plot_QSS_IQ.py
2de6d3d26717master

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: 2019-05-22 10:01:53

			''' 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 plotQSSvars, 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('-A', '--amp', type=float, default=None, help='Amplitude (kPa or mA/m2)')
			ap.add_argument('--tstim', type=float, default=500.,
			help='Stimulus 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('--Ascale', type=str, default='lin',
			help='Scale type for acoustic amplitude ("lin" or "log")')
			ap.add_argument('--Amin', type=float, default=None, help='Amplitude lower bound (kPa or mA/m2)')
			ap.add_argument('--Amax', type=float, default=None, help='Amplitude upper bound (kPa or mA/m2)')
			ap.add_argument('--nA', type=float, default=100, help='Number of amplitude values')
			ap.add_argument('--stim', type=str, default='US', help='Stimulation type ("US" or "elec")')
			ap.add_argument('--vars', type=str, nargs='+', default=None, help='Variables to plot')

			# 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]

			# US parameters
			a = 32e-9 # m
			Fdrive = 500e3 # Hz
			AUS_range = (1., 600.) # kPa

			# E-STIM parameters
			Aelec_range = (-20., 20.) # mA/m2

			# Pulsing parameters
			tstim = args.tstim * 1e-3 # s
			PRF = args.PRF # Hz
			DCs = [100.] if args.DC is None else args.DC # %
			DCs = np.array(DCs) * 1e-2 # (-)

			if args.stim == 'US':
			if args.amp is not None:
			amps = np.array([args.amp * 1e3])
			else:
			Arange = list(AUS_range)
			for i, val in enumerate([args.Amin, args.Amax]):
			if val is not None:
			Arange[i] = val
			amps = {
			'lin': np.linspace(Arange[0], Arange[1], args.nA),
			'log': np.logspace(np.log10(Arange[0]), np.log10(Arange[1]), args.nA)
			}[args.Ascale] * 1e3 # Pa
			cmap = args.cmap
			else:
			a = None
			Fdrive = None
			if args.amp is not None:
			amps = np.array([args.amp]) # mA/m2
			else:
			Arange = list(Aelec_range)
			for i, val in enumerate([args.Amin, args.Amax]):
			if val is not None:
			Arange[i] = val
			amps = np.linspace(Arange[0], Arange[1], args.nA) # mA/m2
			cmap = 'RdBu_r'

			if args.vars is None:
			args.vars = ['dQdt']

			figs = []

			# Plot iNet vs Q for different amplitudes for each neuron and DC
			for i, neuron in enumerate(neurons):
			for DC in DCs:
			if amps.size == 1:
			figs.append(
			plotQSSvars(neuron, a, Fdrive, amps[0]))
			else:
			for var in args.vars:
			figs.append(plotQSSVarVsAmp(
			neuron, a, Fdrive, var, amps=amps, DC=DC, cmap=cmap, zscale=args.Ascale))

			# Plot equilibrium charge as a function of amplitude for each neuron
			if amps.size > 1 and 'dQdt' in args.vars:
			try:
			figs.append(
			plotEqChargeVsAmp(
			neurons, a, Fdrive, amps=amps, tstim=tstim, PRF=PRF, DCs=DCs,
			xscale=args.Ascale, titrate=args.titrate))
			except ValueError as err:
			logger.error(err)
			quit()

			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()

R4670/scripts/plot_QSS_IQ.py2de6d3d26717master

plot_QSS_IQ.pyView Options

R4670/scripts/plot_QSS_IQ.py
2de6d3d26717master

plot_QSS_IQ.py
View Options