def test_envelopGaitPlotPanel(self):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH+"GaitData\\EMG\\Hånnibøl Lecter-nerve block\\"
gaitTrial = "PRE-gait trial 01.c3d"
restTrial = "PRE-repos.c3d"
DATA_PATH_OUT = pyCGM2.TEST_DATA_PATH_OUT+"GaitData\\EMG\\Hånnibøl Lecter-nerve block\\"
files.createDir(DATA_PATH_OUT)
EMG_LABELS=['EMG1','EMG2']
acq = btkTools.smartReader(DATA_PATH +gaitTrial)
bf = emgFilters.BasicEmgProcessingFilter(acq,EMG_LABELS)
bf.setHighPassFrequencies(20.0,200.0)
bf.run()
envf = emgFilters.EmgEnvelopProcessingFilter(acq,EMG_LABELS)
envf.setCutoffFrequency(180.0)
envf.run()
btkTools.smartWriter(acq,DATA_PATH_OUT+"test_envelopGaitPlotPanel.c3d")
modelledFilenames = ["test_envelopGaitPlotPanel.c3d"]
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(DATA_PATH_OUT,modelledFilenames)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableSpatioTemporal(False)
cmf.enableKinematic(False)
cmf.enableKinetic(False)
cmf.enableEmg(True)
trialManager = cmf.generate()
#---- GAIT CYCLES FILTER
#--------------------------------------------------------------------------
cycleBuilder = cycle.GaitCyclesBuilder(spatioTemporalTrials=trialManager.spatioTemporal["Trials"],
kinematicTrials = trialManager.kinematic["Trials"],
kineticTrials = trialManager.kinetic["Trials"],
emgTrials=trialManager.emg["Trials"])
cyclefilter = cycle.CyclesFilter()
cyclefilter.setBuilder(cycleBuilder)
cycles = cyclefilter.build()
modelInfo=None
subjectInfo=None
experimentalInfo=None
analysisBuilder = analysis.GaitAnalysisBuilder(cycles,
kinematicLabelsDict = None,
kineticLabelsDict = None,
emgLabelList = ['EMG1_Rectify_Env','EMG2_Rectify_Env'],
subjectInfos=subjectInfo,
modelInfos=modelInfo,
experimentalInfos=experimentalInfo)
analysisFilter = analysis.AnalysisFilter()
analysisFilter.setBuilder(analysisBuilder)
analysisFilter.setInfo(model = modelInfo)
analysisFilter.build()
analysisInstance = analysisFilter.analysis
envnf = emgFilters.EmgNormalisationProcessingFilter(analysisInstance,"EMG1","Right")
envnf.setMaxMethod(enums.EmgAmplitudeNormalization.MeanMax)
envnf.run()
envnf = emgFilters.EmgNormalisationProcessingFilter(analysisInstance,"EMG2","Right")
envnf.setMaxMethod(enums.EmgAmplitudeNormalization.MeanMax)
envnf.run()
data = analysisInstance.emgStats.data
# viewer
kv = emgPlotViewers.EnvEmgGaitPlotPanelViewer (analysisInstance)
kv.setEmgs([["EMG1","Right","rf"],["EMG2","Right","rf"]])
kv.setNormalActivationLabels(["RECFEM","RECFEM"])
kv.setConcretePlotFunction(plot.gaitDescriptivePlot)
# # filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.plot()
def plotConsistencyEnvelopEMGpanel(DATA_PATH,
analysis,
emgChannels,
muscles,
contexts,
normalActivityEmgs,
normalized=False,
type="Gait",
exportPdf=False,
outputName=None,
show=True,
title=None):
"""
plotConsistencyEnvelopEMGpanel : display all cycle of time-normalized traces of EMG envelops
:param DATA_PATH [str]: path to your data
:param analysis [pyCGM2.Processing.analysis.Analysis]: pyCGM2 analysis instance
:param emgChannels [string list]: labels of your emg channels
:param muscles [string list]: muscle labels associated with your emg channels
:param contexts [string list]: contexts associated with your emg channels
:param normalActivityEmgs [string list]: normal activities associated with your emg channels
**optional**
:param normalized [bool]: (**default**: False) plot normalized amplitude envelops
:param type [string]: display gait events ( other choice than gait [default], display foot strikes only)
:param exportPdf [bool]: save as pdf (False[default])
:param outputName [string]: name of your pdf file (None[default] export your pdf with name : Global Analysis)
:param show [bool]: enable matplotlib show function
:param title [string]: change default title of the plot panel
"""
if outputName is None:
outputName = "Global Analysis"
if exportPdf:
filenameOut = str(outputName + "-ConsistencyEmgEnv" +
"[No Normalized]-") if not normalized else str(
outputName + "-DescriptiveEmgEnv" +
"[Normalized]")
# viewer
combinedEMGcontext = []
for i in range(0, len(emgChannels)):
combinedEMGcontext.append([emgChannels[i], contexts[i], muscles[i]])
kv = emgPlotViewers.EnvEmgGaitPlotPanelViewer(analysis)
kv.setEmgs(combinedEMGcontext)
kv.setNormalActivationLabels(normalActivityEmgs)
kv.setNormalizedEmgFlag(normalized)
if type == "Gait":
kv.setConcretePlotFunction(plot.gaitConsistencyPlot)
else:
kv.setConcretePlotFunction(plot.consistencyPlot)
# # filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
if title is not None:
pf.setTitle(
str(title + "-ConsistencyEmgEnv" + "[No Normalized]-"
) if not normalized else str(title + "-DescriptiveEmgEnv" +
"[Normalized]"))
if exportPdf: pf.setExport(DATA_PATH, filenameOut, "pdf")
pf.plot()
if show: plt.show()
