def test_timestep_constant(self):
rec = Record(self.soma(0.5))
sim = Simulation(constant_timestep=True, dt=1)
sim.run(100)
r1 = rec.as_numpy('v')
sim = Simulation(constant_timestep=False, dt=1)
sim.run(100)
r2 = rec.as_numpy('v')
sim = Simulation(constant_timestep=False, dt=10)
sim.run(100)
r3 = rec.as_numpy('v')
sim = Simulation(constant_timestep=False, dt=0.0001)
sim.run(100)
r4 = rec.as_numpy('v')
sim.remove_immediate_from_neuron()
rec.remove_immediate_from_neuron()
self.assertEqual(101, r1.size)
self.assertEqual(188, r2.size)
self.assertEqual(180, r3.size)
self.assertEqual(189, r4.size)
def test_add_netcon_and_make_event_separately(self):
g1 = self.cell.filter_synaptic_group(mod_name="Exp2Syn", tag="aa")
nc = g1.add_netcon(source=None)
exp2syn_rec = Record(g1['Exp2Syn'][0], variables='i')
expsyn_rec = Record(g1['ExpSyn'][0], variables='i')
sim = Simulation()
sim.run(1)
nc['Exp2Syn'][0].make_event(10)
nc['ExpSyn'][0].make_event(20)
sim.run(100)
exp2syn_np = exp2syn_rec.as_numpy('i')
stim_time_exp2syn = exp2syn_np.time[(exp2syn_np.records != 0).argmax()]
expsyn_np = expsyn_rec.as_numpy('i')
stim_time_expsyn = expsyn_np.time[(expsyn_np.records != 0).argmax()]
self.assertEqual(12.05, round(stim_time_exp2syn, 4))
self.assertEqual(22.025, round(stim_time_expsyn, 4))
# Remove variables and clear NEURON
nc['Exp2Syn'][0].remove_immediate_from_neuron()
nc['ExpSyn'][0].remove_immediate_from_neuron()
nc = {}
g1.remove_immediate_from_neuron()
exp2syn_rec.remove_immediate_from_neuron()
expsyn_rec.remove_immediate_from_neuron()
sim.remove_immediate_from_neuron()
def test_iclamp_after_sim(self):
"""
IClamp works in a regular way after simulation run. in this case (amplitude 3 pA)
we have spike at the soma.
However IClamp delay is in the absolute time.
"""
# Record
rec = Record(self.soma(0.5))
# Run
sim = Simulation(init_v=-70, warmup=20)
sim.run(1)
# IClamp to soma
iclamp = IClamp(segment=self.soma(0.5))
iclamp.stim(delay=25, dur=3, amp=3)
sim.run(100)
r = rec.as_numpy(variable="v")
sim.remove_immediate_from_neuron()
rec.remove_immediate_from_neuron()
iclamp.remove_immediate_from_neuron()
# Make assertions
self.assertEqual(4051, r.size)
self.assertEqual(34.3815, round(r.records.max(), 4))
self.assertEqual(-75.3247, round(r.records.min(), 4))
self.assertEqual(330, r.records.argmax())
# time in ms of max mV value
self.assertEqual(28, round(r.time[r.records.argmax()], 4))
def test_netstim_after_sim(self):
"""
NetStim created after simulation run has no effect, it won't go on this simulation at all.
However NetStim start is in the absolute time.
