def StandardModelSetup(dimension, npoints):
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 = 0.3 #Time from firing order to actual kick
force.SamplingTime = 0.01 # required to normalize delay time.
force.DecayTau = 0.3 # 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(66) #45 worked OK
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
iafHeart.NotifyFunctions = [
fireNotifierHeart.Notify, collector.HeartOpenNotifier
]
mmNotifier = MinMaxNotifier(0)
mmNotifier.MinNotifier = collector.AbpmMinNotifier
mmNotifier.MaxNotifier = collector.AbpmMaxNotifier
seriesNotifier = SeriesNotifier(dimension, npoints)
settings.heartActionForce = HeartActionForceChain(
[iafResp, force, iafHeart])
settings.CoordinateNumberForRespPhase = iafResp.CoordinateNumberForPhase
model = KickedWindkesselModel(settings, dimension)
model.param.Npoints = npoints
chain = NotifierChain((mmNotifier, collector, seriesNotifier))
model.Notify = chain.Notify
return settings, model, force, iafResp, iafHeart, collector, seriesNotifier, fireNotifierResp, fireNotifierHeart, fireNotifier
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_RespiratoryDelayedSmearedHeartActionForceForcedByResp(self):
"""
This test handles the majority of physiological control of heart
rate. Respiratory IAF periodically forces the heart via the
RespiratoryDelayedSmearedHeartActionForce.
The test shows how respiratory kick is converted to delayed smeared kick.
"""
npoints = 240
data = RungeKutta45IntegratorData(10, 0.0)
iafResp = IntegrateAndFire()
iafResp.SetPhaseVelocityFromBPM(20)
iafResp.SamplingTime = 0.1
iafResp.SetInitialPhase(0.0)
iafResp.KickAmplitude = 0.1
iafResp.SamplingTime = 0.1
iafResp.CoordinateNumberForRate = 7
iafResp.CoordinateNumberForPhase = 6
iafResp.CoordinateNumberForForceInput = -1 #not used
# 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
fireNotifier = FiringTimesNotifier()
force = RespiratoryDelayedSmearedHeartActionForce()
force.Drive = 0.0 #Current value of heart drive.
force.CoordinateNumber = 5 #Coordinate number, to which the state will be written
force.KickAmplitude = 1.0 #Kick amplitude
force.DelayTau = 1.53 #Time from firing order to actual kick
force.SamplingTime = 0.1 # required to normalize delay time.
force.StepPeriod = 1.0 #Heart period
#force.FireOrderTime = None #Time of last beat [s]
force.DecayTau = 15.0 # Time by which the drive decays
force.Notify = fireNotifier.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)
force.ApplyDrive(data) # will open or not.
seriesNotifier.Notify(data)
spikes = np.ones(len(fireNotifier.firingTimes))
spikesResp = np.ones(len(fireNotifierResp.firingTimes))
#print("Firing times: %s" % str(fireNotifier.firingTimes))
fig = plt.figure()
plt.subplot(3, 1, 1)
plt.plot(allTimes, seriesNotifier.GetVar(6), "b")
plt.plot(fireNotifierResp.firingTimes, spikesResp, "bo")
plt.ylabel("Resp. phase [1/rad]")
plt.xlabel("Time [s]")
plt.ylim(0.0, 1.2)
plt.subplot(3, 1, 2)
plt.plot(allTimes,
seriesNotifier.GetVar(iafResp.CoordinateNumberForOutput),
"g",
linewidth=2)
plt.xlabel("Time [s]")
plt.ylabel("Force")
plt.ylim(0.0, 5.0 * iafResp.KickAmplitude)
plt.subplot(3, 1, 3)
plt.plot(fireNotifier.firingTimes, spikes, "bo")
plt.plot(allTimes,
seriesNotifier.GetVar(force.CoordinateNumber),
"g",
linewidth=2)
plt.xlabel("Time [s]")
plt.ylabel("Delayed Force")
#plt.ylim(0.0,5.0 * iafResp.KickAmplitude)
fname = sys._getframe().f_code.co_name + ".png"
print("Test result in %s" % fname)
plt.savefig(fname)
def test_RespiratoryDelayedSmearedHeartActionForce(self):
data = RungeKutta45IntegratorData(5, 0.0)
period = 0.5
lastFire = -period #force fire at 0.0
fireNotifier = FiringTimesNotifier()
force = RespiratoryDelayedSmearedHeartActionForce()
force.Drive = 0.0 #Current value of heart drive.
