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_UnperturbedRate(self):
data = RungeKutta45IntegratorData(8, 0.0)
iaf = IntegrateAndFire()
fireNotifier = FiringTimesNotifier()
iaf.Notify = fireNotifier.Notify
npoints = 1000
period = 1.0
seriesNotifier = SeriesNotifier(8, npoints)
allTimes = np.linspace(0.0, 10.0, npoints)
for t in allTimes:
data.t = t
# this is to make the plot visually nicer :-)
data.y[3] = 10.0 * np.cos(2 * np.pi * t / period)
#data.y[0] = data.y[1] = data.y[2] = 0.0
iaf.ApplyDrive(data) # will open or not.
logging.debug(data)
seriesNotifier.Notify(data)
#Print dots at firing times
spikes = np.ones(len(fireNotifier.firingTimes))
#print("Firing times: %s" % str(fireNotifier.firingTimes))
fig = plt.figure()
plt.subplot(2, 1, 1)
#plt.ylim(-12.0,12.0)
plt.plot(allTimes, seriesNotifier.GetVar(3))
plt.subplot(2, 1, 2)
plt.plot(allTimes, seriesNotifier.GetVar(4), "g")
plt.plot(fireNotifier.firingTimes, spikes, "ro")
fname = sys._getframe().f_code.co_name + ".png"
print("Test result in %s" % fname)
plt.savefig(fname)
def test_FrequencyModulation(self):
data = RungeKutta45IntegratorData(8, 0.0)
iaf = IntegrateAndFire()
fireNotifier = FiringTimesNotifier()
iaf.Notify = fireNotifier.Notify
npoints = 1000
period = 20.0
seriesNotifier = SeriesNotifier(8, npoints)
allTimes = np.linspace(0.0, npoints * iaf.SamplingTime, npoints)
for t in allTimes:
data.t = t
data.y[5] = 2.0 * iaf.r * (1.0 + np.cos(2 * np.pi * t / period))
iaf.ApplyDrive(data) # will open or not.
logging.debug(data)
seriesNotifier.Notify(data)
#Print dots at firing times
spikes = np.ones(len(fireNotifier.firingTimes))
#print("Firing times: %s" % str(fireNotifier.firingTimes))
fig = plt.figure()
plt.subplot(2, 1, 1)
#plt.ylim(-12.0,12.0)
plt.plot(allTimes, seriesNotifier.GetVar(5)) #effective rate
plt.subplot(2, 1, 2)
plt.plot(allTimes, seriesNotifier.GetVar(4), "g")
plt.plot(fireNotifier.firingTimes, spikes, "ro")
fname = sys._getframe().f_code.co_name + ".png"
print("Test result in %s" % fname)
plt.savefig(fname)
def test_RectangularHeartActionForce(self):
data = RungeKutta45IntegratorData(5, 0.0)
force = RectangularHeartActionForce()
fireNotifier = FiringTimesNotifier()
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
logging.debug(data)
force.ApplyDrive(data) # will open or not.
seriesNotifier.Notify(data)
allValues4 = seriesNotifier.GetVar(4)
allValues3 = seriesNotifier.GetVar(3)
logging.info("Firing times: %s" % str(fireNotifier.firingTimes))
#fig = plt.figure()
plt.subplot(2, 1, 1)
#plt.ylim(-12.0,12.0)
plt.plot(allTimes, allValues3)
plt.subplot(2, 1, 2)
plt.plot(allTimes, allValues4)
fname = sys._getframe().f_code.co_name + ".png"
logging.info("Test result in %s" % fname)
plt.savefig(fname)
def test_fiducial_points_collector_rect(self):
settings = KickedWindkesselModel.KickedWindkesselModelSettings()
settings.heartActionForce = RectangularHeartActionForce()
model = KickedWindkesselModel(settings)
model.param.Npoints = 10000
collector = AbpmFiducialPointsCollector(
0) #ABPM = 0. Other compartments have different numbers.
