def getWFderivative(self):
sign=1
#print 'Smoothed Data',self.DataSN
self.WFnormP()
for k in range(0,self.length-1):
self.derivative[k]=PPGfunc.getSlope(self.outData[0][k],self.outData[0][k+1],self.outData[1][k],self.outData[1][k+1])
self.derivative[self.length-1]=PPGfunc.getSlope(self.outData[0][self.length-2],self.outData[0][self.length-1],self.outData[1][self.length-2],self.outData[1][self.length-1])
#print "DerivativeNow", self.derivative
self.derivativeN=self.getNormalized(self.derivative)
for k in range(0,self.length-1):
if self.derivativeN[k]==float('nan'):
self.derivativeN[k]=sign
else:
sign=self.derivativeN[k]/self.derivativeN[k]
if self.derivativeN[self.length-1]==float('nan'):
self.derivativeN[k]=sign
#for k in range(0,self.length-1):
#if self.derivativeN[k]==float('nan'):
#print 'NAN= ', k
self.outData[1]=self.derivativeN
return np.copy(self.outData)
def getWFderivative(self):
self.Spectrum()
self.fileteredWave()
for k in range(0, self.length - 1):
self.derivative[k] = PPGfunc.getSlope(self.Time[k],
self.Time[k + 1],
self.filtered_sig[k],
self.filtered_sig[k + 1])
self.derivative[self.length - 1] = PPGfunc.getSlope(
self.Time[self.length - 2], self.Time[self.length - 1],
self.filtered_sig[self.length - 2],
self.filtered_sig[self.length - 1])
sign = 1
for k in range(0, self.length - 1):
if self.derivative[k] == float('nan'):
self.derivative[k] = sign
else:
sign = self.derivative[k] / self.derivative[k]
if self.derivative[self.length - 1] == float('nan'):
self.derivative[k] = sign
return np.copy(self.derivative)
def fileteredWave(self):
n = len(self.Data) / 100
if n < 5:
n = 5
n = 5
#print ('n=',n)
lowcut = 0.5
#print ('lowcut=',lowcut)
highcut = 5
#print ('highcut=',highcut)
fs = 60
#print ('fs=',fs)
b, a = PPGfunc.butter_bandpass(lowcut, highcut, fs, n)
#print ('Butter')
self.filtered_sig = PPGfunc.butter_bandpass_filter(self.Data, b, a)
#print ('Filter')
#self.PlotPPGWave()
#self.PlotPPGWaveFiltered()
min = self.filtered_sig[0]
for i in self.filtered_sig:
if i < min:
min = i
self.filtered_sig = self.filtered_sig - min
def getMinFiltered(self):
self.minFiltered = PPGfunc.getMin(self.filtered_sig)
return self.minFiltered
def getMaxFiltered(self):
self.maxFiltered = PPGfunc.getMax(self.filtered_sig)
return self.maxFiltered
def getMinValue(self):
self.minValue = PPGfunc.getMin(self.Data)
return self.minValue
def getMaxValue(self):
self.maxValue = PPGfunc.getMax(self.Data)
return self.maxValue
def getMinTime(self):
self.minTime = PPGfunc.getMin(self.Time)
return self.minTime
def getMaxTime(self):
self.maxTime = PPGfunc.getMax(self.Time)
return self.maxTime
def make(self,PPGData):
self.ppg=PPGData
# self.smoothS=smoothSpan
# self.smooth= [[0 for x in range(columns)] for y in range(rows)]
# self.smoothN=[
self.PulseWaveSystolicPeakPos=-1
self.PulseWaveEndPos=-1
self.DicroticNotchPos=-1
self.DiastolicPeakPos=-1
self.HalfHeight=-1
self.HalfTimeLow=-1
