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).

NRV WARNING: Deprecated arguments: You migth be using an old script. FEM_stimulation.reshape_fascicle use geometry instead of Fascicle_D, y_c, z_c
NRV WARNING: Deprecated arguments: You migth be using an old script. FEM_stimulation.reshape_fascicle use geometry instead of Fascicle_D, y_c, z_c
NRV WARNING: Deprecated arguments: You migth be using an old script. FEM_stimulation.reshape_fascicle use geometry instead of Fascicle_D, y_c, z_c
NRV WARNING: Deprecated arguments: You migth be using an old script. FEM_stimulation.reshape_fascicle use geometry instead of Fascicle_D, y_c, z_c

import numpy as np
import matplotlib.pyplot as plt
from scipy import signal
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

if __name__ == '__main__':
    #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()