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plot_rheobase_amps.py
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Sat, Oct 12, 09:56

plot_rheobase_amps.py
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# -*- coding: utf-8 -*-
# @Author: Theo
# @Date: 2018-04-30 21:06:10
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2018-11-21 16:27:13
''' Plot duty-cycle dependent rheobase acoustic amplitudes of various neurons
for a specific US frequency and PRF. '''
import logging
import numpy as np
import matplotlib.pyplot as plt
from argparse import ArgumentParser
from PySONIC.utils import logger
# from PySONIC.core import NeuronalBilayerSonophore
from PySONIC.neurons import getNeuronsDict
from PySONIC.plt import plotAstimRheobaseAmps, plotEstimRheobaseAmps
# Set logging level
logger.setLevel(logging.INFO)
# Default parameters
defaults = dict(
neuron='RS',
radii=[32.0],
freqs=[500.0]
)
def main():
ap = ArgumentParser()
# Stimulation parameters
ap.add_argument('-n', '--neuron', type=str, default=defaults['neuron'],
help='Neuron name (string)')
ap.add_argument('-a', '--radii', type=float, nargs='+', default=defaults['radii'],
help='Sonophore radius (nm)')
ap.add_argument('-f', '--freqs', type=float, nargs='+', default=defaults['freqs'],
help='US frequency (kHz)')
ap.add_argument('-m', '--mode', type=str, default='US',
help='Stimulation modality (US or elec)')
# Parse arguments
args = {key: value for key, value in vars(ap.parse_args()).items() if value is not None}
mode = args['mode']
# Get neurons objects from names
neuron_str = args.get('neuron', defaults['neuron'])
if neuron_str not in getNeuronsDict():
logger.error('Invalid neuron type: "%s"', neuron_str)
return
neuron = getNeuronsDict()[neuron_str]()
if mode == 'US':
radii = np.array(args['radii']) * 1e-9 # m
freqs = np.array(args['freqs']) * 1e3 # Hz
plotAstimRheobaseAmps(neuron, radii, freqs)
elif mode == 'elec':
plotEstimRheobaseAmps(neuron)
else:
logger.error('Invalid stimulation type: "%s"', mode)
return
plt.show()
if __name__ == '__main__':
main()

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