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mds_python_model.py
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import matplotlib.pyplot as plt
import numpy as np
import time
import sys
def tagliorette(corr,sim_type):
dur_sign = np.inf
vinc_inf = 700
if corr < vinc_inf and corr > 0:
dur_sign = lin_func_inf = 0.68*corr - 190.0
if sim_type=='corrcostatratti':
vinc_sup = np.inf
if corr > vinc_sup:
dur_sign = lin_func_sup = corr + np.inf
elif sim_type == 'corrcost':
vinc_sup = 1300
if corr > vinc_sup:
dur_sign = lin_func_sup = 76.86-0.028*corr
else:
print("#####################!!! Sim_type not defined!!!!#######")
return
return dur_sign
def V(t, delta, Psi, alpha, beta, IaA0, IdA0, t0, V0):
t_step = t - t0
VV_1 = 0.5 / ((beta -delta) * (pow(beta,2) + (beta-1.0) * delta) * (4.0 * beta - (1.0 + delta) ** 2.0)) * Psi
VV_2 = 2.0 * np.exp(-t_step * beta) * (beta-1.0) * beta * (beta - delta) * Psi
VV_3 = (pow(beta,2) + ((- 1.0) + beta) * delta) * Psi
VV_4 = np.exp((1.0 / 2.0) * t_step * (-1.0 + delta -Psi))
VV_5 = beta * (beta -delta) * (-1.0 -delta + beta * (3.0 + delta -Psi) + Psi)
VV_6 = (pow(beta,2) -delta + beta * delta)
VV_7 = (1.0 + (-2.0) * beta + delta -Psi)
VV_8 = np.exp((1.0 / 2.0) * t_step * (-1.0 + delta + Psi))
VV_9 = beta * (beta-delta) * (-1.0 -delta -Psi + beta * (3.0 + delta + Psi))
VV_10 = (pow(beta,2) - delta + beta * delta)
VV_11 = (1.0 + (-2.0) * beta + delta + Psi)
return VV_1 * (VV_2 * IdA0 + -2.0 * (alpha -beta + delta) * VV_3 + VV_4 * (IdA0 * VV_5 - VV_6 * (alpha * VV_7 + (beta -delta) * (-1.0 + 2.0 * IaA0 * beta -delta + Psi + V0 * (-1.0 -delta + Psi)))) + VV_8 * (-IdA0 * VV_9 + VV_10 * (alpha * VV_11 + (beta -delta) * (-1.0 + 2.0 * IaA0 * beta-delta -Psi -V0 * (1.0 + delta + Psi)))))
def Iadap(t, delta, Psi, alpha, beta, IaA0, IdA0, t0, V0):
AA_1 = -4.0*beta**3.0+beta**2.0*(-1.0+delta)**2.0-delta*(1.0+delta)**2.0+beta*delta*(5+2.0*delta+delta**2.0)
AA_2 = 2.0*np.exp(-(t - t0) * beta)*beta*(4.0*beta**2.0+delta*(1.0+delta)**2.0-beta*(1.0+6*delta+delta**2.0))
AA_3 = np.exp((1.0 / 2.0)*(t-t0)*(-1.0+delta+Psi))
AA_4 = -1.0-2.0*delta-delta**2.0-Psi+delta*Psi+2.0*beta*(2.0+Psi)
AA_5 = (beta**2.0-delta+beta*delta)
AA_6 = (1.0+(-4.0)*beta+2.0*delta+delta**2.0+Psi-delta*Psi)
AA_7 = (1.0+delta)*(-1.0-delta+Psi)
AA_8 = np.exp((-1.0)*(1.0 / 2.0) * (t-t0) * (1.0-delta+Psi))
AA_9 = beta * (beta-delta)*(1.0+2.0*delta+delta**2.0-Psi+delta*Psi+2.0*beta*(-2.0+Psi))
AA_10 = (beta**2.0-delta+beta*delta)
AA_11 = (1.0-4.0*beta+2.0*delta+delta**2.0-Psi+delta*Psi)
