def automaticCPdeviations(DATA_PATH,
analysis,
pointLabelSuffix=None,
filterTrue=False,
export=True,
outputname="Nieuwenhuys2017"):
"""
Detect gait deviation for CP according a Delphi Consensus (Nieuwenhuys2017 et al 2017)
:param analysis [pyCGM2.Processing.analysis.Analysis]: pyCGM2 analysis instance
"""
RULES_PATH = pyCGM2.PYCGM2_SETTINGS_FOLDER + "jointPatterns\\"
rulesXls = RULES_PATH + "Nieuwenhuys2017.xlsx"
jpp = jointPatterns.XlsJointPatternProcedure(rulesXls,
pointSuffix=pointLabelSuffix)
dpf = jointPatterns.JointPatternFilter(jpp, analysis)
dataFrameValues = dpf.getValues()
dataFramePatterns = dpf.getPatterns(filter=filterTrue)
if export:
xlsExport = exporter.XlsExportDataFrameFilter()
xlsExport.setDataFrames([dataFrameValues])
xlsExport.export(str(outputname + "_Data"), path=DATA_PATH)
xlsExport = exporter.XlsExportDataFrameFilter()
xlsExport.setDataFrames([dataFramePatterns])
xlsExport.export(str(outputname + "_Patterns"), path=DATA_PATH)
return dataFramePatterns
def kinematicsOnly_bothSide(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "operations\\gaitDeviations\\gaitPig\\"
modelledFilenames = [
"gait Trial 01 - viconName.c3d", "gait Trial 03 - viconName.c3d"
]
# ----INFOS-----
modelInfo = None
subjectInfo = None
experimentalInfo = None
normativeDataSet = dict()
normativeDataSet["Author"] = "Schwartz2008"
normativeDataSet["Modality"] = "Free"
pointLabelSuffix = ""
#---- c3d manager
#--------------------------------------------------------------------------
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(
DATA_PATH, modelledFilenames)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableEmg(False)
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()
#---- GAIT ANALYSIS FILTER
#--------------------------------------------------------------------------
pointLabelSuffixPlus = pointLabelSuffix if pointLabelSuffix == "" else "_" + pointLabelSuffix
kinematicLabelsDict = {
'Left': [
str("LHipAngles" + pointLabelSuffixPlus),
str("LKneeAngles" + pointLabelSuffixPlus),
str("LAnkleAngles" + pointLabelSuffixPlus),
str("LFootProgressAngles" + pointLabelSuffixPlus),
str("LPelvisAngles" + pointLabelSuffixPlus)
],
'Right': [
str("RHipAngles" + pointLabelSuffixPlus),
str("RKneeAngles" + pointLabelSuffixPlus),
str("RAnkleAngles" + pointLabelSuffixPlus),
str("RFootProgressAngles" + pointLabelSuffixPlus),
str("RPelvisAngles" + pointLabelSuffixPlus)
]
}
kineticLabelsDict = {
'Left': [
str("LHipMoment" + pointLabelSuffixPlus),
str("LKneeMoment" + pointLabelSuffixPlus),
str("LAnkleMoment" + pointLabelSuffixPlus),
str("LHipPower" + pointLabelSuffixPlus),
str("LKneePower" + pointLabelSuffixPlus),
str("LAnklePower" + pointLabelSuffixPlus)
],
'Right': [
str("RHipMoment" + pointLabelSuffixPlus),
str("RKneeMoment" + pointLabelSuffixPlus),
str("RAnkleMoment" + pointLabelSuffixPlus),
str("RHipPower" + pointLabelSuffixPlus),
str("RKneePower" + pointLabelSuffixPlus),
str("RAnklePower" + pointLabelSuffixPlus)
]
}
analysisBuilder = analysis.GaitAnalysisBuilder(
cycles,
kinematicLabelsDict=kinematicLabelsDict,
kineticLabelsDict=kineticLabelsDict,
subjectInfos=subjectInfo,
modelInfos=modelInfo,
experimentalInfos=experimentalInfo)
analysisFilter = analysis.AnalysisFilter()
analysisFilter.setBuilder(analysisBuilder)
analysisFilter.build()
#---- Joint patterns