self.HalfTimeHigh=-1
self.PulseWaveAmplitude=-1
self.SystolicPhase=-1
self.SystolicPeak=-1
self.DiastolicPhase=-1
self.PulseWaveDuration=-1
self.PulsePropogationTme=-1
self.PulseWidthTime=-1
self.RiseTime=-1
self.PulseInflectionPointAmplitude=-1
self.RelectionIndex=-1
self.PulseArea=-1
self.PulseArea1=-1
self.PulseArea2=-1
self.DicroticNotchTime=-1
self.DicroticNotchValue=-1
self.InflectionPointAreaRatio=-1
self.HalfHeightHiPos=-1
self.HalfHeightLowPos=-1
self.AverageWaveForm=self.ppg.getAverageWF()
self.PulseWaveSystolicPeakPos=int(self.AverageWaveForm[2][0])
self.PulseWaveEndPos=int(self.AverageWaveForm[2][1])
self.StdDevPWD=self.AverageWaveForm[2][2]
self.StdDevPWA=self.AverageWaveForm[2][4]
firstD=PPGfunc.derivative(self.AverageWaveForm[0],self.AverageWaveForm[1])
secondD=PPGfunc.derivative(self.AverageWaveForm[0],firstD)
# x1 = self.AverageWaveForm[0]
# y1 = self.AverageWaveForm[1]
# plt.plot(x1, y1,label = "pulse", color= "red")
# x2 = self.AverageWaveForm[0]
# y2 = firstD*10
# plt.plot(x2, y2,label = "First Derivative", color= "blue")
# x2 = self.AverageWaveForm[0]
# y2 = secondD*100
# plt.plot(x2, y2,label = "Second Derivative", color= "green")
# plt.xlabel('Time [ms]')
# plt.ylabel('Pulse Waveform [Arb. Units]')
# plt.legend(loc='upper right')
# plt.title('Pulse Derivatives')
# plt.show()
self.HalfHeight=0.5*self.AverageWaveForm[1][self.PulseWaveSystolicPeakPos]
#print 'Half Height= ',self.HalfHeight
for i in range(0,self.PulseWaveSystolicPeakPos-1):
if self.AverageWaveForm[1][i]>self.HalfHeight:
DeltaX=self.AverageWaveForm[0][i]-self.AverageWaveForm[0][i-1]
DeltaY=self.AverageWaveForm[1][i]-self.AverageWaveForm[1][i-1]
DeltaV=self.HalfHeight-self.AverageWaveForm[1][i-1]
self.HalfTimeLow=self.AverageWaveForm[0][i-1]+DeltaX*DeltaV/DeltaY
self.HalfHeightLowPos=i
break
for i in range(self.PulseWaveSystolicPeakPos+1,self.PulseWaveEndPos-1):
if self.AverageWaveForm[1][i]<self.HalfHeight:
DeltaX=self.AverageWaveForm[0][i]-self.AverageWaveForm[0][i-1]
DeltaY=-self.AverageWaveForm[1][i]+self.AverageWaveForm[1][i-1]
DeltaV=self.HalfHeight-self.AverageWaveForm[1][i]
self.HalfTimeHigh=self.AverageWaveForm[0][i-1]+DeltaX*DeltaV/DeltaY
self.HalfHeightHiPos=i
break
Inflections=PPGfunc.FindNotch(self.AverageWaveForm[0],self.AverageWaveForm[1],self.HalfHeightHiPos-(self.HalfHeightHiPos-self.PulseWaveSystolicPeakPos)/2,self.HalfHeightHiPos+(self.PulseWaveEndPos-self.HalfHeightHiPos)/2,firstD,secondD)
print (self.PulseWaveSystolicPeakPos-self.HalfHeightHiPos)/2,self.HalfHeightHiPos,(self.PulseWaveEndPos-self.HalfHeightHiPos)/2
if(len(Inflections)>1):
self.DiastolicPeakPos=Inflections.pop()
self.DicroticNotchPos=Inflections.pop()
self.DicroticNotchTime=self.AverageWaveForm[0][self.DicroticNotchPos]
self.DicroticNotchValue=self.AverageWaveForm[1][self.DicroticNotchPos]
else:
self.DicroticNotchPos=-1
self.DiastolicPeakPos=-1
self.PulseWaveAmplitude=self.AverageWaveForm[1][self.PulseWaveSystolicPeakPos]
