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batch_ESTIM.py
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Wed, May 29, 09:29

batch_ESTIM.py
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# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2017-08-24 11:55:07
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2018-07-23 17:30:52
""" Run batch electrical simulations of specific "point-neuron" models. """
import sys
import os
import logging
import numpy as np
from argparse import ArgumentParser
from PointNICE.utils import logger, InputError
from PointNICE.solvers import setBatchDir, checkBatchLog, runEStimBatch
from PointNICE.plt import plotBatch
# Neurons
neurons = ['RS']
# Stimulation parameters
stim_params = {
'amps': [10.0], # mA/m2
'durations': [300e-3], # np.array([20, 40, 60, 80, 100, 150, 200, 250, 300]) * 1e-3, # s
'PRFs': [1e2], # np.array([0.1, 0.2, 0.5, 1.0, 2.0, 5.0, 10.0]) * 1e3, # Hz
'DCs': [0.7, 0.9, 1.0], # np.array([1, 2, 5, 10, 25, 50, 75, 100]) * 1e-2
'offsets': [100e-3]
}
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, 'E-STIM')
# Run E-STIM batch
pkl_filepaths = runEStimBatch(batch_dir, log_filepath, neurons, stim_params,
multiprocess=args.multiprocessing)
pkl_dir, _ = os.path.split(pkl_filepaths[0])
# Plot resulting profiles
if args.plot:
yvars = {'V_m': ['Vm']}
plotBatch(pkl_dir, pkl_filepaths, yvars)
except InputError as err:
logger.error(err)
sys.exit(1)

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