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batch_MECH.py
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Mon, Nov 11, 08:49

batch_MECH.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2016-11-21 10:46:56
# @Email: theo.lemaire@epfl.ch
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2018-07-23 14:39:27
""" Run batch simulations of the NICE mechanical model with imposed charge densities """
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, runMechBatch
from PointNICE.neurons import *
from PointNICE.plt import plotBatch
a = 32e-9 # in-plane diameter (m)
# Electrical properties of the membrane
neuron = CorticalRS()
Cm0 = neuron.Cm0
Qm0 = neuron.Vm0 * 1e-5
# Stimulation parameters
stim_params = {
'freqs': [500e3], # Hz
'amps': [50e3], # Pa
'charges': np.linspace(-72, 0, 3) * 1e-5 # C/m2
}
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, 'MECH')
# Run MECH batch
pkl_filepaths = runMechBatch(batch_dir, log_filepath, Cm0, Qm0, stim_params, a,
multiprocess=args.multiprocessing)
pkl_dir, _ = os.path.split(pkl_filepaths[0])
# Plot resulting profiles
if args.plot:
plotBatch(pkl_dir, pkl_filepaths)
except InputError as err:
logger.error(err)
sys.exit(1)

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