class TestSectionFunctions(unittest.TestCase):
def setUp(self):
self.morphology = Morphology(morphology_path)
self.section = self.morphology.section(1)
def test_equality(self):
assert (self.section == self.section)
assert (self.section == self.morphology.section(1))
assert (self.section != self.morphology.section(2))
def test_simple_data(self):
assert (self.section.id() == 1)
assert (self.section.type() == brion.neuron.SectionType.axon)
assert (numpy.isclose(self.section.children()[0].distance_to_soma(),
self.section.length()))
def test_samples(self):
distances = self.section.sample_distances_to_soma()
assert (distances.shape == (11, ))
samples = self.section.samples()
assert (samples.shape == (11, 4))
samples = self.section.samples([0, 0.5, 1.0])
assert (samples.shape == (3, 4))
def test_tree(self):
assert (self.section.parent() == None)
children = self.section.children()
assert (len(children) == 2)
for child in children:
assert (child.parent() == self.section)
def test_transform_errors(self):
self.assertRaises(ValueError,
lambda: Morphology(morphology_path, 'foo'))
transform = numpy.array([[2, 2], [2, 2]])
self.assertRaises(ValueError,
lambda: Morphology(morphology_path, transform))
transform = numpy.array([[1, 0, 0, 7], [0, 'a', 0, 8], [0, 0, 1, 9],
[0, 0, 0, 1]])
class TestMorphologyMemoryManagement(unittest.TestCase):
def setUp(self):
self.morphology = Morphology(morphology_path)
def test_soma(self):
soma = self.morphology.soma()
del self.morphology
points = soma.profile_points()
sum = numpy.zeros(4)
for p in points:
sum += p
def test_section(self):
section = self.morphology.section(1)
del self.morphology
samples = section.samples()
sum = numpy.zeros(4)
for s in samples:
sum += s
def setUp(self):
self.morphology = Morphology(morphology_path)
class TestMorphologyFunctions(unittest.TestCase):
def setUp(self):
self.morphology = Morphology(morphology_path)
def test_array_accessors(self):
points = self.morphology.points()
assert (points.shape == (96, 4))
sections = self.morphology.sections()
assert (sections.shape == (13, 2))
section_types = self.morphology.section_types()
assert (section_types.shape == (13, ))
def test_section(self):
Type = brion.neuron.SectionType
neurites = [Type.axon, Type.dendrite, Type.apical_dendrite]
ids = self.morphology.section_ids([Type.soma])
assert (ids == [0])
self.assertRaises(RuntimeError, lambda: self.morphology.section(0))
ids = self.morphology.section_ids(neurites)
assert (len(ids) == 12)
sections = self.morphology.sections([Type.soma])
assert (len(sections) == 0)
sections = self.morphology.sections(neurites)
assert (len(sections) == 12)
for id in ids:
self.morphology.section(int(id))
self.assertRaises(RuntimeError, lambda: self.morphology.section(1234))
def test_soma(self):
soma = self.morphology.soma()
assert (len(soma.profile_points()) == 4)
for p in soma.profile_points():
assert (len(p) == 4)
assert (numpy.isclose(soma.mean_radius(), 0.1))
assert (soma.centroid() == (0, 0, 0))
assert (len(soma.children()) == 4)
def test_uris(self):
uris = self.circuit.morphology_uris([1, 2, 3])
for uri in uris:
Morphology(uri)
def test_bad(self):
self.assertRaises(RuntimeError, lambda: Morphology("mars"))
def test_transform(self):
transform = numpy.array([[1, 0, 0, 7], [0, 1, 0, 8], [0, 0, 1, 9],
[0, 0, 0, 1]])
morphology = Morphology(morphology_path, transform)
assert (numpy.allclose(morphology.transformation(), transform))
def test_simple(self):
morphology = Morphology(morphology_path)
def setUp(self):
self.morphology = Morphology(morphology_path)
self.section = self.morphology.section(1)