def test_DoubleKickViaSmearedForceWithPRC(self):
"""
This test handles the majority of physiological control of heart
rate. Respiratory IAF periodically forces the heart via the
RespiratoryDelayedSmearedHeartActionForce. The force is applied to heart
drive. Initially the heart is in phase with respiration, as both
periods are commensurate (3:1) and initial phase of both is 0.
"""
npoints = 120
data = RungeKutta45IntegratorData(10, 0.0)
iafResp = IntegrateAndFire()
iafResp.SetPhaseVelocityFromBPM(20)
iafResp.phaseEfectivenessCurve = phaseEfectivenessCurveSH
iafResp.SamplingTime = 0.1
iafResp.SetInitialPhase(0.0)
iafResp.KickAmplitude = 0.1
iafResp.SamplingTime = 0.1
iafResp.CoordinateNumberForRate = 7
iafResp.CoordinateNumberForPhase = 6
iafResp.CoordinateNumberForForceInput = 8 #coupling in opposite direction.
# Coordinate number, to which the state will be written
#this variable will be used for coupling.
iafResp.CoordinateNumberForOutput = 4
fireNotifierResp = FiringTimesNotifier()
iafResp.Notify = fireNotifierResp.Notify
forceCoordinateNumber = 5
iafHeart = IntegrateAndFire()
iafHeart.SamplingTime = 0.1
iafHeart.SetPhaseVelocityFromBPM(67)
iafHeart.phaseEfectivenessCurve = phaseEfectivenessCurveSH
iafHeart.CoordinateNumberForRate = 0
iafHeart.CoordinateNumberForPhase = 1
iafHeart.CoordinateNumberForForceInput = forceCoordinateNumber
# Coordinate number, to which the state will be written
iafHeart.CoordinateNumberForOutput = 2
fireNotifierHeart = FiringTimesNotifier()
iafHeart.Notify = fireNotifierHeart.Notify
fireNotifier = FiringTimesNotifier()
force = RespiratoryDelayedSmearedHeartActionForce()
force.CoordinateNumber = forceCoordinateNumber #Coordinate number, to which the state will be written
force.CoordinateNumberForInput = iafResp.CoordinateNumberForOutput
force.KickAmplitude = -1.0 #Kick amplitude
force.DelayTau = 0.1 #Time from firing order to actual kick
force.SamplingTime = 0.1 # required to normalize delay time.
force.DecayTau = 0.9 # Time by which the drive decays
force.Notify = fireNotifier.Notify
fireNotifierR = FiringTimesNotifier()
forceR = RespiratoryDelayedSmearedHeartActionForce()
forceR.CoordinateNumber = 8 #Coordinate number, to which the state will be written
forceR.KickAmplitude = 1.0 #Kick amplitude
forceR.DelayTau = 0.1 #Time from firing order to actual kick
forceR.SamplingTime = 0.1 # required to normalize delay time.
