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 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 _prepare_iclamp_protocol(self, iclamp: IClampProtocol, global_time):
iclamp_obj = IClamp(iclamp.seg)
current_time = global_time + iclamp.init
for _ in range(iclamp.num):
iclamp_obj.stim(delay=current_time, dur=iclamp.dur, amp=iclamp.amp)
current_time += iclamp.int
current_time = global_time
current_time += iclamp.init
self.iclamp.append(iclamp_obj)
return current_time
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_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 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))
cell.insert("hh")
# Create stim and synapses
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
def make_protocol(self,
protocol: str,
start,
isi=1,
iti=1,
epsp_synapse: [Synapse, ComplexSynapse] = None,
i_clamp_section: Sec = None,
train_number=1,
copy_netconn_params=True):
"""
Create an experimental protocol of EPSPs and APs.
Each element of the experiment (EPSP or AP) is separated by isi (in ms).
:param protocol:
string eg. 3xEPSP[int=10,w=2.5,thr=5,del=2] 3xAP[int=10,dur=3,amp=1.6]
Params ofr EPSP and AP:
int - interval between in ms
Params for EPSP only:
w - weight for netconn (default is 1.0) -> used only when copy_netconn_params=False
del - delay for netconn (default is 1.0) -> used only when copy_netconn_params=False
thr - threshold for netconn (default is 10) -> used only when copy_netconn_params=False
Params for AP only:
dur - duration of AP in ms
amp - amplitude in nA
:param epsp_synapse:
synapse to stimulate. Default is None if you don't want to stimulate synapse
:param i_clamp_section:
section to input IClamp. Default is None if you don't want to stimulate any section by electrode (eg. making AP)
It is assumed that IClamp stimulate i_clamp_section(0.5) segment.
:param start:
start time of the first stimuli in ms, it is absolute time, so bear in mind warmup time.
:param isi:
Inter Stimulus Interval, eg. 3xEPSP,2xAP -isi- 3xEPSP,2xAP
:param iti:
Inter Train Interval eg. 3xEPSP,2xAP -isi- 3xEPSP,2xAP -iti- 3xEPSP,2xAP-isi-3xEPSP,2xAP
:param train_number:
number of trains. Default is 1
:param copy_netconn_params:
If copy_netconn_params=True it will copy NetConn params from the last NetConn added to the synapse.
:return:
tuple(NetStim, IClamp).
If epsp_synapse is None NetStim will be None
If i_clamp_section is None IClamp will be None
"""
#if start < h.t:
# raise ValueError("Experimental protocol 'start' param must > h.t (time of the simulation), but your "
# "start=%s and h.t=%s. Bear in mind that 'start' param is the absolute time" % (start, h.t))
protocol = protocol.lower()
protocols = protocol.split(" ")
netstim = None
if epsp_synapse:
netstim = NetStimCell(name="stim")
self.netstims.append(netstim)
iclamp = None
if i_clamp_section:
iclamp = IClamp(i_clamp_section(0.5))
self.iclamps.append(iclamp)
event_time = start
for train_no in range(train_number):
for p in protocols:
event_time = self._prepare_protocol(p, netstim, iclamp,
event_time, epsp_synapse,
copy_netconn_params)
event_time += isi
event_time += iti
return netstim, iclamp
cell.make_default_mechanisms()
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()