settings.heartActionForce.Notify = collector.HeartOpenNotifier
mmNotifier = MinMaxNotifier(0)
mmNotifier.MinNotifier = collector.AbpmMinNotifier
mmNotifier.MaxNotifier = collector.AbpmMaxNotifier
seriesNotifier = SeriesNotifier(model.param.dimension,
model.param.Npoints)
chain = NotifierChain((mmNotifier, collector, seriesNotifier))
model.Notify = chain.Notify
model.IterateToNotifiers()
allValues = seriesNotifier.GetVar(0)
allTimes = np.linspace(0.0, model.param.dT * model.param.Npoints,
model.param.Npoints)
allItems = collector.GetFiducialPointsList()
fig = plt.figure()
#plt.ylim(-12.0,12.0)
plt.plot(allTimes, allValues)
#pdb.set_trace()
plt.plot(allItems[:, 0], allItems[:, 1], "ro") # systolic
plt.plot(allItems[:, 0], allItems[:, 2], "go") # diastolic
plt.plot(allItems[:, 0], allItems[:, 3], "bo") # mean
plt.savefig("test_fiducial_points_collector_rect.png")
logging.warning("Result in test_fiducial_points_collector_rect.png")
def BasicProcessor():
settings = KickedWindkesselModel.KickedWindkesselModelSettings()
settings.heartActionForce = RectangularHeartActionForce()
model = KickedWindkesselModel(settings)
model.param.Npoints = 1000
series = SeriesNotifier(model.param.dimension, model.param.Npoints + 1)
model.Notify = series.Notify
model.IterateToNotifiers()
fname = "overview.png"
series.PlotSeries((1, 2, 3, 4), fname)
print("Plat data in %s" % fname)
def test_UnperturbedRate(self):
settings = KickedWindkesselModel.KickedWindkesselModelSettings()
settings.heartActionForce = RectangularHeartActionForce()
model = KickedWindkesselModel(settings)
model.param.Npoints = 1000
series = SeriesNotifier(model.param.dimension, model.param.Npoints + 1)
model.Notify = series.Notify
model.IterateToNotifiers()
fname = sys._getframe().f_code.co_name + ".png"
series.PlotSeries((1, 2, 3, 4), fname)
print("Plot data in %s" % 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_min_max_notifier(self):
data = RungeKutta45IntegratorData(2, 0.0)
mmNotifier = MinMaxNotifier(0) #first variable
npoints = 1000
seriesNotifier = SeriesNotifier(2, npoints)
notifier = NotifierChain((mmNotifier, seriesNotifier))
period = 1.0
allTimes = np.linspace(0.0, 10.0, npoints)
for t in allTimes:
data.t = t
data.y[0] = 10.0 * np.cos(2 * np.pi * t / period)
data.y[1] = 10.0 * np.sin(2 * np.pi * t / period)
notifier.Notify(data)
maxTime, maxValue, maxIterator = mmNotifier.getMaxima()
minTime, minValue, minIterator = mmNotifier.getMinima()
allValues = seriesNotifier.GetVar(0)
fig = plt.figure()
plt.ylim(-12.0, 12.0)
plt.plot(allTimes, allValues)
plt.plot(minTime, minValue, "bo")
plt.plot(maxTime, maxValue, "r*")
plt.show()
def PhaseShiftProcessorOld():
logging.basicConfig(level=logging.ERROR)
stepShiftLinspace = np.linspace(0, 1.25, 10)
stepShiftLinspace = np.linspace(0, 2.0 * np.pi, 100)
Sav = []
Ssd = []
Dav = []
Dsd = []
Mav = []
Msd = []
for stepShift in stepShiftLinspace:
settings = KickedWindkesselModel.KickedWindkesselModelSettings()
settings.breathingPhi0 = stepShift
settings.heartActionForce = RectangularHeartActionForce()
settings.heartActionForce.StepShift = stepShift
model = KickedWindkesselModel(settings)
model.param.Npoints = 1000
collector = AbpmFiducialPointsCollector(
0) #ABPM = 0. Other compartments have different numbers.