forceR.DecayTau = 0.9 # Time by which the drive decays
forceR.CoordinateNumberForInput = iafHeart.CoordinateNumberForOutput
forceR.Notify = fireNotifierR.Notify
seriesNotifier = SeriesNotifier(data.dimension, npoints)
allTimes = np.linspace(0.0, npoints * force.SamplingTime, npoints)
for t in allTimes:
data.t = t
data.y[0] = 0.0 # reset only the variable which gets set manually
# to prevent constant firing
iafResp.ApplyDrive(data)
#if data[iafResp.CoordinateNumberForOutput] > 0.0:
# data.y[0] = 1.0
# force.FireOrderTime = t
logging.debug(data)
forceR.ApplyDrive(data)
force.ApplyDrive(data)
iafHeart.ApplyDrive(data)
seriesNotifier.Notify(data)
#print("Firing times: %s" % str(fireNotifier.firingTimes))
fig = plt.figure()
plt.subplot(5, 1, 1)
plt.plot(allTimes, seriesNotifier.GetVar(6), "b")
plt.plot(fireNotifierResp.firingTimes,
fireNotifierResp.firingTimesSpikes(), "bo")
plt.ylabel(r"$\Phi(t)$")
plt.yticks([])
plt.xticks([])
plt.ylim(0.0, 1.2)
plt.subplot(5, 1, 2)
plt.plot(allTimes,
seriesNotifier.GetVar(iafResp.CoordinateNumberForOutput),
"g",
linewidth=2)
plt.plot(fireNotifier.firingTimes, fireNotifier.firingTimesSpikes(),
"go")
plt.plot(allTimes,
seriesNotifier.GetVar(force.CoordinateNumber),
"g",
linewidth=2)
plt.yticks([])
plt.xticks([])
plt.ylabel("Force")
#plt.ylim(0.0,5.0 * iafResp.KickAmplitude)
plt.subplot(5, 1, 3)
plt.ylabel(r"$d\varphi(t)/dt$")
plt.plot(allTimes,
seriesNotifier.GetVar(iafHeart.CoordinateNumberForRate), "v")
plt.yticks([])
plt.xticks([])
plt.subplot(5, 1, 4)
plt.plot(allTimes,
seriesNotifier.GetVar(iafHeart.CoordinateNumberForPhase), "r")
#plt.plot(allTimes,seriesNotifier.GetVar(2),"r")
plt.plot(fireNotifierHeart.firingTimes,
fireNotifierHeart.firingTimesSpikes(), "ro")
plt.ylim(0.0, 1.2)
plt.yticks([])
plt.xticks([])
plt.ylabel(r"$\varphi(t)$")
#plt.ylim(0.0,5.0 * iafResp.KickAmplitude)
plt.subplot(5, 1, 5)
plt.ylabel("RR")
plt.yticks([])
plt.plot(fireNotifierHeart.firingTimes[1:],
fireNotifierHeart.ISI()[1:], "b+-")
plt.xlabel("Time [s]")
fname = sys._getframe().f_code.co_name + ".png"
print("Test result in %s" % fname)
plt.savefig(fname)
def test_FullCoupling(self):
"""
This test handles the majority of physiological control of heart
rate. Respiratory IAF periodically forces the heart via the
RespiratoryDelayedSmearedHeartActionForce. The force is applied to heart
drive. Initially the heart is in phase with respiration, as both
periods are commensurate (3:1) and initial phase of both is 0.
"""
dimension = 10
npoints = 1800
settings = KickedWindkesselModel.KickedWindkesselModelSettings()
fireNotifier = FiringTimesNotifier()
force = RespiratoryDelayedSmearedHeartActionForce()
force.CoordinateNumber = 9 #Coordinate number, to which the state will be written
force.CoordinateNumberForInput = 6
force.KickAmplitude = 1.0 #Kick amplitude
force.DelayTau = 0.1 #Time from firing order to actual kick
force.SamplingTime = 0.01 # required to normalize delay time.
force.DecayTau = 0.9 # Time by which the drive decays
force.Notify = fireNotifier.Notify
iafResp = IntegrateAndFire()
iafResp.SamplingTime = 0.01
iafResp.SetPhaseVelocityFromBPM(20)
iafResp.SetInitialPhase(0.0)
iafResp.KickAmplitude = 0.1
iafResp.CoordinateNumberForRate = -1
iafResp.CoordinateNumberForPhase = 5
iafResp.CoordinateNumberForForceInput = -1 #not used
# Coordinate number, to which the state will be written
#this variable will be used for coupling.
