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_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_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 prepare_da_cells(self, reward_cell, punish_cell):
# make records for DA cells
self.reward_cell = reward_cell
self.punish_cell = punish_cell
reward_soma = reward_cell.filter_secs("soma")
punish_soma = punish_cell.filter_secs("soma")
self.recs_rew_gs = []
for s in self.reward_cell.syns:
r = Record(s.point_process, variables="g")
self.recs_rew_gs.append(r)
self.recs_pun_gs = []
for s in self.punish_cell.syns:
r = Record(s.point_process, variables="g")
self.recs_pun_gs.append(r)
self.rec_v_rew = Record(reward_soma(0.5), variables="v")
self.rec_v_pun = Record(punish_soma(0.5), variables="v")
reward_syn = reward_cell.add_synapse(source=None,
mod_name="ExpSyn",
seg=reward_soma(0.5),
netcon_weight=0.01,
e=0,
tau=1)
punish_syn = punish_cell.add_synapse(source=None,
mod_name="ExpSyn",
seg=punish_soma(0.5),
netcon_weight=0.01,
e=0,
tau=1)
return reward_syn, punish_syn
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_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_record_before_sim(self):
"""
Record created before simulation run is full of data
"""
# Record
rec = Record(self.soma(0.5))
# IClamp to soma
iclamp = IClamp(segment=self.soma(0.5))
iclamp.stim(delay=25, dur=3, amp=3)
# Run
sim = Simulation(init_v=-70, warmup=20)
sim.run(1)
print(h.t)
sim.run(100)
r = rec.as_numpy(variable="v")
# 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 prepare_input_cells(self, input_cells):
self.rec_inps = []
for c in input_cells:
rec_gs = []
for s in c.syns:
r = Record(s.point_process, variables="g")
rec_gs.append(r)
rec_v = Record(c.filter_secs("soma")(0.5), variables="v")
self.rec_inps.append((rec_v, rec_gs))
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_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 add_seg(self, seg: Seg, sec_variables='v'):
if not isinstance(seg, Seg):
raise TypeError(
"Param 'seg' must be of type Seg, but provided '%s'" %
seg.__class__)
rec = Record(elements=seg, variables=sec_variables)
self.sec_recs.append(rec)
def record(self, sec_name="soma", loc=0.5, variable='v'):
d = [
cell.filter_secs(sec_name, as_list=True)[0](loc)
for cell in self.cells
]
rec = Record(d, variables=variable)
self.recs[variable] = rec
def run_and_get_rec():
rec = Record(self.soma(0.5))
iclamp = IClamp(segment=self.soma(0.5))
iclamp.stim(delay=25, dur=3, amp=3)
sim = Simulation(init_v=-70, warmup=20)
sim.run(100)
return rec
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 test_record_after_sim(self):
"""
record created after simulation run is empty
"""
# IClamp to soma
iclamp = IClamp(segment=self.soma(0.5))
iclamp.stim(delay=25, dur=3, amp=3)
# Run
sim = Simulation(init_v=-70, warmup=20)
sim.run(1)
print(h.t)
# Record
rec = Record(self.soma(0.5))
sim.run(100)
r = rec.as_numpy(variable="v")
# Make assertion
self.assertEqual(0, r.size)
def add_syn(self,
syn: Synapse,
syn_variables=None,
key_press=None,
plot=True):
if not isinstance(syn, Synapse):
raise TypeError(
"Param 'syn' must be of type Synapse, but provided '%s'" %
syn.__class__)
if plot and syn_variables:
rec = Record(elements=syn, variables=syn_variables)
self.syn_recs.append(rec)
name = key_press
if name is None:
name = str(len(self.syns))
