def temporalPlotPanel(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "EMG\\SampleNantes\\"
gaitTrial = "gait.c3d"
restTrial = "repos.c3d"
EMG_LABELS = ['EMG1', 'EMG2', 'EMG3', 'EMG4']
acq = btkTools.smartReader(DATA_PATH + gaitTrial)
bf = emgFilters.BasicEmgProcessingFilter(acq, EMG_LABELS)
bf.setHighPassFrequencies(20.0, 200.0)
bf.run()
btkTools.smartWriter(acq, "testBasicPlot.c3d")
trial = trialTools.smartTrialReader(None, "testBasicPlot.c3d")
# # viewer
kv = emgPlotViewers.TemporalEmgPlotViewer(trial)
kv.setEmgs([["EMG1", "Left"], ["EMG2", "Right"], ["EMG3", "Left"],
["EMG4", "Right"]])
kv.setNormalActivationLabels(["RECFEM", "RECFEM", None, "VASLAT"])
kv.setEmgRectify(True)
# # filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.plot()
plt.show()
def noX2d_manualCropping(cls):
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
#DATA_PATH, filenameNoExt = NEXUS.GetTrialName()
DATA_PATH = "C:\\Users\\HLS501\\Documents\\VICON DATA\\pyCGM2-Data\\NexusAPI\\BtkAcquisitionCreator\\sample3\\"
filenameNoExt = "capture 01"
NEXUS.OpenTrial(str(DATA_PATH + filenameNoExt), 30)
NEXUS.SetTrialRegionOfInterest(350, 500)
subject = NEXUS.GetSubjectNames()[0]
acqConstructorFilter = nexusFilters.NexusConstructAcquisitionFilter(
DATA_PATH, filenameNoExt, subject)
acq = acqConstructorFilter.build()
acq0 = btkTools.smartReader(str(DATA_PATH + "Capture 01-cropped.c3d"))
#ipdb.set_trace()
plt.plot(acq.GetPoint("LTHI").GetValues(), "-r")
plt.plot(acq0.GetPoint("LTHI").GetValues(), "-ob")
plt.show()
np.testing.assert_array_almost_equal(acq.GetPoint("LTHI").GetValues(),
acq0.GetPoint("LTHI").GetValues(),
decimal=2)
#np.testing.assert_array_almost_equal(acq.GetAnalog("Force.Fx1").GetValues(),acq0.GetAnalog("Force.Fx1").GetValues(),decimal=2)
btkTools.smartWriter(acq, "noX2d_cropInteractive.c3d")
def temporalPlotSingleEmg(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "EMG\\SampleNantes\\"
gaitTrial = "gait.c3d"
restTrial = "repos.c3d"
EMG_LABELS = ['EMG1']
acq = btkTools.smartReader(DATA_PATH + gaitTrial)
bf = emgFilters.BasicEmgProcessingFilter(acq, EMG_LABELS)
bf.setHighPassFrequencies(20.0, 200.0)
bf.run()
btkTools.smartWriter(acq, "testBasicPlot.c3d")
trial = trialTools.smartTrialReader(None, "testBasicPlot.c3d")
fig = plt.figure()
ax = plt.gca()
plot.temporalPlot(ax,
trial,
"EMG1_Rectify",
0,
color="blue",
title="test",
xlabel="frame",
ylabel="emg",
ylim=None,
legendLabel=None,
customLimits=None)
plot.addTemporalNormalActivationLayer(ax, trial, "RECFEM", "Left")
plt.show()
def croppedC3d(cls):
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
DATA_PATH = "C:\\Users\\HLS501\\Documents\\VICON DATA\\pyCGM2-Data\\NexusAPI\\BtkAcquisitionCreator\\sample_NOx2d\\"
filenameNoExt = "gait_cropped"
NEXUS.OpenTrial(str(DATA_PATH + filenameNoExt), 30)
subject = NEXUS.GetSubjectNames()[0]
acqConstructorFilter = nexusFilters.NexusConstructAcquisitionFilter(
DATA_PATH, filenameNoExt, subject)
acq = acqConstructorFilter.build()
btkTools.smartWriter(acq, "TestsNOX2d_croppedC3d.c3d")
acq0 = btkTools.smartReader(str(DATA_PATH + filenameNoExt + ".c3d"))
# plotPoint(acq,acq0,"LTHI")
# plotAnalog(acq,acq0,"Force.Fz1")
# plotAnalog(acq,acq0,"Force.Fz2")
# plotAnalog(acq,acq0,"Force.Fz3")
np.testing.assert_array_almost_equal(acq.GetPoint("LTHI").GetValues(),
acq0.GetPoint("LTHI").GetValues(),
decimal=2)
np.testing.assert_array_almost_equal(
acq.GetAnalog("Force.Fz1").GetValues(),
acq0.GetAnalog("Force.Fz1").GetValues(),
decimal=2)
np.testing.assert_array_almost_equal(
acq.GetAnalog("Force.Fz2").GetValues(),
acq0.GetAnalog("Force.Fz2").GetValues(),
decimal=2)
np.testing.assert_array_almost_equal(
acq.GetAnalog("Force.Fz3").GetValues(),
acq0.GetAnalog("Force.Fz3").GetValues(),
decimal=2)
def main(args):
DATA_PATH = os.getcwd() + "\\"
file = args.file[0]
if not os.path.isfile(file):
raise Exception("the file (%s) doesn t exist" % (file))
