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plot_QSS_IQ.py
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plot_QSS_IQ.py
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# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2018-09-28 16:13:34
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2019-04-04 13:01:35
''' Phase-plane analysis of neuron behavior under quasi-steady state approximation. '''
import os
import numpy as np
import matplotlib.pyplot as plt
from argparse import ArgumentParser
import logging
from PySONIC.utils import logger, selectDirDialog
from PySONIC.neurons import getNeuronsDict
from PySONIC.plt import plotQSSVarVsAmp, plotEqChargeVsAmp
def main():
ap = ArgumentParser()
# Stimulation parameters
ap.add_argument('-n', '--neurons', type=str, nargs='+', default=None, help='Neuron types')
ap.add_argument('-o', '--outputdir', type=str, default=None, help='Output directory')
ap.add_argument('-c', '--cmap', type=str, default='viridis', help='Colormap name')
ap.add_argument('-v', '--verbose', default=False, action='store_true', help='Increase verbosity')
ap.add_argument('-s', '--save', default=False, action='store_true', help='Save output figures')
ap.add_argument('--titrate', default=False, action='store_true', help='Titrate excitation threshold')
ap.add_argument('--tstim', type=float, default=250., help='Stimulus duration for titration (ms)')
ap.add_argument('--toffset', type=float, default=50., help='Offset duration for titration (ms)')
ap.add_argument('--PRF', type=float, default=100.,
help='Pulse-repetition-frequency for titration (Hz)')
ap.add_argument('--DC', type=float, nargs='+', default=None, help='Duty cycle (%)')
ap.add_argument('--Qi', type=float, default=None,
help='Initial membrane charge density for phase-plane analysis (nC/cm2)')
ap.add_argument('--Ascale', type=str, default='log',
help='Scale type for acoustic amplitude ("lin" or "log")')
# Parse arguments
args = ap.parse_args()
logger.setLevel(logging.DEBUG if args.verbose else logging.INFO)
neurons = ['RS', 'LTS'] if args.neurons is None else args.neurons
neurons = [getNeuronsDict()[n]() for n in neurons]
Qi = args.Qi * 1e-5 if args.Qi is not None else None # C/cm2
a = 32e-9 # m
Fdrive = 500e3 # Hz
Arange = (1., 50.) # kPa
nA = 100
amps = {
'lin': np.linspace(Arange[0], Arange[1], nA),
'log': np.logspace(np.log10(Arange[0]), np.log10(Arange[1]), 100)
}[args.Ascale] * 1e3 # Pa
# amps = np.array([37., 40., 45.]) * 1e3
tstim = args.tstim * 1e-3 # s
toffset = args.toffset * 1e-3 # s
PRF = args.PRF # Hz
DCs = [100.] if args.DC is None else args.DC # %
DCs = np.array(DCs) * 1e-2 # (-)
# Plot iNet vs Q for different amplitudes for each neuron
figs = []
for neuron in neurons:
for DC in DCs:
figs.append(plotQSSVarVsAmp(
neuron, a, Fdrive, 'iNet', amps=amps, DC=DC, Qi=Qi, zscale=args.Ascale))
# Plot equilibrium charge as a function of amplitude for each neuron
figs.append(
plotEqChargeVsAmp(
neurons, a, Fdrive, amps=amps, tstim=tstim, toffset=toffset, PRF=PRF, DCs=DCs,
Qi=Qi, xscale=args.Ascale, titrate=args.titrate))
if args.save:
outputdir = args.outputdir if args.outputdir is not None else selectDirDialog()
if outputdir == '':
logger.error('no output directory')
else:
for fig in figs:
s = fig.canvas.get_window_title()
s = s.replace('(', '- ').replace('/', '_').replace(')', '')
figname = '{}.png'.format(s)
fig.savefig(os.path.join(outputdir, figname), transparent=True)
else:
plt.show()
if __name__ == '__main__':
main()

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