"""
# Record
rec = Record(self.soma(0.5))
# Run
sim = Simulation(init_v=-70, warmup=20)
sim.run(1)
# Netstim to synapse
stim = NetStimCell("stim").add_netstim(start=25, number=10, interval=2)
self.cell.add_synapse(source=stim, netcon_weight=0.5, mod_name="ExpSyn", delay=1,
seg=self.apic1(0.5))
sim.run(100)
r = rec.as_numpy(variable="v")
# Make assertions
self.assertEqual(4051, r.size)
self.assertEqual(-67.1917, round(r.records.max(), 4))
self.assertEqual(-70.0, round(r.records.min(), 4))
self.assertEqual(3, r.records.argmax())
# time in ms of max mV value
self.assertEqual(6, r.time[r.records.argmax()])
stim.remove_immediate_from_neuron()
sim.remove_immediate_from_neuron()
rec.remove_immediate_from_neuron()
def test_netcon_event_after_sim(self):
syn = self.cell.add_synapse(source=None, netcon_weight=1.0, mod_name="ExpSyn", delay=1,
seg=self.apic1(0.5))
# Record
rec = Record(self.soma(0.5))
# Run
sim = Simulation(init_v=-70, warmup=20)
sim.run(1)
syn.make_event(50)
sim.run(100)
r = rec.as_numpy(variable="v")
syn.remove_immediate_from_neuron()
sim.remove_immediate_from_neuron()
rec.remove_immediate_from_neuron()
# Make assertions
self.assertEqual(4051, r.size)
self.assertEqual(34.4582, round(r.records.max(), 4))
self.assertEqual(-75.3478, round(r.records.min(), 4))
self.assertEqual(2159, r.records.argmax())
# time in ms of max mV value
self.assertEqual(73.725, round(r.time[r.records.argmax()], 4))
def test_netstim_before_sim(self):
"""
NetStim run in a regular way before Simulation run, in this cale (netcon weight=1.0)
we have spike of the soma.
However NetStim start is in the absolute time.
"""
# Netstim to synapse
stim = NetStimCell("stim").add_netstim(start=25, number=10, interval=2)
self.cell.add_synapse(source=stim, netcon_weight=1.0, mod_name="ExpSyn", delay=1,
seg=self.apic1(0.5))
# Record
rec = Record(self.soma(0.5))
# Run
sim = Simulation(init_v=-70, warmup=20)
sim.run(1)
sim.run(100)
r = rec.as_numpy(variable="v")
stim.remove_immediate_from_neuron()
sim.remove_immediate_from_neuron()
rec.remove_immediate_from_neuron()
# Make assertions
self.assertEqual(4051, r.size)
self.assertEqual(34.5205, round(r.records.max(), 4))
self.assertEqual(-75.3053, round(r.records.min(), 4))
self.assertEqual(319, r.records.argmax())
# time in ms of max mV value
self.assertEqual(27.725, round(r.time[r.records.argmax()], 4))
def test_warmup(self):
rec = Record(self.soma(0.5))
value_error = False
try:
sim = Simulation(warmup=-100)
sim.run(100)
r1 = rec.as_numpy('v')
except ValueError:
value_error = True
self.assertTrue(value_error)
sim = Simulation(warmup=100, dt=1)
sim.run(100)
r2 = rec.as_numpy('v')
sim = Simulation(warmup=100, dt=1, warmup_dt=1)
sim.run(100)
r3 = rec.as_numpy('v')
sim.remove_immediate_from_neuron()
rec.remove_immediate_from_neuron()
self.assertEqual(111, r2.size)
self.assertEqual(201, r3.size)
def setUpClass(cls):
morpho_path = os.path.join(path, "..",
"commons/morphologies/asc/cell2.asc")
# Create cell
cell = Cell(name="cell")
cell.load_morpho(filepath=morpho_path)
cell.insert("pas")
cell.insert("hh")
soma = cell.filter_secs("soma")
dend = cell.filter_secs("apic[10]")
