def sim_ln_dosc_complex_model_OLD(mu_ext, sigma_ext, L, mu_exp, sigma_exp,
w_m_orig, dt, EW, taum, gL, tauw, a, b,
mu_range, sig_range, f0_grid, tau_grid,
tau_mu_f_grid, tau_sigma_f_grid, Vmean_grid,
r_grid, rec, K, J, delay_type, n_d, taud):
mu_f = np.zeros(L+1, dtype = numba.complex128) \
if use_numba else np.zeros(L+1, dtype=np.complex128)
mu_a = np.zeros(L + 1)
r = np.zeros(L + 1)
r_d = np.zeros(L + 1)
wm = np.zeros(L + 1)
sigma_f = np.zeros(L + 1)
#initial_conditions
mu_a[0] = mu_exp
wm[0] = w_m_orig
sigma_f[0] = sigma_exp
weights_a = interpolate_xy(mu_a[0] - wm[0] / (taum * gL), sigma_f[0],
mu_range, sig_range)
f0 = lookup_xy(f0_grid, weights_a)
tau = lookup_xy(tau_grid, weights_a)
mu_f[0] = (mu_exp * (1 + 1j * 2 * np.pi * f0 * tau))
for i in xrange(L):
#interpolates real numbers
weights_a = interpolate_xy(mu_a[i] - wm[i] / (taum * gL), sigma_f[i],
mu_range, sig_range)
f0 = lookup_xy(f0_grid, weights_a)
tau = lookup_xy(tau_grid, weights_a)
tau_mu_f = lookup_xy(tau_mu_f_grid, weights_a)
tau_sigma_f = lookup_xy(tau_sigma_f_grid, weights_a)
weights_f = interpolate_xy(mu_f[i].real - wm[i] / (taum * gL),
sigma_f[i], mu_range, sig_range)
Vmean_dosc = lookup_xy(Vmean_grid, weights_f)
r_dosc = lookup_xy(r_grid, weights_f)
r[i] = r_dosc
if rec:
mu_syn = get_mu_syn(K, J, mu_ext, delay_type, i, r, r_d, n_d, taud,
dt)
sigma_syn = get_sigma_syn(K, J, sigma_ext, delay_type, i, r, r_d,
n_d, taud, dt)
else:
mu_syn = mu_ext[i]
sigma_syn = sigma_ext[i]
mu_f_rhs = ((2 * np.pi * f0)**2 * tau + 1. / tau) * mu_syn + (
1j * 2 * np.pi * f0 - 1. / tau) * mu_f[i]
sigma_f_rhs = (sigma_syn - sigma_f[i]) / tau_sigma_f
w_rhs = (a[i] *
(Vmean_dosc - EW) - wm[i] + tauw * b[i] * r_dosc) / tauw
mu_a_rhs = (mu_syn - mu_a[i]) / tau_mu_f
#EULER STEP
mu_f[i + 1] = mu_f[i] + dt * mu_f_rhs
mu_a[i + 1] = mu_a[i] + dt * mu_a_rhs
sigma_f[i + 1] = sigma_f[i] + dt * sigma_f_rhs
wm[i + 1] = wm[i] + dt * w_rhs
return (r * 1000., wm)
def sim_spec1_without_HEUN_OLD(mu_ext, sigma_ext, map1_Vmean, map_r_inf, mu_range,
sigma_range, map_lambda_1, tauw, dt, steps, C,a ,b, EW,
s0, r0,w0, rec,K,J,delay_type,n_d,taud):
# optimizations
dt_tauw = dt/tauw
b_tauw = b*tauw
# initialize real arrays
r = np.zeros(steps+1)
r_d = np.zeros(steps+1)
s = np.zeros(steps+1)
wm = np.zeros(steps+1)
lambda_1_real = np.zeros(steps+1)
# write initial condition into array
r[0] = r0
s[0] = s0
wm[0] = w0
for i in range(steps):
#compute mu_syn/sigma_syn from
if rec:
mu_syn = get_mu_syn(K, J, mu_ext,delay_type,i,r,r_d,n_d,taud,dt)
sigma_syn = get_sigma_syn(K, J, sigma_ext,delay_type,i,r,r_d,n_d,taud,dt)
else:
mu_syn = mu_ext[i]
sigma_syn = sigma_ext[i]
#effective mu
mu_eff = mu_syn - wm[i] / C
# interpolate
weights = interpolate_xy(mu_eff, sigma_syn, mu_range, sigma_range)
# lookup
Vm_inf = lookup_xy(map1_Vmean, weights)
r_inf = lookup_xy(map_r_inf, weights)
lambda_1 = lookup_xy(map_lambda_1, weights)
lambda_1_real[i] = lambda_1.real # save real part of lambda(t)
# split lambda in real and imaginary part
Re = lambda_1.real
Im = lambda_1.imag
r_diff = r[i] - r_inf
# integration step
# r[i+1] = r[i] + dt * (Re * r_diff - Im * s[i])
r_prelim = r[i] + dt * (Re * r_diff - Im * s[i])
r[i+1] = r_prelim if r_prelim > 0. else 0.
r[i+1] = r[i] + dt * (Re * r_diff - Im * s[i])
# TODO: add rectify of r via toggle (def: on)
s[i+1] = s[i] + dt * (Im * r_diff + Re * s[i])
wm[i+1] = wm[i] + dt_tauw * (a[i] * (Vm_inf - EW) - wm[i] + b_tauw[i] * r[i])
return (r*1000, wm, lambda_1_real)
def sim_ln_exp_without_HEUN_OLD(mu_ext, sigma_ext, mu_range, sigma_range,
map_Vmean, map_r, map_tau_mu_f, map_tau_sigma_f,
L, muf0, sigma_f0, w_m0, a, b, C, dt, tauW, Ew,
rec, K, J, delay_type, const_delay, taud):
b_tauW = b * tauW
# initialize arrays
r_d = np.zeros(L+1)
mu_f = np.zeros(L+1)
sigma_f = np.zeros(L+1)
w_m = np.zeros(L+1)
rates = np.zeros(L+1)
tau_mu_f = np.zeros(L+1)
tau_sigma_f = np.zeros(L+1)
Vm = np.zeros(L+1)
# set initial values
w_m[0] = w_m0
mu_f[0] = muf0
sigma_f[0] = sigma_f0
for i in xrange(L):
# interpolate
mu_f_eff = mu_f[i]-w_m[i]/C
weights = interpolate_xy(mu_f_eff, sigma_f[i], mu_range, sigma_range)
# lookup
Vm[i] = lookup_xy(map_Vmean, weights)
rates[i] = lookup_xy(map_r, weights)
tau_mu_f[i] = lookup_xy(map_tau_mu_f, weights)
tau_sigma_f[i] = lookup_xy(map_tau_sigma_f, weights)
if rec:
mu_syn = get_mu_syn(K,J,mu_ext,delay_type,i,rates,r_d,const_delay,taud,dt)
sigma_syn = get_sigma_syn(K,J,sigma_ext,delay_type,i,rates,r_d,const_delay,taud,dt)
else:
mu_syn = mu_ext[i]
sigma_syn = sigma_ext[i]
# rhs of equations
mu_f_rhs = (mu_syn - mu_f[i])/tau_mu_f[i]
sigma_f_rhs = (sigma_syn - sigma_f[i])/tau_sigma_f[i]
w_m_rhs = (a[i]*(Vm[i] - Ew) - w_m[i] + b_tauW[i] * (rates[i]))/tauW
# euler step
mu_f[i+1]= mu_f[i] + dt * mu_f_rhs
sigma_f[i+1]= sigma_f[i] + dt * sigma_f_rhs
w_m[i+1]=w_m[i]+ dt * w_m_rhs
#order of return tuple should always be rates, w_m, Vm, etc...
return (rates*1000., w_m, Vm, tau_mu_f, tau_sigma_f, mu_f, sigma_f)
def sim_ln_dosc_UPDATE_without_HEUN(
mu_ext,
sig_ext,
dmu_ext_dt,
t,
dt,
steps,
mu_range,
sig_range,
omega_grid,
tau_grid,
tau_mu_f_grid,
tau_sigma_f_grid,
Vmean_grid,
r_grid,
a,
b,
C,
wm0,
EW,
tauw,
rec,
K,
J,
delay_type,
const_delay,
taud,
):
# initialize arrays
r = np.zeros_like(t)
r_d = np.zeros_like(t)
mu_f = np.zeros_like(t)
dmu_f = np.zeros_like(t) # aux. var for integration
mu_lookup = np.zeros_like(t)
sig_f = np.zeros_like(t)
wm = np.zeros_like(t)
# set initial values
wm[0] = wm0
# mu_f[0] = mu_f0
# sig_f[0] = sig_f0
for i in xrange(steps):