self.syns[name].append(syn)
def get_cell_with_iclamps_as_synapses(warmup, dur, name, input_size, low=0.08, high=0.1):
# Create cell
cell = Cell(name=name)
soma = cell.add_sec("soma", diam=10, l=10, nseg=5)
dend = cell.add_sec("dend", diam=5, l=100, nseg=50)
cell.connect_secs(child=dend, parent=soma)
cell.insert("hh")
# Make synapses
iclamp_syns = []
for i in range(input_size):
iclamp = IClamp(segment=dend(np.random.rand()))
syn = iclamp.stim(delay=warmup, dur=dur, amp=UniformDist(low=low, high=high))
iclamp_syns.append(syn)
# Make recording
rec = Record(elements=soma(0.5), variables='v')
cell.make_spike_detector(seg=soma(0.5))
return cell, iclamp_syns, rec
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)
from neuronpp.utils.record import Record
from neuronpp.utils.simulation import Simulation
path = os.path.dirname(os.path.abspath(__file__))
if __name__ == '__main__':
# Prepare cell
filepath = os.path.join(path, "..",
"commons/mods/sigma3syn")
cell = Cell("cell", compile_paths=filepath)
soma = cell.add_sec("soma", diam=20, l=20, nseg=10)
cell.insert('pas')
cell.insert('hh')
w = 0.003 # LTP
#w = 0.0022 # LTD
syn = cell.add_synapse(source=None, netcon_weight=w, seg=soma(0.5), mod_name="ExcSigma3Exp2Syn")
# prepare plots and spike detector
rec_v = Record(soma(0.5), variables="v")
rec_w = Record(syn, variables="w")
# run
sim = Simulation(init_v=-68, warmup=5)
syn.make_event(5)
sim.run(runtime=50)
# plot
rec_w.plot()
rec_v.plot()
stim = NetStimCell("stim_cell").add_netstim(start=WARMUP + 1,
number=300,
interval=1)
cell.add_random_synapses_with_spine(source=stim,
secs=cell.secs,
mod_name="Syn4P",
netcon_weight=WEIGHT,
delay=1,
head_nseg=10,
neck_nseg=10,
number=10,
**cell.params_4p_syn)
# add mechanisms
cell.make_default_mechanisms()
cell.make_apical_mechanisms(sections='dend head neck')
# make plots
rec_w = Record(cell.filter_point_processes(mod_name="Syn4P",
name="head[0]"),
variables="w")
rec_v = Record(cell.filter_secs(name="head[0]")(1.0), variables="v")
# init and run
sim = Simulation(init_v=-70, warmup=WARMUP)
sim.run(runtime=500)
# plot
rec_w.plot()
rec_v.plot()
ns_cell = NetStimCell("stim_cell")
ns = ns_cell.make_netstim(start=30, number=5, interval=10)
syns = cell.add_synapses_with_spine(source=ns,
secs=cell.filter_secs("apic"),
mod_name="ExpSyn",
netcon_weight=0.01,
delay=1,
number=100)
soma = cell.filter_secs("soma")
# Create IClamp
ic = IClamp(segment=soma(0.5))
ic.stim(delay=100, dur=10, amp=0.1)
# prepare plots and spike detector
rec_v = Record(soma(0.5), variables="v")
cell.make_spike_detector(soma(0.5))
# run
sim = Simulation(init_v=-65,
warmup=20,
init_sleep=2,
with_neuron_gui=True,
shape_plots=[make_shape_plot()])
sim.run(runtime=200, stepsize=1, delay_between_steps=500)
# plot
cell.plot_spikes()
rec_v.plot()
plt.show()
# make VecStim
vs_cell = VecStimCell("vecstim_cell")
stim2 = vs_cell.make_vecstim(np.array([WARMUP+50]))
# make synapses with spines
syns_4p, heads = cell.add_synapses_with_spine(source=None, secs=cell.secs, number=100, netcon_weight=WEIGHT,
mod_name="Syn4PAChDa", delay=1, **cell.params_4p_syn)
for s, h in zip(syns_4p, heads):
syn_ach = cell.add_synapse(source=stim1, mod_name="SynACh", seg=h(1.0), netcon_weight=0.1, delay=1)
syn_da = cell.add_synapse(source=stim2, mod_name="SynDa", seg=h(1.0), netcon_weight=0.1, delay=1)
