def simulate(pool, tstop=1000, vinit=-55):
''' simulation control
Parameters
----------
cell: NEURON cell
cell for simulation
tstop: int (ms)
simulation time
vinit: int (mV)
initialized voltage
'''
h.finitialize(vinit)
for i in pool:
cell = pc.gid2cell(i)
balance(cell)
if h.cvode.active():
h.cvode.active()
else:
h.fcurrent()
h.frecord_init()
h.tstop = tstop
h.v_init = vinit
pc.set_maxstep(0.5)
h.stdinit()
pc.psolve(tstop)
def simulate(pool, tstop=50000, vinit=-55):
''' simulation control
Parameters
----------
cell: NEURON cell
cell for simulation
tstop: int (ms)
simulation time
vinit: int (mV)
initialized voltage
'''
h.finitialize(vinit)
for i in pool:
cell = pc.gid2cell(i)
balance(cell)
if h.cvode.active():
h.cvode.active()
else:
h.fcurrent()
h.frecord_init()
h.tstop = tstop
h.v_init = vinit
pc.set_maxstep(0.5)
h.stdinit()
pc.psolve(tstop)
def FiringOnset(leftI, rightI, precision, apc, stim, T, fr_set):
import neuron
from neuron import h
from I_proc import stimulate
while ((rightI - leftI) > precision * max([abs(rightI), abs(leftI)])):
print("leftI is %f, rightI is %f" % (leftI, rightI))
print("rightI-leftI: %f , precision: %f \n" %
((rightI - leftI), precision))
h.finitialize()
h.fcurrent()
h.frecord_init()
apc.n = 0
mean = (leftI + rightI) / 2
print('mean is %f' % (mean))
h.stim = stimulate([0, stim, mean])
h.tstop = T
h.run()
fr = apc.n / float(T / 1000)
print('fr is %f' % (fr))
if (fr <= fr_set):
leftI = mean # If the firing rate is too small, we will replace lowerbound with middle point
else:
rightI = mean # If the firing rate is too large, we will replace upperbound with middle point
if fr_set > 0:
return rightI
else:
return leftI
def go():
h.dt = 0.1
h.celsius = celsius
h.finitialize(v_init)
#neuron.init()
# params: RERE, RETCa, ***RETCb, TCRE, PYPY, PYIN, INPYa, ***INPYb, PYRE, PYTC, TCPY, TCIN
assign_synapses(RERE * 0.2, RETCa * 0.02, RETCb * 0.04, TCRE * 0.2,
PYPY * 0.6, PYIN * 0.2, INPYa * gabaapercent * 0.15,
INPYb * gababpercent * 0.03, PYRE * 1.2, PYTC * 0.01,
TCPY * 1.2, TCIN * 0.4)
#assign_synapses(gRERE_GABAA, gRETC_GABAA, gRETC_GABAB, gTCRE_AMPA, gPYPY_AMPA, gPYIN_AMPA, gINPY_GABAA, gINPY_GABAB, gPYRE_AMPA, gPYTC_AMPA, gTCPY_AMPA, gTCIN_AMPA)
h.fcurrent()
h.cvode.re_init()
h.frecord_init()
printPYinfo(0)
printINinfo(0)
printTCinfo(0)
printREinfo(0)
printWeight(0)
field.append(0)
while h.t < tstop:
h.fadvance()
field.append(xfield(230, fielddist, watchneuron))
def DetermineStdI(leftStd, rightStd, precision_std, apc, mean, stim, tau, dt,
T, fr_set, seednumber):
import neuron
from neuron import h
from I_proc import stimulate
while ((rightStd - leftStd) >
precision_std * max([abs(rightStd), abs(leftStd)])):
if leftStd == 0 and rightStd < 1e-7:
break
return rightStd
print("leftStd is %f, rightStd is %f" % (leftStd, rightStd))
print("rightStd-leftStd: %f , precision_std: %f \n" %
((rightStd - leftStd), precision_std))
h.finitialize()
h.fcurrent()
h.frecord_init()
apc.n = 0
std = (leftStd + rightStd) / 2
print('std for test is %f' % (std))
h.stim = stimulate([1, stim, mean, std, tau, dt, T, seednumber])
h.tstop = T
h.run()
fr = apc.n / float(T / 1000)
print('fr is %f' % (fr))
if (fr <= fr_set):
leftStd = std
else:
rightStd = std
return std
def initialise(self, vrest=-65):
"""
Initialise the model, to launch before each simulations
"""
for sec in h.allsec():
h.finitialize(vrest, sec)
h.fcurrent(sec)
h.frecord_init()
def simulation(model, tau, posNa, T, threshold, stim_mean, stim_std, frequency, dt=0.025, seednumber=1):
'''
simulation(object) -> va (axonal voltage at the AP initiation site in mV)
Simulate the neuron model based on model setup and stimulus parameters.
