plot_effective_variables.py
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	# -- coding: utf-8 --
	# @Author: Theo Lemaire
	# @Email: theo.lemaire@epfl.ch
	# @Date: 2017-02-15 15:59:37
	# @Last Modified by: Theo Lemaire
	# @Last Modified time: 2020-02-03 21:21:58

	''' Plot the effective variables as a function of charge density with color code. '''

	import numpy as np
	import logging
	import matplotlib.pyplot as plt

	from PySONIC.plt import plotEffectiveVariables
	from PySONIC.utils import logger
	from PySONIC.parsers import MechSimParser

	# Set logging level
	logger.setLevel(logging.INFO)


	def main():

	parser = MechSimParser()
	parser.addNeuron()
	parser.addNColumns()
	parser.addNLevels()
	parser.defaults['neuron'] = 'RS'
	parser.defaults['radius'] = np.nan
	parser.defaults['freq'] = np.nan
	parser.defaults['amp'] = np.nan
	args = parser.parse()
	for k in ['charge', 'embedding', 'Cm0', 'Qm0', 'fs', 'mpi', 'pltscheme', 'plot']:
	del args[k]
	logger.setLevel(args['loglevel'])

	# Restrict radius, frequency and amplitude to single values
	for k in ['radius', 'freq', 'amp']:
	if len(args[k]) > 1:
	logger.error(f'multiple {k} values not allowed')
	val = args[k][0]
	if np.isnan(val):
	args[k] = None
	else:
	args[k] = val

	for pneuron in args['neuron']:
	plotEffectiveVariables(
	pneuron, a=args['radius'], f=args['freq'], A=args['amp'],
	zscale=args['cscale'], cmap=args['cmap'], ncolmax=args['ncol'], nlevels=args['nlevels'])

	plt.show()


	if __name__ == '__main__':
	main()