settings.heartActionForce.Notify = collector.HeartOpenNotifier
mmNotifier = MinMaxNotifier(0)
mmNotifier.MinNotifier = collector.AbpmMinNotifier
mmNotifier.MaxNotifier = collector.AbpmMaxNotifier
seriesNotifier = SeriesNotifier(model.param.dimension,
model.param.Npoints)
chain = NotifierChain((mmNotifier, collector, seriesNotifier))
model.Notify = chain.Notify
model.IterateToNotifiers()
allItems = collector.GetFiducialPointsList()
averages = []
standard_deviations = []
for channel in [1, 2, 3]: # 1-systloic 2-diastolic 3-mean
averages.append(np.mean(allItems[:, channel]))
standard_deviations.append(np.std(allItems[:, channel]))
Sav.append(averages[0])
Ssd.append(standard_deviations[0])
Dav.append(averages[1])
Dsd.append(standard_deviations[1])
Mav.append(averages[2])
Msd.append(standard_deviations[2])
print("%f\t%f\t%f\t%f\t%f\t%f\t%f" %
(settings.heartActionForce.StepShift, averages[0],
standard_deviations[0], averages[1], standard_deviations[1],
averages[2], standard_deviations[2]))
#normalize values
basalValue = Ssd[0]
for i, v in enumerate(Ssd):
Ssd[i] = 100.0 * (v / basalValue)
basalValue = Dsd[0]
for i, v in enumerate(Dsd):
Dsd[i] = 100.0 * (v / basalValue)
basalValue = Msd[0]
for i, v in enumerate(Msd):
Msd[i] = 100.0 * (v / basalValue)
#pdb.set_trace()
fig, ax = plt.subplots()
ax.ticklabel_format(useOffset=False)
#plt.subplot(3,1,1)
ax.plot(stepShiftLinspace, Ssd, "r", linestyle="-",
linewidth=1) # SAP thin curve
#plt.subplot(3,1,2)
ax.plot(stepShiftLinspace, Dsd, "g", linestyle="--",
linewidth=3) # DAP thick dashed
#plt.subplot(3,1,3)
ax.plot(stepShiftLinspace, Msd, "b", linestyle="-",
linewidth=3) # MAP thick solid
for y in (100.0, ): # 80.0,100.0,120.0):
plt.axhline(y=y, color='k', linestyle='-')
#ax.fill(30, 30, fill=False, hatch='\\')
#pdb.set_trace()
ylim = copy.deepcopy(ax.get_ylim()) # keep original limits.\
xlim = copy.deepcopy(ax.get_xlim()) # keep original limits.\
ax.set_ylim([ylim[0], ylim[1]])
ax.set_xlim([xlim[0], xlim[1]])
plt.savefig("phaseShiftFunction100.png")
plt.show()
return (Sav, Ssd, Dav, Dsd, Mav,
Msd), (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_TwoIAFOneWayCoupledInSeconds(self):
"""
This test is a comparison of two IAFs: one with PRC and one without.
"""
npoints = 240
data = RungeKutta45IntegratorData(10, 0.0)
iafResp = IntegrateAndFire()
iafResp.SetPhaseVelocityFromBPM(20)
iafResp.SetInitialPhase(1.0 / 7.0)
iafResp.KickAmplitude = 0.1
iafResp.SamplingTime = 0.01
iafResp.CoordinateNumberForRate = 7
iafResp.CoordinateNumberForPhase = 6
iafResp.CoordinateNumberForForceInput = 5 #not used
# Coordinate number, to which the state will be written
#this variable will be used for coupling.
iafResp.CoordinateNumberForOutput = 4
fireNotifier = FiringTimesNotifier()
iafResp.Notify = fireNotifier.Notify
seriesNotifier = SeriesNotifier(10, npoints)
iafHeart = IntegrateAndFire()
iafHeart.SamplingTime = 0.01
iafHeart.SetPhaseVelocityFromBPM(67)
iafHeart.CoordinateNumberForRate = 0
iafHeart.CoordinateNumberForPhase = 1
iafHeart.CoordinateNumberForForceInput = 4 #essential
#iafHeart.CoordinateNumberForForceInput = 9 # void #essential
# Coordinate number, to which the state will be written
#this variable will be used for coupling.
iafHeart.CoordinateNumberForOutput = 2
fireNotifierHeart = FiringTimesNotifier()
iafHeart.Notify = fireNotifierHeart.Notify
allTimes = np.linspace(0.0, npoints * iafHeart.SamplingTime, npoints)
for t in allTimes:
data.t = t
iafResp.ApplyDrive(data) # will open or not.