Parameters: Meanings [Example Values]
model: model name ['Brette']
tau: correlation time of stimulus (ms) [5]
posNa: position of sodium channels (um) [20]
T: duration of stimulus and simulation (ms) [20000]
threshold: axonal reset voltage for finishing spikes (mV) [-23]
stim_mean: mean of stochastic stimulus (nA) [0.0185]
stim_std: std of stochastic stimulus (nA) [0.046]
dt: time step of model simulation (ms) [0.025]
seednumber: random seed number for stimulus generation [1]
'''
import os, sys
from neuron import h
from math import pi
import numpy as np
# Load parameters into NEURON.
h('dt=%f'%(dt))
h('posNa=%f'%(posNa))
h('threshold=%f'%(threshold))
# Set up neuron model.
h.load_file('nrngui.hoc') # Load nrngui.
h.load_file('../Models/%s/Neuron.hoc'%(model)) # Load hoc file of neuron model.
h('access soma')
h('objref APgen, stimulus, stim, vAIS, vSoma')
h('axon APgen = new NetCon(&v(posNa/axon_L), sodiumchan,threshold,0,0)') # Define action potential generation.
h('axon {sodiumchan.loc(posNa/axon_L)}') # Insert sodium channels in axon.
# Set up stimulus.
h.stimulus = h.IClamp(0.5) # Stimulus is injected in the middle of soma.
h.stimulus.dur = T # duration of simulus
h.stim = h.Vector()
sinwave = 0.01*np.sin(2*pi*frequency*np.arange(int(T/dt))*dt/1000.0) # NEW!! sinewave
h.stim.from_python(sinwave) # Generate the stimulus with the OU process. # !!!
h('stim.play(&stimulus.amp, dt)')
# Axonal voltage recording
h.vAIS = h.Vector(int(T/dt))
h.vSoma = h.Vector(int(T/dt))
h('vAIS.record(&axon.v(posNa/axon_L))') # Axonal voltage is recorded at the position of sodium channels.
h('vSoma.record(&soma.v(0.5))')
h.tstop = T # duration of simulation
# Initiate model simulation
h.finitialize()
h.frecord_init()
h.run()
va = h.vAIS.to_python() # Convert NEURON vector to numpy array.
vs = h.vSoma.to_python()
return va, vs
def runsim():
t0 = time.time() # clock start time
pc.set_maxstep(
10) # sets the default max solver step in ms (purposefully large)
for elec in lelec:
elec.setup()
elec.LFPinit()
h.finitialize(
) # initialize cells to -65 mV, after all the NetCon delays have been specified
if pcID == 0:
for tt in range(0, int(h.tstop), printdt):
h.cvode.event(tt, prsimtime) # print time callbacks
h.fcurrent()
h.frecord_init(
) # set state variables if they have been changed since h.finitialize
pc.psolve(h.tstop) # actual simulation - run the solver
pc.barrier()
# these calls aggregate data across procs/nodes
pc.allreduce(dp_rec_L2, 1)
pc.allreduce(
dp_rec_L5,
1) # combine dp_rec on every node, 1=add contributions together
for elec in lelec:
elec.lfp_final()
net.aggregate_currents(
) # aggregate the currents independently on each proc
# combine net.current{} variables on each proc
pc.allreduce(net.current['L5Pyr_soma'], 1)
pc.allreduce(net.current['L2Pyr_soma'], 1)
pc.barrier()
# write time and calculated dipole to data file only if on the first proc
# only execute this statement on one proc
savedat(p, pcID, t_vec, dp_rec_L2, dp_rec_L5, net)
for elec in lelec:
print('end; t_vec.size()', t_vec.size(), 'elec.lfp_t.size()',
elec.lfp_t.size())
if pcID == 0:
if debug: print("Simulation run time: %4.4f s" % (time.time() - t0))
if debug: print("Simulation directory is: %s" % ddir.dsim)
if paramrw.find_param(doutf['file_param'],
'save_spec_data') or usingOngoingInputs(
doutf['file_param']):
runanalysis(p, doutf['file_param'], doutf['file_dpl_norm'],
doutf['file_spec']) # run spectral analysis
if paramrw.find_param(doutf['file_param'], 'save_figs'):
savefigs(ddir, p, p_exp) # save output figures
pc.barrier() # make sure all done in case multiple trials
def prun(runState):
h.stdinit()
if runState == 1:
pnm.psolve(h.tstop / 2.)
