def test_ASTIM_hybrid(self, is_profiled=False):
logger.info('Test: running ASTIM hybrid simulation')
pp = PulsedProtocol(0.6e-3, 0.1e-3)
pneuron = getPointNeuron('RS')
nbls = NeuronalBilayerSonophore(self.a, pneuron)
self.execute(lambda: nbls.simulate(self.USdrive, pp, method='hybrid'),
is_profiled)
def test_ASTIM_full(self, is_profiled=False):
logger.info('Test: running ASTIM detailed simulation')
pp = PulsedProtocol(1e-6, 1e-6)
pneuron = getPointNeuron('RS')
nbls = NeuronalBilayerSonophore(self.a, pneuron)
self.execute(lambda: nbls.simulate(self.USdrive, pp, method='full'),
is_profiled)
def test_ASTIM_sonic(self, is_profiled=False):
logger.info('Test: ASTIM sonic simulation')
pp = PulsedProtocol(50e-3, 10e-3)
pneuron = getPointNeuron('RS')
nbls = NeuronalBilayerSonophore(self.a, pneuron)
# test error 1: sonophore radius outside of lookup range
try:
nbls = NeuronalBilayerSonophore(100e-9, pneuron)
nbls.simulate(self.USdrive, pp, method='sonic')
except ValueError:
logger.debug('Out of range radius: OK')
# test error 2: frequency outside of lookups range
try:
nbls = NeuronalBilayerSonophore(self.a, pneuron)
nbls.simulate(AcousticDrive(10e3, self.USdrive.A),
pp,
method='sonic')
except ValueError:
logger.debug('Out of range frequency: OK')
# test error 3: amplitude outside of lookups range
try:
nbls = NeuronalBilayerSonophore(self.a, pneuron)
nbls.simulate(AcousticDrive(self.USdrive.f, 1e6),
pp,
method='sonic')
except ValueError:
logger.debug('Out of range amplitude: OK')
# Run simulation on all neurons
for name, neuron_class in getNeuronsDict().items():
if name not in ('template', 'LeechP', 'LeechT', 'LeechR',
'SWnode'):
pneuron = neuron_class()
nbls = NeuronalBilayerSonophore(self.a, pneuron)
self.execute(
lambda: nbls.simulate(self.USdrive, pp, method='sonic'),
is_profiled)
def main():
''' The code must be wrappped inside a main function in order to allow MPI usage. '''
# Parameters
root = selectDirDialog()
pneuron = getPointNeuron('TC')
a = 32e-9 # m
coverages = [0.8, 1.0]
f = 500e3 # Hz
tstim = 100e-3 # s
PRF = 100 # Hz
amps = np.logspace(np.log10(10.), np.log10(600.), 5) * 1e3 # Pa
DCs = np.linspace(5, 100, 5) * 1e-2 # (-)
# Define variable-dependent z-bounds and colormaps
zbounds = {
'FR': (1e0, 1e3), # Hz
'Cai': (1e0, 1e2) # uM
}
cmap = {'FR': 'viridis', 'Cai': 'cividis'}
# For each coevrage fraction
for fs in coverages:
# For each map class
for zkey in ['FR', 'Cai']:
# Create activation map object
actmap = getActivationMap(zkey, root, pneuron, a, fs, f, tstim,
PRF, amps, DCs)
# Run simulations for populate the 2D map
actmap.run(mpi=True)
# Render the 2D map
actmap.render(interactive=True,
zbounds=zbounds[zkey],
cmap=cmap[zkey])
plt.show()
import itertools
import logging
import numpy as np
from PySONIC.core import NeuronalBilayerSonophore, AcousticDrive, Batch
from PySONIC.neurons import getPointNeuron
from PySONIC.utils import logger
from PySONIC.constants import *
logger.setLevel(logging.DEBUG)
# Model
a = 32e-9
fs = 1.
pneuron = getPointNeuron('RS')
nbls = NeuronalBilayerSonophore(a, pneuron)
# Stimulus
Fdrive = 500e3
Adrive = 100e3
drive = AcousticDrive(Fdrive, Adrive)
# Charge range
Qmin, Qmax = pneuron.Qbounds
Q_ref = np.arange(Qmin, Qmax + DQ_LOOKUP, DQ_LOOKUP) # C/m2
# Charge oscillations
AQ_ref = np.linspace(0, 100e-5, 5) # C/m2
phiQ_ref = np.linspace(0, 2 * np.pi, 5, endpoint=False) # rad
NFS = 2
def test_ESTIM(self, is_profiled=False):
logger.info('Test: running ESTIM simulation')
ELdrive = ElectricDrive(10.0) # mA/m2
pp = PulsedProtocol(100e-3, 50e-3)
pneuron = getPointNeuron('RS')
self.execute(lambda: pneuron.simulate(ELdrive, pp), is_profiled)