def test_children_of(self):
morphology = test_morphology_small()
node = test_node(id=1,
type=SOMA,
x=800,
y=610,
z=30,
radius=35,
parent_node_id=-1)
children = morphology.children_of(node)
expected_children = [
test_node(id=2,
type=BASAL_DENDRITE,
x=400,
y=600,
z=10,
radius=3,
parent_node_id=1),
test_node(id=4,
type=APICAL_DENDRITE,
x=600,
y=300,
z=20,
radius=3,
parent_node_id=1),
test_node(id=6,
type=AXON,
x=900,
y=600,
z=30,
radius=3,
parent_node_id=1)
]
self.assertEqual(children, expected_children)
def test_get_leaf_nodes(self):
morphology = test_morphology_small()
leaf_nodes = morphology.get_leaf_nodes()
expected_leaf_node_ids = set([3, 5, 7])
self.assertEqual(set([leaf_node['id'] for leaf_node in leaf_nodes]),
expected_leaf_node_ids)
def test_get_root(self):
morphology = test_morphology_small()
expected_root = test_node(id=1,
type=SOMA,
x=800,
y=610,
z=30,
radius=35,
parent_node_id=-1)
self.assertEqual(expected_root, morphology.get_root())
def test_node_by_id(self):
morphology = test_morphology_small()
expected_node = test_node(id=4,
type=APICAL_DENDRITE,
x=600,
y=300,
z=20,
radius=3,
parent_node_id=1)
node_by_id = morphology.node_by_id(4)
self.assertEqual(expected_node, node_by_id)
def test_get_compartment_for_node_with_type(self):
morphology = test_morphology_small()
node_types = [AXON]
node = test_node(id=2,
type=BASAL_DENDRITE,
x=400,
y=600,
z=10,
radius=3,
parent_node_id=1)
compartment = morphology.get_compartment_for_node(node, node_types)
expected_compartment = None
self.assertEqual(expected_compartment, compartment)
def test_get_non_soma_nodes(self):
morphology = test_morphology_small()
expected_nodes = [
test_node(id=2,
type=BASAL_DENDRITE,
x=400,
y=600,
z=10,
radius=3,
parent_node_id=1),
test_node(id=3,
type=BASAL_DENDRITE,
x=400,
y=600,
z=10,
radius=3,
parent_node_id=2),
test_node(id=4,
type=APICAL_DENDRITE,
x=600,
y=300,
z=20,
radius=3,
parent_node_id=1),
test_node(id=5,
type=APICAL_DENDRITE,
x=600,
y=300,
z=20,
radius=3,
parent_node_id=4),
test_node(id=6,
type=AXON,
x=900,
y=600,
z=30,
radius=3,
parent_node_id=1),
test_node(id=7,
type=AXON,
x=900,
y=600,
z=30,
radius=3,
parent_node_id=6)
]
nodes = morphology.get_non_soma_nodes()
self.assertEqual(expected_nodes, nodes)
def test_get_compartment_volume(self):
morphology = test_morphology_small() # not actually using nodes
compartment = [{
"x": 0,
"y": 0,
"z": 0,
"radius": 10
}, {
"x": 0,
"y": 0,
"z": 5,
"radius": 5
}]
self.assertAlmostEqual(morphology.get_compartment_volume(compartment),
916.297857,
places=6)
def test_get_compartment_surface_area(self):
morphology = test_morphology_small() # not actually using nodes
compartment = [{
"x": 0,
"y": 0,
"z": 0,
"radius": 10
}, {
"x": 0,
"y": 0,
"z": 5,
"radius": 5
}]
self.assertAlmostEqual(
morphology.get_compartment_surface_area(compartment),
333.21622,
places=6)
def test_parent_of(self):
morphology = test_morphology_small()
node = test_node(id=2,
type=BASAL_DENDRITE,
x=400,
y=600,
z=10,
radius=3,
parent_node_id=1)
expected_parent = test_node(id=1,
type=SOMA,
x=800,
y=610,
z=30,
radius=35,
parent_node_id=-1)
parent = morphology.parent_of(node)
self.assertEqual(expected_parent, parent)
def test_get_children_of_node_by_type(self):
morphology = test_morphology_small()
node = test_node(id=1,