savestate()
else:
restorestate()
h.frecord_init()
pnm.psolve(h.tstop)
pspike()
def simulate(cell, tstop=400, vinit=-55):
''' simulation control
Parameters
----------
cell: NEURON cell
cell for simulation
tstop: int (ms)
simulation time
vinit: int (mV)
initialized voltage
'''
h.finitialize(vinit)
balance(cell)
if h.cvode.active():
h.cvode.active()
else:
h.fcurrent()
h.frecord_init()
h.tstop = tstop
h.v_init = vinit
h.run()
if cell.numofmodel == 9 or cell.numofmodel == 10 or cell.numofmodel == 12:
running_ = 1
if cell.numofmodel == 9:
dl = 0
d_t = 60000
elif cell.numofmodel == 10:
dl = 1000
d_t = 40
else:
dl = 800
d_t = 10
h.stdinit()
for n in range(3):
cell.x_application = cell.x_application + dl
if n == 0:
cell.dl = 5000
cell.x_application = 0
print(cell.x_application)
else:
cell.dl = 30050
cell.x_application = -400
cell.distance()
for item in cell.diffs:
item.tx1 = h.t + 5
# item.initial = 0#item.atp
# if n == 0:
# item.c0cleft = 0.01#item.c0cleft
# else:
item.c0cleft = item.c0cleft
item.h = cell.distances.get(cell.diffusions.get(item))
h.continuerun(h.t + d_t)
h.continuerun(h.t + 500)
def reset(self):
print("Simulation initialization.")
h.initnrn()
h.frecord_init()
h.finitialize(self.init_v * mV)
if self.init_sleep > 0:
print("sleep before run for: %s seconds" % self.init_sleep)
time.sleep(self.init_sleep)
if self.warmup > 0:
h.dt = self.warmup / 10
h.continuerun(self.warmup * ms)
h.dt = self.dt
def min_sim(self):
"""
Launch a minimal simulation to test the model and determine its
resting potential empirically
"""
for sec in h.allsec():
h.finitialize(-65, sec)
h.fcurrent(sec)
h.frecord_init()
while h.t < 200: # Launch a simulation
h.fadvance()
# Record the soma voltage after this minimal stimulation to find v_rest
soma = getattr(h, "soma")
self.vrest = getattr(soma, "v")
def min_sim(self, TSTOP=100):
"""
Launch a minimal simulation to test the model and determine its resting potential empirically
"""
vrec = h.Vector()
vrec.record(self.soma(0.5)._ref_v)
for sec in h.allsec():
h.finitialize(-65, sec)
h.fcurrent(sec)
h.frecord_init()
while h.t < TSTOP: #Launch a simulation
h.fadvance()
vrest = np.array(vrec)[-1]
return vrest
def run(self, cell, cmd, temp=22, dt=0.025):
"""
Run a single current-clamp recording on *section*.
