689593], [5.1272364, 1.4825425, 4.9689593]])
def test_find_axon():
axon = find_axon(SIMPLE)
assert_array_equal(axon.points,
[[0, 0, 0], [0, -4, 0]])
with assert_raises(MorphToolException) as obj:
dendrite = SIMPLE.root_sections[0]
find_axon(dendrite)
with assert_raises(MorphToolException) as obj:
find_axon(Morphology(os.path.join(_path, 'no_axon.swc')))
assert_equal(str(obj.exception), 'No axon found!')
with assert_raises(MorphToolException) as obj:
find_axon(Morphology(os.path.join(_path, 'two_axons.asc')))
assert_equal(str(obj.exception), 'Too many axons found!')
def test_find_axon():
axon = graft.find_axon(SIMPLE)
assert_array_equal(axon.points, [[0, 0, 0], [0, -4, 0]])
# section is not an axon
with pytest.raises(MorphToolException):
dendrite = SIMPLE.root_sections[0]
graft.find_axon(dendrite)
# no axon found
with pytest.raises(MorphToolException, match='No axon found!'):
graft.find_axon(Morphology(DATA / 'no_axon.swc'))
# first axon is chosen
axon = graft.find_axon(Morphology(DATA / 'two_axons.asc'))
assert_array_equal(axon.points, [[0, 0, 0], [0, -4, 0]])
def test_find_axon():
axon = graft.find_axon(SIMPLE)
assert_array_equal(axon.points, [[0, 0, 0], [0, -4, 0]])
# section is not an axon
with assert_raises(MorphToolException):
dendrite = SIMPLE.root_sections[0]
graft.find_axon(dendrite)
# no axon found
with assert_raises(MorphToolException) as obj:
graft.find_axon(Morphology(os.path.join(_path, 'no_axon.swc')))
assert_equal(str(obj.exception), 'No axon found!')
# first axon is chosen
axon = graft.find_axon(Morphology(os.path.join(_path, 'two_axons.asc')))
assert_array_equal(axon.points, [[0, 0, 0], [0, -4, 0]])