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R4670/sim/batch_ASTIM.py
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batch_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: 2018-08-21 16:07:35
""" Run batch acoustic simulations of specific "point-neuron" models. """
import sys
import os
import logging
import numpy as np
from argparse import ArgumentParser
from PySONIC.utils import logger, InputError
from PySONIC.solvers import setBatchDir, checkBatchLog, runAStimBatch
from PySONIC.plt import plotBatch
# Set logging level
logger.setLevel(logging.INFO)
# Neurons
neurons = ['RS']
# Stimulation parameters
stim_params = {
'freqs': [500e3], # Hz
'amps': [100e3], # Pa
'durations': [100e-3], # s
'PRFs': [100.0], # Hz
'DCs': [0.1, 0.5, 1.],
'offsets': [0]
}
if __name__ == '__main__':
# Define argument parser
ap = ArgumentParser()
ap.add_argument('-m', '--multiprocessing', default=False, action='store_true',
help='Use multiprocessing')
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()
if args.verbose:
logger.setLevel(logging.DEBUG)
else:
logger.setLevel(logging.INFO)
try:
# Select output directory
batch_dir = setBatchDir()
log_filepath, _ = checkBatchLog(batch_dir, 'A-STIM')
# Run A-STIM batch
pkl_filepaths = runAStimBatch(batch_dir, log_filepath, neurons, stim_params,
int_method='effective', multiprocess=args.multiprocessing)
pkl_dir, _ = os.path.split(pkl_filepaths[0])
# Plot resulting profiles
if args.plot:
yvars = {'Q_m': ['Qm']}
plotBatch(pkl_dir, pkl_filepaths, yvars)
except InputError as err:
logger.error(err)
sys.exit(1)
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