def test_spoofing(self):
"""
Assert that fake detailed connections can be made
"""
config = JSONConfig(file=_config)
scaffold = Scaffold(config)
scaffold.compile_network()
original_connections = len(
scaffold.cell_connections_by_tag["connection"])
sd = SpoofDetails()
sd.presynaptic = "from_cell"
sd.postsynaptic = "to_cell"
sd.scaffold = scaffold
# Raise error because here's no morphologies registered for the cell types.
with self.assertRaises(
MorphologyDataError,
msg="Missing morphologies during spoofing not caught."):
sd.after_connectivity()
# Add some morphologies
setattr(
config.cell_types["from_cell"].morphology,
"detailed_morphologies",
{"names": ["GranuleCell"]},
)
setattr(
config.cell_types["to_cell"].morphology,
"detailed_morphologies",
{"names": ["GranuleCell"]},
)
# Run the spoofing again
sd.after_connectivity()
cs = scaffold.get_connectivity_set("connection")
scaffold.compile_output()
# Use the intersection property. It throws an error should the detailed
# information be missing
try:
i = cs.intersections
for inter in i:
fl = inter.from_compartment.labels
tl = inter.to_compartment.labels
self.assertIn("axon", fl,
"From compartment type is not an axon")
self.assertIn("dendrites", tl,
"From compartment type is not a dendrite")
self.assertNotEqual(len(i), 0, "Empty intersection data")
self.assertEqual(len(i), original_connections,
"Different amount of spoofed connections")
except MissingMorphologyError:
self.fail("Could not find the intersection data on spoofed set")
# Set both types to relays and try spoofing again
config.cell_types["from_cell"].relay = True
config.cell_types["to_cell"].relay = True
with self.assertRaises(MorphologyError,
msg="Did not catch double relay spoofing!"):
sd.after_connectivity()
class TestFiberIntersection(unittest.TestCase):
@classmethod
def setUpClass(self):
super(TestFiberIntersection, self).setUpClass()
# Make sure the MR exists
test_setup.prep_morphologies()
# The scaffold has only the Granular layer (100x100x150) with 20 GrCs
# and 1 GoC placed, as specified in the config file
self.config = JSONConfig(file=fiber_transform_config)
# Defining quivers field to include also voxels outside the scaffold
# volume
self.quivers_field = np.zeros(
shape=(3, 80, 80, 80)) # Each voxel in the volume has vol_res=25um
# Fake quiver, oriented as original fibers
basic_quiver = np.array([0, 1.0, 0.0])
self.quivers_field[0, :] = basic_quiver[0]
self.quivers_field[1, :] = basic_quiver[1]
self.quivers_field[2, :] = basic_quiver[2]
self.config.connection_types[
"parallel_fiber_to_golgi_bended"].transformation.quivers = self.quivers_field
self.config.connection_types[
"parallel_fiber_to_golgi_bended"].transformation.vol_start = [
-500.0, -500.0, -500.0
]
self.scaffold = Scaffold(self.config)
self.scaffold.morphology_repository = MorphologyRepository(morpho_file)
self.scaffold.compile_network()
def test_fiber_connections(self):
pre_type = "granule_cell"
pre_neu = self.scaffold.get_placement_set(pre_type)
conn_type = "parallel_fiber_to_golgi"
cs = self.scaffold.get_connectivity_set(conn_type)
num_conn = len(cs.connections)
# Check that no more connections are formed than the number of
# presynaptic neurons - how could happen otherwise?
self.assertTrue(num_conn <= len(pre_neu.identifiers))
# Check that increasing resolution in FiberIntersection does not change
# connection number if there are no transformations (and thus the fibers
# are parallel to main axes)
conn_type_HR = "parallel_fiber_to_golgi_HR"
cs_HR = self.scaffold.get_connectivity_set(conn_type_HR)
self.assertEqual(num_conn, len(cs_HR.connections))
# Check that half (+- 5) connections are obtained with half the affinity
conn_type_affinity = "parallel_fiber_to_golgi_affinity"
cs_affinity = self.scaffold.get_connectivity_set(conn_type_affinity)
self.assertAlmostEqual(num_conn / 2,
len(cs_affinity.connections),
delta=5)
# Check that same number of connections are obtained when a fake quiver
# transformation is applied
conn_type_transform = "parallel_fiber_to_golgi_bended"
cs_fake_transform = self.scaffold.get_connectivity_set(
conn_type_transform)
self.assertEqual(len(cs_fake_transform.connections), num_conn)
# Check that less connections are obtained when the PC surface is
# oriented according to orientation vector of 45° rotation in yz plane,
# for how the Golgi cell is placed and the parallel fibers are rotated
basic_quiver = np.array([0, 0.7, 0.7])
self.quivers_field[0, :] = basic_quiver[0]
self.quivers_field[1, :] = basic_quiver[1]
self.quivers_field[2, :] = basic_quiver[2]
self.config.connection_types[
"parallel_fiber_to_golgi_bended"].transformation.quivers = self.quivers_field
self.scaffold = Scaffold(self.config)
self.scaffold.compile_network()
cs_transform = self.scaffold.get_connectivity_set(conn_type_transform)
self.assertTrue(len(cs_transform.connections) <= num_conn)