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plot_activation_map.py
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Mon, May 13, 15:30

plot_activation_map.py
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# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2018-09-26 09:51:43
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2018-12-14 18:14:29
''' Plot (duty-cycle x amplitude) US activation map of a neuron at a given frequency and PRF. '''
import numpy as np
import logging
import matplotlib.pyplot as plt
from argparse import ArgumentParser
from PySONIC.utils import logger, selectDirDialog, Intensity2Pressure
from PySONIC.plt import plotActivationMap
# Default parameters
defaults = dict(
neuron='RS',
radius=32, # nm
freq=500, # kHz
duration=1000, # ms
PRF=100, # Hz
amps=np.logspace(np.log10(10), np.log10(600), num=30), # kPa
DCs=np.arange(1, 101), # %
Ascale='log',
FRscale='log',
FRbounds=(1e0, 1e3), # Hz
tmax=240, # ms
Vbounds=(-150, 50), # mV
)
def main():
ap = ArgumentParser()
# Runtime options
ap.add_argument('-v', '--verbose', default=False, action='store_true', help='Increase verbosity')
ap.add_argument('-i', '--inputdir', type=str, default=None, help='Input directory')
ap.add_argument('-r', '--threshold', default=False, action='store_true',
help='Show threshold amplitudes')
ap.add_argument('-c', '--connect', default=False, action='store_true',
help='Show traces on click')
# Stimulation parameters
ap.add_argument('-n', '--neuron', type=str, default=defaults['neuron'],
help='Neuron name (string)')
ap.add_argument('-a', '--radius', type=float, default=defaults['radius'],
help='Sonophore radius (nm)')
ap.add_argument('-f', '--freq', type=float, default=defaults['freq'],
help='US frequency (kHz)')
ap.add_argument('-d', '--duration', type=float, default=defaults['duration'],
help='Stimulus duration (ms)')
ap.add_argument('-A', '--amps', nargs='+', type=float, help='Acoustic pressure amplitude (kPa)')
ap.add_argument('-I', '--intensities', nargs='+', type=float, help='Acoustic intensity (W/cm2)')
ap.add_argument('--PRF', type=float, default=defaults['PRF'], help='PRF (Hz)')
ap.add_argument('--DC', nargs='+', type=float, help='Duty cycle (%%)')
# Plot options
ap.add_argument('--Ascale', type=str, default=defaults['Ascale'],
help='y-axis scale ("log" or "lin")')
ap.add_argument('--FRscale', type=str, default=defaults['FRscale'],
help='map color scale ("log" or "lin")')
ap.add_argument('--FRbounds', type=float, nargs='+', default=defaults['FRbounds'],
help='Lower and upper bounds for firing rate (Hz)')
ap.add_argument('--tmax', type=float, default=defaults['tmax'],
help='Max time value for callback graphs (ms)')
ap.add_argument('--Vbounds', type=float, nargs='+', default=defaults['Vbounds'],
help='Y-axis extent for callback graphs (mV)')
# Parse arguments
args = {key: value for key, value in vars(ap.parse_args()).items() if value is not None}
# Runtime options
loglevel = logging.DEBUG if args['verbose'] is True else logging.INFO
logger.setLevel(loglevel)
inputdir = args['inputdir'] if 'inputdir' in args else selectDirDialog()
if inputdir == '':
logger.error('Operation cancelled')
return
# Parameters
neuron = args['neuron']
a = args['radius'] * 1e-9 # m
Fdrive = args['freq'] * 1e3 # Hz
tstim = args['duration'] * 1e-3 # s
PRF = args['PRF'] # Hz
DCs = np.array(args.get('DCs', defaults['DCs'])) * 1e-2 # (-)
if 'amps' in args:
amps = np.array(args['amps']) * 1e3 # Pa
elif 'intensities' in args:
amps = Intensity2Pressure(np.array(args['intensities']) * 1e4) # Pa
else:
amps = np.array(defaults['amps']) * 1e3 # Pa
# Plot options
for item in ['Ascale', 'FRscale']:
assert args[item] in ('lin', 'log'), 'Unknown {}'.format(item)
Ascale = args['Ascale']
FRscale = args['FRscale']
tmax = args['tmax'] # ms
Vbounds = args['Vbounds'] # mV
FRbounds = args['FRbounds'] # Hz
# Plot activation map
plotActivationMap(
inputdir, neuron, a, Fdrive, tstim, PRF, amps, DCs,
Ascale=Ascale, FRscale=FRscale, FRbounds=FRbounds,
thrs=args['threshold'], connect=args['connect'],
tmax=tmax, Vbounds=Vbounds)
plt.show()
if __name__ == '__main__':
main()

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