Parameters:
cell : Cell
The Cell instance to test. IClamp will be attached to
cell.soma(0.5).
cmd : array
Array of current command values
temp :
temperature of simulation (22)
dt :
timestep of simulation (0.025)
"""
self.reset()
self.cell = cell
self.current_cmd = cmd
self.dt = dt
self.temp = temp
tend = len(cmd) * dt
# Configure IClamp
istim = h.iStim(0.5, sec=cell.soma)
istim.delay = 0
istim.dur = 1e9 # these actually do not matter...
istim.iMax = 0.0
i_stim = h.Vector(cmd)
i_stim.play(istim._ref_i, h.dt, 0)
# Connect recording vectors
self['vm'] = cell.soma(0.5)._ref_v
self['i_inj'] = istim._ref_i
self['time'] = h._ref_t
# GO
h.dt = dt
h.celsius = temp
h.tstop = tend
cell.initialize()
h.frecord_init()
while h.t < h.tstop:
h.fadvance()
def simulate(cell, tstop=1500, vinit=-55):
''' simulation control
Parameters
----------
cell: NEURON cell
cell for simulation
tstop: int (ms)
simulation time
vinit: int (mV)
initialized voltage
'''
h.finitialize(vinit)
balance(cell)
if h.cvode.active():
h.cvode.active()
else:
h.fcurrent()
h.frecord_init()
h.tstop = tstop
h.v_init = vinit
h.run()
def simulate(cell, tstop=500, vinit=-60):
''' simulation control
Parameters
----------
cell: NEURON cell
cell for simulation
tstop: int (ms)
simulation time
vinit: int (mV)
initialized voltage
'''
h.finitialize(vinit)
balance(cell)
if h.cvode.active():
h.cvode.active()
else:
h.fcurrent()
h.frecord_init()
h.tstop = tstop
h.v_init = vinit
h.run()
def run_neuron_simulator(warmup=2000,
dt_warmup=10,
dt_sim=0.1,
t_start=0,
t_stop=600,
v_init=-60):
h.cvode.active(0)
dt = 0.1
h.steps_per_ms = 1.0 / dt
h.finitialize(v_init)
h.t = -warmup
h.secondorder = 0
h.dt = dt_warmup
while h.t < -100:
h.fadvance()
h.secondorder = 2
h.t = 0
h.dt = dt_sim
"""Setup run control for -100 to 1500"""
h.frecord_init() # Necessary after changing t to restart the vectors
while h.t < t_stop:
h.fadvance()
"""Initialization for -2000 to -100"""
h.cvode.active(0)
dt = 0.1
h.steps_per_ms = 1.0 / dt
h.finitialize(-60)
h.t = -2000
h.secondorder = 0
h.dt = 10
while h.t < -100:
h.fadvance()
h.secondorder = 2
h.t = 0
h.dt = 0.1
"""Setup run control for -100 to 1500"""
h.frecord_init() # Necessary after changing t to restart the vectors
while h.t < 600:
h.fadvance()
print("Done Running")
tuned_save_file_name = (str(nw) + "_data_paradigm_local-pattern" +
"-separation_run_scale_seed_" + str(run).zfill(3) +
'_' + str(input_scale).zfill(3) + '_' + str(seed))
nw.shelve_network(savedir, tuned_save_file_name)
fig = nw.plot_aps(time=600)
tuned_fig_file_name = (str(nw) + "_spike-plot_paradigm_local-pattern" +
"-separation_run_scale_seed_" + str(run).zfill(3) +
'_' + str(input_scale).zfill(3) + '_' + str(seed))
nw.save_ap_fig(fig, savedir, tuned_fig_file_name)
def simulation(model,
tau,
posNa,
T,
stim_mean,
stim_std,
dt=0.025,
seednumber=1,
stim_type='OU',
amplitude=[0],
frequency=[0],
electrode_place='soma'):
'''
simulation(object) -> va (axonal voltage at the AP initiation site in mV)
Simulate the neuron model based on model setup and stimulus parameters.
Parameters: Meanings [Example Values]
model: model name ['GE_diam_0']
tau: correlation time of stimulus (ms) [5]
posNa: AP initiation site on axon (um) [47]
T: duration of stimulus and simulation (ms) [20000]
stim_mean: mean of stochastic stimulus (nA) [0.0]
stim_std: std of stochastic stimulus (nA) [0.0346]
dt: time step of model simulation (ms) [0.025]
seednumber: random seed number for stimulus generation [1]
stim_type: type of stimulus ['OU']
amplitude: amplitude of the sinusoidal signal in unit of stim_std [0.1]
frequency: frequency of the sinusoidal signal added to background noise (Hz) [1, 2, 5, 10, 20, ..., 1000]
electrode_place: the place of the input stimulus ['soma']
'''
import os, sys
from neuron import h
# Load parameters into NEURON.
h('dt=%f' % (dt))
h('posNa=%f' % (posNa))
# Set up neuron model.
h.load_file('nrngui.hoc') # Load nrngui.
