Activation function for a LIFE

This script investigates the activation function for a longitudinal intrafascicular electrode (LIFE). It is similar to the previous example but include geometrical consideration, and computations are evaluated with the FEM solver in background (transparent for user).

import numpy as np
import matplotlib.pyplot as plt
from scipy import signal
import sys
sys.path.append("../")
import nrv

nrv.parameters.set_nrv_verbosity(2)

d_elect_list = [100,200]
LIFE_length_list = [100,1000]

def move_mean(A, N):
    A = signal.savgol_filter(A, N, 3)
    #A = np.convolve(A, np.ones(N)/N, mode='valid')
    return A

def derivate(A, n_order, N=99):
    for _ in range(n_order):
        A = np.diff(A)
        A = move_mean(A, N)
    return A

#dummy stimulus def
start = 1
I_cathod = 500
I_anod = I_cathod/5
T_cathod = 60e-3
T_inter = 40e-3
stim1 = nrv.stimulus()
stim1.biphasic_pulse(start, I_cathod, T_cathod, I_anod, T_inter)

#nerve
L = 10000
Nerve_D = 1500
Fascicle_D = 1000
Outer_D = 6

##### electrodes
D_1 = 25
y_c_1 = 0
z_c_1 = 0

##### compute footprints
x_ftp = np.linspace(0,L,num=1000)

plt.figure()

for d_elect in d_elect_list:
    for length_1 in LIFE_length_list:

        ##### extracellular context
        test_stim = nrv.FEM_stimulation()
        test_stim.reshape_outerBox(Outer_D)
        test_stim.reshape_nerve(Nerve_D, L)
        test_stim.reshape_fascicle(Fascicle_D)
        x_1_offset = L/2 - (length_1/2)
        elec_1 = nrv.LIFE_electrode('LIFE', D_1, length_1, x_1_offset, d_elect, z_c_1)
        test_stim.add_electrode(elec_1, stim1)

        test_stim.compute_electrodes_footprints(x_ftp, y=0, z=0, ID=0)
        ftp = elec_1.footprint
        acti_function = derivate(ftp, 2)
        acti_function = acti_function/np.max(acti_function)

        x_plot = np.linspace(0,L, len(acti_function))
        plt.plot(x_plot, acti_function, label=f'd={d_elect}µm - l={length_1}µm')


        del elec_1,test_stim

plt.ylabel(r'Activation Function ($\Delta^2V_e$)')
plt.xlabel('x-axis (µm)')
plt.legend()
plt.title('Activation function of LIFE for different geometries')
#plt.show()