modelledTrials = [file]
for trial in modelledTrials:
logging.info("[pyCGM2]: Zeni Event Detection on trial %s" %
(str(trial)))
acqGait = btkTools.smartReader(str(DATA_PATH + trial))
acqGait.ClearEvents()
# ----------------------EVENT DETECTOR-------------------------------
evp = events.ZeniProcedure()
evp.setFootStrikeOffset(args.footStrikeOffset)
evp.setFootOffOffset(args.footOffOffset)
# event filter
evf = events.EventFilter(evp, acqGait)
evf.detect()
btkTools.smartWriter(acqGait, str(DATA_PATH + trial))
logging.info("[pyCGM2]: Zeni Event Detection on trial %s ----> Done" %
(str(trial)))
if args.MokkaCheck:
cmd = "Mokka.exe \"%s\"" % (str(DATA_PATH + trial))
os.system(cmd)
def test_temporalPlotPanel(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','EMG3','EMG4']
acq = btkTools.smartReader(DATA_PATH +gaitTrial)
bf = emgFilters.BasicEmgProcessingFilter(acq,EMG_LABELS)
bf.setHighPassFrequencies(20.0,200.0)
bf.run()
btkTools.smartWriter(acq,DATA_PATH_OUT+"test_temporalPlotPanel.c3d")
trial =trialTools.smartTrialReader(DATA_PATH_OUT,"test_temporalPlotPanel.c3d")
# # viewer
kv = emgPlotViewers.TemporalEmgPlotViewer(trial)
kv.setEmgs([["EMG1","Left","RF"],["EMG2","Right","RF"],["EMG3","Left","vaste"],["EMG4","Right","vaste"]])
kv.setNormalActivationLabels(["RECFEM","RECFEM",None,"VASLAT"])
kv. setEmgRectify(True)
# # filter
pf = plotFilters.PlottingFilter()
pf.setViewer(kv)
pf.setExport(DATA_PATH_OUT,"hän-test_temporalPlotPanel","png")
pf.plot()
def analysisAdvancedEMG(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH+"operations\\analysis\\gaitEMG\\"
inputFile = ["pre.c3d","post.c3d"]
EMG_LABELS = ["EMG1","EMG2"]
#
for file in inputFile:
acq = btkTools.smartReader(DATA_PATH+file)
pyCGM2.Lib.analysis.processEMG_fromBtkAcq(acq, EMG_LABELS, highPassFrequencies=[20,200],envelopFrequency=6.0)
btkTools.smartWriter(acq,DATA_PATH+file[:-4]+"-emgProcessed.c3d")
inputFileProcessed = [file[:-4]+"-emgProcessed.c3d" for file in inputFile]
emgAnalysis = pyCGM2.Lib.analysis.makeEmgAnalysis(DATA_PATH, inputFileProcessed, EMG_LABELS,None, None)
exportFilter = exporter.XlsAnalysisExportFilter()
exportFilter.setAnalysisInstance(emgAnalysis)
exportFilter.export("testAdvancedEMG", path=DATA_PATH,excelFormat = "xls",mode="Advanced")
# exportFilter = exporter.AnalysisExportFilter()
# exportFilter.setAnalysisInstance(emgAnalysis)
# exportFilter.export("testAdvancedEMG.json", path=DATA_PATH)
exportFilter = exporter.AnalysisC3dExportFilter()
exportFilter.setAnalysisInstance(emgAnalysis)
exportFilter.export("testAdvanced", path=DATA_PATH)
def noIK_6dof(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.4\\fullBody\\"
staticFilename = "PN01OP01S01STAT.c3d"
gaitFilename = "PN01OP01S01STAT.c3d"
markerDiameter = 14
mp = {
'Bodymass': 83.0,
'LeftLegLength': 874.0,
'RightLegLength': 876.0,
'LeftKneeWidth': 106.0,
'RightKneeWidth': 103.0,
'LeftAnkleWidth': 74.0,
'RightAnkleWidth': 72.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
}
# --- Calibration ---
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
translators = files.getTranslators(MAIN_PATH, "CGM2_4.translators")
acqStatic = btkTools.applyTranslators(acqStatic, translators)
model = cgm2.CGM2_4()
model.configure()
model.addAnthropoInputParameters(mp)
# ---- Calibration ----
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
print "----"
print model.getSegment("Left Shank").getReferential(
"TF").relativeMatrixAnatomic
print "----"
# # cgm decorator
modelDecorator.HipJointCenterDecorator(model).hara()
modelDecorator.KneeCalibrationDecorator(model).midCondyles(
acqStatic, markerDiameter=markerDiameter, side="both")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="both")
#
# # final
modelFilters.ModelCalibrationFilter(
scp, acqStatic, model, markerDiameter=markerDiameter).compute()
# ------ Fitting -------
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