AA_12 = (2.0*(beta-delta)*(beta**2.0+(-1.0+beta)*delta)*(4.0*beta-(1.0+delta)**2.0))
to_return = (-2.0 * alpha * AA_1 + IdA0 * AA_2 + AA_3 * (-IdA0 * beta * (beta - delta) * AA_4 + AA_5 * (alpha * AA_6 + (beta - delta) * (4.0 * IaA0 * beta -2.0 * (1.0 + V0) * Psi + IaA0 * AA_7))) + AA_8 * (IdA0 * AA_9 + AA_10 * (alpha * AA_11 - (beta-delta) * (-4.0 * IaA0 * beta - 2.0*(1.0+V0)*Psi+IaA0*(1.0+delta)*(1.0+delta+Psi)))))/ AA_12
return to_return
def Idep(t, beta, IdA0, t0):
return np.exp(((-1) * t + t0) * beta) * IdA0
def exp_cum(x, a, b):
return a * (1 - np.exp(-b * x))
def monod(x, a, b, c, alp):
to_return = c + (a * np.exp(b) * x) / (alp + x)
return to_return
def mds_sim(sim_type, total_current, sim_id, d_dt):
EL = -72.5
vres = -65
vtm = -52
Cm = 2047.4164432004916
ith = 300.9987901902274
tao_m = 3310.462136574088
sc = 4526.328798037026
bet = 0.24522251335200956
delta1 = 0.009906254244852036
cost_idep_ini = 0.017625482908326662
Idep_ini_vr = 1.0122905259090516
psi1 = 0.1975362978159442
a=14.2787
b=-2.10966
c=0.0608809
alp=225.491
istim_min_spikinig_exp=400
istim_max_spikinig_exp=1000
time_scale = 1 / (-sc / (Cm * EL))
H = (90+EL)*sc*(bet-delta1)/(EL*(-200))
cor = total_current
sim_length = 1000
if sim_type=='corrcostatratti':
corrcostatratti = 1
corrcost = 0
elif sim_type == 'corrcost':
corrcostatratti = 0
corrcost = 1
else:
print("#####################!!! Sim_type not defined!!!!#######")
return
tic = time.perf_counter()
Vconvfact = -EL
vth = vtm/Vconvfact
vrm = vres/Vconvfact
t0_val = 0
vini_neg = EL
ts = np.inf
dt = d_dt/time_scale
init_sign = 0
ref_t = 2
t0_val = 0
psi1 = ((-4)*bet+((1+delta1)**2))**(0.5)
Idep_ini = 0
Iadap_ini = 0
out = []
t_out = []
t_final = t0_val+dt
v_ini = -1
vini_prec = v_ini
mul = 15
f = open('t_spk_simulated_SIM4before_contheta_newinit_codicepulito'+sim_id+'.txt', 'w')
i = 0
soglia_sign = 10
Ide = []
Iada = []
Ide2 = []
Iada2 = []
tetalist = []
monod_plot = []
Iadap0max_plot = []
init_sign_plot = []
t_spk = -3*d_dt
afirst = 0
meancorlastis = 0
stdcorlastis = 0
sis = 0
firstSpikeFlag = False
counter = 0
while(t_final*time_scale < sim_length):
if (t_final-init_sign)*time_scale >= tagliorette(cor[i],sim_type):
if corrcostatratti:
if cor[i] > ith:
if cor[i-1] < ith or i == 0:
init_sign = t_final
Idep_ini = cost_idep_ini*(cor[i]-ith)
Iadap_ini = 0
if cor[i-1] > ith and cor[i-1] < cor[i]:
init_sign = init_sign*(1+(cor[i-1]-ith)/cor[i-1])
Idep_ini = cost_idep_ini*(cor[i]-ith)
if corrcost:
if cor[i] > ith:
if cor[i-1] < ith or i == 0:
init_sign = t_final
Idep_ini = cost_idep_ini*(cor[i]-ith)
Iadap_ini = 0
