def processEMG_fromBtkAcq(acq,
emgChannels,
highPassFrequencies=[20, 200],
envelopFrequency=6.0):
"""
processEMG_fromBtkAcq : filt emg from a btk acq
:param acq [btk::Acquisition]: btk acquisition
:param emgChannels [string list]: label of your emg channels
**optional**
:param highPassFrequencies [list of float]: boundaries of the bandpass filter
:param envelopFrequency [float]: cut-off frequency for creating an emg envelop
"""
bf = emgFilters.BasicEmgProcessingFilter(acq, emgChannels)
bf.setHighPassFrequencies(highPassFrequencies[0], highPassFrequencies[1])
bf.run()
envf = emgFilters.EmgEnvelopProcessingFilter(acq, emgChannels)
envf.setCutoffFrequency(envelopFrequency)
envf.run()
return acq
def processEMG(DATA_PATH,
gaitTrials,
emgChannels,
highPassFrequencies=[20, 200],
envelopFrequency=6.0,
fileSuffix=None):
"""
processEMG_fromC3dFiles : filters emg channels from a list of c3d files
:param DATA_PATH [String]: path to your folder
:param gaitTrials [string List]:c3d files with emg signals
:param emgChannels [string list]: label of your emg channels
**optional**
:param highPassFrequencies [list of float]: boundaries of the bandpass filter
:param envelopFrequency [float]: cut-off frequency for creating an emg envelop
:param fileSuffix [string]: suffix added to your ouput c3d files
"""
if fileSuffix is None: fileSuffix = ""
for gaitTrial in gaitTrials:
acq = btkTools.smartReader(DATA_PATH + gaitTrial)
flag = False
for channel in emgChannels:
if not btkTools.isAnalogExist(acq, channel):
logging.error("channel [%s] not detected in the c3d [%s]" %
(channel, gaitTrial))
flag = True
if flag:
raise Exception(
"[pyCGM2] One label has not been detected as analog. see above"
)
bf = emgFilters.BasicEmgProcessingFilter(acq, emgChannels)
bf.setHighPassFrequencies(highPassFrequencies[0],
highPassFrequencies[1])
bf.run()
envf = emgFilters.EmgEnvelopProcessingFilter(acq, emgChannels)
envf.setCutoffFrequency(envelopFrequency)
envf.run()
outFilename = gaitTrial if fileSuffix == "" else gaitTrial + "_" + fileSuffix
btkTools.smartWriter(acq, DATA_PATH + outFilename)
def EnveloppeProcessing(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH+"EMG\\SampleNantes\\"
gaitTrial = "gait.c3d"
restTrial = "repos.c3d"
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,"test.c3d")
values = acq.GetAnalog("EMG1_Rectify").GetValues()
def processEMG(DATA_PATH,
gaitTrials,
emgChannels,
highPassFrequencies=[20, 200],
envelopFrequency=6.0,
fileSuffix=None):
"""
processEMG_fromC3dFiles : filters emg channels from a list of c3d files
:param DATA_PATH [String]: path to your folder
:param gaitTrials [string List]:c3d files with emg signals
:param emgChannels [string list]: label of your emg channels
**optional**
:param highPassFrequencies [list of float]: boundaries of the bandpass filter
:param envelopFrequency [float]: cut-off frequency for creating an emg envelop
:param fileSuffix [string]: suffix added to your ouput c3d files
"""
if fileSuffix is None: fileSuffix = ""
for gaitTrial in gaitTrials:
acq = btkTools.smartReader(DATA_PATH + gaitTrial)
bf = emgFilters.BasicEmgProcessingFilter(acq, emgChannels)
bf.setHighPassFrequencies(highPassFrequencies[0],
highPassFrequencies[1])
bf.run()
envf = emgFilters.EmgEnvelopProcessingFilter(acq, emgChannels)
envf.setCutoffFrequency(envelopFrequency)
envf.run()
outFilename = gaitTrial if fileSuffix == "" else gaitTrial + "_" + fileSuffix
btkTools.smartWriter(acq, DATA_PATH + outFilename)
def psd(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH+"EMG\\SampleNantes\\"
gaitTrial = "gait.c3d"
restTrial = "repos.c3d"
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,"test.c3d")
values = acq.GetAnalog("EMG1_Rectify").GetValues()
fpcntile, mpf, fmax, Ptotal, f, P = signal_processing.psd(values[:,0],1000,show=True)
def test_envelopPlotSingleEmg(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_envelopPlotSingleEmg.c3d")
modelledFilenames = ["test_envelopPlotSingleEmg.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","Left")
envnf.setMaxMethod(enums.EmgAmplitudeNormalization.MeanMax)
envnf.run()
fig = plt.figure()
ax = plt.gca()
plot.gaitDescriptivePlot(ax,analysisInstance.emgStats,
"EMG1_Rectify_Env","Left",0,
color=None,
title="title", xlabel=None, ylabel=None,ylim=None,legendLabel=None,
customLimits=None)
footOff = analysisInstance.emgStats.pst['stancePhase', "Left"]["mean"]
plot.addNormalActivationLayer(ax,"RECFEM", footOff)
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 EnvelopCoactivationPlot(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "EMG\\SampleNantes\\"
gaitTrial = "gait.c3d"
restTrial = "repos.c3d"
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 + "test.c3d")
modelledFilenames = ["test.c3d"]
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(
DATA_PATH, 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", "Left")
envnf.setMaxMethod(enums.EmgAmplitudeNormalization.MeanMax)
envnf.run()
envnf = emgFilters.EmgNormalisationProcessingFilter(
analysisInstance, "EMG2", "Left")
envnf.setMaxMethod(enums.EmgAmplitudeNormalization.MeanMax)
envnf.run()
# viewer
kv = emgPlotViewers.CoactivationEmgPlotViewer(analysisInstance)
kv.setEmgs("EMG1", "EMG2")
kv.setMuscles("RF1", "RF2")
kv.setConcretePlotFunction(plot.gaitDescriptivePlot)
kv.setContext("Left")
# # filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.plot()
plt.show()
def cycleAnalysis(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH+"EMG\\SampleNantes\\"
gaitTrial = "gait.c3d"
restTrial = "repos.c3d"
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+"test.c3d")
modelledFilenames = ["test.c3d"]
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(DATA_PATH,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