Page MenuHomec4science
Files F91462004

test_basic.py
No OneTemporary
Actions

File Metadata

Created
Mon, Nov 11, 08:51

test_basic.py
View Options

#!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2017-06-14 18:37:45
# @Email: theo.lemaire@epfl.ch
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2017-09-12 18:48:35
''' Test the basic functionalities of the package. '''
import os
import sys
import logging
import time
import cProfile
import pstats
from argparse import ArgumentParser
from PointNICE.utils import logger
from PointNICE import BilayerSonophore, SolverElec, SolverUS
from PointNICE.channels import *
def test_MECH(is_profiled=False):
''' Mechanical simulation. '''
logger.info('Test: running MECH simulation')
# Create BLS instance
a = 32e-9 # m
Fdrive = 350e3 # Hz
Cm0 = 1e-2 # membrane resting capacitance (F/m2)
Qm0 = -80e-5 # membrane resting charge density (C/m2)
bls = BilayerSonophore(a, Fdrive, Cm0, Qm0)
# Stimulation parameters
Adrive = 100e3 # Pa
Qm = 50e-5 # C/m2
# Run simulation
if is_profiled:
pfile = 'tmp.stats'
cProfile.runctx('bls.runMech(Fdrive, Adrive, Qm)', globals(), locals(), pfile)
stats = pstats.Stats(pfile)
os.remove(pfile)
stats.strip_dirs()
stats.sort_stats('cumulative')
stats.print_stats()
else:
bls.runMech(Fdrive, Adrive, Qm)
def test_ESTIM(is_profiled=False):
''' Electrical simulation '''
logger.info('Test: running ESTIM simulation')
# Initialize neuron
neuron = CorticalRS()
# Initialize solver
solver = SolverElec()
# Stimulation parameters
Astim = 10.0 # mA/m2
tstim = 100e-3 # s
toffset = 50e-3 # s
# Run simulation
if is_profiled:
pfile = 'tmp.stats'
cProfile.runctx('solver.run(neuron, Astim, tstim, toffset)',
globals(), locals(), pfile)
stats = pstats.Stats(pfile)
os.remove(pfile)
stats.strip_dirs()
stats.sort_stats('cumulative')
stats.print_stats()
else:
solver.run(neuron, Astim, tstim, toffset, PRF=None, DF=1.0)
def test_ASTIM_effective(is_profiled=False):
''' Effective acoustic simulation '''
logger.info('Test: running ASTIM effective simulation')
# Initialize neuron
neuron = CorticalRS()
# Stimulation parameters
Fdrive = 350e3 # Hz
Adrive = 100e3 # Pa
tstim = 50e-3 # s
toffset = 30e-3 # s
# Initialize solver
a = 32e-9 # m
solver = SolverUS(a, neuron, Fdrive)
# Run simulation
if is_profiled:
pfile = 'tmp.stats'
cProfile.runctx("solver.run(neuron, Fdrive, Adrive, tstim, toffset, sim_type='effective')",
globals(), locals(), pfile)
stats = pstats.Stats(pfile)
os.remove(pfile)
stats.strip_dirs()
stats.sort_stats('cumulative')
stats.print_stats()
else:
solver.run(neuron, Fdrive, Adrive, tstim, toffset, sim_type='effective')
def test_ASTIM_classic(is_profiled=False):
''' Classic acoustic simulation '''
logger.info('Test: running ASTIM classic simulation')
# Initialize neuron
neuron = CorticalRS()
# Stimulation parameters
Fdrive = 350e3 # Hz
Adrive = 100e3 # Pa
tstim = 1e-6 # s
toffset = 1e-6 # s
# Initialize solver
a = 32e-9 # m
solver = SolverUS(a, neuron, Fdrive)
# Run simulation
if is_profiled:
pfile = 'tmp.stats'
cProfile.runctx("solver.run(neuron, Fdrive, Adrive, tstim, toffset, sim_type='classic')",
globals(), locals(), pfile)
stats = pstats.Stats(pfile)
os.remove(pfile)
stats.strip_dirs()
stats.sort_stats('cumulative')
stats.print_stats()
else:
solver.run(neuron, Fdrive, Adrive, tstim, toffset, sim_type='classic')
def test_ASTIM_hybrid(is_profiled=False):
''' Hybrid acoustic simulation '''
logger.info('Test: running ASTIM hybrid simulation')
# Initialize neuron
neuron = CorticalRS()
# Stimulation parameters
Fdrive = 350e3 # Hz
Adrive = 100e3 # Pa
tstim = 1e-3 # s
toffset = 1e-3 # s
# Initialize solver
a = 32e-9 # m
solver = SolverUS(a, neuron, Fdrive)
# Run simulation
if is_profiled:
pfile = 'tmp.stats'
cProfile.runctx("solver.run(neuron, Fdrive, Adrive, tstim, toffset, sim_type='hybrid')",
globals(), locals(), pfile)
stats = pstats.Stats(pfile)
os.remove(pfile)
stats.strip_dirs()
stats.sort_stats('cumulative')
stats.print_stats()
else:
solver.run(neuron, Fdrive, Adrive, tstim, toffset, sim_type='hybrid')
def test_all():
t0 = time.time()
test_MECH()
test_ESTIM()
test_ASTIM_effective()
test_ASTIM_classic()
test_ASTIM_hybrid()
tcomp = time.time() - t0
logger.info('All tests completed in %.0f s', tcomp)
def main():
# Define valid test sets
valid_testsets = [
'MECH',
'ESTIM',
'ASTIM_effective',
'ASTIM_classic',
'ASTIM_hybrid',
'all'
]
# Define argument parser
ap = ArgumentParser()
ap.add_argument('-t', '--testset', type=str, default='all', choices=valid_testsets,
help='Specific test set')
ap.add_argument('-v', '--verbose', default=False, action='store_true',
help='Increase verbosity')
ap.add_argument('-p', '--profile', default=False, action='store_true',
help='Profile test set')
# Parse arguments
args = ap.parse_args()
if args.verbose:
logger.setLevel(logging.DEBUG)
else:
logger.setLevel(logging.INFO)
if args.profile and args.testset == 'all':
logger.error('profiling can only be run on individual tests')
sys.exit(2)
# Run test
if args.testset == 'all':
test_all()
else:
possibles = globals().copy()
possibles.update(locals())
method = possibles.get('test_{}'.format(args.testset))
method(args.profile)
sys.exit(0)
if __name__ == '__main__':
main()

Event Timeline

c4science · Help