# 1st interpolation and lookup with
# exponentially filtered mu_ext for looking up omega,tau ..
weights_1 = interpolate_xy(mu_lookup[i] - wm[i] / C, sig_f[i], mu_range, sig_range)
omega = lookup_xy(omega_grid, weights_1)
tau = lookup_xy(tau_grid, weights_1)
tau_mu_f = lookup_xy(tau_mu_f_grid, weights_1)
tau_sigma_f = lookup_xy(tau_sigma_f_grid, weights_1)
# 2nd interpolation and lookup with
# mu_ext filtered by damped oscillatory function for looking up Vm and r
weights_2 = interpolate_xy(mu_f[i] - wm[i] / C, sig_f[i], mu_range, sig_range)
Vm = lookup_xy(Vmean_grid, weights_2)
r[i] = lookup_xy(r_grid, weights_2)
if rec:
mu_syn = get_mu_syn(K, J, mu_ext, delay_type, i, r, r_d, const_delay, taud, dt)
sigma_syn = get_sigma_syn(K, J, sig_ext, delay_type, i, r, r_d, const_delay, taud, dt)
else:
mu_syn = mu_ext[i]
sigma_syn = sig_ext[i]
# rhs of the equations
mu_lookup_rhs = (mu_syn - mu_lookup[i]) / tau_mu_f
sig_f_rhs = (sigma_syn - sig_f[i]) / tau_sigma_f
wm_rhs = (a[i] * (Vm - EW) - wm[i] + tauw * b[i] * r[i]) / tauw
# euler step
A = (tau ** 2 * omega ** 2 + 1) / tau
mu_f[i + 1] = mu_f[i] + dt * dmu_f[i]
dmu_f[i + 1] = dmu_f[i] + dt * (
(-2.0 / tau) * dmu_f[i] - (1.0 / tau ** 2 + omega ** 2) * mu_f[i] + A * (mu_syn / tau + dmu_ext_dt[i])
)
# indentical to the old model
mu_lookup[i + 1] = mu_lookup[i] + dt * mu_lookup_rhs
sig_f[i + 1] = sig_f[i] + dt * sig_f_rhs
wm[i + 1] = wm[i] + dt * wm_rhs
return (r * 1000.0, wm)
def sim_ln_bexdos(mu_ext, sig_ext, mu_range, sigma_range, B_mu_grid,
tau_mu_1_grid, tau_mu_2_grid, f0_mu_grid, tau_mua_grid,
tau_sigma_grid, Vm_grid, r_grid, dmu_ext_dt, C, K, J,
const_delay, delay_type, rec, taud, a, b, tauw, EW, t, dt,
steps, uni_int_order):
# todo: figure out how to deal with
# initialize arrays
x_mu = np.zeros_like(t)
y_mu = np.zeros_like(t)
z_mu = np.zeros_like(t)
mu_f = np.zeros_like(t)
mu_a = np.zeros_like(t)
mu_syn = np.zeros_like(t)
dmu_syn_dt = np.zeros_like(t)
sigma_syn = np.zeros_like(t)
sigma_f = np.zeros_like(t)
wm = np.zeros_like(t)
Vm = np.zeros_like(t)
r = np.zeros_like(t)
r_d = np.zeros_like(t)
inv_tau1 = np.zeros_like(t)
B_mu = np.zeros_like(t)
tau_mu_1 = np.zeros_like(t)
tau_mu_2 = np.zeros_like(t)
f0_mu = np.zeros_like(t)
tau_mua = np.zeros_like(t)
tau_sigma = np.zeros_like(t)
A_mu = np.zeros_like(t)
for i in xrange(steps):
for j in range(int(uni_int_order)):
# mu_a lookup
weights_1 = interpolate_xy(mu_a[i + j] - wm[i + j] / C,
sigma_f[i + j], mu_range, sigma_range)
B_mu[i + j] = lookup_xy(B_mu_grid, weights_1)
tau_mu_1[i + j] = lookup_xy(tau_mu_1_grid, weights_1)
inv_tau1[i + j] = tau_mu_1[i + j]
tau_mu_2[i + j] = lookup_xy(tau_mu_2_grid, weights_1)
# todo change this to omega
f0_mu[i + j] = lookup_xy(f0_mu_grid, weights_1)
# this is tau_mu_exp
tau_mua[i + j] = lookup_xy(tau_mua_grid, weights_1)
# this is tau_sigma_exp
tau_sigma[i + j] = lookup_xy(tau_sigma_grid, weights_1)
A_mu[i+j] = 1./tau_mu_1[i+j] - B_mu[i+j]*tau_mu_2[i+j]/\
((1.+(2.*np.pi*f0_mu[i+j]*tau_mu_2[i+j])**2)
*tau_mu_1[i+j])
# mu_f lookup
weights_2 = interpolate_xy(mu_f[i + j] - wm[i + j] / C,
sigma_f[i + j], mu_range, sigma_range)
Vm[i + j] = lookup_xy(Vm_grid, weights_2)
r[i + j] = lookup_xy(r_grid, weights_2)
if rec:
mu_syn[i + j] = get_mu_syn(K, J, mu_ext, delay_type, i + j, r,
r_d, const_delay, taud, dt)
sigma_syn[i + j] = get_sigma_syn(K, J, sig_ext, delay_type,
i + j, r, r_d, const_delay,
taud, dt)
# also compute the derivatives of the synaptic input
# in the case of exponentially distributed
# delays; compute dmu_syn_dt analytically
if delay_type == 2:
dmu_syn_dt[
i +
j] = dmu_ext_dt[i + j] + (r[i + j] - r_d[i + j]) / taud
# else finite differences mu_syn
else:
dmu_syn_dt[i +
j] = (mu_syn[i + j] - mu_syn[i + j - 1]) / dt
# this case corresponds to an UNCOUPLED POPULATION of neurons, i.e. K=0.
#todo: double check thist comutation
else:
mu_syn[i + j] = mu_ext[i + j]
sigma_syn[i + j] = sig_ext[i + j]
dmu_syn_dt[i + j] = dmu_ext_dt[i + j]
#euler step
if j == 0:
x_mu[i + 1] = x_mu[i] + dt * (A_mu[i] * mu_syn[i] -
x_mu[i] / tau_mu_1[i])
y_mu[i + 1] = y_mu[i] + dt * z_mu[i]
z_mu[i + 1] = z_mu[i] + dt * (
B_mu[i] * mu_syn[i] / tau_mu_2[i] +
B_mu[i] * dmu_ext_dt[i] - 2. * z_mu[i] / tau_mu_2[i] -
(1. / tau_mu_2[i]**2 +
(2. * np.pi * f0_mu[i])**2) * y_mu[i])
mu_f[i + 1] = x_mu[i + 1] + y_mu[i + 1]
mu_a[i + 1] = mu_a[i] + dt * (mu_syn[i] -
mu_a[i]) / dt #dt #tau_mua[i]
sigma_f[i + 1] = sigma_f[i] + dt * (sigma_syn[i] -
sigma_f[i]) / tau_sigma[i]
wm[i + 1] = wm[i] + dt * (a[i] * (Vm[i] - EW) - wm[i] +
tauw * b[i] * r[i]) / tauw
#additional heun step #TODO: adjust according to euler above
if j == 1:
x_mu[i + 1] = x_mu[i] + dt / 2. * (
(mu_syn[i] - x_mu[i] / tau_mu_1[i]) +
(mu_syn[i + 1] - x_mu[i + 1] / tau_mu_1[i + 1]))
y_mu[i + 1] = y_mu[i] + dt / 2. * (z_mu[i] + z_mu[i + 1])
z_mu[i + 1] = z_mu[i] + dt / 2. * (
(mu_syn[i] / tau_mu_2[i] + dmu_ext_dt[i] -
2. * z_mu[i] / tau_mu_2[i] -
(1. / tau_mu_2[i]**2 +
(2. * np.pi * f0_mu[i])**2) * y_mu[i]) +
(mu_syn[i + 1] / tau_mu_2[i + 1] + dmu_ext_dt[i + 1] -
2. * z_mu[i + 1] / tau_mu_2[i + 1] -
(1. / tau_mu_2[i + 1]**2 +
(2. * np.pi * f0_mu[i + 1])**2) * y_mu[i + 1]))
# no heun scheme for that step
mu_f[i + 1] = A_mu[i] * x_mu[i + 1] + B_mu[i] * y_mu[i + 1]
mu_a[i + 1] = mu_a[i] + dt / 2. * (
(mu_syn[i] - mu_a[i]) / tau_mua[i] +
(mu_syn[i + 1] - mu_a[i + 1]) / tau_mua[i + 1])
sigma_f[i + 1] = sigma_f[i] + dt / 2. * (
(sigma_syn[i] - sigma_f[i]) / tau_sigma[i] +
(sigma_syn[i + 1] - sigma_f[i + 1]) / tau_sigma[i + 1])
wm[i + 1] = wm[i] + dt / 2. * (
(a[i] * (Vm[i] - EW) - wm[i] + tauw * b[i] * r[i]) / tauw +
(a[i + 1] * (Vm[i + 1] - EW) - wm[i + 1] +
tauw * b[i + 1] * r[i + 1]) / tauw)
return (r * 1000., wm, Vm)
def sim_spec1(mu_ext,
sigma_ext,
map1_Vmean,
map_r_inf,
mu_range,
sigma_range,
map_lambda_1,
tauw,
dt,
steps,
C,
a,
b,
EW,
s0,
r0,
w0,
rec,
K,
J,
delay_type,
n_d,
taud,
uni_int_order,
rectify,
grid_warn=True):
# small optimization(s)
dt_tauw = dt / tauw
b_tauw = b * tauw
# initialize arrays
r = np.zeros(steps + 1)
r_d = np.zeros(steps + 1)
s = np.zeros(steps + 1)
wm = np.zeros(steps + 1)
Re = np.zeros(steps + 1)
Im = np.zeros(steps + 1)
Vm_inf = np.zeros(steps + 1)
r_inf = np.zeros(steps + 1)
r_diff = np.zeros(steps + 1)
lambda_1_real = np.zeros(steps + 1)
mu_total = np.zeros(steps + 1)
# write initial condition into array
r[0] = r0
s[0] = s0
wm[0] = w0
for i in range(steps):
for j in xrange(int(uni_int_order)):
if rec:
mu_syn = get_mu_syn(K, J, mu_ext, delay_type, i + j, r, r_d,
n_d, taud, dt)
sigma_syn = get_sigma_syn(K, J, sigma_ext, delay_type, i + j,
r, r_d, n_d, taud, dt)
# this case corresponds to an UNCOUPLED POPULATION of neurons, i.e. K=0.
else:
mu_syn = mu_ext[i + j]
sigma_syn = sigma_ext[i + j]
#effective mu
mu_eff = mu_syn - wm[i + j] / C
# grid warning
if grid_warn and j == 0:
outside_grid_warning(mu_eff, sigma_syn, mu_range, sigma_range,
dt * i)
# interpolate
weights = interpolate_xy(mu_eff, sigma_syn, mu_range, sigma_range)
# lookup
Vm_inf[i + j] = lookup_xy(map1_Vmean, weights)
r_inf[i + j] = lookup_xy(map_r_inf, weights)
lambda_1 = lookup_xy(map_lambda_1, weights)
lambda_1_real[i + j] = lambda_1.real # save real part of lambda(t)
# split lambda in real and imaginary part
Re[i + j] = lambda_1.real
Im[i + j] = lambda_1.imag
r_diff[i + j] = r[i + j] - r_inf[i + j]