iafHeart.ApplyDrive(data)
#print("%lf\t%lf" % (iaf.Phase,data.y[6]))
logging.debug(data)
seriesNotifier.Notify(data)
#Print dots at firing times
spikes = np.ones(len(fireNotifier.firingTimes))
spikes2 = np.ones(len(fireNotifierHeart.firingTimes))
#print("Firing times: %s" % str(fireNotifier.firingTimes))
fig = plt.figure()
plt.subplot(3, 1, 1)
#plt.ylim(-12.0,12.0)
#plt.plot(allTimes,seriesNotifier.GetVar(5))#effective rate
plt.plot(allTimes, seriesNotifier.GetVar(4), "g", linewidth=2)
plt.xlabel("Time [s]")
plt.ylabel("Force")
plt.ylim(0.0, 0.1)
plt.subplot(3, 1, 2)
#pdb.set_trace()
plt.plot(allTimes, seriesNotifier.GetVar(6), "b")
plt.plot(fireNotifier.firingTimes, spikes, "bo")
plt.xlabel("Time [s]")
plt.ylim(0.0, 1.2)
plt.subplot(3, 1, 3)
plt.plot(allTimes, seriesNotifier.GetVar(1), "r")
#plt.plot(allTimes,seriesNotifier.GetVar(2),"r")
plt.plot(fireNotifierHeart.firingTimes, spikes2, "ro")
plt.ylim(0.0, 1.2)
plt.xlabel("Time [s]")
fname = sys._getframe().f_code.co_name + ".png"
print("Test result in %s" % fname)
plt.savefig(fname)
def test_FrequencyModulationWithPRCandKick(self):
"""
This test is a comparison of two IAFs: one with PRC and one without.
"""
npoints = 1000
period = 20.0
data = RungeKutta45IntegratorData(8, 0.0)
iaf = IntegrateAndFire()
iaf.phaseEfectivenessCurve = phaseEfectivenessCurveSH
fireNotifier = FiringTimesNotifier()
iaf.Notify = fireNotifier.Notify
seriesNotifier = SeriesNotifier(8, npoints)
data2 = RungeKutta45IntegratorData(8, 0.0)
iaf2 = IntegrateAndFire()
fireNotifier2 = FiringTimesNotifier()
iaf2.Notify = fireNotifier2.Notify
seriesNotifier2 = SeriesNotifier(8, npoints)
allTimes = np.linspace(0.0, npoints * iaf.SamplingTime, npoints)
binaryKick = np.zeros(npoints)
for i in range(npoints):
if random.randint(0, 10) == 1:
binaryKick[i] = 0.2
for i, t in enumerate(allTimes):
data.t = t
data[5] = binaryKick[i]
data2.t = t
data2[5] = binaryKick[i]
#data.y[5] = 2.0 * iaf.r * (1.0 + np.cos(2 * np.pi * t / period))
#data.y[6] = iaf.Phase+phaseEfectivenessCurveSH(iaf.Phase)
iaf.ApplyDrive(data) # will open or not.
iaf2.ApplyDrive(data2)
#print("%lf\t%lf" % (iaf.Phase,data.y[6]))
logging.debug(data)
seriesNotifier.Notify(data)
seriesNotifier2.Notify(data2)
#Print dots at firing times
spikes = np.ones(len(fireNotifier.firingTimes))
spikes2 = np.ones(len(fireNotifier2.firingTimes))
#print("Firing times: %s" % str(fireNotifier.firingTimes))
fig = plt.figure()
plt.subplot(3, 1, 1)
#plt.ylim(-12.0,12.0)
plt.plot(allTimes, seriesNotifier.GetVar(5)) #effective rate
plt.subplot(3, 1, 2)
plt.plot(allTimes, seriesNotifier.GetVar(4), "g")
plt.plot(allTimes, seriesNotifier.GetVar(6), "r")
plt.plot(fireNotifier.firingTimes, spikes, "ro")
plt.subplot(3, 1, 3)
plt.plot(allTimes, seriesNotifier2.GetVar(4), "g")
plt.plot(allTimes, seriesNotifier2.GetVar(6), "r")
plt.plot(fireNotifier2.firingTimes, spikes2, "ro")
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)
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)