acqGait = btkTools.applyTranslators(acqGait, translators)
# Motion FILTER
modMotion = modelFilters.ModelMotionFilter(
scp, acqGait, model, enums.motionMethod.Sodervisk)
modMotion.compute()
btkTools.smartWriter(acqGait, "cgm24_noIK6dof_staticMotion.c3d")
def basicCGM1_manualTibialTorsion(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\basic-tibialTorsion\\"
staticFilename = "MRI-US-01, 2008-08-08, 3DGA 02.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model=cgm.CGM1
model.configure()
markerDiameter=14
mp={
'Bodymass' : 71.0,
'LeftLegLength' : 860.0,
'RightLegLength' : 865.0 ,
'LeftKneeWidth' : 102.0,
'RightKneeWidth' : 103.4,
'LeftAnkleWidth' : 75.3,
'RightAnkleWidth' : 72.9,
'LeftSoleDelta' : 0,
'RightSoleDelta' : 0,
}
optional_mp={
'LeftTibialTorsion' : -30.0,
'RightTibialTorsion' : -30.0
}
model.addAnthropoInputParameters(mp,optional=optional_mp)
# -----------CGM STATIC CALIBRATION--------------------
scp=modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,acqStatic,model,
viconCGM1compatible=True).compute()
# TESTS ------------------------------------------------
# offset testing
offsetTesting(acqStatic,model,display = True, unitTesting=True)
# nodes
# np.testing.assert_equal(model.getSegment("Left Thigh").getReferential("TF").static.getNode_byLabel("LKJC").m_desc ,"Chord")
# np.testing.assert_equal(model.getSegment("Right Thigh").getReferential("TF").static.getNode_byLabel("RKJC").m_desc ,"Chord")
#
# np.testing.assert_equal(model.getSegment("Left Shank").getReferential("TF").static.getNode_byLabel("LKJC").m_desc ,"Chord")
# np.testing.assert_equal(model.getSegment("Right Shank").getReferential("TF").static.getNode_byLabel("RKJC").m_desc ,"Chord")
np.testing.assert_equal(model.m_useRightTibialTorsion,True )
np.testing.assert_equal(model.m_useLeftTibialTorsion,True )
# joint centres
np.testing.assert_almost_equal(acqStatic.GetPoint("LFEP").GetValues().mean(axis=0),acqStatic.GetPoint("LHJC").GetValues().mean(axis=0),decimal = 3)
np.testing.assert_almost_equal(acqStatic.GetPoint("RFEP").GetValues().mean(axis=0),acqStatic.GetPoint("RHJC").GetValues().mean(axis=0),decimal = 3)
np.testing.assert_almost_equal(acqStatic.GetPoint("LFEO").GetValues().mean(axis=0),acqStatic.GetPoint("LKJC").GetValues().mean(axis=0),decimal = 3)
np.testing.assert_almost_equal(acqStatic.GetPoint("RFEO").GetValues().mean(axis=0),acqStatic.GetPoint("RKJC").GetValues().mean(axis=0),decimal = 3)
np.testing.assert_almost_equal(acqStatic.GetPoint("LTIO").GetValues().mean(axis=0),acqStatic.GetPoint("LAJC").GetValues().mean(axis=0),decimal = 3)
np.testing.assert_almost_equal(acqStatic.GetPoint("RTIO").GetValues().mean(axis=0),acqStatic.GetPoint("RAJC").GetValues().mean(axis=0),decimal = 3)
btkTools.smartWriter(acqStatic, "outStatic_advancedCGM1_kad_manualTibial.c3d")
def test_temporalPlotSingleEmg(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']
acq = btkTools.smartReader(DATA_PATH +gaitTrial)
bf = emgFilters.BasicEmgProcessingFilter(acq,EMG_LABELS)
bf.setHighPassFrequencies(20.0,200.0)
bf.run()
btkTools.smartWriter(acq,DATA_PATH_OUT+"test_temporalPlotSingleEmg.c3d")
trial =trialTools.smartTrialReader(DATA_PATH_OUT,"test_temporalPlotSingleEmg.c3d")
fig = plt.figure()
ax = plt.gca()
plot.temporalPlot(ax,trial,"EMG1_Rectify",0,
color="blue",
title="test", xlabel="frame", ylabel="emg",ylim=None,legendLabel=None,
customLimits=None)
plot.addTemporalNormalActivationLayer(ax,trial,"RECFEM","Left")
def cgm24(cls):
"""
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "operations\\markerDecomposition\\CGM24decomposeTracking\\"
#
staticFilename = "PN01OP01S01STAT.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model=cgm2.CGM2_4LowerLimbs()
model.setVersion("CGM2.4e")
model.configure()
markerDiameter=14
mp={
'Bodymass' : 83.0,
'LeftLegLength' : 874.0,
'RightLegLength' : 876.0 ,