if cor[i-1] == 0:
v_ini = vini_prec
else:
v_ini= (EL+(1-np.exp(-cor[i]/1000))*(vtm-EL))/Vconvfact
vini_prec = v_ini
else:
vini_prec = v_ini
if (cor[i] < ith and cor[i] >= 0) or i == 0:
if cor[i-1] < 0:
Iadap_ini = 90/EL + 1
Idep_ini = 0
v_ini = vini_prec
if ((cor[i] / sc) / (bet - delta1) - 1) <= v_ini:
Idep_ini = 0
Iadap_ini = (cor[i] / sc) / (bet - delta1)
v_ini = ((cor[i] / sc) / (bet - delta1) - 1)
else:
v_ini = V(t_final, delta1, psi1,
cor[i]/sc, bet, Iadap_ini, Idep_ini, t0_val, v_ini)
Iadap_ini = Iadap(
t_final, delta1, psi1, cor[i] / sc, bet, Iadap_ini, Idep_ini, t0_val, v_ini)
Idep_ini = Idep(t_final, bet, Idep_ini, t0_val)
if v_ini * Vconvfact < -90:
v_ini = -90 / Vconvfact
Iadap_ini = 0
else:
if cor[i] < cor[i-1] and cor[i] > 0 and (t_spk+2*d_dt) < t_final*time_scale:
teta = (out[i-1]/(cor[i-1] / sc))*(1/dt-delta1) - \
(out[i-2]/((cor[i-1] / sc)*dt))-delta1/(cor[i-1] / sc)-1
if teta < 0:
teta = 0
Idep_ini = Iadap_ini + teta * (cor[i] / sc) / bet
tetalist.append(teta)
v_ini = V(t=t_final, delta=delta1, Psi=psi1,
alpha=cor[i]/sc, beta=bet, IaA0=Iadap_ini, IdA0=Idep_ini, t0=t0_val, V0=v_ini)
Iadap_ini = Iadap(t=t_final, delta=delta1, Psi=psi1,
alpha=cor[i]/sc, beta=bet, IaA0=Iadap_ini, IdA0=Idep_ini, t0=t0_val, V0=v_ini)
Idep_ini = Idep(t=t_final, beta=bet,
IdA0=Idep_ini, t0=t0_val)
else:
if cor[i] > 0:
v_ini = V(t=t_final, delta=delta1, Psi=psi1,
alpha=cor[i]/sc, beta=bet, IaA0=Iadap_ini, IdA0=Idep_ini, t0=t0_val, V0=v_ini)
Iadap_ini = Iadap(t=t_final, delta=delta1, Psi=psi1,
alpha=cor[i]/sc, beta=bet, IaA0=Iadap_ini, IdA0=Idep_ini, t0=t0_val, V0=v_ini)
Idep_ini = Idep(t=t_final, beta=bet,
IdA0=Idep_ini, t0=t0_val)
if cor[i-1] != cor[i] and (cor[i] < 0 and cor[i] > -200):
Iadap_ini = (90+EL)*cor[i]/(EL*(-200))
Idep_ini = 0
v_ini = vini_prec
if cor[i] < 0 and cor[i] > -200:
v_ini = V(t=t_final, delta=delta1, Psi=psi1, alpha=H *
cor[i]/sc, beta=bet, IaA0=Iadap_ini, IdA0=Idep_ini, t0=t0_val, V0=v_ini)
Iadap_ini = Iadap(t=t_final, delta=delta1, Psi=psi1, alpha=H *
cor[i]/sc, beta=bet, IaA0=Iadap_ini, IdA0=Idep_ini, t0=t0_val, V0=v_ini)
Idep_ini = Idep(t=t_final, beta=bet,
IdA0=Idep_ini, t0=t0_val)
if cor[i-1] != cor[i] and cor[i] <= -200:
Iadap_ini = 90/EL + 1
Idep_ini = 0
v_ini = vini_prec
if cor[i] <= -200:
v_ini = V(t=t_final, delta=delta1, Psi=psi1, alpha=H *
cor[i]/sc, beta=bet, IaA0=Iadap_ini, IdA0=Idep_ini, t0=t0_val, V0=v_ini)
Iadap_ini = Iadap(t=t_final, delta=delta1, Psi=psi1, alpha=H *
cor[i]/sc, beta=bet, IaA0=Iadap_ini, IdA0=Idep_ini, t0=t0_val, V0=v_ini)
Idep_ini = Idep(t=t_final, beta=bet,
