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R4670/scripts/plot_rheobase_amps.py
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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: 2018-09-28 14:12:31
''' 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, si_format
from PySONIC.core import NeuronalBilayerSonophore
from PySONIC.neurons import getNeuronsDict
# Set logging level
logger.setLevel(logging.INFO)
# Default parameters
defaults = dict(
neurons=['RS', 'FS', 'RE'],
diam=32.0,
freq=500.0
)
def plotAstimRheobaseAmps(neurons, a, Fdrive, fs=15):
fig, ax = plt.subplots()
ax.set_title('Rheobase amplitudes @ {}Hz ({:.0f} nm sonophore)'.format(
si_format(Fdrive, 1, space=' '), a * 1e9), fontsize=fs)
ax.set_xlabel('Duty cycle (%)', fontsize=fs)
ax.set_ylabel('Threshold amplitude (kPa)', fontsize=fs)
for item in ax.get_xticklabels() + ax.get_yticklabels():
item.set_fontsize(fs)
ax.set_yscale('log')
ax.set_ylim([10, 600])
DCs = np.arange(1, 101) / 1e2
for neuron in neurons:
nbls = NeuronalBilayerSonophore(a, neuron)
Athrs = nbls.findRheobaseAmps(DCs, Fdrive, neuron.VT)
ax.plot(DCs * 1e2, Athrs * 1e-3, label='{} neuron'.format(neuron.name))
ax.legend(fontsize=fs, frameon=False)
fig.tight_layout()
return fig
def plotEstimRheobaseAmps(neurons, fs=15):
fig, ax = plt.subplots()
ax.set_title('Rheobase amplitudes', fontsize=fs)
ax.set_xlabel('Duty cycle (%)', fontsize=fs)
ax.set_ylabel('Threshold amplitude (mA/m2)', fontsize=fs)
for item in ax.get_xticklabels() + ax.get_yticklabels():
item.set_fontsize(fs)
ax.set_yscale('log')
ax.set_ylim([1e0, 1e3])
DCs = np.arange(1, 101) / 1e2
for neuron in neurons:
Athrs = neuron.findRheobaseAmps(DCs, neuron.VT)
ax.plot(DCs * 1e2, Athrs, label='{} neuron'.format(neuron.name))
ax.legend(fontsize=fs, frameon=False)
fig.tight_layout()
return fig
def main():
ap = ArgumentParser()
# Stimulation parameters
ap.add_argument('-n', '--neurons', type=str, nargs='+', default=defaults['neurons'],
help='Neuron name (string)')
ap.add_argument('-a', '--diam', type=float, default=defaults['diam'],
help='Sonophore diameter (nm)')
ap.add_argument('-f', '--freq', type=float, default=defaults['freq'],
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}
neurons_str = args.get('neurons', defaults['neurons'])
neurons = []
for n in neurons_str:
if n not in getNeuronsDict():
logger.error('Invalid neuron type: "%s"', n)
return
neurons.append(getNeuronsDict()[n]())
mode = args['mode']
if mode == 'US':
diam = args.get('diam', defaults['diam']) * 1e-9 # m
Fdrive = args.get('freq', defaults['freq']) * 1e3 # Hz
plotAstimRheobaseAmps(neurons, diam, Fdrive)
elif mode == 'elec':
plotEstimRheobaseAmps(neurons)
else:
logger.error('Invalid stimulation type: "%s"', mode)
return
plt.show()
if __name__ == '__main__':
main()
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