'LeftKneeWidth' : 106.0,
'RightKneeWidth' : 103.0,
'LeftAnkleWidth' : 74.0,
'RightAnkleWidth' : 72.0,
'LeftSoleDelta' : 0,
'RightSoleDelta' : 0,
}
model.addAnthropoInputParameters(mp)
# CALIBRATION
scp=modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,acqStatic,model,
leftFlatFoot = 1, rightFlatFoot = 1,
markerDiameter=markerDiameter,
).compute()
modelDecorator.KneeCalibrationDecorator(model).midCondyles(acqStatic, markerDiameter=markerDiameter, side="left")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="left")
modelDecorator.KneeCalibrationDecorator(model).midCondyles(acqStatic, markerDiameter=markerDiameter, side="right")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="right")
modelDecorator.HipJointCenterDecorator(model).hara(side = "Both")
scp=modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,acqStatic,model,
leftFlatFoot = 1, rightFlatFoot = 1,
markerDiameter=markerDiameter,
).compute()
# --- Test 1 Motion Axe X -------
gaitFilename="PN01OP01S01SS01.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion=modelFilters.ModelMotionFilter(scp,acqGait,model,pyCGM2Enums.motionMethod.Sodervisk )
modMotion.compute()
mtf = modelFilters.TrackingMarkerDecompositionFilter(model,acqGait)
mtf.decompose()
btkTools.smartWriter(acqGait, "cgm24-decompose.c3d")
def prepare_folder_and_run_event_detection(sessionXML, work_folder,
processed_folder):
utils.create_directory_if_needed(processed_folder)
staticMeasurement = utils.find_static(sessionXML)
filename = qtmTools.getFilename(staticMeasurement)
calibrated_file_path = os.path.join(processed_folder, filename)
if not os.path.isfile(calibrated_file_path):
shutil.copyfile(os.path.join(work_folder, filename),
calibrated_file_path)
logging.info(
"qualisys exported c3d file [%s] copied to processed folder" %
(filename))
dynamicMeasurements = qtmTools.findDynamic(sessionXML)
for dynamicMeasurement in dynamicMeasurements:
filename = qtmTools.getFilename(dynamicMeasurement)
no_events_file_path = os.path.join(work_folder, filename)
processed_file_path = os.path.join(processed_folder, filename)
if not os.path.isfile(processed_file_path):
shutil.copyfile(no_events_file_path, processed_file_path)
logging.info(
"qualisys exported c3d file [%s] copied to processed folder" %
(filename))
acq = btkTools.smartReader(processed_file_path)
if "5" in btkTools.smartGetMetadata(acq, "FORCE_PLATFORM", "TYPE"):
forceplates.correctForcePlateType5(acq)
acq, state = eventDetector.zeni(acq)
btkTools.smartWriter(acq, processed_file_path)
def test_btkWriter(self):
filename = pyCGM2.TEST_DATA_PATH + "LowLevel\\IO\\Hånnibøl_c3d\\static.c3d"
acq = btkTools.smartReader(filename, translators=None)
filenameOUT = pyCGM2.TEST_DATA_PATH_OUT + "LowLevel\\IO\\Hånnibøl_c3d\\static.c3d"
files.createDir(pyCGM2.TEST_DATA_PATH_OUT +
"LowLevel\\IO\\Hånnibøl_c3d")
btkTools.smartWriter(acq, filenameOUT)
def exportC3d(self, filenameNoExt=None):
if filenameNoExt is None:
btkTools.smartWriter(
self.m_acq, self.m_dataPath + self.m_filenameNoExt + ".c3d")
else:
btkTools.smartWriter(self.m_acq,
self.m_dataPath + filenameNoExt + ".c3d")
def noIK_6dof_Garches(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "Datasets Tests\\didier\\08_02_18_Vincent Pere\\"
staticFilename = "08_02_18_Vincent_Pere_Statique_000_MOKKA.c3d"
gaitFilename = "08_02_18_Vincent_Pere_Statique_000_MOKKA.c3d"
markerDiameter = 14
mp = {
'Bodymass': 70.0,
'LeftLegLength': 890.0,
'RightLegLength': 890.0,
'LeftKneeWidth': 150.0,
'RightKneeWidth': 150.0,
'LeftAnkleWidth': 88.0,
'RightAnkleWidth': 99.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
}
# --- Calibration ---
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm2.CGM2_4()
model.configure()
model.addAnthropoInputParameters(mp)
# ---- Calibration ----
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
print "----"
print model.getSegment("Left Shank").getReferential(