h('objref cell') # create neuron model
h.load_file('../Models/%s/%s.hoc' % (model, model))
exec('h.cell = h.%s()' % (model))
h.cell.create_model()
h.cell.biophys()
h('v_init = -90') # initial voltage
h('objref stimulus, stim, vAIS')
if electrode_place == 'soma':
h.stimulus = h.IClamp(0.5)
else:
h.stimulus = h.IClamp(h.cell.axon[0](0.94))
h.stimulus.dur = T
h.stim = h.Vector()
h.stim.from_python(
stimulate([
stim_mean, stim_std, tau, dt, T, seednumber, stim_type, amplitude,
frequency
])) # Generate the stimulus with the OU process.
h('stim.play(&stimulus.amp, dt)')
h.finitialize()
h.frecord_init()
# Axonal voltage recording
h.vAIS = h.Vector(int(T / dt))
h.vAIS.record(
h.cell.axon[0](h.posNa / h.cell.axon[0].L)._ref_v
) # Axonal voltage is recorded on the AIS with a distance of posNa. Total length of AIS is L.
# h.vAIS.record(h.cell.soma[0](0.5)._ref_v)
h.tstop = T # duration of simulation
# Initiate model simulation
h.finitialize()
h.frecord_init()
h.run()
va = h.vAIS.to_python() # Convert NEURON vector to numpy array.
return va
for prs, post in np.genfromtxt("../se.ssv").astype(int):
scons.append(h.NetCon(S[prs].s, E[post].cell))
sys.stderr.write("====== Network Created! =======\n")
for econ in econs:
econ.weight[0], econ.delay = excw, excd
for icon in icons:
icon.weight[0], icon.delay = inhw, inhd
for scon in scons:
scon.weight[0], scon.delay = stmw, stmd
h.dt = 0.1
h.finitialize()
h.fcurrent()
h.frecord_init()
endbuild = time.time()
while h.t < 1000.:
h.fadvance()
endsimulate = time.time()
print("Building time : %.2f s" % (endbuild - startbuild))
print("Simulation time : %.2f s" % (endsimulate - endbuild))
print("Time step : %.2f ms" % (h.dt))
spkse = np.array([(x, ni) for ni, nE in enumerate(E)
for x in list(np.array(nE.spk))])
spksi = np.array([(x, ni + Ne + 100) for ni, nI in enumerate(I)
def pyDentate(input_grid_out, seed_2, n_traj, dur_ms):
savedir = os.getcwd()
