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R4670/scripts/plot_QSS.py
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plot_QSS.py
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# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Email: theo.lemaire@epfl.ch
# @Date: 2018-09-28 16:13:34
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2019-10-09 15:18:55
''' Phase-plane analysis of neuron behavior under quasi-steady state approximation. '''
import os
import numpy as np
import matplotlib.pyplot as plt
from PySONIC.utils import logger
from PySONIC.plt import plotQSSdynamics, plotQSSVarVsQm, plotEqChargeVsAmp, plotQSSThresholdCurve
from PySONIC.parsers import AStimParser
def main():
# Parse command line arguments
parser = AStimParser()
# parser.addCmap(default='viridis')
parser.addAscale()
parser.outputdir_dep_key = 'save'
parser.addInputDir(dep_key='compare')
parser.defaults['amp'] = np.logspace(np.log10(1), np.log10(600), 100) # kPa
parser.defaults['tstim'] = 1000. # ms
parser.defaults['toffset'] = 0. # ms
args = parser.parse()
logger.setLevel(args['loglevel'])
if args['plot'] is None:
args['plot'] = ['dQdt']
a, Fdrive, tstim, toffset, PRF = [
args[k][0] for k in ['radius', 'freq', 'tstim', 'toffset', 'PRF']]
figs = []
for i, pneuron in enumerate(args['neuron']):
if args['DC'].size == 1:
DC = args['DC'][0]
if args['amp'].size == 1:
Adrive = args['amp'][0]
figs.append(plotQSSdynamics(pneuron, a, Fdrive, Adrive, DC))
else:
# Plot evolution of QSS vars vs Q for different amplitudes
# for pvar in args['plot']:
# figs.append(plotQSSVarVsQm(
# pneuron, a, Fdrive, pvar, amps=args['amp'], DC=DC,
# cmap=args['cmap'], zscale=args['Ascale'], mpi=args['mpi'],
# loglevel=args['loglevel']))
# Plot equilibrium charge as a function of amplitude
if 'dQdt' in args['plot']:
figs.append(plotEqChargeVsAmp(
pneuron, a, Fdrive, amps=args['amp'], tstim=tstim, toffset=toffset, PRF=PRF,
DC=DC, xscale=args['Ascale'], compdir=args['inputdir'], mpi=args['mpi'],
loglevel=args['loglevel']))
else:
figs.append(plotQSSThresholdCurve(
pneuron, a, Fdrive, tstim=tstim, toffset=toffset, PRF=PRF, DCs=args['DC'],
Ascale=args['Ascale'], comp=args['compare'], mpi=args['mpi'],
loglevel=args['loglevel']))
if args['save']:
for fig in figs:
s = fig.canvas.get_window_title()
s = s.replace('(', '- ').replace('/', '_').replace(')', '')
figname = '{}.png'.format(s)
fig.savefig(os.path.join(args['outputdir'], figname), transparent=True)
else:
plt.show()
if __name__ == '__main__':
main()
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