def run_WN(photoreceptor, I):
Z_dictionary = {}
V_dictionary = {}
Vl_dictionary = {}
I_dictionary = {}
for i, V in enumerate(Vr):
DepolarisePhotoreceptor.WithLight(photoreceptor, V)
## Filtering signal
print("Processing V=", V, " mV")
## Run HH
print("Running HH...")
Vm, g = Experiment.inject_current(photoreceptor, I, dt)
Vl = Linearise.inject_current(photoreceptor, I, dt)
print("Variance of voltage is ", var(Vm), "mV2")
## Calculate impedance
Vmm = (Vm - mean(Vm)) #without DC
CPSD = zeros(round(len(time) / 2 + 1), dtype=complex_)
PSD = zeros(round(len(time) / 2 + 1))
window = hamming(len(time))
print("len(window)", len(window))
for ii in range(repetitions):
I_cut = I[ii * len(time):(ii + 1) * len(time)]
V_cut = Vmm[ii * len(time):(ii + 1) * len(time)]
PSD += power(absolute(rfft(I_cut * window)), 2)
CPSD += rfft(V_cut * window) * rfft(I_cut * window).conjugate()
Z = CPSD / PSD #MOhm
Z_dictionary[V] = Z
I_dictionary[V] = I[sample * len(time):(sample + 1) * len(time)]
V_dictionary[V] = Vm[sample * len(time):(sample + 1) * len(time)]
Vl_dictionary[V] = Vl[sample * len(time):(sample + 1) * len(time)]
return (Z_dictionary, V_dictionary, Vl_dictionary, I_dictionary)
ax.text(-0.12,
1.02,
label,
transform=ax.transAxes,
fontsize=14,
va='top',
ha='right')
ax_bw_gain, ax_cost_bw, ax_cost_gain = axes
## Only the values in Vr to plot fat circles
for i, V in enumerate(Vr):
label_str = str(V) + ' mV'
photoreceptor = FlyFactory.DrosophilaR16(shift="none")
DepolarisePhotoreceptor.WithLight(photoreceptor, V=V)
Z_cut = photoreceptor.body.impedance(
f_from_medium
) #Only frequencies above f_medium, to calculate bandwidth
gain_max_r[N, i] = max(
abs(photoreceptor.body.voltage_contrast_gain(f_from_medium)))
Bandwidth_r[N, i] = Calculate_Bandwidth(Z_cut, f_from_medium)
Cost_r[N, i] = photoreceptor.energy_consumption() * delta_cost
if gain_max_r[N, i] > epsilon:
#ax_gain_vs_bw.plot(gain_max_r[N, i], Bandwidth_r[N, i], colour_graph[i] + '.', markersize=15)
#ax_cost_vs_gbwp.plot(Cost_r[N, i], gain_max_r[N, i] * Bandwidth_r[N, i], colour_graph[i] + '.', markersize=15)
ax_bw_gain.plot(gain_max_r[N, i],
Bandwidth_r[N, i],
colour_graph[i] + '.',
colour_graph = ['y', 'b', 'g', 'r', 'c']
Bandwidth = zeros_like(Vr)
Bandwidth_fixed = zeros_like(Vr)
gain_max = zeros_like(Vr)
gain_max_fixed = zeros_like(Vr)
gain_bandwidth_product = zeros_like(Vr)
gain_bandwidth_product_fixed = zeros_like(Vr)
HH_RC = []
for i, V in enumerate(Vr):
label_str = str(V) + ' mV'
DepolarisePhotoreceptor.WithLight(HH, V)
gain_max[i], Bandwidth[i] = Gain_Bandwidth(HH.body.voltage_contrast_gain,
f_min=f_medium)
gain = abs(HH.body.voltage_contrast_gain(f))
gain_bandwidth_product[i] = gain_max[i] * Bandwidth[i]
Experiment.freeze_conductances(HH)
gain_max_fixed[i], Bandwidth_fixed[i] = Gain_Bandwidth(
HH.body.voltage_contrast_gain, f_min=f_medium)
gain_fixed = abs(HH.body.voltage_contrast_gain(f))