type=SOMA,
x=800,
y=610,
z=30,
radius=35,
parent_node_id=-1)
expected_children_by_type = {
BASAL_DENDRITE: [
test_node(id=2,
type=BASAL_DENDRITE,
x=400,
y=600,
z=10,
radius=3,
parent_node_id=1)
],
APICAL_DENDRITE: [
test_node(id=4,
type=APICAL_DENDRITE,
x=600,
y=300,
z=20,
radius=3,
parent_node_id=1)
],
AXON: [
test_node(id=6,
type=AXON,
x=900,
y=600,
z=30,
radius=3,
parent_node_id=1)
]
}
for node_type in [BASAL_DENDRITE, APICAL_DENDRITE, AXON]:
child = morphology.get_children_of_node_by_types(node, [node_type])
self.assertEqual(expected_children_by_type[node_type], child)
def test_get_compartment_for_node_with_no_type(self):
morphology = test_morphology_small()
node = test_node(id=2,
type=BASAL_DENDRITE,
x=400,
y=600,
z=10,
radius=3,
parent_node_id=1)
compartment = morphology.get_compartment_for_node(node)
expected_compartment = [
test_node(id=1,
type=SOMA,
x=800,
y=610,
z=30,
radius=35,
parent_node_id=-1), node
]
self.assertEqual(expected_compartment, compartment)
def test_get_compartment_midpoint(self):
morphology = test_morphology_small()
compartment = [
test_node(id=1,
type=SOMA,
x=800,
y=610,
z=30,
radius=35,
parent_node_id=-1),
test_node(id=2,
type=BASAL_DENDRITE,
x=400,
y=600,
z=10,
radius=3,
parent_node_id=1)
]
midpoint = morphology.get_compartment_midpoint(compartment)
expected_midpoint = [600.0, 605.0, 20.0]
self.assertEqual(expected_midpoint, midpoint)
def test_get_compartment_length(self):
morphology = test_morphology_small()
compartment = [
test_node(id=1,
type=SOMA,
x=800,
y=610,
z=30,
radius=35,
parent_node_id=-1),
test_node(id=2,
type=BASAL_DENDRITE,
x=400,
y=600,
z=10,
radius=3,
parent_node_id=1)
]
expected_legnth = 400.6245124802026
length = morphology.get_compartment_length(compartment)
self.assertEqual(expected_legnth, length)
def test_get_compartment_list(self):
morphology = test_morphology_small()
compartments = morphology.compartments
expected_compartments = [[
test_node(id=1,
type=SOMA,
x=800,
y=610,
z=30,
radius=35,
parent_node_id=-1),
test_node(id=2,
type=BASAL_DENDRITE,
x=400,
y=600,
z=10,
radius=3,
parent_node_id=1)
],
[
test_node(id=2,
type=BASAL_DENDRITE,
x=400,
y=600,
z=10,
radius=3,
parent_node_id=1),
test_node(id=3,
type=BASAL_DENDRITE,
x=400,
y=600,
z=10,
radius=3,
parent_node_id=2)
],
[
test_node(id=1,
type=SOMA,
x=800,
y=610,
z=30,
radius=35,
parent_node_id=-1),
test_node(id=4,
type=APICAL_DENDRITE,
x=600,
y=300,
z=20,
radius=3,
parent_node_id=1)
],
[
test_node(id=4,
type=APICAL_DENDRITE,
x=600,
y=300,
z=20,
radius=3,
parent_node_id=1),
test_node(id=5,
type=APICAL_DENDRITE,
x=600,
y=300,
z=20,
radius=3,
parent_node_id=4)
],
[
test_node(id=1,
type=SOMA,
x=800,
y=610,
z=30,
radius=35,
parent_node_id=-1),
test_node(id=6,
type=AXON,
x=900,
y=600,
z=30,
radius=3,
parent_node_id=1)
],
[
test_node(id=6,
type=AXON,
x=900,
y=600,
z=30,
radius=3,
parent_node_id=1),
test_node(id=7,
type=AXON,
x=900,
y=600,
z=30,
radius=3,
parent_node_id=6)
]]
self.assertEqual(expected_compartments, compartments)
def test_len(self):
morphology = test_morphology_small()
expected_length = 7
self.assertEqual(expected_length, len(morphology))
def test_get_root_id(self):
morphology = test_morphology_small()
expected_root_id = 1
root_id = morphology.get_root_id()
self.assertEqual(expected_root_id, root_id)