mu_total[i + j] = mu_eff
# j == 0: corresponds to a simple Euler method.
# If j reaches 1 (-> j!=0) the ELSE block is executed
# which updates using the HEUN scheme.
if j == 0:
r[i + 1] = r[i] + dt * (Re[i] * r_diff[i] - Im[i] * s[i])
s[i + 1] = s[i] + dt * (Im[i] * r_diff[i] + Re[i] * s[i])
wm[i+1] = wm[i] + dt_tauw * \
(a[i] * (Vm_inf[i] - EW) - wm[i] + b_tauw[i] * r[i])
# only perform Heun integration step if 'uni_int_order' == 2
else:
r[i + 1] = r[i] + dt / 2 * (
(Re[i] * r_diff[i] - Im[i] * s[i]) +
(Re[i + 1] * r_diff[i + 1] - Im[i + 1] * s[i + 1]))
s[i + 1] = s[i] + dt / 2 * (
(Im[i] * r_diff[i] + Re[i] * s[i]) +
(Im[i + 1] * r_diff[i + 1] + Re[i + 1] * s[i + 1]))
wm[i + 1] = wm[i] + dt_tauw / 2 * (
(a[i] * (Vm_inf[i] - EW) - wm[i] + b_tauw[i] * r[i]) +
(a[i + 1] * (Vm_inf[i + 1] - EW) - wm[i + 1] +
b_tauw[i + 1] * r[i + 1]))
# set variables to zero if they would be integrated below 0
if rectify and r[i + 1] < 0.:
r[i + 1] = 0.
s[i + 1] = 0.
return (r * 1000, wm, lambda_1_real, mu_total, Vm_inf)
def sim_spec2m_simple_HEUN(mu_ext, sigma_ext,steps,dt,EW, a,b,C, tauw,
map_Vmean, map_rss, mu_range2, sigma_range2,
map_eig1, map_eig_mattia, rec,K,J,delay_type,n_d,
taud, r0, s0, w0, uni_int_order):
# optimazations
dt_tauw = dt/tauw
b_tauw = b*tauw
# initialize arrays
r = np.zeros(steps+1)
dr = np.zeros(steps+1)
r_d = np.zeros(steps+1)
s = np.zeros(steps+1)
wm = np.zeros(steps+1)
# more arrays for HEUN method
Vm_inf = np.zeros(steps+1)
r_inf = np.zeros(steps+1)
lambda1_plus_lambda2 = np.zeros(steps+1)
lambda1_times_lambda2 = np.zeros(steps+1)
# write initial condition into array
r[0] = r0
s[0] = s0
wm[0] = w0
for i in xrange(steps):
for j in xrange(int(uni_int_order)): # i --> i + j = i + 1 (for second round)
if rec:
mu_syn = get_mu_syn(K,J,mu_ext,delay_type,i+j,r,r_d,n_d,taud,dt)
sigma_syn = get_sigma_syn(K,J,sigma_ext,delay_type,i+j,r,r_d,n_d,taud,dt)
else:
mu_syn = mu_ext[i+j]
sigma_syn = sigma_ext[i+j]
# compute effective mu
mu_tot = mu_syn - wm[i+j] / C
# interpolate
# weights_quant = interpolate_xy(mu_tot, sigma_syn, mu_range1, sigma_range1)
weights_eig = interpolate_xy(mu_tot, sigma_syn, mu_range2, sigma_range2)
# lookup
Vm_inf[i+j] = lookup_xy(map_Vmean, weights_eig)
r_inf[i+j] = lookup_xy(map_rss, weights_eig)
lambda1 = lookup_xy(map_eig1, weights_eig)
lambda2 = lookup_xy(map_eig_mattia, weights_eig)
# results of lambda1+lambda2 and lambda1*lambda2
# are always real --> eliminate imaginary parts
lambda1_plus_lambda2[i+j] = (lambda1+lambda2).real
lambda1_times_lambda2[i+j] = (lambda1*lambda2).real
# TODO: add rectify of r via toggle (def: on)
if j == 0:
dr[i+1] = dr[i] + dt * (lambda1_times_lambda2[i] * (r_inf[i]-r[i])
+ lambda1_plus_lambda2[i] * dr[i])
r[i+1] = r[i] + dt * dr[i]
wm[i+1] = wm[i] + dt_tauw * (a[i] * (Vm_inf[i] - EW)
- wm[i] + b_tauw[i] * r[i])
# only perform Heun integration step if 'uni_int_order' == 2
# to compute the updates state variables with the trapezian rule
elif j == 1:
dr[i+1] = dr[i] + dt/2. * ( (lambda1_times_lambda2[i] * (r_inf[i]-r[i])
+ lambda1_plus_lambda2[i] * dr[i])
+ (lambda1_times_lambda2[i+1] * (r_inf[i+1]-r[i+1])
+ lambda1_plus_lambda2[i+1] * dr[i+1]))
r[i+1] = r[i] + dt/2. * (dr[i]+dr[i+1])
wm[i+1] = wm[i] + dt_tauw/2. * ( (a[i] * (Vm_inf[i] - EW)
- wm[i] + b_tauw[i] * r[i])
+(a[i+1] * (Vm_inf[i+1] - EW)
- wm[i+1] + b_tauw[i+1] * r[i+1]))
# re
return (r*1000., wm)
def sim_spec2m_simple(mu_ext, sigma_ext,steps,dt,EW, a,b,C, tauw,
map_Vmean, map_rss, mu_range2, sigma_range2,
map_eig1, map_eig_mattia, rec,K,J,delay_type,n_d,
taud, r0, s0, w0):
# optimazations
dt_tauw = dt/tauw
b_tauw = b*tauw
# initialize arrays
r = np.zeros(steps+1)
dr = np.zeros(steps+1)
r_d = np.zeros(steps+1)
s = np.zeros(steps+1)
wm = np.zeros(steps+1)
# write initial condition into array
r[0] = r0
s[0] = s0
wm[0] = w0
for i in xrange(steps):
if rec:
mu_syn = get_mu_syn(K,J,mu_ext,delay_type,i,r,r_d,n_d,taud,dt)
sigma_syn = get_sigma_syn(K,J,sigma_ext,delay_type,i,r,r_d,n_d,taud,dt)
else:
mu_syn = mu_ext[i]
sigma_syn = sigma_ext[i]
# compute effective mu
mu_tot = mu_syn - wm[i] / C
# interpolate
# weights_quant = interpolate_xy(mu_tot, sigma_syn, mu_range1, sigma_range1)
weights_eig = interpolate_xy(mu_tot, sigma_syn, mu_range2, sigma_range2)
# lookup
Vm_inf = lookup_xy(map_Vmean, weights_eig)
r_inf = lookup_xy(map_rss, weights_eig)
lambda1 = lookup_xy(map_eig1, weights_eig)
lambda2 = lookup_xy(map_eig_mattia, weights_eig)
# results of lambda1+lambda2 and lambda1*lambda2
# are always real --> eliminate imaginary parts
lambda1_plus_lambda2 = (lambda1+lambda2).real
lambda1_times_lambda2 = (lambda1*lambda2).real
# euler step
# the model equations below are equal to the ones of
# the spectral2m model for a feedforward setting without coupling and without adaptation
dr[i+1] = dr[i] + dt * (lambda1_times_lambda2 * (r_inf-r[i]) + lambda1_plus_lambda2 * dr[i])
