Page MenuHomec4science
Files F60213441

lookups_ASTIM.py
No OneTemporary
Actions

File Metadata

Created
Sun, Apr 28, 08:47

lookups_ASTIM.py
View Options

#!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2017-06-02 17:50:10
# @Email: theo.lemaire@epfl.ch
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2018-08-21 16:07:36
""" Create lookup table for specific neuron. """
import os
import pickle
import logging
import numpy as np
from argparse import ArgumentParser
from PySONIC.solvers import computeAStimLookups
from PySONIC.utils import logger, InputError, getNeuronsDict, getLookupDir
from PySONIC.neurons import *
# Default parameters
default = {
'neuron': 'RS',
'a': 32.0, # nm
'freqs': np.array([20., 100., 500., 1e3, 2e3, 3e3, 4e3]), # kHz
'amps': np.insert(np.logspace(np.log10(0.1), np.log10(600), num=50), 0, 0.0), # kPa
}
def main():
# Define argument parser
ap = ArgumentParser()
# Stimulation 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', '--frequencies', nargs='+', type=float, default=None,
help='Acoustic drive frequencies (kHz)')
ap.add_argument('-A', '--amplitudes', nargs='+', type=float, default=None,
help='Acoustic pressure amplitudes (kPa)')
# Boolean parameters
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')
# Parse arguments
args = ap.parse_args()
neuron_str = args.neuron
a = args.diameter * 1e-9 # m
freqs = (default['freqs'] if args.frequencies is None else np.array(args.frequencies)) * 1e3 # Hz
amps = (default['amps'] if args.amplitudes is None else np.array(args.amplitudes)) * 1e3 # Pa
if args.verbose:
logger.setLevel(logging.DEBUG)
else:
logger.setLevel(logging.INFO)
# Check neuron name validity
if neuron_str not in getNeuronsDict():
raise InputError('Unknown neuron type: "{}"'.format(neuron_str))
neuron = getNeuronsDict()[neuron_str]()
# Check if lookup file already exists
lookup_file = '{}_lookups_a{:.1f}nm.pkl'.format(neuron.name, a * 1e9)
lookup_filepath = '{0}/{1}'.format(getLookupDir(), lookup_file)
if os.path.isfile(lookup_filepath):
logger.warning('"%s" file already exists and will be overwritten. ' +
'Continue? (y/n)', lookup_file)
user_str = input()
if user_str not in ['y', 'Y']:
logger.info('%s Lookup creation canceled', neuron.name)
sys.exit(0)
try:
# Compute lookups
lookup_dict = computeAStimLookups(neuron, a, freqs, amps,
multiprocess=args.multiprocessing)
# Save dictionary in lookup file
logger.info('Saving %s neuron lookup table in file: "%s"', neuron.name, lookup_file)
with open(lookup_filepath, 'wb') as fh:
pickle.dump(lookup_dict, fh)
except InputError as err:
logger.error(err)
sys.exit(1)
if __name__ == '__main__':
main()

Event Timeline

c4science · Help