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_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 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_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)