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test_basic.py
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#!/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: 2017-08-25 14:40:55
''' Test the basic functionalities of the package. '''
import logging
import numpy as np
import PointNICE
from PointNICE.utils import LoadParams
from PointNICE.solvers import detectSpikes, titrateAStim
from PointNICE.channels import CorticalRS
from PointNICE.constants import *
# Set logging options
logging.basicConfig(format='%(asctime)s %(message)s', datefmt='%d/%m/%Y %H:%M:%S:')
logger = logging.getLogger('PointNICE')
logger.setLevel(logging.DEBUG)
# Set geometry of NBLS structure
geom = {"a": 32e-9, "d": 0.0e-6}
# Defining general stimulation parameters
Fdrive = 3.5e5 # Hz
Adrive = 1e5 # Pa
PRF = 1.5e3 # Hz
DF = 1
logger.info('Starting basic tests')
logger.info('Test 1: Loading parameters')
params = LoadParams()
# logger.info('Test 2: Creating typical BLS instance')
# Cm0 = 1e-2 # membrane resting capacitance (F/m2)
# Qm0 = -89e-5 # membrane resting charge density (C/m2)
# bls = PointNICE.BilayerSonophore(geom, params, Fdrive, Cm0, Qm0)
# logger.info('Test 3: Running simulation of the mechanical system')
# charges = np.linspace(-100, 50, 10) * 1e-5 # C/m2
# for Qm in charges:
# bls.runMech(Fdrive, 2e4, Qm)
logger.info('Test 4: Creating channel mechanism')
rs_mech = CorticalRS()
logger.info('Test 5: Creating typical SolverUS instance')
solver = PointNICE.SolverUS(geom, params, rs_mech, Fdrive)
# logger.info('Test 6: running short classic simulation of the full system')
# tstim = 1e-3 # s
# toffset = 1e-3 # s
# (t, y, _) = solver.run(rs_mech, Fdrive, Adrive, tstim, toffset, PRF, DF, 'classic')
# Qm = y[2]
# n_spikes, _, _ = detectSpikes(t, Qm, SPIKE_MIN_QAMP, SPIKE_MIN_DT)
# assert n_spikes == 0, 'Error: number of spikes should be 0'
# logger.info('0 spike detected --> OK')
# logger.info('Test 7: running hybrid simulation')
# tstim = 30e-3 # s
# toffset = 10e-3 # s
# (t, y, _) = solver.run(rs_mech, Fdrive, Adrive, tstim, toffset, PRF, DF, 'hybrid')
# Qm = y[2]
# n_spikes, _, _ = detectSpikes(t, Qm, SPIKE_MIN_QAMP, SPIKE_MIN_DT)
# assert n_spikes == 1, 'Error: number of spikes should be 1'
# logger.info('1 spike detected --> OK')
# logger.info('Test 8: creating dummy lookup file')
# amps = np.array([1, 2]) * 1e5 # Pa
# charges = np.array([-80.0, 30.0]) * 1e-5 # C/m2
# tmp = rs_mech.name
# rs_mech.name = 'test'
# solver.createLookup(rs_mech, Fdrive, amps, charges)
# rs_mech.name = tmp
# logger.info('Test 9: running effective simulation')
# tstim = 30e-3 # s
# toffset = 10e-3 # s
# (t, y, _) = solver.run(rs_mech, Fdrive, Adrive, tstim, toffset, PRF, DF, 'effective')
# Qm = y[2]
# n_spikes, _, _ = detectSpikes(t, Qm, SPIKE_MIN_QAMP, SPIKE_MIN_DT)
# assert n_spikes == 1, 'Error: number of spikes should be 1'
# logger.info('1 spike detected --> OK')
logger.info('Test 10: running effective amplitude titration')
tstim = 30e-3 # s
toffset = 10e-3 # s
Arange = (0.0, 2 * TITRATION_ASTIM_A_MAX) # Pa
(Athr, t, y, _, latency) = titrateAStim(solver, rs_mech, Fdrive, Arange, tstim, toffset, PRF, DF)
Qm = y[2]
n_spikes, _, _ = detectSpikes(t, Qm, SPIKE_MIN_QAMP, SPIKE_MIN_DT)
assert n_spikes == 1, 'Error: number of spikes should be 1'
logger.info('1 spike detected --> OK')
# logger.info('Test 11: running effective duration titration')
# trange = (0.0, 2 * TITRATION_T_MAX) # s
# toffset = 10e-3 # s
# (tthr, t, y, _, latency) = solver.titrateDur(rs_mech, Fdrive, Adrive, trange, toffset,
# PRF, DF, 'effective')
# Qm = y[2]
# n_spikes, _, _ = detectSpikes(t, Qm, SPIKE_MIN_QAMP, SPIKE_MIN_DT)
# assert n_spikes == 1, 'Error: number of spikes should be 1'
# logger.info('1 spike detected --> OK')
logger.info('All tests successfully completed')

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