run_actmaps.py
35e89619726amaster

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()