# r_prelim = r[i] + dt * dr[i]
# assert that r[i+1] is leq than 0
# r[i+1] = r[i] + dt * dr[i]
# r[i+1] = r_prelim if r_prelim > 0. else 0.
r[i+1] = r[i] + dt * dr[i]
# TODO: add rectify of r via toggle (def: on)
# adaptation
wm[i+1] = wm[i] + dt_tauw * (a[i] * (Vm_inf - EW) - wm[i] + b_tauw[i] * r[i])
# rates computed in [kHz] or [1/ms] therefore change to [Hz]
# return (r*1000., wm)
return (r*1000., wm)
def sim_spec2m_simple(mu_ext, sigma_ext, steps, dt, EW, a, b, C, tauw,
map_Vmean, map_rss, mu_range2, sigma_range2, map_eig1,
map_eig_mattia, rec, K, J, delay_type, n_d, taud, r0, s0,
w0):
# optimazations
dt_tauw = dt / tauw
b_tauw = b * tauw
# initialize arrays
r = np.zeros(steps + 1)
dr = np.zeros(steps + 1)
r_d = np.zeros(steps + 1)
s = np.zeros(steps + 1)
wm = np.zeros(steps + 1)
# write initial condition into array
r[0] = r0
s[0] = s0
wm[0] = w0
for i in xrange(steps):
if rec:
mu_syn = get_mu_syn(K, J, mu_ext, delay_type, i, r, r_d, n_d, taud,
dt)
sigma_syn = get_sigma_syn(K, J, sigma_ext, delay_type, i, r, r_d,
n_d, taud, dt)
else:
mu_syn = mu_ext[i]
sigma_syn = sigma_ext[i]
# compute effective mu
mu_tot = mu_syn - wm[i] / C
# interpolate
# weights_quant = interpolate_xy(mu_tot, sigma_syn, mu_range1, sigma_range1)
weights_eig = interpolate_xy(mu_tot, sigma_syn, mu_range2,
sigma_range2)
# lookup
Vm_inf = lookup_xy(map_Vmean, weights_eig)
r_inf = lookup_xy(map_rss, weights_eig)
lambda1 = lookup_xy(map_eig1, weights_eig)
lambda2 = lookup_xy(map_eig_mattia, weights_eig)
# results of lambda1+lambda2 and lambda1*lambda2
# are always real --> eliminate imaginary parts
lambda1_plus_lambda2 = (lambda1 + lambda2).real
lambda1_times_lambda2 = (lambda1 * lambda2).real
# euler step
# the model equations below are equal to the ones of
# the spectral2m model for a feedforward setting without coupling and without adaptation
dr[i +
1] = dr[i] + dt * (lambda1_times_lambda2 *
(r_inf - r[i]) + lambda1_plus_lambda2 * dr[i])
# r_prelim = r[i] + dt * dr[i]
# assert that r[i+1] is leq than 0
# r[i+1] = r[i] + dt * dr[i]
# r[i+1] = r_prelim if r_prelim > 0. else 0.
r[i + 1] = r[i] + dt * dr[i]
# TODO: add rectify of r via toggle (def: on)
# adaptation
wm[i +
1] = wm[i] + dt_tauw * (a[i] *
(Vm_inf - EW) - wm[i] + b_tauw[i] * r[i])
# rates computed in [kHz] or [1/ms] therefore change to [Hz]
# return (r*1000., wm)
return (r * 1000., wm)
def sim_spec1(mu_ext, sigma_ext, map1_Vmean, map_r_inf, mu_range,
sigma_range, map_lambda_1, tauw, dt, steps, C,a ,b, EW,
s0, r0,w0, rec,K,J,delay_type,n_d,taud, uni_int_order,
rectify):
# optimizations
dt_tauw = dt/tauw
b_tauw = b*tauw
# initialize real arrays
r = np.zeros(steps+1)
r_d = np.zeros(steps+1)
s = np.zeros(steps+1)
wm = np.zeros(steps+1)
Re = np.zeros(steps+1)
Im = np.zeros(steps+1)
Vm_inf = np.zeros(steps+1)
r_inf = np.zeros(steps+1)
r_diff = np.zeros(steps+1)
lambda_1_real = np.zeros(steps+1)
mu_total = np.zeros(steps+1)
# write initial condition into array
r[0] = r0
s[0] = s0
wm[0] = w0
for i in range(steps):
# break loop after 1 iteration for Euler
# two for Heun
for j in xrange(int(uni_int_order)): # i --> i + j = i + 1 (for second round)
if rec:
mu_syn = get_mu_syn(K, J, mu_ext,delay_type,i+j,r,r_d,n_d,taud,dt)
sigma_syn = get_sigma_syn(K, J, sigma_ext,delay_type,i+j,r,r_d,n_d,taud,dt)
# this case corresponds to an UNCOUPLED POPULATION of neurons, i.e. K=0.
else:
mu_syn = mu_ext[i+j]
sigma_syn = sigma_ext[i+j]
#effective mu
mu_eff = mu_syn - wm[i+j] / C
# interpolate
weights = interpolate_xy(mu_eff, sigma_syn, mu_range, sigma_range)
# lookup
Vm_inf[i+j] = lookup_xy(map1_Vmean, weights)
r_inf[i+j] = lookup_xy(map_r_inf, weights)
lambda_1 = lookup_xy(map_lambda_1, weights)
lambda_1_real[i+j] = lambda_1.real # save real part of lambda(t)
# split lambda in real and imaginary part
Re[i+j] = lambda_1.real
Im[i+j] = lambda_1.imag
r_diff[i+j] = r[i+j] - r_inf[i+j]
mu_total[i+j] = mu_eff
# TODO: add rectify of r via toggle (def: on)
# integration step Euler
if j == 0:
r[i+1] = r[i] + dt * (Re[i] * r_diff[i] - Im[i] * s[i])
s[i+1] = s[i] + dt * (Im[i] * r_diff[i] + Re[i] * s[i])
wm[i+1] = wm[i] + dt_tauw * \
(a[i] * (Vm_inf[i] - EW) - wm[i] + b_tauw[i] * r[i])
# only perform Heun integration step if 'uni_int_order' == 2
elif j == 1:
r[i+1] = r[i] + dt/2 * ( (Re[i] * r_diff[i] - Im[i] * s[i])
+ (Re[i+1] * r_diff[i+1] - Im[i+1] * s[i+1]))
s[i+1] = s[i] + dt/2 * ( (Im[i] * r_diff[i] + Re[i] * s[i])
+ (Im[i+1] * r_diff[i+1] + Re[i+1] * s[i+1]))
wm[i+1] = wm[i] + dt_tauw/2 * ( (a[i] * (Vm_inf[i] - EW) -
wm[i] + b_tauw[i] * r[i])
+(a[i+1] * (Vm_inf[i+1] - EW) -
wm[i+1] + b_tauw[i+1] * r[i+1]))
# set variables to zero if they would be integrated below 0
if rectify and r[i+1] < 0.:
r[i+1] = 0.
s[i+1] = 0.
return (r*1000, wm, lambda_1_real, mu_total, Vm_inf)
def sim_ln_dos(mu_ext, sig_ext, dmu_ext_dt, t, dt, steps,
mu_range, sig_range, omega_grid,tau_grid,
tau_mu_f_grid, tau_sigma_f_grid, Vmean_grid,
r_grid,a,b,C,wm0, EW, tauw, rec, K, J, delay_type,
const_delay,taud,uni_int_order, grid_warn = True):
# small optimization(s)
b_tauW = b * tauw
# initialize arrays
r = np.zeros_like(t)
r_d = np.zeros_like(t)
mu_f = np.zeros_like(t)
mu_total = np.zeros_like(t)
dmu_f = np.zeros_like(t) #aux. var for integration
dmu_syn_dt = np.zeros_like(t)
sig_f = np.zeros_like(t)
wm = np.zeros_like(t)
Vm = np.zeros_like(t)
mu_syn = np.zeros_like(t)
sigma_syn = np.zeros_like(t)
omega = np.zeros_like(t)
tau = np.zeros_like(t)
tau_mu_f = np.zeros_like(t)
tau_sigma_f = np.zeros_like(t)
A = np.zeros_like(t)
# set initial value of wm
wm[0] = wm0
for i in xrange(steps):
for j in range(int(uni_int_order)):
# outside grid warning
if grid_warn and j == 0:
outside_grid_warning(mu_f[i+j]-wm[i+j]/C, sig_f[i+j],
mu_range, sig_range, dt*i)
# weights for looking up mean membrane voltage (Vm)
# and the firing rate (r)
weights_2 = interpolate_xy(mu_f[i+j]-wm[i+j]/C, sig_f[i+j],
mu_range, sig_range)
Vm[i+j] = lookup_xy(Vmean_grid,weights_2)
r[i+j] = lookup_xy(r_grid,weights_2)
# with recurrency compute the synaptic mean and sigma
# by generative functions
if rec:
mu_syn[i+j] = get_mu_syn(K,J,mu_ext,delay_type,i+j,
r,r_d,const_delay,taud,dt)
sigma_syn[i+j] = get_sigma_syn(K,J,sig_ext,delay_type,i+j,
r,r_d,const_delay,taud,dt)
# exponentially distributed delays -> compute dmu_syn_dt analytically
if delay_type == 2:
dmu_syn_dt[i+j] = dmu_ext_dt[i+j] + (r[i+j]-r_d[i+j])/taud
# in all other rec cases compute dmu_syn by finite differences
else:
dmu_syn_dt[i+j] = (mu_syn[i+j]-mu_syn[i+j-1])/dt
# w/o recurrency (i.e. in the case of an upcoupled populatoin of neurons, K=0)
# -> mu_syn, sigma_syn and dmu_syn_dt equal the external quantities
else:
mu_syn[i+j] = mu_ext[i+j]
sigma_syn[i+j] = sig_ext[i+j]
dmu_syn_dt[i+j] = dmu_ext_dt[i+j]
# save total mu
mu_total[i+j] = mu_syn[i+j]-wm[i+j]/C
# weights for looking up omega, tau, tau_mu_f, tau_sigma_f
weights_1 = interpolate_xy(mu_total[i+j],sigma_syn[i+j],
mu_range, sig_range)
omega[i+j] = lookup_xy(omega_grid, weights_1)
tau[i+j] = lookup_xy(tau_grid, weights_1)
tau_mu_f[i+j] = lookup_xy(tau_mu_f_grid, weights_1)
tau_sigma_f[i+j] = lookup_xy(tau_sigma_f_grid, weights_1)
A[i+j] = (tau[i+j]**2*omega[i+j]**2+1)/tau[i+j]