"TF").relativeMatrixAnatomic
print "----"
# # cgm decorator
modelDecorator.HipJointCenterDecorator(model).hara()
modelDecorator.KneeCalibrationDecorator(model).midCondyles(
acqStatic, markerDiameter=markerDiameter, side="both")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="both")
#
# # final
modelFilters.ModelCalibrationFilter(
scp, acqStatic, model, markerDiameter=markerDiameter).compute()
# ------ Fitting -------
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
# Motion FILTER
modMotion = modelFilters.ModelMotionFilter(
scp, acqGait, model, enums.motionMethod.Sodervisk)
modMotion.compute()
btkTools.smartWriter(acqGait,
"cgm24_noIK6dof_staticMotion_Garches.c3d")
def twoPF_FP1left_FP2right(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "operations\\forceplates\\FootAssignementAutoamticGeneralEvent\\"
# --- Motion 1
gaitFilename = "MRI-US-01, 2008-08-08, 3DGA 13.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
#forceplates.appendForcePlateCornerAsMarker(acqGait)
mappedForcePlate = forceplates.matchingFootSideOnForceplate(acqGait)
forceplates.addForcePlateGeneralEvents(acqGait, "LR")
btkTools.smartWriter(acqGait,
str(MAIN_PATH + "twoPF_FP1left_FP2right.c3d"))
modelledFilenames = ["twoPF_FP1left_FP2right.c3d"]
#---- GAIT CYCLES FILTER PRELIMARIES
#--------------------------------------------------------------------------
# distinguishing trials for kinematic and kinetic processing
# - kinematic Trials
kinematicTrials = []
kinematicFilenames = []
for kinematicFilename in modelledFilenames:
kinematicFileNode = ma.io.read(str(MAIN_PATH + kinematicFilename))
kinematicTrial = kinematicFileNode.findChild(ma.T_Trial)
trialTools.sortedEvents(kinematicTrial)
longitudinalAxis, forwardProgression, globalFrame = trialTools.findProgression(
kinematicTrial, "LHEE")
kinematicTrials.append(kinematicTrial)
kinematicFilenames.append(kinematicFilename)
# - kinetic Trials ( check if kinetic events)
kineticTrials, kineticFilenames, flag_kinetics = trialTools.automaticKineticDetection(
MAIN_PATH, modelledFilenames)
#---- GAIT CYCLES FILTER
#--------------------------------------------------------------------------
cycleBuilder = cycle.GaitCyclesBuilder(
spatioTemporalTrials=kinematicTrials,
kinematicTrials=kinematicTrials,
kineticTrials=kineticTrials,
emgTrials=None)
cyclefilter = cycle.CyclesFilter()
cyclefilter.setBuilder(cycleBuilder)
cycles = cyclefilter.build()
# TESTING
np.testing.assert_equal(len(cycles.kineticCycles), 2)
np.testing.assert_equal(cycles.kineticCycles[0].context, "Left")
np.testing.assert_equal(cycles.kineticCycles[0].begin, 253)
np.testing.assert_equal(cycles.kineticCycles[1].context, "Right")
np.testing.assert_equal(cycles.kineticCycles[1].begin, 201)
def calibration_FlatFoot(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.4\\medial\\"
staticFilename = "static.c3d"
markerDiameter = 14
mp = {
'Bodymass': 69.0,
'LeftLegLength': 930.0,
'RightLegLength': 930.0,
'LeftKneeWidth': 94.0,
'RightKneeWidth': 64.0,
'LeftAnkleWidth': 67.0,
'RightAnkleWidth': 62.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
"LeftToeOffset": 0,
"RightToeOffset": 0,
}
# --- Calibration ---
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm2.CGM2_4()
model.configure()
model.addAnthropoInputParameters(mp)
# ---- Calibration ----
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
# cgm decorator
modelDecorator.HipJointCenterDecorator(model).hara()
modelDecorator.KneeCalibrationDecorator(model).midCondyles(
acqStatic, markerDiameter=markerDiameter, side="both")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="both")
# final
modelFilters.ModelCalibrationFilter(scp,
acqStatic,
model,
markerDiameter=markerDiameter,
leftFlatFoot=True,
rightFlatFoot=True).compute()
# display CS
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csf = modelFilters.CoordinateSystemDisplayFilter(csp, model, acqStatic)
