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R4670/scripts/plot_effective_variables.py
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plot_effective_variables.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2017-02-15 15:59:37
# @Email: theo.lemaire@epfl.ch
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2019-03-11 14:35:27
''' Plot the effective variables as a function of charge density with color code. '''
import logging
import matplotlib.pyplot as plt
from argparse import ArgumentParser
from PySONIC.plt import plotEffectiveVariables
from PySONIC.utils import logger, Intensity2Pressure, getLowIntensitiesSTN
from PySONIC.neurons import getNeuronsDict
# Set logging level
logger.setLevel(logging.INFO)
def main():
ap = ArgumentParser()
# Stimulation parameters
ap.add_argument('-n', '--neuron', type=str, default='RS',
help='Neuron name (string)')
ap.add_argument('-a', '--radius', type=float, default=None,
help='Sonophore radius (nm)')
ap.add_argument('-f', '--freq', type=float, default=None,
help='US frequency (kHz)')
ap.add_argument('-A', '--amp', type=float, default=None,
help='Acoustic pressure amplitude (kPa)')
ap.add_argument('--log', action='store_true', default=False,
help='Log color scale')
ap.add_argument('-c', '--cmap', type=str, default=None,
help='Colormap name')
ap.add_argument('--ncol', type=int, default=1,
help='Number of columns in figure')
ap.add_argument('-v', '--verbose', default=False, action='store_true', help='Increase verbosity')
# Parse arguments
args = {key: value for key, value in vars(ap.parse_args()).items() if value is not None}
neuron_str = args['neuron']
a = args['radius'] * 1e-9 if 'radius' in args else None # m
Fdrive = args['freq'] * 1e3 if 'freq' in args else None # Hz
Adrive = args['amp'] * 1e3 if 'amp' in args else None # Pa
# Range of intensities
if neuron_str == 'STN':
intensities = getLowIntensitiesSTN() # W/m2
Adrive = Intensity2Pressure(intensities) # Pa
zscale = 'log' if args['log'] else 'lin'
cmap = args.get('cmap', None)
ncol = args['ncol']
loglevel = logging.DEBUG if args['verbose'] is True else logging.INFO
logger.setLevel(loglevel)
# Plot effective variables
if neuron_str not in getNeuronsDict():
logger.error('Unknown neuron type: "%s"', neuron_str)
return
neuron = getNeuronsDict()[neuron_str]()
plotEffectiveVariables(neuron, a=a, Fdrive=Fdrive, Adrive=Adrive,
zscale=zscale, cmap=cmap, ncolmax=ncol)
plt.show()
if __name__ == '__main__':
main()
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