input_scale = 1000
seed_3 = seed_2 + 150 #seed_3 for network generation & simulation
# Where to search for nrnmech.dll file. Must be adjusted for your machine.
# dll_files = [("C:\\Users\\DanielM\\Repos\\models_dentate\\"
# "dentate_gyrus_Santhakumar2005_and_Yim_patterns\\"
# "dentategyrusnet2005\\nrnmech.dll"),
# "C:\\Users\\daniel\\Repos\\nrnmech.dll",
# ("C:\\Users\\Holger\\danielm\\models_dentate\\"
# "dentate_gyrus_Santhakumar2005_and_Yim_patterns\\"
# "dentategyrusnet2005\\nrnmech.dll"),
# ("C:\\Users\\Daniel\\repos\\"
# "dentate_gyrus_Santhakumar2005_and_Yim_patterns\\"
# "dentategyrusnet2005\\nrnmech.dll"),
# ("/home/baris/Python/mechs_7-6_linux/"
# "x86_64/.libs/libnrnmech.so")]
# for x in dll_files:
# if os.path.isfile(x):
# dll_dir = x
# print("DLL loaded from: " + dll_dir)
# h.nrn_load_dll(dll_dir)
#number of cells
n_grid = 200
n_granule = 2000
n_mossy = 60
n_basket = 24
n_hipp = 24
np.random.seed(seed_3) # seed_3 for connections in the network
# Randomly choose target cells for the GridCell lines
gauss_gc = stats.norm(loc=1000, scale=input_scale)
gauss_bc = stats.norm(loc=12,
scale=(input_scale / float(n_granule)) * n_basket)
pdf_gc = gauss_gc.pdf(np.arange(n_granule))
pdf_gc = pdf_gc / pdf_gc.sum()
pdf_bc = gauss_bc.pdf(np.arange(n_basket))
pdf_bc = pdf_bc / pdf_bc.sum()
GC_indices = np.arange(n_granule)
start_idc = np.random.randint(0, n_granule - 1, size=n_grid)
PP_to_GCs = []
for x in start_idc:
curr_idc = np.concatenate((GC_indices[x:n_granule], GC_indices[0:x]))
PP_to_GCs.append(
np.random.choice(curr_idc, size=100, replace=False, p=pdf_gc))
PP_to_GCs = np.array(PP_to_GCs)
BC_indices = np.arange(n_basket)
start_idc = np.array(((start_idc / float(n_granule)) * 24), dtype=int)
PP_to_BCs = []
for x in start_idc:
curr_idc = np.concatenate((BC_indices[x:24], BC_indices[0:x]))
PP_to_BCs.append(
np.random.choice(curr_idc, size=1, replace=False, p=pdf_bc))
PP_to_BCs = np.array(PP_to_BCs)
# generate temporal patterns out of grid cell act profiles as an input for pyDentate
# input_grid_out = inhom_poiss(par_traj, n_traj, dt_s=0.0001, seed=seed_2)
np.random.seed(seed_3) #seed_3 again for network generation & simulation
granule_output = np.empty((n_granule, n_traj), dtype=np.ndarray)
mossy_output = np.empty((n_mossy, n_traj), dtype=np.ndarray)
basket_output = np.empty((n_basket, n_traj), dtype=np.ndarray)
hipp_output = np.empty((n_hipp, n_traj), dtype=np.ndarray)
for trj in range(n_traj):
nw = net_tunedrev.TunedNetwork(seed_3, input_grid_out[:, trj],
PP_to_GCs, PP_to_BCs)
# Attach voltage recordings to all cells
nw.populations[0].voltage_recording(range(n_granule))
nw.populations[1].voltage_recording(range(n_mossy))
nw.populations[2].voltage_recording(range(n_basket))
nw.populations[3].voltage_recording(range(n_hipp))
# Run the model
"""Initialization for -2000 to -100"""
h.cvode.active(0)
dt = 0.1
h.steps_per_ms = 1.0 / dt
h.finitialize(-60)
h.t = -2000
h.secondorder = 0
h.dt = 10
while h.t < -100:
h.fadvance()
h.secondorder = 2
h.t = 0
h.dt = 0.1
"""Setup run control for -100 to 1500"""
h.frecord_init() # Necessary after changing t to restart the vectors
while h.t < dur_ms:
h.fadvance()
print("Done Running")
granule_output[:, trj] = np.array(
[cell[0].as_numpy() for cell in nw.populations[0].ap_counters])
# mossy_output[:,trj] = np.array([cell[0].as_numpy() for cell in nw.populations[1].ap_counters])
# basket_output[:,trj] = np.array([cell[0].as_numpy() for cell in nw.populations[2].ap_counters])
# hipp_output[:,trj] = np.array([cell[0].as_numpy() for cell in nw.populations[3].ap_counters])
return granule_output, mossy_output, basket_output, hipp_output
def simulate():
h.frecord_init()
h.tstop = tstop
h.run()
def simulate(tau_facil,
tau_rec,
stim_freq,
celltype,
tau_1=0.3,
tau_2=0.6,
u0=0.078,
sampling_interval=0.5,
v_clamp=-70.42,
sec='proxd'):
"""Simulates a frequency stimulation of the tmgexp2syn meachnism onto a
neuron and measure the conductance at the soma.