# xls Processing
RULES_PATH = pyCGM2.PYCGM2_SETTINGS_FOLDER + "jointPatterns\\"
rulesXls = RULES_PATH + "Nieuwenhuys2017.xlsx"
jpp = jointPatterns.XlsJointPatternProcedure(rulesXls)
dpf = jointPatterns.JointPatternFilter(jpp, analysisFilter.analysis)
dataFrameValues = dpf.getValues()
dataFramePatterns = dpf.getPatterns()
xlsExport = exporter.XlsExportDataFrameFilter()
xlsExport.setDataFrames([dataFrameValues])
xlsExport.export("TestsPointData", path=DATA_PATH)
xlsExport = exporter.XlsExportDataFrameFilter()
xlsExport.setDataFrames([dataFramePatterns])
xlsExport.export("TestsPatternsData", path=DATA_PATH)
def test(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "operations\\analysis\\gait\\"
modelledFilenames = [
"gait Trial 01 - viconName.c3d", "gait Trial 03 - viconName.c3d"
]
# ----INFOS-----
modelInfo = None
subjectInfo = None
experimentalInfo = None
normativeDataSet = dict()
normativeDataSet["Author"] = "Schwartz2008"
normativeDataSet["Modality"] = "Free"
pointLabelSuffix = ""
#---- c3d manager
#--------------------------------------------------------------------------
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(
DATA_PATH, modelledFilenames)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableEmg(False)
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()
#---- GAIT ANALYSIS FILTER
#--------------------------------------------------------------------------
pointLabelSuffixPlus = pointLabelSuffix if pointLabelSuffix == "" else "_" + pointLabelSuffix
kinematicLabelsDict = {
'Left': [
str("LHipAngles" + pointLabelSuffixPlus),
str("LKneeAngles" + pointLabelSuffixPlus),
str("LAnkleAngles" + pointLabelSuffixPlus),
str("LFootProgressAngles" + pointLabelSuffixPlus),
str("LPelvisAngles" + pointLabelSuffixPlus)
],
'Right': [
str("RHipAngles" + pointLabelSuffixPlus),
str("RKneeAngles" + pointLabelSuffixPlus),
str("RAnkleAngles" + pointLabelSuffixPlus),
str("RFootProgressAngles" + pointLabelSuffixPlus),
str("RPelvisAngles" + pointLabelSuffixPlus)
]
}
kineticLabelsDict = {
'Left': [
str("LHipMoment" + pointLabelSuffixPlus),
str("LKneeMoment" + pointLabelSuffixPlus),
str("LAnkleMoment" + pointLabelSuffixPlus),
str("LHipPower" + pointLabelSuffixPlus),
str("LKneePower" + pointLabelSuffixPlus),
str("LAnklePower" + pointLabelSuffixPlus)
],
'Right': [
str("RHipMoment" + pointLabelSuffixPlus),
str("RKneeMoment" + pointLabelSuffixPlus),
str("RAnkleMoment" + pointLabelSuffixPlus),
str("RHipPower" + pointLabelSuffixPlus),
str("RKneePower" + pointLabelSuffixPlus),
str("RAnklePower" + pointLabelSuffixPlus)
]
}
analysisBuilder = analysis.GaitAnalysisBuilder(
cycles,
kinematicLabelsDict=kinematicLabelsDict,
kineticLabelsDict=kineticLabelsDict,
subjectInfos=subjectInfo,
modelInfos=modelInfo,
experimentalInfos=experimentalInfo)
analysisFilter = analysis.AnalysisFilter()
analysisFilter.setBuilder(analysisBuilder)
analysisFilter.build()
#---- DISCRETE POINT FILTER
#-----------------------------------------------------------------------
# Benedetti Processing
dpProcedure = discretePoints.GoldbergProcedure()
dpf = discretePoints.DiscretePointsFilter(dpProcedure,
analysisFilter.analysis)
dataFrame = dpf.getOutput()
xlsExport = exporter.XlsExportDataFrameFilter()
xlsExport.setDataFrames(dataFrame)
xlsExport.export("discretePointsGoldberg", path=DATA_PATH)