force.CoordinateNumber = 4 #Coordinate number, to which the state will be written
force.CoordinateNumberForInput = 0
force.KickAmplitude = 1.0 #Kick amplitude
force.DelayTau = 0.13 #Time from firing order to actual kick
force.SamplingTime = 0.1 # required to normalize delay time.
force.DecayTau = 15.0 # Time by which the drive decays
force.Notify = fireNotifier.Notify
npoints = 1000
period = 1.0
seriesNotifier = SeriesNotifier(5, npoints)
allTimes = np.linspace(0.0, 10.0, npoints)
for t in allTimes:
data.t = t
data.y[3] = 10.0 * np.cos(2 * np.pi * t / period)
data.y[0] = data.y[1] = data.y[2] = 0.0
if t >= lastFire + period:
data.y[0] = 1.0
lastFire = t
logging.debug(data)
force.ApplyDrive(data) # will open or not.
seriesNotifier.Notify(data)
#print("Firing times: %s" % str(fireNotifier.firingTimes))
fig = plt.figure()
plt.subplot(2, 1, 1)
plt.plot(allTimes, seriesNotifier.GetVar(3))
plt.subplot(2, 1, 2)
plt.plot(allTimes, seriesNotifier.GetVar(0), "r")
plt.plot(allTimes, seriesNotifier.GetVar(4))
fname = sys._getframe().f_code.co_name + ".png"
logging.info("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)
def test_HighAmplitude(self):
"""
Is the influence of high intrathoracic pressure amplitude visible
at disabled heart control
"""
dimension = 10
npoints = 2400
settings = KickedWindkesselModel.KickedWindkesselModelSettings()
fireNotifier = FiringTimesNotifier()
force = RespiratoryDelayedSmearedHeartActionForce()
force.CoordinateNumber = 9 #Coordinate number, to which the state will be written
force.CoordinateNumberForInput = 6
force.KickAmplitude = 0.0 #Kick amplitude
force.DelayTau = 0.3 #Time from firing order to actual kick
force.SamplingTime = 0.01 # required to normalize delay time.
force.DecayTau = 0.3 # Time by which the drive decays
force.Notify = fireNotifier.Notify
iafResp = IntegrateAndFire()
iafResp.SamplingTime = 0.01
iafResp.SetPhaseVelocityFromBPM(6)
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
iafHeart.NotifyFunctions = [
fireNotifierHeart.Notify, collector.HeartOpenNotifier
]
mmNotifier = MinMaxNotifier(0)
mmNotifier.MinNotifier = collector.AbpmMinNotifier
mmNotifier.MaxNotifier = collector.AbpmMaxNotifier
seriesNotifier = SeriesNotifier(dimension, npoints)
allTimes = np.linspace(0.0, npoints * force.SamplingTime, npoints)
settings.heartActionForce = HeartActionForceChain(
[iafResp, force, iafHeart])
settings.CoordinateNumberForRespPhase = iafResp.CoordinateNumberForPhase
settings.p_I1 = 3.0 # default is 0.1
model = KickedWindkesselModel(settings, dimension)
model.param.Npoints = npoints
chain = NotifierChain((mmNotifier, collector, seriesNotifier))
model.Notify = chain.Notify
model.IterateToNotifiers()
allItems = collector.GetFiducialPointsList()
series = {}
series["systolicABP"] = np.array(allItems[:, 1])
series["diastolicABP"] = np.array(allItems[:, 2])
series["meanABP"] = np.array(allItems[:, 3])
for key in series.keys():
av = np.average(series[key])
sd = np.std(series[key])
logging.info("%s: av: %.2lf sd: %.2lf, npoints: %d" %
(key, av, sd, len(series[key])))
print(allItems)
fname = sys._getframe().f_code.co_name + ".png"
KickedWindkesselModelVisualization(
fname, allTimes, allItems, seriesNotifier, fireNotifierResp,
fireNotifier, fireNotifierHeart, iafResp.CoordinateNumberForPhase,
force.CoordinateNumber, iafHeart.CoordinateNumberForRate,
iafHeart.CoordinateNumberForPhase)