def temporalPlot(figAxis,
trial,
pointLabel,
axis,
pointLabelSuffix=None,
color=None,
title=None,
xlabel=None,
ylabel=None,
ylim=None,
legendLabel=None,
customLimits=None):
'''
**Description :** plot descriptive statistical (average and sd corridor) gait traces from a pyCGM2.Processing.analysis.Analysis instance
:Parameters:
- `figAxis` (matplotlib::Axis )
- `trial` (ma.Trial) - a Structure item of an Analysis instance built from AnalysisFilter
:Return:
- matplotlib figure
**Usage**
.. code:: python
'''
pointLabel = pointLabel + "_" + pointLabelSuffix if pointLabelSuffix is not None else pointLabel
flag = trialTools.isTimeSequenceExist(trial, pointLabel)
if flag:
timeseq = trial.findChild(ma.T_TimeSequence, pointLabel)
lines = figAxis.plot(timeseq.data()[:, axis], '-', color=color)
if legendLabel is not None and flag: lines[0].set_label(legendLabel)
if title is not None: figAxis.set_title(title, size=8)
figAxis.tick_params(axis='x', which='major', labelsize=6)
figAxis.tick_params(axis='y', which='major', labelsize=6)
if xlabel is not None: figAxis.set_xlabel(xlabel, size=8)
if ylabel is not None: figAxis.set_ylabel(ylabel, size=8)
if ylim is not None: figAxis.set_ylim(ylim)
if flag:
for ev in trial.findChildren(ma.T_Event):
colorContext = plotUtils.colorContext(ev.context())
if ev.name() == "Foot Strike":
figAxis.axvline(x=(ev.time() - timeseq.startTime()) *
timeseq.sampleRate(),
color=colorContext,
linestyle="-")
elif ev.name() == "Foot Off":
figAxis.axvline(x=(ev.time() - timeseq.startTime()) *
timeseq.sampleRate(),
color=colorContext,
linestyle="--")
def getAnalogTimeSequenceData(self,analogLabel):
"""
Get analog data of the cycle
:Parameters:
- `analogLabel` (str) - analog Label
"""
if trialTools.isTimeSequenceExist(self.trial,analogLabel):
return self.trial.findChild(ma.T_TimeSequence, utils.str(analogLabel)).data()[int((self.begin-self.firstFrame) * self.appf) : int((self.end-self.firstFrame+1) * self.appf),:]
else:
logging.debug("[pyCGM2] the Analog Label %s doesn t exist in %s" % (analogLabel,self.trial.name()))
return None
def getPointTimeSequenceData(self,pointLabel):
"""
Get temporal point data of the cycle
:Parameters:
- `pointLabel` (str) - point Label
"""
if trialTools.isTimeSequenceExist(self.trial,pointLabel):
return self.trial.findChild(ma.T_TimeSequence, utils.str(pointLabel)).data()[self.begin-self.firstFrame:self.end-self.firstFrame+1,0:3] # 0.3 because openma::Ts includes a forth column (i.e residual)
else:
logging.debug("[pyCGM2] the point Label %s doesn t exist in %s" % (pointLabel,self.trial.name()))
return None
def getPointTimeSequenceData(self, pointLabel):
"""
Get temporal point data of the cycle
:Parameters:
- `pointLabel` (str) - point Label
"""
if trialTools.isTimeSequenceExist(self.trial, pointLabel):
return self.trial.findChild(ma.T_TimeSequence, pointLabel).data(
)[self.begin - self.firstFrame:self.end - self.firstFrame + 1, 0:
3] # 0.3 because openma::Ts includes a forth column (i.e residual)
else:
raise Exception("[pyCGM2] marker %s doesn t exist" % pointLabel)
def getAnalogTimeSequenceData(self, analogLabel):
"""
Get analog data of the cycle
:Parameters:
- `analogLabel` (str) - analog Label
"""
if trialTools.isTimeSequenceExist(self.trial, analogLabel):
return self.trial.findChild(
ma.T_TimeSequence,
analogLabel).data()[int((self.begin - self.firstFrame) *
self.appf):int((self.end -
self.firstFrame + 1) *
self.appf), :]
else:
raise Exception("[pyCGM2] Analog %s doesn t exist" % analogLabel)
def __computeSpatioTemporalParameter(self):
duration = np.divide((self.end-self.begin),self.pointfrequency)
stanceDuration=np.divide(np.abs(self.m_contraFO - self.begin) , self.pointfrequency)