csf.setStatic(True)
csf.display()
btkTools.smartWriter(acqStatic, "cgm2.4_FlatFoot.c3d")
def calibration_GarchesFlatFoot(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "Datasets Tests\\didier\\08_02_18_Vincent Pere\\"
staticFilename = "08_02_18_Vincent_Pere_Statique_000_MOKKA.c3d"
markerDiameter = 14
mp = {
'Bodymass': 70.0,
'LeftLegLength': 890.0,
'RightLegLength': 890.0,
'LeftKneeWidth': 150.0,
'RightKneeWidth': 150.0,
'LeftAnkleWidth': 88.0,
'RightAnkleWidth': 99.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
"LeftToeOffset": 0,
"RightToeOffset": 0,
}
# --- Calibration ---
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm2.CGM2_4()
model.configure()
model.addAnthropoInputParameters(mp)
# ---- Calibration ----
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
# cgm decorator
modelDecorator.HipJointCenterDecorator(model).hara()
modelDecorator.KneeCalibrationDecorator(model).midCondyles(
acqStatic, markerDiameter=markerDiameter, side="both")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="both")
# final
modelFilters.ModelCalibrationFilter(scp,
acqStatic,
model,
markerDiameter=markerDiameter,
leftFlatFoot=True,
rightFlatFoot=True).compute()
# display CS
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csf = modelFilters.CoordinateSystemDisplayFilter(csp, model, acqStatic)
csf.setStatic(True)
csf.display()
btkTools.smartWriter(acqStatic, "cgm2.4_GarchesFlatFoot.c3d")
def processC3d(self):
for c3d in self.m_c3ds:
filenameOut = c3d[:-4] + "_" + self.m_fileSuffix+".c3d" if self.m_fileSuffix is not None else c3d
acq = btkTools.smartReader((self.m_c3dPath+c3d))
values = acq.GetAnalog(utils.str(self.m_label)).GetValues()
valuesNorm = values / self.m_threshold
btkTools.smartAppendAnalog(acq,self.m_label+"_Norm",valuesNorm, desc= "Normalization)")
btkTools.smartWriter(acq, (self.m_c3dPath+filenameOut))
def test_correctForcePlateType5(self):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "LowLevel\\ForcePlate\\ForcePlateTypeManagement\\"
DATA_PATH_OUT = pyCGM2.TEST_DATA_PATH_OUT + "LowLevel\\ForcePlate\\ForcePlateTypeManagement\\"
files.createDir(DATA_PATH_OUT)
btkAcq = btkTools.smartReader(MAIN_PATH + "HUG_gait_type5.c3d")
forceplates.correctForcePlateType5(btkAcq)
btkTools.smartWriter(btkAcq, DATA_PATH_OUT + "HUG_gait_type5.c3d")
def basicCGM1_bodyBuilderFoot(cls):
"""
goal : know effet on Foot kinematics of a foot referential built according ta sequence metionned in some bodybuilder code:
LFoot = [LTOE,LAJC-LTOE,LAJC-LKJC,zyx]
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\basic\\"
staticFilename = "MRI-US-01, 2008-08-08, 3DGA 02.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model=cgm.CGM1LowerLimbs()
model.configure()
mp={
'Bodymass' : 71.0,
'LeftLegLength' : 860.0,
'RightLegLength' : 865.0 ,
'LeftKneeWidth' : 102.0,
'RightKneeWidth' : 103.4,
'LeftAnkleWidth' : 75.3,
'RightAnkleWidth' : 72.9,
'LeftSoleDelta' : 0,
'RightSoleDelta' : 0,
}
model.addAnthropoInputParameters(mp)
scp=modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,acqStatic,model,
useBodyBuilderFoot=True).compute()
# ------ Test 1 Motion Axe X -------
gaitFilename="MRI-US-01, 2008-08-08, 3DGA 14.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
# Motion FILTER
# optimisation segmentaire et calibration fonctionnel
modMotion=modelFilters.ModelMotionFilter(scp,acqGait,model,pyCGM2Enums.motionMethod.Determinist)
modMotion.compute()
# relative angles
modelFilters.ModelJCSFilter(model,acqGait).compute(description="vectoriel", pointLabelSuffix="cgm1_6dof")
# absolute angles
longitudinalAxis,forwardProgression,globalFrame = btkTools.findProgressionAxisFromPelvicMarkers(acqGait,["LASI","LPSI","RASI","RPSI"])
modelFilters.ModelAbsoluteAnglesFilter(model,acqGait,
segmentLabels=["Left Foot","Right Foot","Pelvis"],
angleLabels=["LFootProgress", "RFootProgress","Pelvis"],
