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 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(
Vm=-65, # Initial membrane voltage (mV)
tempK=300, # Temperature (Kelvin)
rL=10000, # Axial resistivity (Ω cm)
cm=0.01, # Membrane capacitance (F/m**2)
)
# set passive mechanism all over
# passive mech w. leak reversal potential (mV)
pas = arbor.mechanism('pas/e=-65')
pas.set('g', 0.0001) # leak conductivity (S/cm2)
decor.paint('(all)', arbor.density(pas))
# set number of CVs per branch
policy = arbor.cv_policy_fixed_per_branch(cvs_per_branch)
decor.discretization(policy)
# place sinusoid input current
iclamp = arbor.iclamp(
5, # stimulation onset (ms)
1E8, # stimulation duration (ms)
-0.001, # stimulation amplitude (nA)
frequency=0.1, # stimulation frequency (kHz)
phase=0) # stimulation phase)
decor.place(str(clamp_location), iclamp, '"iclamp"')
# create ``arbor.place_pwlin`` object
p = arbor.place_pwlin(morphology)
# create cell and set properties
cell = arbor.cable_cell(morphology, labels, decor)
return p, cell
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)
V_m_samples = V_m_samples[:, np.r_[True, inds]]
V_m_meta = np.array(V_m_meta)[inds].tolist()
# note: the cables comprising the metadata for each probe
# should be the same, as well as the reported sample times.
assert V_m_meta == I_m_meta
assert (V_m_samples[:, 0] == I_m_samples[:, 0]).all()
# prep recorded data for plotting
time = V_m_samples[:, 0]
V_m = V_m_samples[:, 1:].T
I_m = I_m_samples[:, 1:].T
I_c = I_c_samples[:, 1:].T
# gather geometry of CVs and assign segments to each CV
p = arbor.place_pwlin(morphology)
x, y, z, d = [np.array([], dtype=float).reshape((0, 2))] * 4
CV_ind = np.array([], dtype=int) # tracks which CV owns segment
for i, m in enumerate(I_m_meta):
segs = p.segments([m])
for j, seg in enumerate(segs):
x = np.row_stack([x, [seg.prox.x, seg.dist.x]])
y = np.row_stack([y, [seg.prox.y, seg.dist.y]])
z = np.row_stack([z, [seg.prox.z, seg.dist.z]])
d = np.row_stack([d, [seg.prox.radius * 2, seg.dist.radius * 2]])
CV_ind = np.r_[CV_ind, i]
###############################################################################
# compute extracellular potential using segment information
###############################################################################
cell_geometry = lfpykit.CellGeometry(x=x, y=y, z=z, d=d)