iafResp.CoordinateNumberForOutput = 6
fireNotifierResp = FiringTimesNotifier()
iafResp.Notify = fireNotifierResp.Notify
iafHeart = IntegrateAndFire()
iafHeart.SamplingTime = 0.01
iafHeart.SetPhaseVelocityFromBPM(67)
iafHeart.phaseEfectivenessCurve = phaseEfectivenessCurveSH
iafHeart.CoordinateNumberForRate = 8
iafHeart.CoordinateNumberForPhase = 7
iafHeart.CoordinateNumberForForceInput = force.CoordinateNumber
# Coordinate number, to which the state will be written
iafHeart.CoordinateNumberForOutput = 4
fireNotifierHeart = FiringTimesNotifier()
iafHeart.Notify = fireNotifierHeart.Notify
collector = AbpmFiducialPointsCollector(0) #ABPM = 0
seriesNotifier = SeriesNotifier(dimension, npoints)
allTimes = np.linspace(0.0, npoints * force.SamplingTime, npoints)
settings.heartActionForce = HeartActionForceChain(
[iafResp, force, iafHeart])
model = KickedWindkesselModel(settings, dimension)
model.param.Npoints = npoints
chain = NotifierChain((collector, seriesNotifier))
model.Notify = chain.Notify
model.IterateToNotifiers()
#print("Firing times: %s" % str(fireNotifier.firingTimes))
fig = plt.figure()
gs = gridspec.GridSpec(6, 1, height_ratios=[1, 2, 2, 2, 2, 4])
ax = plt.subplot(gs[0])
plt.plot(allTimes,
seriesNotifier.GetVar(iafResp.CoordinateNumberForPhase), "b")
plt.plot(fireNotifierResp.firingTimes,
fireNotifierResp.firingTimesSpikes(), "bo")
plt.yticks([0.0, 1.0])
plt.ylabel(r"$\Phi(t)$")
#plt.xlabel("Time [s]")
plt.ylim(0.0, 1.2)
plt.setp(ax.get_xticklabels(), visible=False)
ax = plt.subplot(gs[1])
#todo: the guy below is all flat.
#plt.plot(allTimes,seriesNotifier.GetVar(iafResp.CoordinateNumberForOutput),"g",linewidth=2)
plt.plot(fireNotifier.firingTimes, fireNotifier.firingTimesSpikes(),
"go")
plt.plot(allTimes,
seriesNotifier.GetVar(force.CoordinateNumber),
"g",
linewidth=2)
plt.yticks([])
plt.setp(ax.get_xticklabels(), visible=False)
#plt.xlabel("Time [s]")
plt.ylabel(r"$r_{n}(t)$")
#plt.ylim(0.0,5.0 * iafResp.KickAmplitude)
ax = plt.subplot(gs[2])
plt.yticks([])
plt.ylabel(r"$r(t)$")
plt.plot(allTimes,
seriesNotifier.GetVar(iafHeart.CoordinateNumberForRate), "v")
plt.setp(ax.get_xticklabels(), visible=False)
ax = plt.subplot(gs[3])
plt.plot(allTimes,
seriesNotifier.GetVar(iafHeart.CoordinateNumberForPhase), "r")
#plt.plot(allTimes,seriesNotifier.GetVar(2),"r")
plt.plot(fireNotifierHeart.firingTimes,
fireNotifierHeart.firingTimesSpikes(), "ro")
plt.ylim(0.0, 1.2)
plt.yticks([0.0, 1.0])
#plt.xlabel("Time [s]")
plt.ylabel(r"$\varphi(t)$")
#plt.ylim(0.0,5.0 * iafResp.KickAmplitude)
plt.setp(ax.get_xticklabels(), visible=False)
ax = plt.subplot(gs[4])
plt.ylabel("ISI")
plt.plot(fireNotifierHeart.firingTimes[1:],
fireNotifierHeart.ISI()[1:], "b+-")
plt.setp(ax.get_xticklabels(), visible=False)
plt.subplot(gs[5])
for varNumber in (0, 1, 2, 3):
plt.plot(allTimes, seriesNotifier.GetVar(varNumber))
plt.ylim(0.0, 300.0)
plt.xlabel("Time [s]")
plt.ylabel("BP [mmHg]")
fname = sys._getframe().f_code.co_name + ".png"
print("Test result in %s" % fname)
plt.savefig(fname)
plt.close(fig)