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run_ASTIM.py
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run_ASTIM.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2017-02-13 18:16:09
# @Email: theo.lemaire@epfl.ch
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2018-07-23 13:27:52
""" Script to run ASTIM simulations from command line. """
import sys
import os
import logging
from argparse import ArgumentParser
from PointNICE.utils import logger, getNeuronsDict, InputError
from PointNICE.solvers import checkBatchLog, SolverUS, AStimWorker
from PointNICE.plt import plotBatch
# Default parameters
default = {
'neuron': 'RS',
'a': 32.0, # nm
'f': 500.0, # kHz
'A': 100.0, # kPa
't': 150.0, # ms
'off': 100.0, # ms
'PRF': 100.0, # Hz
'DC': 100.0, # %
'int_method': 'effective'
}
def main():
# Define argument parser
ap = ArgumentParser()
# ASTIM parameters
ap.add_argument('-n', '--neuron', type=str, default=default['neuron'],
help='Neuron name (string)')
ap.add_argument('-a', '--diameter', type=float, default=default['a'],
help='Sonophore diameter (nm)')
ap.add_argument('-f', '--frequency', type=float, default=default['f'],
help='Acoustic drive frequency (kHz)')
ap.add_argument('-A', '--amplitude', type=float, default=default['A'],
help='Acoustic pressure amplitude (kPa)')
ap.add_argument('-t', '--duration', type=float, default=default['t'],
help='Stimulus duration (ms)')
ap.add_argument('--offset', type=float, default=default['off'],
help='Offset duration (ms)')
ap.add_argument('--PRF', type=float, default=default['PRF'],
help='PRF (Hz)')
ap.add_argument('--DC', type=float, default=default['DC'],
help='Duty cycle (%%)')
ap.add_argument('-o', '--outputdir', type=str, default=os.getcwd(),
help='Output directory')
ap.add_argument('-m', '--method', type=str, default=default['int_method'],
help='Numerical integration method ("classic", "hybrid" or "effective"')
# Boolean parameters
ap.add_argument('-v', '--verbose', default=False, action='store_true',
help='Increase verbosity')
ap.add_argument('-p', '--plot', default=False, action='store_true',
help='Plot results')
# Parse arguments
args = ap.parse_args()
neuron_str = args.neuron
a = args.diameter * 1e-9 # m
Fdrive = args.frequency * 1e3 # Hz
Adrive = args.amplitude * 1e3 # Pa
tstim = args.duration * 1e-3 # s
toffset = args.offset * 1e-3 # s
PRF = args.PRF # Hz
DC = args.DC * 1e-2
output_dir = args.outputdir
int_method = args.method
if args.verbose:
logger.setLevel(logging.DEBUG)
else:
logger.setLevel(logging.INFO)
try:
if neuron_str not in getNeuronsDict():
raise InputError('Unknown neuron type: "{}"'.format(neuron_str))
log_filepath, _ = checkBatchLog(output_dir, 'A-STIM')
neuron = getNeuronsDict()[neuron_str]()
worker = AStimWorker(1, output_dir, log_filepath, SolverUS(a, neuron, Fdrive), neuron,
Fdrive, Adrive, tstim, toffset, PRF, DC, int_method, 1)
logger.info('%s', worker)
outfile = worker.__call__()
logger.info('Finished')
if args.plot:
plotBatch(output_dir, [outfile])
except InputError as err:
logger.error(err)
sys.exit(1)
if __name__ == '__main__':
main()

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