cell.set_synaptic_pointers(s, syn_ach, syn_da)
# add mechanisms
cell.make_default_mechanisms()
cell.make_apical_mechanisms(sections='head neck')
# make plots
rec_4psyn = Record(cell.filter_point_processes(mod_name="Syn4PAChDa", name="head[0]"), variables="w")
# init and run
sim = Simulation(init_v=-70, warmup=WARMUP)
sim.run(runtime=200)
# Event delivery
syns_4p[0].make_event(10)
sim.run(runtime=200)
# plot
rec_4psyn.plot()
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()
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)
rec.plot()
v_soma = rec.as_numpy('v', segment_name=soma(.5).name)
v_dend = rec.as_numpy('v', segment_name=dend(.5).name)
spine_number=10,
spine_secs_names="apic",
spine_seed=13)
soma = cell.filter_secs("soma")
syns = cell.filter_complex_synapses(tag="combe")
# Prepare STDP protocol
stdp = Experiment()
stdp.make_protocol("3xEPSP[int=10] 3xAP[int=10,dur=3,amp=1.6]",
start=1,
isi=10,
epsp_synapse=syns[0],
i_clamp_section=soma)
# Prepare plots
v_soma_rec = Record([soma(0.5), syns[0].parent], variables='v')
cai_head0_rec = Record(syns[0].parent, variables='cai')
# Run
sim = Simulation(init_v=-70,
warmup=20,
with_neuron_gui=True,
constant_timestep=False)
sim.run(runtime=100, debug=True)
# Plot
cai_head0_rec.plot()
v_soma_rec.plot()
v_soma_rec.to_csv("vrec.csv")
netcon_weight=0.1,
delay=1)
cell.set_synaptic_pointers(s, syn_ach, syn_da)
cell.group_synapses(tag="input_syn", synapses=[s, syn_ach, syn_da])
# add mechanisms
cell.make_default_mechanisms()
cell.make_apical_mechanisms(sections='dend head neck')
soma = cell.filter_secs("soma")
syns = cell.filter_synaptic_group()
syn4p = syns[0]['Syn4PAChDa']
synach = syns[0]['SynACh']
rec_syn = Record(syn4p, variables="w stdp_ach ach_stdp ACh ACh_w")
rec_soma = Record(soma(0.5), variables="v")
sim = Simulation(init_v=-80, warmup=WARMUP, warmup_on_create=True)
event = 0
inter = 5
for i in range(10):
for syn in syns:
syn['Syn4PAChDa'][0].make_event(event)
syn['SynACh'][0].make_event(event)
event += inter
sim.run(runtime=150)
# plot
# 2) Recommended synapse
syn1 = cell.add_synapse(source=stim,
seg=soma(0.5),
netcon_weight=0.01,
mod_name="Syn4P",
delay=1)
# 3) Event synapse
syn2 = cell.add_synapse(source=None,
seg=soma(0.5),
netcon_weight=0.01,
mod_name="Syn4P",
delay=1)
# prepare plots
rec_v = Record(soma(0.5), variables="v")
# run
sim = Simulation(init_v=-55, warmup=20)
# Making external events to the synapse
syn2.make_event(10)
syn2.make_event(20)
syn2.make_event(30)
syn2.make_event(40)
# Example of online update of the graph, however sim.run(runtime=1000) can be call in a single run
for i in range(1000):
sim.run(runtime=1)
rec_v.plot(animate=True)
soma = cell.filter_secs("soma")
# Netstim to synapse
stim = NetStimCell("stim").add_netstim(start=WARMUP,
number=REPS,
interval=interval)
syn = cell.add_synapse(source=stim,
netcon_weight=WEIGHT,
mod_name="Syn4P",
delay=1,
seg=cell.filter_secs('apic[1]')(0.5))
# IClamp to soma
iclamp = IClamp(segment=cell.filter_secs("soma")(0.5))
for i in range(REPS):
start_t = WARMUP + delta_t + i * interval
iclamp.stim(delay=start_t, dur=DUR, amp=AMP)
# Record
rec = Record([s(0.5) for s in cell.filter_secs("apic[1],apic[50]")])
# Run
sim = Simulation(init_v=-70, warmup=WARMUP, dt=DT)
total_time = REPS * interval + COOL_DOWN
sim.run(total_time)
# Plot
rec.plot(position="merge")
plt.show()