# j == 0: corresponds to a simple Euler method.
# If j reaches 1 (-> j!=0) the ELSE block is executed
# which updates using the HEUN scheme.
if j == 0:
mu_f[i+1] = mu_f[i] + dt*dmu_f[i]
dmu_f[i+1] = dmu_f[i] + dt*( (-2./tau[i])*dmu_f[i]
-(1./tau[i]**2 + omega[i]**2)*mu_f[i]
+A[i]*(mu_syn[i]/tau[i]+dmu_syn_dt[i]))
sig_f[i+1] = sig_f[i] + dt*(sigma_syn[i]-sig_f[i])/tau_sigma_f[i]
wm[i+1] = wm[i] + dt*(a[i]*(Vm[i] - EW) - wm[i] + b_tauW[i] * r[i])/tauw
# only perform Heun integration step if 'uni_int_order' == 2
else:
mu_f[i+1] = mu_f[i] + dt/2.*(dmu_f[i]+dmu_f[i+1])
dmu_f[i+1] = dmu_f[i] + dt/2. * (( (-2./tau[i])*dmu_f[i]
-(1./tau[i]**2 + omega[i]**2)*mu_f[i]
+A[i]*(mu_syn[i]/tau[i]+dmu_syn_dt[i]))
+( (-2./tau[i+1])*dmu_f[i+1]
-(1./tau[i+1]**2 + omega[i+1]**2)*mu_f[i+1]
+A[i+1]*(mu_syn[i+1]/tau[i+1]+dmu_syn_dt[i+1])))
sig_f[i+1] = sig_f[i] + dt/2.*((sigma_syn[i]-sig_f[i])/tau_sigma_f[i]
+(sigma_syn[i+1]-sig_f[i+1])/tau_sigma_f[i+1])
wm[i+1] = wm[i] + dt/2.*((a[i]*(Vm[i] - EW) - wm[i] + b_tauW[i] * r[i])/tauw
+(a[i+1]*(Vm[i+1] - EW) - wm[i+1] + b_tauW[i+1] * r[i+1])/tauw)
# return results tuple
return (r*1000., wm, mu_total, Vm)
def sim_ln_exp(mu_ext,
sigma_ext,
mu_range,
sigma_range,
map_Vmean,
map_r,
map_tau_mu_f,
map_tau_sigma_f,
L,
muf0,
sigma_f0,
w_m0,
a,
b,
C,
dt,
tauW,
Ew,
rec,
K,
J,
delay_type,
const_delay,
taud,
uni_int_order,
grid_warn=True):
# small optimization(s)
b_tauW = b * tauW
# initialize arrays
r_d = np.zeros(L + 1)
mu_f = np.zeros(L + 1)
sigma_f = np.zeros(L + 1)
mu_syn = np.zeros(L + 1)
mu_total = np.zeros(L + 1)
sigma_syn = np.zeros(L + 1)
w_m = np.zeros(L + 1)
rates = np.zeros(L + 1)
tau_mu_f = np.zeros(L + 1)
tau_sigma_f = np.zeros(L + 1)
Vm = np.zeros(L + 1)
# set initial values
w_m[0] = w_m0
mu_f[0] = muf0
sigma_f[0] = sigma_f0
for i in xrange(L):
for j in xrange(int(uni_int_order)):
# interpolate
mu_f_eff = mu_f[i + j] - w_m[i + j] / C
# save for param exploration
# todo remove this again
mu_total[i + j] = mu_f_eff
# grid warning
if grid_warn and j == 0:
outside_grid_warning(mu_f_eff, sigma_f[i + j], mu_range,
sigma_range, dt * i)
# interpolate
weights = interpolate_xy(mu_f_eff, sigma_f[i + j], mu_range,
sigma_range)
# lookup
Vm[i + j] = lookup_xy(map_Vmean, weights)
rates[i + j] = lookup_xy(map_r, weights)
tau_mu_f[i + j] = lookup_xy(map_tau_mu_f, weights)
tau_sigma_f[i + j] = lookup_xy(map_tau_sigma_f, weights)
if rec:
mu_syn[i + j] = get_mu_syn(K, J, mu_ext, delay_type, i + j,
rates, r_d, const_delay, taud, dt)
sigma_syn[i + j] = get_sigma_syn(K, J, sigma_ext, delay_type,
i + j, rates, r_d,
const_delay, taud, dt)
# this case corresponds to an UNCOUPLED POPULATION of neurons, i.e. K=0.
else:
mu_syn[i + j] = mu_ext[i + j]
sigma_syn[i + j] = sigma_ext[i + j]
# j == 0: corresponds to a simple Euler method.
# If j reaches 1 (-> j!=0) the ELSE block is executed
# which updates using the HEUN scheme.
if j == 0:
mu_f[i+1] = mu_f[i] \
+ dt * (mu_syn[i] - mu_f[i])/tau_mu_f[i]
sigma_f[i+1] = sigma_f[i] \
+ dt * (sigma_syn[i] - sigma_f[i])/tau_sigma_f[i]
w_m[i+1] = w_m[i] + dt \
* (a[i]*(Vm[i] - Ew) - w_m[i]
+ b_tauW[i] * (rates[i]))/tauW
# only perform Heun integration step if 'uni_int_order' == 2
else:
mu_f[i+1] = mu_f[i] \
+ dt/2. * ((mu_syn[i] - mu_f[i])/tau_mu_f[i]
+(mu_syn[i+1] - mu_f[i+1])/tau_mu_f[i+1])
sigma_f[i+1] = sigma_f[i] \
+ dt/2. * ((sigma_syn[i] - sigma_f[i])/tau_sigma_f[i]
+(sigma_syn[i+1] - sigma_f[i+1])/tau_sigma_f[i+1])
w_m[i+1] = w_m[i] \
+ dt/2. * (((a[i]*(Vm[i] - Ew) - w_m[i]
+ b_tauW[i] * (rates[i]))/tauW)
+((a[i+1]*(Vm[i+1] - Ew) - w_m[i+1]
+ b_tauW[i+1] * (rates[i+1]))/tauW))
#order of return tuple should always be rates, w_m, Vm, etc...
return (rates * 1000., w_m, Vm, tau_mu_f, tau_sigma_f, mu_f, sigma_f,
mu_total)
def sim_ln_bexdos(mu_ext, sig_ext, mu_range, sigma_range,
B_mu_grid, tau_mu_1_grid, tau_mu_2_grid,
f0_mu_grid, tau_mua_grid, tau_sigma_grid,
Vm_grid, r_grid, dmu_ext_dt,
C, K, J, const_delay, delay_type,
rec, taud,
a,b,tauw, EW,
t, dt, steps, uni_int_order):
# todo: figure out how to deal with
# initialize arrays
x_mu = np.zeros_like(t)
y_mu = np.zeros_like(t)
z_mu = np.zeros_like(t)
mu_f = np.zeros_like(t)
mu_a = np.zeros_like(t)
mu_syn = np.zeros_like(t)
dmu_syn_dt = np.zeros_like(t)
sigma_syn = np.zeros_like(t)
sigma_f = np.zeros_like(t)
wm = np.zeros_like(t)
Vm = np.zeros_like(t)
r = np.zeros_like(t)
r_d = np.zeros_like(t)
inv_tau1 = np.zeros_like(t)
B_mu = np.zeros_like(t)
tau_mu_1 = np.zeros_like(t)
tau_mu_2 = np.zeros_like(t)
f0_mu = np.zeros_like(t)
tau_mua = np.zeros_like(t)
tau_sigma = np.zeros_like(t)
A_mu = np.zeros_like(t)
for i in xrange(steps):
for j in range(int(uni_int_order)):
# mu_a lookup
weights_1 = interpolate_xy(mu_a[i+j]-wm[i+j]/C, sigma_f[i+j], mu_range, sigma_range)
B_mu[i+j] = lookup_xy(B_mu_grid, weights_1)
tau_mu_1[i+j] = lookup_xy(tau_mu_1_grid,weights_1)
inv_tau1[i+j] = tau_mu_1[i+j]
tau_mu_2[i+j] = lookup_xy(tau_mu_2_grid,weights_1)
# todo change this to omega
f0_mu[i+j] = lookup_xy(f0_mu_grid, weights_1)
# this is tau_mu_exp
tau_mua[i+j] = lookup_xy(tau_mua_grid, weights_1)
# this is tau_sigma_exp
tau_sigma[i+j] = lookup_xy(tau_sigma_grid, weights_1)
A_mu[i+j] = 1./tau_mu_1[i+j] - B_mu[i+j]*tau_mu_2[i+j]/\
((1.+(2.*np.pi*f0_mu[i+j]*tau_mu_2[i+j])**2)
*tau_mu_1[i+j])
# mu_f lookup
weights_2 = interpolate_xy(mu_f[i+j]-wm[i+j]/C, sigma_f[i+j], mu_range, sigma_range)
Vm[i+j] = lookup_xy(Vm_grid, weights_2)
r[i+j] = lookup_xy(r_grid, weights_2)
if rec:
mu_syn[i+j] = get_mu_syn(K,J,mu_ext,delay_type,i+j,
r,r_d,const_delay,taud,dt)
sigma_syn[i+j] = get_sigma_syn(K,J,sig_ext,delay_type,i+j,
r,r_d,const_delay,taud,dt)
# also compute the derivatives of the synaptic input
# in the case of exponentially distributed
# delays; compute dmu_syn_dt analytically
if delay_type == 2:
dmu_syn_dt[i+j] = dmu_ext_dt[i+j] + (r[i+j]-r_d[i+j])/taud
# else finite differences mu_syn
else:
dmu_syn_dt[i+j] = (mu_syn[i+j]-mu_syn[i+j-1])/dt
# this case corresponds to an UNCOUPLED POPULATION of neurons, i.e. K=0.
#todo: double check thist comutation
else:
mu_syn[i+j] = mu_ext[i+j]
sigma_syn[i+j] = sig_ext[i+j]
dmu_syn_dt[i+j] = dmu_ext_dt[i+j]
#euler step
if j == 0:
x_mu[i+1] = x_mu[i] + dt*(A_mu[i]*mu_syn[i] - x_mu[i]/tau_mu_1[i])
y_mu[i+1] = y_mu[i] + dt*z_mu[i]
z_mu[i+1] = z_mu[i] + dt*(B_mu[i]*mu_syn[i]/tau_mu_2[i] + B_mu[i]*dmu_ext_dt[i]-2.*z_mu[i]/tau_mu_2[i]
-(1./tau_mu_2[i]**2 + (2.*np.pi*f0_mu[i])**2)*y_mu[i])
mu_f[i+1] = x_mu[i+1] + y_mu[i+1]
mu_a[i+1] = mu_a[i] + dt*(mu_syn[i]-mu_a[i])/dt #dt #tau_mua[i]
sigma_f[i+1] = sigma_f[i] + dt*(sigma_syn[i]-sigma_f[i])/tau_sigma[i]
wm[i+1] = wm[i] + dt*(a[i]*(Vm[i] - EW) - wm[i] + tauw * b[i] * r[i])/tauw
#additional heun step #TODO: adjust according to euler above
if j == 1:
x_mu[i+1] = x_mu[i] + dt/2.*((mu_syn[i] - x_mu[i]/tau_mu_1[i])
+(mu_syn[i+1] - x_mu[i+1]/tau_mu_1[i+1]))
y_mu[i+1] = y_mu[i] + dt/2.*(z_mu[i]+z_mu[i+1])
z_mu[i+1] = z_mu[i] + dt/2.*((mu_syn[i]/tau_mu_2[i] + dmu_ext_dt[i]-2.*z_mu[i]/tau_mu_2[i]
-(1./tau_mu_2[i]**2 + (2.*np.pi*f0_mu[i])**2)*y_mu[i])
+(mu_syn[i+1]/tau_mu_2[i+1] + dmu_ext_dt[i+1]-2.*z_mu[i+1]/tau_mu_2[i+1]
-(1./tau_mu_2[i+1]**2 + (2.*np.pi*f0_mu[i+1])**2)*y_mu[i+1]))
# no heun scheme for that step
mu_f[i+1] = A_mu[i]*x_mu[i+1] + B_mu[i]*y_mu[i+1]
mu_a[i+1] = mu_a[i] + dt/2.*((mu_syn[i]-mu_a[i])/tau_mua[i]
+(mu_syn[i+1]-mu_a[i+1])/tau_mua[i+1])
sigma_f[i+1] = sigma_f[i] + dt/2.*((sigma_syn[i]-sigma_f[i])/tau_sigma[i]
+(sigma_syn[i+1]-sigma_f[i+1])/tau_sigma[i+1])
wm[i+1] = wm[i] + dt/2.*((a[i]*(Vm[i] - EW) - wm[i] + tauw * b[i] * r[i])/tauw
+(a[i+1]*(Vm[i+1] - EW) - wm[i+1] + tauw * b[i+1] * r[i+1])/tauw)
return (r*1000., wm, Vm)
def sim_ln_dosc_UPDATE_without_HEUN(mu_ext, sig_ext, dmu_ext_dt, t, dt, steps,
mu_range, sig_range, omega_grid, tau_grid,
tau_mu_f_grid, tau_sigma_f_grid,
Vmean_grid, r_grid, a, b, C, wm0, EW, tauw,
rec, K, J, delay_type, const_delay, taud):
# initialize arrays
r = np.zeros_like(t)
r_d = np.zeros_like(t)
mu_f = np.zeros_like(t)
dmu_f = np.zeros_like(t) #aux. var for integration
mu_lookup = np.zeros_like(t)
sig_f = np.zeros_like(t)
wm = np.zeros_like(t)
# set initial values
wm[0] = wm0
# mu_f[0] = mu_f0
# sig_f[0] = sig_f0
for i in xrange(steps):
# 1st interpolation and lookup with
# exponentially filtered mu_ext for looking up omega,tau ..
weights_1 = interpolate_xy(mu_lookup[i] - wm[i] / C, sig_f[i],
mu_range, sig_range)
omega = lookup_xy(omega_grid, weights_1)
tau = lookup_xy(tau_grid, weights_1)
tau_mu_f = lookup_xy(tau_mu_f_grid, weights_1)
tau_sigma_f = lookup_xy(tau_sigma_f_grid, weights_1)
# 2nd interpolation and lookup with
# mu_ext filtered by damped oscillatory function for looking up Vm and r
weights_2 = interpolate_xy(mu_f[i] - wm[i] / C, sig_f[i], mu_range,
sig_range)
Vm = lookup_xy(Vmean_grid, weights_2)
r[i] = lookup_xy(r_grid, weights_2)
if rec:
mu_syn = get_mu_syn(K, J, mu_ext, delay_type, i, r, r_d,
const_delay, taud, dt)
sigma_syn = get_sigma_syn(K, J, sig_ext, delay_type, i, r, r_d,
const_delay, taud, dt)
else:
mu_syn = mu_ext[i]
sigma_syn = sig_ext[i]
# rhs of the equations
mu_lookup_rhs = (mu_syn - mu_lookup[i]) / tau_mu_f
sig_f_rhs = (sigma_syn - sig_f[i]) / tau_sigma_f
wm_rhs = (a[i] * (Vm - EW) - wm[i] + tauw * b[i] * r[i]) / tauw
# euler step
A = (tau**2 * omega**2 + 1) / tau
mu_f[i + 1] = mu_f[i] + dt * dmu_f[i]
dmu_f[i +
1] = dmu_f[i] + dt * ((-2. / tau) * dmu_f[i] -
(1. / tau**2 + omega**2) * mu_f[i] + A *
(mu_syn / tau + dmu_ext_dt[i]))
# indentical to the old model
mu_lookup[i + 1] = mu_lookup[i] + dt * mu_lookup_rhs
sig_f[i + 1] = sig_f[i] + dt * sig_f_rhs
wm[i + 1] = wm[i] + dt * wm_rhs
return (r * 1000., wm)
def sim_ln_dosc(
mu_ext,
sig_ext,
dmu_ext_dt,
t,
dt,
steps,
mu_range,
sig_range,
omega_grid,
tau_grid,
tau_mu_f_grid,
tau_sigma_f_grid,
Vmean_grid,
r_grid,
a,
b,
C,
wm0,
EW,
tauw,
rec,
K,
J,
delay_type,
const_delay,
taud,
uni_int_order,
):
# initialize arrays
r = np.zeros_like(t)
r_d = np.zeros_like(t)
mu_f = np.zeros_like(t)
mu_total = np.zeros_like(t)
dmu_f = np.zeros_like(t) # aux. var for integration
dmu_syn_dt = np.zeros_like(t)
sig_f = np.zeros_like(t)
wm = np.zeros_like(t)
# new arrays for HEUN method
Vm = np.zeros_like(t)
mu_syn = np.zeros_like(t)
sigma_syn = np.zeros_like(t)
omega = np.zeros_like(t)
tau = np.zeros_like(t)
tau_mu_f = np.zeros_like(t)
tau_sigma_f = np.zeros_like(t)
A = np.zeros_like(t)
# set initial values
wm[0] = wm0
# mu_f[0] = mu_f0
# sig_f[0] = sig_f0
for i in xrange(steps):
for j in range(int(uni_int_order)):
# mu_ext filtered by damped oscillatory function for looking up Vm and r
weights_2 = interpolate_xy(mu_f[i + j] - wm[i + j] / C, sig_f[i + j], mu_range, sig_range)
Vm[i + j] = lookup_xy(Vmean_grid, weights_2)
r[i + j] = lookup_xy(r_grid, weights_2)
if rec:
mu_syn[i + j] = get_mu_syn(K, J, mu_ext, delay_type, i + j, r, r_d, const_delay, taud, dt)
sigma_syn[i + j] = get_sigma_syn(K, J, sig_ext, delay_type, i + j, r, r_d, const_delay, taud, dt)
# in the case of exponentially distributed
# delays; compute dmu_syn_dt analytically
if delay_type == 2:
dmu_syn_dt[i + j] = dmu_ext_dt[i + j] + K * J * (r[i + j] - r_d[i + j]) / taud
# else finite differences mu_syn
else:
dmu_syn_dt[i + j] = (mu_syn[i + j] - mu_syn[i + j - 1]) / dt
# this case corresponds to an UNCOUPLED POPULATION of neurons, i.e. K=0.
else:
mu_syn[i + j] = mu_ext[i + j]
sigma_syn[i + j] = sig_ext[i + j]
dmu_syn_dt[i + j] = dmu_ext_dt[i + j]
# save mu_total for param exploration
# todo: remove this again
mu_total[i + j] = mu_syn[i + j] - wm[i + j] / C
# todo
weights_1 = interpolate_xy(mu_total[i + j], sig_f[i + j], mu_range, sig_range)
omega[i + j] = lookup_xy(omega_grid, weights_1)
tau[i + j] = lookup_xy(tau_grid, weights_1)
tau_mu_f[i + j] = lookup_xy(tau_mu_f_grid, weights_1)
tau_sigma_f[i + j] = lookup_xy(tau_sigma_f_grid, weights_1)
# 2nd interpolation and lookup with
# euler step
A[i + j] = (tau[i + j] ** 2 * omega[i + j] ** 2 + 1) / tau[i + j]
if j == 0:
mu_f[i + 1] = mu_f[i] + dt * dmu_f[i]
dmu_f[i + 1] = dmu_f[i] + dt * (
(-2.0 / tau[i]) * dmu_f[i]
- (1.0 / tau[i] ** 2 + omega[i] ** 2) * mu_f[i]
+ A[i] * (mu_syn[i] / tau[i] + dmu_syn_dt[i])
)
# indentical to the old model
# mu_lookup[i+1] = mu_lookup[i] + dt*(mu_syn[i]-mu_lookup[i])/tau_mu_f[i]
sig_f[i + 1] = sig_f[i] + dt * (sigma_syn[i] - sig_f[i]) / tau_sigma_f[i]
wm[i + 1] = wm[i] + dt * (a[i] * (Vm[i] - EW) - wm[i] + tauw * b[i] * r[i]) / tauw
if j == 1:
mu_f[i + 1] = mu_f[i] + dt / 2.0 * (dmu_f[i] + dmu_f[i + 1])
dmu_f[i + 1] = dmu_f[i] + dt / 2.0 * (
(
(-2.0 / tau[i]) * dmu_f[i]
- (1.0 / tau[i] ** 2 + omega[i] ** 2) * mu_f[i]
+ A[i] * (mu_syn[i] / tau[i] + dmu_syn_dt[i])
)
+ (
(-2.0 / tau[i + 1]) * dmu_f[i + 1]
- (1.0 / tau[i + 1] ** 2 + omega[i + 1] ** 2) * mu_f[i + 1]
+ A[i + 1] * (mu_syn[i + 1] / tau[i + 1] + dmu_syn_dt[i + 1])
)
)
# indentical to the old model
# mu_lookup[i+1] = mu_lookup[i] + dt/2.*((mu_syn[i]-mu_lookup[i])/tau_mu_f[i]
# +(mu_syn[i+1]-mu_lookup[i+1])/tau_mu_f[i+1])
sig_f[i + 1] = sig_f[i] + dt / 2.0 * (
(sigma_syn[i] - sig_f[i]) / tau_sigma_f[i] + (sigma_syn[i + 1] - sig_f[i + 1]) / tau_sigma_f[i + 1]
)
wm[i + 1] = wm[i] + dt / 2.0 * (
(a[i] * (Vm[i] - EW) - wm[i] + tauw * b[i] * r[i]) / tauw
+ (a[i + 1] * (Vm[i + 1] - EW) - wm[i + 1] + tauw * b[i + 1] * r[i + 1]) / tauw
)
return (r * 1000.0, wm, mu_total, Vm)
def sim_ln_dosc_complex_model_OLD(
mu_ext,
sigma_ext,
L,
mu_exp,
sigma_exp,
w_m_orig,
dt,
EW,
taum,
gL,
tauw,
a,
b,
mu_range,
sig_range,
f0_grid,
tau_grid,
tau_mu_f_grid,
tau_sigma_f_grid,
Vmean_grid,
r_grid,
rec,
K,
J,
delay_type,
n_d,
taud,
):
mu_f = np.zeros(L + 1, dtype=numba.complex128) if use_numba else np.zeros(L + 1, dtype=np.complex128)
mu_a = np.zeros(L + 1)
r = np.zeros(L + 1)
r_d = np.zeros(L + 1)
wm = np.zeros(L + 1)
sigma_f = np.zeros(L + 1)
# initial_conditions
mu_a[0] = mu_exp
wm[0] = w_m_orig
sigma_f[0] = sigma_exp
weights_a = interpolate_xy(mu_a[0] - wm[0] / (taum * gL), sigma_f[0], mu_range, sig_range)
f0 = lookup_xy(f0_grid, weights_a)
tau = lookup_xy(tau_grid, weights_a)
mu_f[0] = mu_exp * (1 + 1j * 2 * np.pi * f0 * tau)
for i in xrange(L):
# interpolates real numbers
weights_a = interpolate_xy(mu_a[i] - wm[i] / (taum * gL), sigma_f[i], mu_range, sig_range)
f0 = lookup_xy(f0_grid, weights_a)
tau = lookup_xy(tau_grid, weights_a)
tau_mu_f = lookup_xy(tau_mu_f_grid, weights_a)
tau_sigma_f = lookup_xy(tau_sigma_f_grid, weights_a)
weights_f = interpolate_xy(mu_f[i].real - wm[i] / (taum * gL), sigma_f[i], mu_range, sig_range)
Vmean_dosc = lookup_xy(Vmean_grid, weights_f)
r_dosc = lookup_xy(r_grid, weights_f)
r[i] = r_dosc
if rec:
mu_syn = get_mu_syn(K, J, mu_ext, delay_type, i, r, r_d, n_d, taud, dt)
sigma_syn = get_sigma_syn(K, J, sigma_ext, delay_type, i, r, r_d, n_d, taud, dt)
else:
mu_syn = mu_ext[i]
sigma_syn = sigma_ext[i]
mu_f_rhs = ((2 * np.pi * f0) ** 2 * tau + 1.0 / tau) * mu_syn + (1j * 2 * np.pi * f0 - 1.0 / tau) * mu_f[i]
sigma_f_rhs = (sigma_syn - sigma_f[i]) / tau_sigma_f
w_rhs = (a[i] * (Vmean_dosc - EW) - wm[i] + tauw * b[i] * r_dosc) / tauw
mu_a_rhs = (mu_syn - mu_a[i]) / tau_mu_f
# EULER STEP
mu_f[i + 1] = mu_f[i] + dt * mu_f_rhs
mu_a[i + 1] = mu_a[i] + dt * mu_a_rhs
sigma_f[i + 1] = sigma_f[i] + dt * sigma_f_rhs
wm[i + 1] = wm[i] + dt * w_rhs
return (r * 1000.0, wm)
def sim_ln_exp(mu_ext, sigma_ext, mu_range, sigma_range,
map_Vmean, map_r, map_tau_mu_f, map_tau_sigma_f,
L, muf0, sigma_f0, w_m0, a, b, C, dt, tauW, Ew,
rec, K, J, delay_type, const_delay, taud, uni_int_order):
b_tauW = b * tauW
# initialize arrays
r_d = np.zeros(L+1)
mu_f = np.zeros(L+1)
sigma_f = np.zeros(L+1)
mu_syn = np.zeros(L+1)
mu_total = np.zeros(L+1)
sigma_syn = np.zeros(L+1)
w_m = np.zeros(L+1)
rates = np.zeros(L+1)
tau_mu_f = np.zeros(L+1)
tau_sigma_f = np.zeros(L+1)
Vm = np.zeros(L+1)
# set initial values
w_m[0] = w_m0
mu_f[0] = muf0
sigma_f[0] = sigma_f0
for i in xrange(L):
for j in xrange(int(uni_int_order)):
# interpolate
mu_f_eff = mu_f[i+j]-w_m[i+j]/C
# save for param exploration
# todo remove this again
mu_total[i+j] = mu_f_eff
weights = interpolate_xy(mu_f_eff, sigma_f[i+j], mu_range, sigma_range)
# lookup
Vm[i+j] = lookup_xy(map_Vmean, weights)
rates[i+j] = lookup_xy(map_r, weights)
tau_mu_f[i+j] = lookup_xy(map_tau_mu_f, weights)
tau_sigma_f[i+j] = lookup_xy(map_tau_sigma_f, weights)
if rec:
mu_syn[i+j] = get_mu_syn(K,J,mu_ext,delay_type,i+j,
rates,r_d,const_delay,taud,dt)
sigma_syn[i+j] = get_sigma_syn(K,J,sigma_ext,delay_type,i+j,
rates,r_d,const_delay,taud,dt)
# this case corresponds to an UNCOUPLED POPULATION of neurons, i.e. K=0.
else:
mu_syn[i+j] = mu_ext[i+j]
sigma_syn[i+j] = sigma_ext[i+j]
# euler step
if j == 0:
mu_f[i+1] = mu_f[i] \
+ dt * (mu_syn[i] - mu_f[i])/tau_mu_f[i]
sigma_f[i+1] = sigma_f[i] \
+ dt * (sigma_syn[i] - sigma_f[i])/tau_sigma_f[i]
w_m[i+1] = w_m[i] + dt \
* (a[i]*(Vm[i] - Ew) - w_m[i]
+ b_tauW[i] * (rates[i]))/tauW
if j == 1:
mu_f[i+1] = mu_f[i] \
+ dt/2. * ((mu_syn[i] - mu_f[i])/tau_mu_f[i]
+(mu_syn[i+1] - mu_f[i+1])/tau_mu_f[i+1])
sigma_f[i+1] = sigma_f[i] \
+ dt/2. * ((sigma_syn[i] - sigma_f[i])/tau_sigma_f[i]
+(sigma_syn[i+1] - sigma_f[i+1])/tau_sigma_f[i+1])
w_m[i+1] = w_m[i] \
+ dt/2. * (((a[i]*(Vm[i] - Ew) - w_m[i]
+ b_tauW[i] * (rates[i]))/tauW)
+((a[i+1]*(Vm[i+1] - Ew) - w_m[i+1]
+ b_tauW[i+1] * (rates[i+1]))/tauW))
#order of return tuple should always be rates, w_m, Vm, etc...