eulerSequences=["TOR","TOR", "TOR"],
globalFrameOrientation = globalFrame,
forwardProgression = forwardProgression).compute(pointLabelSuffix="cgm1_6dof")
btkTools.smartWriter(acqGait, "testuseBodyBuilderFoot.c3d")
def advancedCGM11_KneeMedKad_TrueEquinus(cls):
"""
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\kad-med-TrueEquinus\\"
staticFilename = "static.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm.CGM1
model.configure()
markerDiameter = 14
mp = {
'Bodymass': 36.9,
'LeftLegLength': 665.0,
'RightLegLength': 655.0,
'LeftKneeWidth': 102.7,
'RightKneeWidth': 100.2,
'LeftAnkleWidth': 64.5,
'RightAnkleWidth': 63.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
}
optional_mp = {
'InterAsisDistance': 0,
'LeftAsisTrocanterDistance': 0,
'LeftThighRotation': 0,
'LeftShankRotation': 0,
'LeftTibialTorsion': 0,
'RightAsisTrocanterDistance': 0,
'RightThighRotation': 0,
'RightShankRotation': 0,
'RightTibialTorsion': 0
}
model.addAnthropoInputParameters(mp, optional=optional_mp)
# -----------CGM STATIC CALIBRATION--------------------
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
# cgm decorator
modelDecorator.Kad(model, acqStatic).compute()
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, side="both")
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
btkTools.smartWriter(acqStatic, "Kad-med-TrueEquinus.c3d")
def test_FullBody_noOptions(self):
DATA_PATH = MAIN_PATH = pyCGM2.TEST_DATA_PATH + "LowLevel\\uncropped data\\cgm1\\"
staticFilename = "static.c3d"
DATA_PATH_OUT = pyCGM2.TEST_DATA_PATH_OUT+"LowLevel\\uncropped data\\cgm1\\"
files.createDir(DATA_PATH_OUT)
markerDiameter=14
leftFlatFoot = True
rightFlatFoot = True
headStraight = True
pointSuffix = ""
vskFile = vskTools.getVskFiles(DATA_PATH)
vsk = vskTools.Vsk(DATA_PATH + "New Subject.vsk")
required_mp,optional_mp = vskTools.getFromVskSubjectMp(vsk, resetFlag=True)
model,finalAcqStatic = cgm1.calibrate(DATA_PATH,
staticFilename,
None,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headStraight,
markerDiameter,
pointSuffix,
displayCoordinateSystem=True)
# btkTools.smartWriter(finalAcqStatic, str( staticFilename[:-4]+"-pyCGM2modelled.c3d"))
# logging.info("Static Calibration -----> Done")
gaitFilename="gait1.c3d"
acqGait0 = btkTools.smartReader(DATA_PATH + gaitFilename)
trackingMarkers = model.getTrackingMarkers(acqGait0)
validFrames,vff,vlf = btkTools.findValidFrames(acqGait0,trackingMarkers)
mfpa = None
reconstructFilenameLabelled = gaitFilename
acqGait = cgm1.fitting(model,DATA_PATH, reconstructFilenameLabelled,
None,
markerDiameter,
pointSuffix,
mfpa,
enums.MomentProjection.Proximal,
displayCoordinateSystem=True)
btkTools.smartWriter(acqGait, DATA_PATH_OUT+"//gait1-processed.c3d")
def advancedCGM11_KneeMedKad(cls):
"""
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\CGM1.1\medial\\"
staticFilename = "static-all.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm.CGM1
model.configure()
markerDiameter = 14
mp = {
'Bodymass': 71.0,
'LeftLegLength': 860.0,
'RightLegLength': 865.0,
'LeftKneeWidth': 102.0,
'RightKneeWidth': 103.4,
'LeftAnkleWidth': 75.3,
'RightAnkleWidth': 72.9,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
}
optional_mp = {
'InterAsisDistance': 0,
'LeftAsisTrocanterDistance': 0,
'LeftThighRotation': 0,
'LeftShankRotation': 0,
'LeftTibialTorsion': -10,
'RightAsisTrocanterDistance': 0,
'RightThighRotation': 0,
'RightShankRotation': 0,
'RightTibialTorsion': 15
}
model.addAnthropoInputParameters(mp, optional=optional_mp)
# -----------CGM STATIC CALIBRATION--------------------
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
# cgm decorator
modelDecorator.KneeCalibrationDecorator(model).midCondyles_KAD(
acqStatic)
#modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, side="both")
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
