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run_mech.py
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run_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: 2019-06-02 22:11:24
''' Run simulations of the NICE mechanical model. '''
import logging
import numpy as np
import matplotlib.pyplot as plt
from argparse import ArgumentParser
from PySONIC.core import BilayerSonophore, Batch
from PySONIC.utils import logger, selectDirDialog, parseUSAmps, getInDict
from PySONIC.neurons import CorticalRS
from PySONIC.plt import plotBatch
# Default parameters
defaults = dict(
Cm0=CorticalRS().Cm0 * 1e2, # uF/m2
Qm0=CorticalRS().Vm0, # nC/m2
radius=[32.0], # nm
embedding=[0.], # um
freq=[500.0], # kHz
amp=[100.0], # kPa
charge=[0.] # nC/cm2
)
def main():
ap = ArgumentParser()
# Runtime options
ap.add_argument('--mpi', 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', type=str, nargs='+', help='Variables to plot')
ap.add_argument('-o', '--outputdir', type=str, default=None, help='Output directory')
# Stimulation parameters
ap.add_argument('-a', '--radius', nargs='+', type=float, help='Sonophore radius (nm)')
ap.add_argument('--Cm0', type=float, default=defaults['Cm0'],
help='Resting membrane capacitance (uF/cm2)')
ap.add_argument('--Qm0', type=float, default=defaults['Qm0'],
help='Resting membrane charge density (nC/cm2)')
ap.add_argument('-d', '--embedding', nargs='+', type=float, help='Embedding depth (um)')
ap.add_argument('-f', '--freq', nargs='+', type=float, help='US frequency (kHz)')
ap.add_argument('-A', '--amp', nargs='+', type=float, help='Acoustic pressure amplitude (kPa)')
ap.add_argument('--Arange', type=str, nargs='+', help='Amplitude range [scale min max n] (kPa)')
ap.add_argument('-I', '--intensity', nargs='+', type=float, help='Acoustic intensity (W/cm2)')
ap.add_argument('--Irange', type=str, nargs='+',
help='Intensity range [scale min max n] (W/cm2)')
ap.add_argument('-Q', '--charge', nargs='+', type=float,
help='Membrane charge density (nC/cm2)')
# Parse arguments
args = {key: value for key, value in vars(ap.parse_args()).items() if value is not None}
loglevel = logging.DEBUG if args['verbose'] is True else logging.INFO
logger.setLevel(loglevel)
outdir = getInDict(args, 'outputdir', selectDirDialog)
if outdir == '':
logger.error('No output directory selected')
return
mpi = args['mpi']
Cm0 = args['Cm0'] * 1e-2 # F/m2
Qm0 = args['Qm0'] * 1e-5 # C/m2
radii = np.array(args.get('radius', defaults['radius'])) * 1e-9 # m
embeddings = np.array(args.get('embedding', defaults['embedding'])) * 1e-6 # m
freqs = np.array(args.get('freq', defaults['freq'])) * 1e3 # Hz
try:
amps = parseUSAmps(args, defaults)
except ValueError as err:
logger.error(err)
return
charges = np.array(args.get('charge', defaults['charge'])) * 1e-5 # C/m2
# Run MECH batch
pkl_filepaths = []
logger.info("Starting mechanical simulation batch")
for a in radii:
for d in embeddings:
bls = BilayerSonophore(a, Cm0, Qm0, embedding_depth=d)
queue = bls.simQueue(freqs, amps, charges)
for item in queue:
item.insert(0, outdir)
batch = Batch(bls.runAndSave, queue)
pkl_filepaths += batch(mpi=mpi, loglevel=loglevel)
# Plot resulting profiles
if 'plot' in args:
if args['plot'] == ['all']:
pltscheme = None
else:
pltscheme = {x: [x] for x in args['plot']}
plotBatch(pkl_filepaths, pltscheme=pltscheme)
plt.show()
if __name__ == '__main__':
main()

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