return (rates*1000., w_m, Vm, tau_mu_f, tau_sigma_f, mu_f, sigma_f, mu_total)
def sim_spec2m_simple_HEUN(mu_ext, sigma_ext, steps, dt, EW, a, b, C, tauw,
map_Vmean, map_rss, mu_range2, sigma_range2,
map_eig1, map_eig_mattia, rec, K, J, delay_type,
n_d, taud, r0, s0, w0, uni_int_order):
# optimazations
dt_tauw = dt / tauw
b_tauw = b * tauw
# initialize arrays
r = np.zeros(steps + 1)
dr = np.zeros(steps + 1)
r_d = np.zeros(steps + 1)
s = np.zeros(steps + 1)
wm = np.zeros(steps + 1)
# more arrays for HEUN method
Vm_inf = np.zeros(steps + 1)
r_inf = np.zeros(steps + 1)
lambda1_plus_lambda2 = np.zeros(steps + 1)
lambda1_times_lambda2 = np.zeros(steps + 1)
# write initial condition into array
r[0] = r0
s[0] = s0
wm[0] = w0
for i in xrange(steps):
for j in xrange(
int(uni_int_order)): # i --> i + j = i + 1 (for second round)
if rec:
mu_syn = get_mu_syn(K, J, mu_ext, delay_type, i + j, r, r_d,
n_d, taud, dt)
sigma_syn = get_sigma_syn(K, J, sigma_ext, delay_type, i + j,
r, r_d, n_d, taud, dt)
else:
mu_syn = mu_ext[i + j]
sigma_syn = sigma_ext[i + j]
# compute effective mu
mu_tot = mu_syn - wm[i + j] / C
# interpolate
# weights_quant = interpolate_xy(mu_tot, sigma_syn, mu_range1, sigma_range1)
weights_eig = interpolate_xy(mu_tot, sigma_syn, mu_range2,
sigma_range2)
# lookup
Vm_inf[i + j] = lookup_xy(map_Vmean, weights_eig)
r_inf[i + j] = lookup_xy(map_rss, weights_eig)
lambda1 = lookup_xy(map_eig1, weights_eig)
lambda2 = lookup_xy(map_eig_mattia, weights_eig)
# results of lambda1+lambda2 and lambda1*lambda2
# are always real --> eliminate imaginary parts
lambda1_plus_lambda2[i + j] = (lambda1 + lambda2).real
lambda1_times_lambda2[i + j] = (lambda1 * lambda2).real
# TODO: add rectify of r via toggle (def: on)
if j == 0:
dr[i + 1] = dr[i] + dt * (lambda1_times_lambda2[i] *
(r_inf[i] - r[i]) +
lambda1_plus_lambda2[i] * dr[i])
r[i + 1] = r[i] + dt * dr[i]
wm[i + 1] = wm[i] + dt_tauw * (a[i] * (Vm_inf[i] - EW) -
wm[i] + b_tauw[i] * r[i])
# only perform Heun integration step if 'uni_int_order' == 2
# to compute the updates state variables with the trapezian rule
elif j == 1:
dr[i + 1] = dr[i] + dt / 2. * (
(lambda1_times_lambda2[i] *
(r_inf[i] - r[i]) + lambda1_plus_lambda2[i] * dr[i]) +
(lambda1_times_lambda2[i + 1] * (r_inf[i + 1] - r[i + 1]) +
lambda1_plus_lambda2[i + 1] * dr[i + 1]))
r[i + 1] = r[i] + dt / 2. * (dr[i] + dr[i + 1])
wm[i + 1] = wm[i] + dt_tauw / 2. * (
(a[i] * (Vm_inf[i] - EW) - wm[i] + b_tauw[i] * r[i]) +
(a[i + 1] * (Vm_inf[i + 1] - EW) - wm[i + 1] +
b_tauw[i + 1] * r[i + 1]))
# re
return (r * 1000., wm)
def sim_ln_dosc(mu_ext, sig_ext, dmu_ext_dt, t, dt, steps, mu_range, sig_range,
omega_grid, tau_grid, tau_mu_f_grid, tau_sigma_f_grid,
Vmean_grid, r_grid, a, b, C, wm0, EW, tauw, rec, K, J,
delay_type, const_delay, taud, uni_int_order):
# initialize arrays
r = np.zeros_like(t)
r_d = np.zeros_like(t)
mu_f = np.zeros_like(t)
mu_total = np.zeros_like(t)
dmu_f = np.zeros_like(t) #aux. var for integration
dmu_syn_dt = np.zeros_like(t)
sig_f = np.zeros_like(t)
wm = np.zeros_like(t)
# new arrays for HEUN method
Vm = np.zeros_like(t)
mu_syn = np.zeros_like(t)
sigma_syn = np.zeros_like(t)
omega = np.zeros_like(t)
tau = np.zeros_like(t)
tau_mu_f = np.zeros_like(t)
tau_sigma_f = np.zeros_like(t)
A = np.zeros_like(t)
# set initial values
wm[0] = wm0
# mu_f[0] = mu_f0
# sig_f[0] = sig_f0
for i in xrange(steps):
for j in range(int(uni_int_order)):
# mu_ext filtered by damped oscillatory function for looking up Vm and r
weights_2 = interpolate_xy(mu_f[i + j] - wm[i + j] / C,
sig_f[i + j], mu_range, sig_range)
Vm[i + j] = lookup_xy(Vmean_grid, weights_2)
r[i + j] = lookup_xy(r_grid, weights_2)
if rec:
mu_syn[i + j] = get_mu_syn(K, J, mu_ext, delay_type, i + j, r,
r_d, const_delay, taud, dt)
sigma_syn[i + j] = get_sigma_syn(K, J, sig_ext, delay_type,
i + j, r, r_d, const_delay,
taud, dt)
# in the case of exponentially distributed
# delays; compute dmu_syn_dt analytically
if delay_type == 2:
dmu_syn_dt[i + j] = dmu_ext_dt[
i + j] + K * J * (r[i + j] - r_d[i + j]) / taud
# else finite differences mu_syn
else:
dmu_syn_dt[i +
j] = (mu_syn[i + j] - mu_syn[i + j - 1]) / dt
# this case corresponds to an UNCOUPLED POPULATION of neurons, i.e. K=0.
else:
mu_syn[i + j] = mu_ext[i + j]
sigma_syn[i + j] = sig_ext[i + j]
dmu_syn_dt[i + j] = dmu_ext_dt[i + j]
# save mu_total for param exploration
# todo: remove this again
mu_total[i + j] = mu_syn[i + j] - wm[i + j] / C
# todo
weights_1 = interpolate_xy(mu_total[i + j], sig_f[i + j], mu_range,
sig_range)
omega[i + j] = lookup_xy(omega_grid, weights_1)
tau[i + j] = lookup_xy(tau_grid, weights_1)
tau_mu_f[i + j] = lookup_xy(tau_mu_f_grid, weights_1)
tau_sigma_f[i + j] = lookup_xy(tau_sigma_f_grid, weights_1)
# 2nd interpolation and lookup with
# euler step
A[i + j] = (tau[i + j]**2 * omega[i + j]**2 + 1) / tau[i + j]
if j == 0:
mu_f[i + 1] = mu_f[i] + dt * dmu_f[i]
dmu_f[i + 1] = dmu_f[i] + dt * (
(-2. / tau[i]) * dmu_f[i] -
(1. / tau[i]**2 + omega[i]**2) * mu_f[i] + A[i] *
(mu_syn[i] / tau[i] + dmu_syn_dt[i]))
# indentical to the old model
# mu_lookup[i+1] = mu_lookup[i] + dt*(mu_syn[i]-mu_lookup[i])/tau_mu_f[i]
sig_f[i + 1] = sig_f[i] + dt * (sigma_syn[i] -
sig_f[i]) / tau_sigma_f[i]
wm[i + 1] = wm[i] + dt * (a[i] * (Vm[i] - EW) - wm[i] +
tauw * b[i] * r[i]) / tauw
if j == 1:
mu_f[i + 1] = mu_f[i] + dt / 2. * (dmu_f[i] + dmu_f[i + 1])
dmu_f[i + 1] = dmu_f[i] + dt / 2. * (
((-2. / tau[i]) * dmu_f[i] -
(1. / tau[i]**2 + omega[i]**2) * mu_f[i] + A[i] *
(mu_syn[i] / tau[i] + dmu_syn_dt[i])) +
((-2. / tau[i + 1]) * dmu_f[i + 1] -
(1. / tau[i + 1]**2 + omega[i + 1]**2) * mu_f[i + 1] +
A[i + 1] *
(mu_syn[i + 1] / tau[i + 1] + dmu_syn_dt[i + 1])))
# indentical to the old model
# mu_lookup[i+1] = mu_lookup[i] + dt/2.*((mu_syn[i]-mu_lookup[i])/tau_mu_f[i]
# +(mu_syn[i+1]-mu_lookup[i+1])/tau_mu_f[i+1])
sig_f[i + 1] = sig_f[i] + dt / 2. * (
(sigma_syn[i] - sig_f[i]) / tau_sigma_f[i] +
(sigma_syn[i + 1] - sig_f[i + 1]) / tau_sigma_f[i + 1])
wm[i + 1] = wm[i] + dt / 2. * (
(a[i] * (Vm[i] - EW) - wm[i] + tauw * b[i] * r[i]) / tauw +
(a[i + 1] * (Vm[i + 1] - EW) - wm[i + 1] +
tauw * b[i + 1] * r[i + 1]) / tauw)
return (r * 1000., wm, mu_total, Vm)
