def model(Duration,Freq,DFreq,Amps,YY):
fs = 1000*50*4 # Hz, sampling rate
h.cvode_active(0) # turn off variable time step
h.steps_per_ms = fs*1e-3 # steps per ms for NEURON simulation
h.dt = 1/(fs*1e-3) # ms, sample spacing
h.celsius = h.celsius # temperature at which to run simulation
h.v_init = -80. # mV, initial voltage to begin simulations
ZZ=0
MyTraj = np.array([[-50e-3,YY,ZZ], [+51e-3,YY,ZZ]])
MyPath = os.getcwd() + '/'
CELL_DIR = MyPath+'cells/'
CELL_FILE_NAME = 'NewMRGaxon_for_Python.hoc'
MyD = 8.7
MyCell = MRG(axon_trajectory=MyTraj, fiberD=MyD,
CELL_FILE_NAME=CELL_FILE_NAME, CELL_DIR=CELL_DIR)
I = 1. # current source amplitude in A
# find xyz coordinates of center of each axon compartment
nrn_xyz = list()
for sec in MyCell.get_secs():
nrn_xyz.append(MyCell.center_3Dcoords(sec))
nrn_xyz = np.array(nrn_xyz)*1e-6 # m, convert from um to m
sigmaXX=0.6
sigmaYY=0.083
sigmaZZ=0.083
VS1=Voltages(nrn_xyz[:,0],nrn_xyz[:,1],nrn_xyz[:,2],-5e-3,+5e-3,+0e-3,+I,sigmaXX,sigmaYY,sigmaZZ,'V')['V']
VS2=Voltages(nrn_xyz[:,0],nrn_xyz[:,1],nrn_xyz[:,2],+5e-3,+5e-3,+0e-3,-I,sigmaXX,sigmaYY,sigmaZZ,'V')['V']
VS3=Voltages(nrn_xyz[:,0],nrn_xyz[:,1],nrn_xyz[:,2],-5e-3,-5e-3,+0e-3,+I,sigmaXX,sigmaYY,sigmaZZ,'V')['V']
VS4=Voltages(nrn_xyz[:,0],nrn_xyz[:,1],nrn_xyz[:,2],+5e-3,-5e-3,+0e-3,-I,sigmaXX,sigmaYY,sigmaZZ,'V')['V']
V1 = VS1+VS2 # voltage of first pair
V2 = VS3+VS4 # voltage of second pair
recordingDict = dict()
location = 0.5
variable = {'v'}
iSec=0
# MyPoints = list()
for Sec in MyCell.get_secs():
Sec.rx1_xtra=V1[iSec]
Sec.rx2_xtra=V2[iSec]
iSec=iSec+1
if ("node" in Sec.name()):
for vars in variable:
rec_dict(recordingDict, Sec, location, vars)
MyCell.record(recordingDict)
h.load_file("stdrun.hoc")
h.init()
h.finitialize(h.v_init)
h.fcurrent()
h.tstop = Duration
Times=np.arange(0,h.tstop+h.dt,h.dt)
Sim1=Amps*np.sin(2*np.pi*Freq/1000.0*Times)
Sim2=Amps*np.sin(2*np.pi*(Freq+DFreq)/1000.0*Times)
t = h.Vector(Times)
Stim1=h.Vector(Sim1*1e-3)
Stim2=h.Vector(Sim2*1e-3)
Stim1.play(h._ref_is1_xtra, t, 0)
Stim2.play(h._ref_is2_xtra, t, 0)
h.run()
return MyCell
sys.path.append('.')
from neuron import h
import numpy as np
import pickle
import os
import matplotlib.pyplot as plt
from functions.Voltages import Voltages
from classes.Cell_rdg import MRG
MyTraj = np.array([[-50e-3, 0, 0], [51e-3, 0, 0]])
MyPath = os.getcwd() + '/'
CELL_DIR = MyPath + 'cells/'
CELL_FILE_NAME = 'NewMRGaxon_for_Python.hoc'
MyD = 8.7
MyCell = MRG(axon_trajectory=MyTraj,
fiberD=MyD,
CELL_FILE_NAME=CELL_FILE_NAME,
CELL_DIR=CELL_DIR)
MyPoints = list()
for sec in MyCell.get_secs():
if ("node" in sec.name()):
MyPoints.append(MyCell.center_3Dcoords(sec))
MyPoints = np.array(MyPoints) * 1e-6
NumNodes = len(MyPoints[:, 0])
AllAPT = []
AllAPL = []
APTs = np.empty(0)
APLs = np.empty(0)