Parameters
----------
tau_facil : numeric
facilitation time constant of the tmgexp2syn mechanism
tau_rec : numeric
recovery time constant of the tmgexp2syn mechanism
stim_freq : numeric
stimulation frequency in Hz
celltype : ouropy.GenNeuron
A class that inherits from ouropy.GenNeuron
tau_1 : numeric
Synaptic rise time
tau_2 : numeric
Synaptic decay time
u0 : float
The u0 parameters as specified in tmgexp2syn
sampling_interval : numeric
The sampling interval in ms
v_clamp : numeric
Holding potential of the
Returns
-------
peaks_norm : ndarray
Peak conductances normalized to first peak
garr_norm : ndarray
Conductance array normalized to first peak
"""
# Resolve simulation hyperparameters
left_pad, right_pad = 50, 100 # in ms
simdur = left_pad + right_pad + 10 * (1000 / stim_freq)
# Create cell
mycell = celltype()
# Create synapse
syn = h.tmgexp2syn(mycell.get_segs_by_name(sec)[0](0.5))
syn.tau_1 = tau_1
syn.tau_2 = tau_2
syn.tau_facil = tau_facil
syn.tau_rec = tau_rec
syn.u0 = u0
syn.e = 0
# Create stimulation
stim_period_ms = 1000 / stim_freq
stim = h.NetStim()
stim.interval = stim_period_ms
stim.start = left_pad
stim.number = 10
nc = h.NetCon(stim, syn)
nc.weight[0] = 0.001
# Create voltage clamp
c = h.SEClamp(mycell.soma(0.5))
c.dur1 = simdur
c.amp1 = v_clamp
c.rs = 0.1
# Create recording vector
ivec = h.Vector()
ivec.record(c._ref_i)
# Start simulation
sample_period_ms = sampling_interval
h.cvode.active(0)
h.finitialize(-70.42)
h.t = -2000
h.secondorder = 0
h.dt = 10
while h.t < -100:
h.fadvance()
h.secondorder = 0
h.t = 0
h.dt = sample_period_ms
h.steps_per_ms = 1.0 / h.dt
h.frecord_init() # Necessary after changing t to restart the vectors
while h.t < simdur:
h.fadvance()
# Get Peaks from output
iarr = np.array(ivec)
garr = (iarr - iarr[0:50].mean()) / v_clamp
stim_dtp = int(np.around(stim.interval / sampling_interval))
pad_dtp = int(left_pad / sampling_interval)
t_stim = np.arange(pad_dtp, stim_dtp * 11 + pad_dtp, stim_dtp)
#dtp_stim = np.array(t_stim / sampling_interval, dtype=np.int)
dtp_stim = np.array(t_stim, dtype=np.int)
gvec_split = np.array(np.split(garr, dtp_stim)[1:-1])
peaks = gvec_split.max(axis=1)
peaks_norm = peaks / peaks[0]
garr_norm = garr / peaks[0]
return peaks_norm, garr_norm
def _simulate_single_trial(net):
"""Simulate one trial."""
from .parallel import rank, nhosts, pc, cvode
from neuron import h
h.load_file("stdrun.hoc")
# Now let's simulate the dipole
if rank == 0:
print("running on %d cores" % nhosts)
# global variables, should be node-independent
h("dp_total_L2 = 0.")
h("dp_total_L5 = 0.")