gain_bandwidth_product_fixed[i] = gain_max_fixed[i] * Bandwidth_fixed[i]
Experiment.unfreeze_conductances(HH)
fig2 = figure(5, figsize=[9, 5])
ax_Z = fig2.add_subplot(1, 3, 1)
ax_bw = fig2.add_subplot(2, 3, 3)
ax_cost = fig2.add_subplot(2, 3, 6)
ax_Z_V_low = fig2.add_subplot(2, 3, 2)
ax_Z_V_medium = fig2.add_subplot(2, 3, 5)
###### CONTINUOUS ACROSS VOLTAGES
Vr = arange(-70.0, -30.0, 0.5)
Z_array = zeros(len(Vr))
Z_fixed_array = zeros(len(Vr))
total_resistance_array = zeros_like(Vr)
total_K_conductance = zeros_like(Vr)
for i, V in enumerate(Vr): #Impedances at lowest frequency
if depolarise_with_light:
DepolarisePhotoreceptor.WithLight(HH, V)
else:
DepolarisePhotoreceptor.WithCurrent(HH, V)
Z_array[i] = abs(HH.body.impedance(f_low))
Experiment.freeze_conductances(HH)
Z_fixed_array[i] = abs(HH.body.impedance(f_low))
Experiment.unfreeze_conductances(HH)
total_resistance_array[i] = HH.body.resistance()
total_K_conductance[i] = HH.body.total_K_conductance()
ax_Z_V_low.plot(Vr,
Z_array / 1000,
'k',
linewidth=2,
label="Fixed conductances")
ax_Z_V_low.plot(Vr,
T = 300 #ms
dt = 0.05 #ms
time_array = arange(0, T + dt, dt)
I = zeros_like(time_array)
fig1 = plt.figure(1)
ax = fig1.add_subplot(211)
ax_t = fig1.add_subplot(212)
fig2 = plt.figure(2)
ax_curr = fig2.add_subplot(211)
V_membrane = -38 #mV
photoreceptor = Drone.Vallet92()
DepolarisePhotoreceptor.WithLight(photoreceptor, V=V_membrane)
fig1.text(0.06,
0.5,
'Membrane potential deflection (mV)',
ha='center',
va='center',
rotation='vertical')
for ii in range(5):
for i, t in enumerate(time_array):
if 10 <= t <= 110: I[i] = 1e-3 * (-0.02 + 0.01 * ii) # nA->uA
DepolarisePhotoreceptor.WithLight(photoreceptor, V=V_membrane)
V_array, g_Ch = Experiment.inject_current(photoreceptor, I, dt)
ax_curr.plot(time_array, I, 'k')
option = 1 # 1:Compare with full conductance freeze, 2: Compare with inactivation freeze
V_membrane_ = [-68,-59,-41] #mV
plot_window = array([-.5,3.5])
drosophila = FlyFactory.DrosophilaR16()
fig1 = figure(1)
T=200 #ms
dt=0.5 #ms
time_array = arange(0,T+dt,dt)
I = zeros_like(time_array)
for ii,V_membrane in enumerate(V_membrane_) :
for i, t in enumerate(time_array):
if 10 <= t <= 160: I[i] = 1e-3*(0.01) # nA->uA
DepolarisePhotoreceptor.WithLight(drosophila, V = V_membrane)
V_array, g_Ch = Experiment.inject_current(drosophila,I,dt)
ax = fig1.add_subplot(3,1,ii+1)
ax.plot(time_array, V_array,color='black') #mV
#Experiment.unfreeze_conductances(drosophila)
DepolarisePhotoreceptor.WithLight(drosophila, V = V_membrane) #To make sure that all channels are back at rest
Experiment.freeze_inactivations(drosophila)
V_array, g_Ch = Experiment.inject_current(drosophila,I,dt)
Experiment.unfreeze_inactivations(drosophila)
ax.plot(time_array, V_array,'k:') #mV
DepolarisePhotoreceptor.WithLight(drosophila, V = V_membrane) #To make sure that all channels are back at rest