IdA0=Idep_ini, t0=t0_val)
if v_ini*Vconvfact < -90:
v_ini = -90/Vconvfact
Iadap_ini = 0
if corrcostatratti:
if cor[i] > ith:
if cor[i-1] < ith or i == 0:
init_sign = t_final
Idep_ini = cost_idep_ini*(cor[i]-ith)
Iadap_ini = 0
if cor[i-1] > ith and cor[i-1] < cor[i]:
init_sign = init_sign*(1+(cor[i-1]-ith)/cor[i-1])
Idep_ini = cost_idep_ini*(cor[i]-ith)
Iadap_ini = 0
if corrcost:
if cor[i] > ith:
if cor[i-1] < ith or i == 0:
init_sign = t_final
Idep_ini = cost_idep_ini*(cor[i]-ith)
Iadap_ini = 0
if v_ini > vth:
t_spk = t_final*time_scale
f.write(str(round(t_spk, 3)) + ' \n')
v_ini = vrm
print('***spike***')
print('t ', t_final, 'val_ist V', v_ini * Vconvfact, 'adap',
Iadap_ini, 'adap', Iadap_ini, 't_ini', init_sign)
print('************')
if cor[i] < istim_min_spikinig_exp or cor[i] > istim_max_spikinig_exp:
if corrcost or corrcostatratti:
if firstSpikeFlag == False or cor[i-1]!=cor[i]:
firstSpikeFlag=True
paramL = monod((t_final-init_sign)*time_scale,a,b*cor[i]/1000,c,alp)
if paramL<0:
if a > 0:
c_aux = c - paramL
else:
c_aux = -a*np.exp(b*cor[i]/1000)
else:
c_aux = c
Iadap_ini = monod((t_final-init_sign) *
time_scale, a, b*cor[i]/1000, c_aux, alp)
else:
c_aux = c
Iadap_ini = monod((t_final-init_sign) *
time_scale, a, b*cor[i]/1000, c_aux, alp)
else:
Iadap_ini = monod((t_final-init_sign) *
time_scale, a, b*cor[i]/1000, c, alp)
if Iadap_ini<0:
if firstSpikeFlag == False or cor[i-1]!=cor[i]:
firstSpikeFlag=True
paramL = monod((t_final-init_sign)*time_scale,a,b*cor[i]/1000,c,alp)
if counter<2:
Iadap_ini = 0
counter = counter + 1
elif counter == 2:
c_aux = c
if a > 0:
c_aux = c - paramL
else:
c_aux = -a*np.exp(b*cor[i]/1000)
Iadap_ini = monod((t_final-init_sign) * time_scale, a, b*cor[i]/1000, c_aux, alp)
counter = counter + 1
else:
Iadap_ini = monod((t_final-init_sign) * time_scale, a, b*cor[i]/1000, c_aux, alp)
if cor[i] < ith:
Idep_ini = 0
Iadap_ini = 0
else:
Idep_ini = Idep_ini_vr
for k in range(int(ref_t / d_dt)):
out.append(v_ini)
t_out.append(t_final)
t_final = t_final + dt
Iada.append(Iadap_ini)
Ide.append(Idep_ini)
i = i + 1
vini_prec = v_ini
out.append(v_ini)
t_out.append(t_final)
Iada.append(Iadap_ini)
Ide.append(Idep_ini)
i = i + 1
t0_val = t_final
t_final = t0_val+dt
membrane_voltage = np.array(out) * Vconvfact
I_adapt = np.array(Iada)
I_dep = np.array(Ide)
monod_plot = np.array(monod_plot)
Iadap0max_plot = np.array(Iadap0max_plot)
init_sign_plot = np.array(init_sign_plot)* time_scale
return np.array(t_out)*time_scale, membrane_voltage, I_adapt, I_dep, monod_plot, Iadap0max_plot, init_sign_plot