btkTools.smartWriter(acqStatic, "advancedCGM11_KneeMedKad.c3d")
def cgm1(cls):
"""
GOAL : compare Joint centres and foot Offset
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "operations\\markerDecomposition\\CGM1decomposeTracking\\"
#
staticFilename = "static.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm.CGM1LowerLimbs()
model.configure()
markerDiameter = 14
mp = {
'Bodymass': 36.9,
'LeftLegLength': 665,
'RightLegLength': 655.0,
'LeftKneeWidth': 102.7,
'RightKneeWidth': 100.2,
'LeftAnkleWidth': 64.5,
'RightAnkleWidth': 63.4,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
}
model.addAnthropoInputParameters(mp)
# CALIBRATION
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
print model.m_useRightTibialTorsion
# --- Test 1 Motion Axe X -------
gaitFilename = "gait trial 01.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion = modelFilters.ModelMotionFilter(
scp,
acqGait,
model,
pyCGM2Enums.motionMethod.Determinist,
useForMotionTest=True)
modMotion.compute()
mtf = modelFilters.TrackingMarkerDecompositionFilter(model, acqGait)
mtf.decompose()
btkTools.smartWriter(acqGait, "cgm1-decompose.c3d")
def detection(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "operations\\event detection\\events\\"
# --- Motion 1
gaitFilename = "gait-noEvents.c3d"
acq = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
evp = events.ZeniProcedure()
evf = events.EventFilter(evp, acq)
evf.detect()
btkTools.smartWriter("testEvent0.c3d", 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 test_CGM1_FullBody_noOptions_noFP(self):
DATA_PATH = pyCGM2.TEST_DATA_PATH + "GaitModels\CGM1\\fullBody-native-noOptions - noFP\\"
staticFilename = "static.c3d"
acqStatic = btkTools.smartReader(DATA_PATH + staticFilename)
markerDiameter=14
leftFlatFoot = False
rightFlatFoot = False
headStraight = False
pointSuffix = "test"
vskFile = vskTools.getVskFiles(DATA_PATH)
vsk = vskTools.Vsk(DATA_PATH + "New Subject.vsk")
required_mp,optional_mp = vskTools.getFromVskSubjectMp(vsk, resetFlag=True)
model,finalAcqStatic = cgm1.calibrate(DATA_PATH,
staticFilename,
None,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headStraight,
markerDiameter,
pointSuffix,
displayCoordinateSystem=True)
# btkTools.smartWriter(finalAcqStatic, str( staticFilename[:-4]+"-pyCGM2modelled.c3d"))
# logging.info("Static Calibration -----> Done")
gaitFilename="gait1.c3d"
mfpa = None
reconstructFilenameLabelled = gaitFilename
acqGait = cgm1.fitting(model,DATA_PATH, reconstructFilenameLabelled,
None,
markerDiameter,
pointSuffix,
mfpa,
enums.MomentProjection.Proximal,
displayCoordinateSystem=True)
btkTools.smartWriter(acqGait, "gait1-pyCGM2modelled.c3d")
def cgm1_sacrum(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "operations\\Translators\\cgm1-sacr\\"
staticFilename = "static.c3d"
translators = files.getTranslators(MAIN_PATH,
translatorType="CGM1.translators")
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
acqStatic2 = btkTools.applyTranslators(acqStatic, translators)
btkTools.smartWriter(acqStatic2, "staticCGM1Sacrum.c3d")
np.testing.assert_equal(
acqStatic2.GetPoint("LPSI").GetValues(),
acqStatic.GetPoint("SACR").GetValues())
np.testing.assert_equal(
acqStatic2.GetPoint("RPSI").GetValues(),
acqStatic.GetPoint("SACR").GetValues())
def fit_model_to_measurements(model, model_type, model_manager, data_path,
point_suffix):
processing_module = get_processing_module_alias(model_type)
for dynamic_measurement in model_manager.dynamicTrials:
fitting_settings = get_model_fitting_settings(model_type,
dynamic_measurement,
model, data_path,
model_manager,
point_suffix)
filename = qtmTools.getFilename(dynamic_measurement)
logging.info("----Processing of [%s]-----" % filename)
file_path = os.path.join(data_path, filename)
filter_data(file_path, dynamic_measurement)
acqGait = processing_module.fitting(*fitting_settings)
btkTools.smartWriter(acqGait, file_path)