self.SystolicPhase=self.RiseTime=self.AverageWaveForm[0][self.PulseWaveSystolicPeakPos]
self.SystolicPeak=self.AverageWaveForm[1][self.PulseWaveSystolicPeakPos]
self.DiastolicPhase=self.AverageWaveForm[0][self.PulseWaveEndPos]-self.AverageWaveForm[0][self.PulseWaveSystolicPeakPos]
self.PulseWaveDuration=self.AverageWaveForm[0][self.PulseWaveEndPos]
self.PulsePropogationTme=self.AverageWaveForm[0][self.DiastolicPeakPos]-self.AverageWaveForm[0][self.PulseWaveSystolicPeakPos]
self.PulseWidthTime=self.HalfTimeHigh-self.HalfTimeLow
self.PulseInflectionPointAmplitude=self.AverageWaveForm[1][self.DiastolicPeakPos]
self.RelectionIndex=self.PulseInflectionPointAmplitude/self.PulseWaveAmplitude*100
self.PulseArea1=0
for i in range(1,self.DicroticNotchPos):
self.PulseArea1=self.PulseArea1+abs((self.AverageWaveForm[1][i]+self.AverageWaveForm[1][i-1])/2*(self.AverageWaveForm[0][i]-self.AverageWaveForm[0][i-1]))
self.PulseArea2=0
for i in range(self.DicroticNotchPos,self.PulseWaveEndPos):
self.PulseArea2=self.PulseArea2+abs((self.AverageWaveForm[1][i]+self.AverageWaveForm[1][i-1])/2*(self.AverageWaveForm[0][i]-self.AverageWaveForm[0][i-1]))
self.PulseArea=self.PulseArea1+self.PulseArea2
self.InflectionPointAreaRatio=self.PulseArea2/self.PulseArea1
def make(self, PPGData):
self.ppg = PPGData
# self.smoothS=smoothSpan
# self.smooth= [[0 for x in range(columns)] for y in range(rows)]
# self.smoothN=[
self.InflectionPoints = []
self.PulseWaveSystolicPeakPos = -1
self.PulseWaveEndPos = -1
self.DicroticNotchPos = -1
self.DiastolicPeakPos = -1
self.HalfHeight = -1
self.HalfTimeLow = -1
self.HalfTimeHigh = -1
self.PulseWaveAmplitude = -1
self.SystolicPhase = -1
self.DiastolicPhase = -1
self.PulseWaveDuration = -1
self.PulseWavePropogationTme = -1
self.PulseWidthTime = -1
self.RiseTime = -1
self.wf1 = self.ppg.getWFnormP()
#print "Waveform0", self.wf1[1]
#data_obj = Data(self.wf1[0], self.wf1[1], smoothness=11)
#print "Waveform1", self.wf1[1]
#data_obj.get_peaks(method='slope')
#print "Waveform2", self.wf1[1]
self.wfD = self.ppg.getWFderivative()
self.wfCP = self.ppg.getWFCriticalP()
self.AverageWaveForm = []
#print "Waveform3", self.wf1[1]
#print data_obj.peaks
#print data_obj.peaks['peaks'][0]
#print data_obj.peaks['peaks'][1]
#print data_obj.peaks['valleys']
#print 'Critical Points',self.wfCP
# Pulse = go.Scatter(x=self.wf1[0],y=self.wf1[1],mode = 'markers',marker = dict(size = 1,color = 'rgba(255, 0, 0, .8)'),name='Pulse',)
# Trace4 = go.Scatter(x=self.wfCP[0],y=self.wfCP[1],mode = 'markers',marker = dict(size = 3,color = 'rgba(255, 0, 0, .8)'),name='Pulse',)
#Valleys = go.Scatter(x=data_obj.peaks['peaks'][0],y=data_obj.peaks['peaks'][1],mode = 'markers',marker = dict(size = 5,color = 'rgba(0, 255, 100, .8)'),name='Valleys',)
#Peaks = go.Scatter(x=data_obj.peaks['valleys'][0],y=data_obj.peaks['valleys'][1],mode = 'markers',marker = dict(size = 5,color = 'rgba(0, 0, 255, .8)'),name='Peaks',)
