run_actmaps.py
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	# -- coding: utf-8 --
	# @Author: Theo Lemaire
	# @Email: theo.lemaire@epfl.ch
	# @Date: 2020-04-09 10:52:49
	# @Last Modified by: Theo Lemaire
	# @Last Modified time: 2020-04-18 18:10:13

	''' Example script showing how to build neuron activation maps. '''

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

	from PySONIC.utils import logger, selectDirDialog
	from PySONIC.neurons import getPointNeuron
	from PySONIC.plt import getActivationMap

	logger.setLevel(logging.INFO)


	def main():
	''' The code must be wrappped inside a main function in order to allow MPI usage. '''
	# Parameters
	root = selectDirDialog()
	pneuron = getPointNeuron('TC')
	a = 32e-9 # m
	coverages = [0.8, 1.0]
	f = 500e3 # Hz
	tstim = 100e-3 # s
	PRF = 100 # Hz
	amps = np.logspace(np.log10(10.), np.log10(600.), 5) * 1e3 # Pa
	DCs = np.linspace(5, 100, 5) * 1e-2 # (-)

	# Define variable-dependent z-bounds and colormaps
	zbounds = {
	'FR': (1e0, 1e3), # Hz
	'Cai': (1e0, 1e2) # uM
	}
	cmap = {'FR': 'viridis', 'Cai': 'cividis'}

	# For each coevrage fraction
	for fs in coverages:
	# For each map class
	for zkey in ['FR', 'Cai']:
	# Create activation map object
	actmap = getActivationMap(zkey, root, pneuron, a, fs, f, tstim, PRF, amps, DCs)

	# Run simulations for populate the 2D map
	actmap.run(mpi=True)

	# Render the 2D map
	actmap.render(interactive=True, zbounds=zbounds[zkey], cmap=cmap[zkey])

	plt.show()


	if __name__ == '__main__':
	main()