syn = cell.add_synapse(source=None, mod_name="ExpSyn", seg=dend(0.5))
# Prepare EPSP and AP (IClamp) protocols
experiment = Experiment(iti=40)
experiment.add_epsp(num=3,
synapse=syn,
init=20,
interval=20,
weight=0.02)
experiment.add_iclamp(num=3,
segment=soma(0.5),
init=60,
interval=20,
dur=3,
amp=1.6)
experiment.build()
# Prepare plots
rec = Record([soma(0.5), dend(0.5)], variables='v')
# Run
sim = Simulation(init_v=-70,
warmup=20,
with_neuron_gui=False,
constant_timestep=True)
sim.run(runtime=100)
cls.v_soma = rec.as_numpy('v', segment_name=soma(.5).name)
cls.v_apic = rec.as_numpy('v', segment_name=dend(.5).name)
syn.remove_immediate_from_neuron()
soma.remove_immediate_from_neuron()
dend.remove_immediate_from_neuron()
rec.remove_immediate_from_neuron()
experiment.remove_immediate_from_neuron()
cell.remove_immediate_from_neuron()
sim.remove_immediate_from_neuron()
cls.sections_left = len(list(h.allsec()))
def test_init_v(self):
rec = Record(self.soma(0.5))
sim = Simulation(init_v=-100)
sim.run(100)
r1 = rec.as_numpy('v')
sim = Simulation(init_v=100)
sim.run(100)
r2 = rec.as_numpy('v')
sim.remove_immediate_from_neuron()
rec.remove_immediate_from_neuron()
self.assertEqual(-100, r1.records[0])
self.assertEqual(100, r2.records[0])
def test_dt(self):
rec = Record(self.soma(0.5))
sim = Simulation(dt=10)
sim.run(100)
r1 = rec.as_numpy('v')
sim = Simulation(dt=0.01)
sim.run(100)
r2 = rec.as_numpy('v')
sim.remove_immediate_from_neuron()
rec.remove_immediate_from_neuron()
self.assertEqual(11, r1.size)
self.assertEqual(10001, r2.size)
def test_stim_syns(self):
gs = self.cell.filter_synaptic_group()
gs0_exp2syn_rec = Record(gs[0]['Exp2Syn'][0], variables='i')
gs0_expsyn_rec = Record(gs[0]['ExpSyn'][0], variables='i')
gs1_exp2syn_rec = Record(gs[1]['Exp2Syn'][0], variables='i')
gs1_expsyn_rec = Record(gs[1]['ExpSyn'][0], variables='i')
sim = Simulation()
sim.run(1)
gs[0].make_event(10)
gs[1].make_event(20)
sim.run(100)
# Test stim time of synaptic group 1
gs0_exp2syn_np = gs0_exp2syn_rec.as_numpy('i')
stim_time_gs0_exp2syn = gs0_exp2syn_np.time[(gs0_exp2syn_np.records != 0).argmax()]
gs0_expsyn_np = gs0_expsyn_rec.as_numpy('i')
stim_time_gs0_expsyn = gs0_expsyn_np.time[(gs0_expsyn_np.records != 0).argmax()]
self.assertEqual(round(stim_time_gs0_exp2syn, 1), round(stim_time_gs0_expsyn, 1))
# Test stim time of synaptic group 2
gs1_exp2syn_np = gs1_exp2syn_rec.as_numpy('i')
stim_time_gs1_exp2syn = gs1_exp2syn_np.time[(gs1_exp2syn_np.records != 0).argmax()]
gs1_expsyn_np = gs1_expsyn_rec.as_numpy('i')
stim_time_gs1_expsyn = gs1_expsyn_np.time[(gs1_expsyn_np.records != 0).argmax()]
self.assertEqual(round(stim_time_gs1_exp2syn, 1), round(stim_time_gs1_expsyn, 1))
# Test values of mV in soma
self.assertEqual(31.3285, round(gs0_exp2syn_np.records.max(), 4))
self.assertEqual(-61.309, round(gs0_exp2syn_np.records.min(), 4))
# Remove variables and clear NEURON
gs0_exp2syn_rec.remove_immediate_from_neuron()
gs0_expsyn_rec.remove_immediate_from_neuron()
gs1_exp2syn_rec.remove_immediate_from_neuron()
gs1_expsyn_rec.remove_immediate_from_neuron()
gs[0].remove_immediate_from_neuron()
gs[1].remove_immediate_from_neuron()
sim.remove_immediate_from_neuron()