# data = [Pulse,Trace4]
# layout = go.Layout(title='PPG',hovermode='closest',
# xaxis=dict(title='Time [ms]',),
# yaxis=dict(title='Pulse Waveform [Arb. Units]',),)
# fig = go.Figure(data=data, layout=layout)
#print data
# py.plot(fig, filename='basic-scatter')
#print "Out"
self.AverageWaveForm = self.ppg.AverageWF()
self.InflectionPoints = PPGfunc.inflection(self.AverageWaveForm[0],
self.AverageWaveForm[1])
self.PulseWaveSystolicPeakPos = int(self.AverageWaveForm[2][0])
self.PulseWaveEndPos = int(self.AverageWaveForm[2][1])
#print "Inflection Points= ", self.InflectionPoints, 'Length= ',len(self.InflectionPoints)
if (len(self.InflectionPoints) > 0):
temp = self.InflectionPoints.pop()
self.DicroticNotchPos = temp[0]
self.DiastolicPeakPos = temp[1]
else:
self.DicroticNotchPos = -1
self.DiastolicPeakPos = -1
self.HalfHeight = 0.5 * self.AverageWaveForm[1][
self.PulseWaveSystolicPeakPos]
print 'Half Height= ', self.HalfHeight
for i in range(0, self.PulseWaveSystolicPeakPos - 1):
if self.AverageWaveForm[1][i] > self.HalfHeight:
# print 'Point i=(',self.AverageWaveForm[0][i],self.AverageWaveForm[1][i],')'
# print 'Point i-1=(',self.AverageWaveForm[0][i-1],self.AverageWaveForm[1][i-1],')'
DeltaX = self.AverageWaveForm[0][i] - self.AverageWaveForm[0][
i - 1]
# print "Delta X=", DeltaX
DeltaY = self.AverageWaveForm[1][i] - self.AverageWaveForm[1][
i - 1]
# print "Delta y=", DeltaY
DeltaV = self.HalfHeight - self.AverageWaveForm[1][i - 1]
# print "Delta V=", DeltaV
self.HalfTimeLow = self.AverageWaveForm[0][
i - 1] + DeltaX * DeltaV / DeltaY
# print "Half Time Low=", self.HalfTimeLow
break
for i in range(self.PulseWaveSystolicPeakPos + 1,
self.PulseWaveEndPos - 1):
if self.AverageWaveForm[1][i] < self.HalfHeight:
# print 'Point i=(',self.AverageWaveForm[0][i],self.AverageWaveForm[1][i],')'
# print 'Point i-1=(',self.AverageWaveForm[0][i-1],self.AverageWaveForm[1][i-1],')'
DeltaX = self.AverageWaveForm[0][i] - self.AverageWaveForm[0][
i - 1]
# print "Delta X=", DeltaX
DeltaY = -self.AverageWaveForm[1][i] + self.AverageWaveForm[1][
i - 1]
# print "Delta y=", DeltaY
DeltaV = self.HalfHeight - self.AverageWaveForm[1][i]
# print "Delta V=", DeltaV
self.HalfTimeHigh = self.AverageWaveForm[0][
i - 1] + DeltaX * DeltaV / DeltaY
# print "Half Time Low=", self.HalfTimeLow
break
self.PulseWaveAmplitude = self.AverageWaveForm[1][
self.PulseWaveSystolicPeakPos]
self.SystolicPhase = self.RiseTime = self.AverageWaveForm[0][
self.PulseWaveSystolicPeakPos]
self.DiastolicPhase = self.AverageWaveForm[0][
self.PulseWaveEndPos] - self.AverageWaveForm[0][
self.PulseWaveSystolicPeakPos]
self.PulseWaveDuration = self.AverageWaveForm[0][self.PulseWaveEndPos]
self.PulseWavePropogationTme = self.AverageWaveForm[0][
self.DicroticNotchPos] - self.AverageWaveForm[0][
self.PulseWaveSystolicPeakPos]
self.PulseWidthTime = self.HalfTimeHigh - self.HalfTimeLow