# Set tstop before instantiating any classes
h.tstop = net.params['tstop']
h.dt = net.params['dt'] # simulation duration and time-step
h.celsius = net.params['celsius'] # 37.0 - set temperature
# We define the arrays (Vector in numpy) for recording the signals
t_vec = h.Vector()
t_vec.record(h._ref_t) # time recording
dp_rec_L2 = h.Vector()
dp_rec_L2.record(h._ref_dp_total_L2) # L2 dipole recording
dp_rec_L5 = h.Vector()
dp_rec_L5.record(h._ref_dp_total_L5) # L5 dipole recording
net.move_cells_to_pos() # position cells in 2D grid
# sets the default max solver step in ms (purposefully large)
pc.set_maxstep(10)
# initialize cells to -65 mV, after all the NetCon
# delays have been specified
h.finitialize()
def prsimtime():
print('Simulation time: {0} ms...'.format(round(h.t, 2)))
printdt = 10
if rank == 0:
for tt in range(0, int(h.tstop), printdt):
cvode.event(tt, prsimtime) # print time callbacks
h.fcurrent()
# set state variables if they have been changed since h.finitialize
h.frecord_init()
# actual simulation - run the solver
pc.psolve(h.tstop)
pc.barrier()
# these calls aggregate data across procs/nodes
pc.allreduce(dp_rec_L2, 1)
# combine dp_rec on every node, 1=add contributions together
pc.allreduce(dp_rec_L5, 1)
# aggregate the currents independently on each proc
net.aggregate_currents()
# combine net.current{} variables on each proc
pc.allreduce(net.current['L5Pyr_soma'], 1)
pc.allreduce(net.current['L2Pyr_soma'], 1)
pc.barrier() # get all nodes to this place before continuing
dpl_data = np.c_[np.array(dp_rec_L2.to_python()) +
np.array(dp_rec_L5.to_python()),
np.array(dp_rec_L2.to_python()),
np.array(dp_rec_L5.to_python())]
pc.gid_clear()
pc.done()
dpl = Dipole(np.array(t_vec.to_python()), dpl_data)
if rank == 0:
if net.params['save_dpl']:
dpl.write('rawdpl.txt')
dpl.baseline_renormalize(net.params)
dpl.convert_fAm_to_nAm()
dpl.scale(net.params['dipole_scalefctr'])
dpl.smooth(net.params['dipole_smooth_win'] / h.dt)
return dpl, net.spiketimes.to_python(), net.spikegids.to_python()
def __call__(self, input_spikes, bin_size=10, el=1):
"""
Launch a simulation of a given time with a binary event happening
or not in each time bin
Parameters
----------
input_spikes: 2-D numpy array of Bool
contain the occurence or not of an event. Each line is a set of
signals
and each column corresponds to a time bin
bin_size: float
the size of a time bin in ms.
el: float
elementary weight, it will scale all the weights
Comments
--------
It seems that when multiple go method are done it does not
change the output vector.
"""
# Set the time to 0
h.t = 0
try:
weights = self.weights*el
where_what = self.input_locations
assert len(self.weights) == len(self.input_locations)
except AttributeError:
return "Weights or the input_locations not set. Simulation aborted"
except AssertionError:
print("Weights or the input_locations not match. Set default w")
self.weights = np.ones(len(self.input_locations))
# Test if signal and stimulation match.
try:
assert len(input_spikes) == len(self.input_locations)
except AssertionError:
print(self.where_what)
print(input_spikes)
print("Number of input neuron does not match number of synapses")
print("Aborting simulation")
return
# Set the input spike time
self.tstims = bin2time(input_spikes, bin_size)
self.TSTOP = bin_size * input_spikes.shape[1]
tstims = self.tstims
# This is to prevent remanescence of the synapse
# Otherwise you can become crazy!!
if len(self.syn) >= 1:
for key in self.syn.keys():
del self.syn[key]
# Set the inputs
for i, tstim in enumerate(tstims):
self.add_stim(where_what[i],
name='Stream'+str(i),
tstim=tstim,
w=weights[i])
# Set the initial membrane potential
if not hasattr(self, 'vrest'):
self.min_sim()
# Record Time
record_time = h.Vector()
record_time.record(h._ref_t)
# Record Voltage
self.record_v()
# Set the time at zero
h.t = 0
# ReInitialise the sections
for sec in h.allsec():
h.finitialize(self.vrest, sec)
h.fcurrent(sec)
h.frecord_init()
# Launch a simulation with or without adding spikes
if self.spike:
# Need to hasck the recording of the data
self.data['soma'] = [[]]
self.data['soma'][0].append(h.soma.v)
refrac_abs = 200
threshold = -40
spk = False
refrac = 0
h.t = 0
while h.t < self.TSTOP:
h.fadvance()
# Spike if voltage cross threshold and no refractoriness
if h.soma.v >= threshold and not refrac:
h.soma.v = 20
spk = True
# If the neuron spiked add one to the refractory period
if spk:
refrac += 1
# Put the soma back to a reset voltage
if refrac == 2:
h.soma.v = threshold - 10
# Reset the absolute refrac period
if refrac >= refrac_abs:
refrac = 0
spk = False
self.data['soma'][0].append(h.soma.v)
else:
while h.t < self.TSTOP:
h.fadvance()
# Copy time into a vector
self.rec_t = np.array(record_time)