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test_sims.py
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test_sims.py
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# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Email: theo.lemaire@epfl.ch
# @Date: 2017-06-14 18:37:45
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2019-11-13 12:31:55
''' Test the basic functionalities of the package. '''
from PySONIC.core import BilayerSonophore, NeuronalBilayerSonophore, PulsedProtocol
from PySONIC.utils import logger
from PySONIC.neurons import getPointNeuron, getNeuronsDict
from PySONIC.test import TestBase
class TestSims(TestBase):
def test_MECH(self, is_profiled=False):
logger.info('Test: running MECH simulation')
a = 32e-9 # m
Qm0 = -80e-5 # membrane resting charge density (C/m2)
Cm0 = 1e-2 # membrane resting capacitance (F/m2)
Fdrive = 350e3 # Hz
Adrive = 100e3 # Pa
Qm = 50e-5 # C/m2
bls = BilayerSonophore(a, Cm0, Qm0)
self.execute('bls.simulate(Fdrive, Adrive, Qm)', globals(), locals(), is_profiled)
def test_ESTIM(self, is_profiled=False):
logger.info('Test: running ESTIM simulation')
Astim = 10.0 # mA/m2
pp = PulsedProtocol(100e-3, 50e-3)
pneuron = getPointNeuron('RS')
self.execute('pneuron.simulate(Astim, pp)', globals(), locals(), is_profiled)
def test_ASTIM_sonic(self, is_profiled=False):
logger.info('Test: ASTIM sonic simulation')
a = 32e-9 # m
Fdrive = 500e3 # Hz
Adrive = 100e3 # Pa
pp = PulsedProtocol(50e-3, 10e-3)
pneuron = getPointNeuron('RS')
nbls = NeuronalBilayerSonophore(a, pneuron)
# test error 1: sonophore radius outside of lookup range
try:
nbls = NeuronalBilayerSonophore(100e-9, pneuron)
nbls.simulate(Fdrive, Adrive, pp, method='sonic')
except ValueError:
logger.debug('Out of range radius: OK')
# test error 2: frequency outside of lookups range
try:
nbls = NeuronalBilayerSonophore(a, pneuron)
nbls.simulate(10e3, Adrive, pp, method='sonic')
except ValueError:
logger.debug('Out of range frequency: OK')
# test error 3: amplitude outside of lookups range
try:
nbls = NeuronalBilayerSonophore(a, pneuron)
nbls.simulate(Fdrive, 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', 'SW', 'sundt'):
pneuron = neuron_class()
nbls = NeuronalBilayerSonophore(a, pneuron)
self.execute("nbls.simulate(Fdrive, Adrive, pp, method='sonic')",
globals(), locals(), is_profiled)
def test_ASTIM_full(self, is_profiled=False):
logger.info('Test: running ASTIM detailed simulation')
a = 32e-9 # m
Fdrive = 500e3 # Hz
Adrive = 100e3 # Pa
pp = PulsedProtocol(1e-6, 1e-6)
pneuron = getPointNeuron('RS')
nbls = NeuronalBilayerSonophore(a, pneuron)
self.execute("nbls.simulate(Fdrive, Adrive, pp, method='full')",
globals(), locals(), is_profiled)
def test_ASTIM_hybrid(self, is_profiled=False):
logger.info('Test: running ASTIM hybrid simulation')
a = 32e-9 # m
Fdrive = 350e3 # Hz
Adrive = 100e3 # Pa
pp = PulsedProtocol(0.6e-3, 0.1e-3)
pneuron = getPointNeuron('RS')
nbls = NeuronalBilayerSonophore(a, pneuron)
self.execute("nbls.simulate(Fdrive, Adrive, pp, method='hybrid')",
globals(), locals(), is_profiled)
if __name__ == '__main__':
tester = TestSims()
tester.main()

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