swingDuration=np.divide(np.abs(self.m_contraFO - self.end) , self.pointfrequency)
stepDuration=np.divide(np.abs(self.m_oppositeFS - self.begin) , self.pointfrequency)
pst = ma.Node("stp",self)
pst.setProperty("duration", duration)
pst.setProperty("cadence", np.divide(60.0,duration))
pst.setProperty("stanceDuration", stanceDuration)
pst.setProperty("swingDuration", swingDuration)
pst.setProperty("stepDuration", stepDuration)
pst.setProperty("doubleStance1Duration", np.divide(np.abs(self.m_oppositeFO - self.begin) , self.pointfrequency))
pst.setProperty("doubleStance2Duration", np.divide(np.abs(self.m_contraFO - self.m_oppositeFS) , self.pointfrequency))
pst.setProperty("simpleStanceDuration", np.divide(np.abs(self.m_oppositeFO - self.m_oppositeFS) , self.pointfrequency))
pst.setProperty("stancePhase", round(np.divide(stanceDuration,duration)*100))
pst.setProperty("swingPhase", round(np.divide(swingDuration,duration)*100 ))
pst.setProperty("doubleStance1", round(np.divide(np.divide(np.abs(self.m_oppositeFO - self.begin) , self.pointfrequency),duration)*100))
pst.setProperty("doubleStance2", round(np.divide(np.divide(np.abs(self.m_contraFO - self.m_oppositeFS) , self.pointfrequency),duration)*100))
pst.setProperty("simpleStance", round(np.divide(np.divide(np.abs(self.m_oppositeFO - self.m_oppositeFS) , self.pointfrequency),duration)*100))
pst.setProperty("stepPhase", round(np.divide(stepDuration,duration)*100))
#pst.setProperty("simpleStance3 ",15.0 )
if self.context == "Left":
if trialTools.isTimeSequenceExist(self.trial,"LHEE") and trialTools.isTimeSequenceExist(self.trial,"RHEE") and trialTools.isTimeSequenceExist(self.trial,"LTOE"):
progressionAxis,forwardProgression,globalFrame = trialTools.findProgression(self.trial,"LHEE")
longitudinal_axis=0 if progressionAxis =="X" else 1
lateral_axis=1 if progressionAxis =="X" else 0
strideLength=np.abs(self.getPointTimeSequenceData("LHEE")[self.end-self.begin,longitudinal_axis] -\
self.getPointTimeSequenceData("LHEE")[0,longitudinal_axis])/1000.0
pst.setProperty("strideLength", strideLength)
stepLength = np.abs(self.getPointTimeSequenceData("RHEE")[self.m_oppositeFS-self.begin,longitudinal_axis] -\
self.getPointTimeSequenceData("LHEE")[0,longitudinal_axis])/1000.0
pst.setProperty("stepLength", stepLength)
strideWidth = np.abs(self.getPointTimeSequenceData("LTOE")[self.end-self.begin,lateral_axis] -\
self.getPointTimeSequenceData("RHEE")[0,lateral_axis])/1000.0
pst.setProperty("strideWidth", strideWidth)
pst.setProperty("speed",np.divide(strideLength,duration))
if self.context == "Right":
if trialTools.isTimeSequenceExist(self.trial,"RHEE") and trialTools.isTimeSequenceExist(self.trial,"LHEE") and trialTools.isTimeSequenceExist(self.trial,"RTOE"):
progressionAxis,forwardProgression,globalFrame = trialTools.findProgression(self.trial,"RHEE")
longitudinal_axis=0 if progressionAxis =="X" else 1
lateral_axis=1 if progressionAxis =="X" else 0
strideLength=np.abs(self.getPointTimeSequenceData("RHEE")[self.end-self.begin,longitudinal_axis] -\
self.getPointTimeSequenceData("RHEE")[0,longitudinal_axis])/1000.0
strideWidth = np.abs(self.getPointTimeSequenceData("RTOE")[self.end-self.begin,lateral_axis] -\
self.getPointTimeSequenceData("LHEE")[0,lateral_axis])/1000.0
pst.setProperty("strideLength", strideLength)
pst.setProperty("strideWidth", strideWidth)
stepLength = np.abs(self.getPointTimeSequenceData("RHEE")[self.m_oppositeFS-self.begin,longitudinal_axis] -\
self.getPointTimeSequenceData("LHEE")[0,longitudinal_axis])/1000.0
pst.setProperty("stepLength", stepLength)
pst.setProperty("speed",np.divide(strideLength,duration))