def test_place_pwlin_id(self):
# Single branch, discontiguous segments.
s0p = A.mpoint(0, 0, 0, 10)
s0d = A.mpoint(1, 0, 0, 10)
s1p = A.mpoint(3, 0, 0, 10)
s1d = A.mpoint(4, 0, 0, 10)
tree = A.segment_tree()
i = tree.append(A.mnpos, s0p, s0d, 1)
tree.append(i, s1p, s1d, 2)
m = A.morphology(tree)
place = A.place_pwlin(m)
L0 = place.at(A.location(0, 0))
L0s = place.all_at(A.location(0, 0))
self.assertEqual(s0p, L0)
self.assertEqual([s0p], L0s)
Lhalf = place.at(A.location(0, 0.5))
Lhalfs = place.all_at(A.location(0, 0.5))
self.assertTrue(s0d == Lhalf or s1p == Lhalf)
self.assertTrue([s0d, s1p] == Lhalfs)
Chalf = [(s.prox, s.dist)
for s in place.segments([A.cable(0, 0., 0.5)])]
self.assertEqual([(s0p, s0d)], Chalf)
Chalf_all = [(s.prox, s.dist)
for s in place.all_segments([A.cable(0, 0., 0.5)])]
self.assertEqual([(s0p, s0d), (s1p, s1p)], Chalf_all)
def test_probe_meta(self):
sim = self.init_sim(cc2_recipe())
self.assertEqual([A.location(1, 1)], sim.probe_metadata((0, 0)))
self.assertEqual([A.location(2, 1)], sim.probe_metadata((0, 1)))
self.assertEqual([A.location(1, 1), A.location(2, 1)],
sorted(sim.probe_metadata((0, 2)),
key=lambda x: (x.branch, x.pos)))
# Default CV policy is one per branch, which also gives a tivial CV over the branch point.
# Expect metadata cables to be one for each full branch, plus three length-zero cables corresponding to the branch point.
self.assertEqual([
A.cable(0, 0, 1),
A.cable(0, 1, 1),
A.cable(1, 0, 0),
A.cable(1, 0, 1),
A.cable(2, 0, 0),
A.cable(2, 0, 1)
],
sorted(sim.probe_metadata((1, 0))[0],
key=lambda x: (x.branch, x.prox, x.dist)))
# Four expsyn synapses; the two on branch zero should be coalesced, giving a multiplicity of 2.
# Expect entries to be in target index order.
m11 = sim.probe_metadata((1, 1))[0]
self.assertEqual(4, len(m11))
self.assertEqual([0, 1, 2, 3], [x.target for x in m11])
self.assertEqual([2, 2, 1, 1], [x.multiplicity for x in m11])
self.assertEqual([
A.location(0, 0.3),
A.location(0, 0.6),
A.location(1, 0.3),
A.location(2, 0.3)
], [x.location for x in m11])
def test_place_pwlin_isometry(self):
# Single branch, discontiguous segments.
s0p = A.mpoint(0, 0, 0, 10)
s0d = A.mpoint(1, 0, 0, 10)
s1p = A.mpoint(3, 0, 0, 10)
s1d = A.mpoint(4, 0, 0, 10)
tree = A.segment_tree()
i = tree.append(A.mnpos, s0p, s0d, 1)
tree.append(i, s1p, s1d, 2)
m = A.morphology(tree)
iso = A.isometry.translate(2, 3, 4)
place = A.place_pwlin(m, iso)
x0p = iso(s0p)
x0d = iso(s0d)
x1p = iso(s1p)
x1d = iso(s1d)
L0 = place.at(A.location(0, 0))
L0s = place.all_at(A.location(0, 0))
self.assertEqual(x0p, L0)
self.assertEqual([x0p], L0s)
Lhalf = place.at(A.location(0, 0.5))
Lhalfs = place.all_at(A.location(0, 0.5))
self.assertTrue(x0d == Lhalf or x1p == Lhalf)
self.assertTrue([x0d, x1p] == Lhalfs)
Chalf = [(s.prox, s.dist)
for s in place.segments([A.cable(0, 0., 0.5)])]
self.assertEqual([(x0p, x0d)], Chalf)
Chalf_all = [(s.prox, s.dist)
for s in place.all_segments([A.cable(0, 0., 0.5)])]
self.assertEqual([(x0p, x0d), (x1p, x1p)], Chalf_all)
def test_probe_scalar_recorders(self):
sim = self.init_sim(cc2_recipe())
ts = [0, 0.1, 0.3, 0.7]
h = sim.sample((0, 0), A.explicit_schedule(ts))
dt = 0.01
sim.run(10., dt)
s, meta = sim.samples(h)[0]
self.assertEqual(A.location(1, 1), meta)
for i, t in enumerate(s[:, 0]):
