run_astim.py
82b931897c27master

run_astim.py
View Options

			# -- coding: utf-8 --
			# @Author: Theo Lemaire
			# @Email: theo.lemaire@epfl.ch
			# @Date: 2017-02-13 18:16:09
			# @Last Modified by: Theo Lemaire
			# @Last Modified time: 2020-04-17 20:23:11

			''' Run A-STIM simulations of a specific point-neuron. '''

			from PySONIC.core import NeuronalBilayerSonophore, Batch
			from PySONIC.utils import logger
			from PySONIC.parsers import AStimParser


			def main():
			# Parse command line arguments
			parser = AStimParser()
			args = parser.parse()
			logger.setLevel(args['loglevel'])
			sim_inputs = parser.parseSimInputs(args)
			simQueue_func = {9: 'simQueue', 10: 'simQueueBurst'}[len(sim_inputs)]

			# Run A-STIM batch
			logger.info("Starting A-STIM simulation batch")
			queue = getattr(NeuronalBilayerSonophore, simQueue_func)(
			*sim_inputs, outputdir=args['outputdir'], overwrite=args['overwrite'])
			output = []
			for a in args['radius']:
			for pneuron in args['neuron']:
			nbls = NeuronalBilayerSonophore(a, pneuron)
			batch = Batch(nbls.simAndSave if args['save'] else nbls.simulate, queue)
			output += batch(mpi=args['mpi'], loglevel=args['loglevel'])

			# Plot resulting profiles
			if args['plot'] is not None:
			parser.parsePlot(args, output)


			if __name__ == '__main__':
			main()