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run_estim.py
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Wed, May 8, 23:18

run_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: 2019-05-27 15:28:27
''' Run E-STIM simulations of a specific point-neuron. '''
import os
import logging
import numpy as np
import matplotlib.pyplot as plt
from argparse import ArgumentParser
from PySONIC.utils import logger, selectDirDialog, parseElecAmps
from PySONIC.neurons import *
from PySONIC.batches import createEStimQueue, runBatch
from PySONIC.plt import plotBatch
# Default parameters
defaults = dict(
neuron='RS',
amp=[10.0], # mA/m2
duration=[100.0], # ms
PRF=[100.0], # Hz
DC=[100.0], # %
offset=[50.], # ms
method='sonic'
)
def runEStimBatch(outdir, neuron, stim_params, mpi=False):
''' Run batch E-STIM simulations of the system for various neuron types and
stimulation parameters.
:param outdir: full path to output directory
:param stim_params: dictionary containing sweeps for all stimulation parameters
:param mpi: boolean statting wether or not to use multiprocessing
:return: list of full paths to the output files
'''
mandatory_params = ['durations', 'offsets', 'PRFs', 'DCs']
for mparam in mandatory_params:
if mparam not in stim_params:
raise ValueError('Missing stimulation parameter field: "{}"'.format(mparam))
logger.info("Starting E-STIM simulation batch")
# Generate simulations queue
queue = createEStimQueue(
stim_params.get('amps', None),
stim_params['durations'],
stim_params['offsets'],
stim_params['PRFs'],
stim_params['DCs']
)
# Run batch
return runBatch(neuron, 'runAndSave', queue, extra_params=[outdir], mpi=mpi)
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')
ap.add_argument('-t', '--titrate', default=False, action='store_true', help='Perform titration')
# Stimulation parameters
ap.add_argument('-n', '--neuron', type=str, default=defaults['neuron'],
help='Neuron name (string)')
ap.add_argument('-A', '--amp', nargs='+', type=float, help='Injected current density (mA/m2)')
ap.add_argument('--Arange', type=str, nargs='+', help='Amplitude range [scale min max n] (mA/m2)')
ap.add_argument('-d', '--duration', nargs='+', type=float, help='Stimulus duration (ms)')
ap.add_argument('--offset', nargs='+', type=float, help='Offset duration (ms)')
ap.add_argument('--PRF', nargs='+', type=float, help='PRF (Hz)')
ap.add_argument('--DC', nargs='+', type=float, help='Duty cycle (%%)')
# 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 = args['outputdir'] if 'outputdir' in args else selectDirDialog()
if outdir == '':
logger.error('No output directory selected')
quit()
titrate = args['titrate']
neuron_str = args['neuron']
try:
amps = parseElecAmps(args, defaults)
except ValueError as err:
logger.error(err)
quit()
stim_params = dict(
amps=amps,
durations=np.array(args.get('duration', defaults['duration'])) * 1e-3, # s
PRFs=np.array(args.get('PRF', defaults['PRF'])), # Hz
DCs=np.array(args.get('DC', defaults['DC'])) * 1e-2, # (-)
offsets=np.array(args.get('offset', defaults['offset'])) * 1e-3 # s
)
if titrate:
stim_params['amps'] = None
# Run E-STIM batch
if neuron_str not in getNeuronsDict():
logger.error('Unknown neuron type: "%s"', neuron_str)
return
neuron = getNeuronsDict()[neuron_str]()
pkl_filepaths = runEStimBatch(outdir, neuron, stim_params, mpi=args['mpi'])
pkl_dir, _ = os.path.split(pkl_filepaths[0])
# 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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