self.assertLess(abs(t - ts[i]), dt)
sim.remove_sampler(h)
sim.reset()
h = sim.sample(A.cell_member(0, 0), A.explicit_schedule(ts),
A.sampling_policy.exact)
sim.run(10., dt)
s, meta = sim.samples(h)[0]
for i, t in enumerate(s[:, 0]):
self.assertEqual(t, ts[i])
def get_probe(self, id):
loc = arbor.location(0, 0) # at the soma
return arbor.cable_probe('voltage', id, loc)
def get_probes(self, gid):
loc = arbor.location(0, 0) # at the soma
return [arbor.cable_probe('voltage', loc)]
def test_probe_addr_metadata(self):
recipe = cc_recipe()
context = A.context()
dd = A.partition_load_balance(recipe, context)
sim = A.simulation(recipe, dd, context)
all_cv_cables = [A.cable(0, 0, 1)]
m = sim.probe_metadata((0, 0))
self.assertEqual(1, len(m))
self.assertEqual(A.location(0, 0.0), m[0])
m = sim.probe_metadata((0, 1))
self.assertEqual(1, len(m))
self.assertEqual(all_cv_cables, m[0])
m = sim.probe_metadata((0, 2))
self.assertEqual(1, len(m))
self.assertEqual(A.location(0, 0.02), m[0])
m = sim.probe_metadata((0, 3))
self.assertEqual(1, len(m))
self.assertEqual(A.location(0, 0.03), m[0])
m = sim.probe_metadata((0, 4))
self.assertEqual(1, len(m))
self.assertEqual(all_cv_cables, m[0])
m = sim.probe_metadata((0, 5))
self.assertEqual(1, len(m))
self.assertEqual(all_cv_cables, m[0])
m = sim.probe_metadata((0, 6))
self.assertEqual(1, len(m))
self.assertEqual(A.location(0, 0.06), m[0])
m = sim.probe_metadata((0, 7))
self.assertEqual(1, len(m))
self.assertEqual(all_cv_cables, m[0])
m = sim.probe_metadata((0, 8))
self.assertEqual(1, len(m))
self.assertEqual(A.location(0, 0.08), m[0].location)
self.assertEqual(1, m[0].multiplicity)
self.assertEqual(0, m[0].target)
m = sim.probe_metadata((0, 9))
self.assertEqual(1, len(m))
self.assertEqual(1, len(m[0]))
self.assertEqual(A.location(0, 0.09), m[0][0].location)
self.assertEqual(1, m[0][0].multiplicity)
self.assertEqual(1, m[0][0].target)
m = sim.probe_metadata((0, 10))
self.assertEqual(1, len(m))
self.assertEqual(A.location(0, 0.10), m[0])
m = sim.probe_metadata((0, 11))
self.assertEqual(1, len(m))
self.assertEqual(all_cv_cables, m[0])
m = sim.probe_metadata((0, 12))
self.assertEqual(1, len(m))
self.assertEqual(A.location(0, 0.12), m[0])
m = sim.probe_metadata((0, 13))
self.assertEqual(1, len(m))
self.assertEqual(all_cv_cables, m[0])
m = sim.probe_metadata((0, 14))
self.assertEqual(1, len(m))
self.assertEqual(A.location(0, 0.14), m[0])
m = sim.probe_metadata((0, 15))
self.assertEqual(1, len(m))
self.assertEqual(all_cv_cables, m[0])
m = sim.probe_metadata((0, 16))
self.assertEqual(1, len(m))
self.assertEqual(all_cv_cables, m[0])
]
# Read the SWC filename from input
# Example from docs: single_cell_detailed.swc
if len(sys.argv) < 2:
print("No SWC file passed to the program")
sys.exit(0)
filename = sys.argv[1]
# define morphology (needed for ``arbor.place_pwlin`` and ``arbor.cable_cell`` below)
morphology = arbor.load_swc_arbor(filename)
# define a location on morphology for current clamp
clamp_location = arbor.location(4, 1 / 6)
def make_cable_cell(morphology, clamp_location):
# number of CVs per branch
cvs_per_branch = 3
# Label dictionary
defs = {}
labels = arbor.label_dict(defs)
# decor
decor = arbor.decor()
# set initial voltage, temperature, axial resistivity, membrane capacitance
decor.set_property(
