def analysisAdvanced(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH+"operations\\analysis\\gait\\"
modelledFilenames = ["gait Trial 03 - viconName.c3d" ]
#---- c3d manager
#--------------------------------------------------------------------------
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(DATA_PATH,modelledFilenames)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableEmg(False)
trialManager = cmf.generate()
#---- Analysis
#--------------------------------------------------------------------------
# ----INFOS-----
modelInfo={"Type":"cgm2", "hjc":"hara"}
subjectInfo={"Id":"1", "Name":"Lecter"}
experimentalInfo={"Condition":"Barefoot", "context":"block"}
analysisInstance = pyCGM2.Lib.analysis.makeAnalysis("Gait", DATA_PATH,modelledFilenames,subjectInfo, experimentalInfo, modelInfo)
exportFilter = exporter.XlsAnalysisExportFilter()
exportFilter.setAnalysisInstance(analysisInstance)
exportFilter.export("testAdvanced", path=DATA_PATH,excelFormat = "xls",mode="Advanced")
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 analysisBasic(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "operations\\analysis\\gait\\"
modelledFilenames = ["gait Trial 03 - viconName.c3d"]
#---- c3d manager
#--------------------------------------------------------------------------
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(
DATA_PATH, modelledFilenames)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableEmg(False)
trialManager = cmf.generate()
#---- Analysis
#--------------------------------------------------------------------------
# ----INFOS-----
modelInfo = {"Type": "cgm2", "hjc": "hara"}
subjectInfo = {"Id": "1", "Name": "Lecter"}
experimentalInfo = {"Condition": "Barefoot", "context": "block"}
analysis = gaitSmartFunctions.make_analysis(
trialManager, cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT,
cgm.CGM1LowerLimbs.ANALYSIS_KINETIC_LABELS_DICT, modelInfo,
subjectInfo, experimentalInfo)
exportFilter = exporter.XlsAnalysisExportFilter()
exportFilter.setAnalysisInstance(analysis)
exportFilter.export("test",
path=DATA_PATH,
excelFormat="xls",
mode="Basic")
def standardProcessing(DATA_PATH, modelledFilenames, modelVersion,
modelInfo, subjectInfo, experimentalInfo,
pointSuffix,
outputPath=None,
outputFilename="standardProcessing",
exportXls=False):
if outputPath is None:
outputPath= DATA_PATH
if isinstance(modelledFilenames,str) or isinstance(modelledFilenames,unicode):
modelledFilenames = [modelledFilenames]
#---- c3d manager
#--------------------------------------------------------------------------
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(DATA_PATH,modelledFilenames)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableEmg(False)
trialManager = cmf.generate()
#---- make analysis
#-----------------------------------------------------------------------
# pycgm2-filter pipeline are gathered in a single function
if modelVersion in["CGM1.0","CGM1.1","CGM2.1","CGM2.2","CGM2.2e","CGM2.3","CGM2.3e","CGM2.4","CGM2.4e"]:
if modelVersion in ["CGM2.4","CGM2.4e"]:
cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT["Left"].append("LForeFoot")
cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT["Right"].append("RForeFoot")
analysis = standardSmartFunctions.make_analysis(trialManager,
cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT,
cgm.CGM1LowerLimbs.ANALYSIS_KINETIC_LABELS_DICT,
modelInfo, subjectInfo, experimentalInfo,
pointLabelSuffix=pointSuffix)
#---- export
#-----------------------------------------------------------------------
if exportXls:
exportFilter = exporter.XlsAnalysisExportFilter()
exportFilter.setAnalysisInstance(analysis)
exportFilter.export(outputFilename, path=outputPath,excelFormat = "xls",mode="Advanced")
def exportAnalysis(analysisInstance, DATA_PATH, name, mode="Advanced"):
"""
exportAnalysis : export the pyCGM2.Processing.analysis.Analysis instance in a xls spreadsheet
:param analysisInstance [pyCGM2.Processing.analysis.Analysis]: pyCGM2 analysis instance
:param DATA_PATH [str]: path to your data
:param name [string]: name of the output file
**optional**
:param mode [string]: structure of the output xls (choice: Advanced[Default] or Basic)
.. note::
the advanced xls organizes data by row ( one raw = on cycle)
whereas the Basic mode exports each model output in a new sheet
"""
exportFilter = exporter.XlsAnalysisExportFilter()
exportFilter.setAnalysisInstance(analysisInstance)
exportFilter.export(name, path=DATA_PATH, excelFormat="xls", mode=mode)
def analysisAdvancedAndBasic_nonExistingLabel(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH+"operations\\analysis\\gait\\"
modelledFilenames = ["gait Trial 03 - viconName.c3d","gait Trial 01 - viconName.c3d" ]
#---- 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
#--------------------------------------------------------------------------
# ----INFOS-----
modelInfo={"type":"S01"}
subjectInfo=None
experimentalInfo=None
kinematicLabelsDict ={ 'Left': ["LHipAngles","LKneeAngles","LAnkleAngles","LForeFootAngles"],
'Right': ["RHipAngles","RKneeAngles","RAnkleAngles"] }
kineticLabelsDict =None#{ 'Left': ["LHipMoment","LKneeMoment"],
#'Right': ["RHipMoment","RKneeMoment"]}
analysisBuilder = analysis.GaitAnalysisBuilder(cycles,
kinematicLabelsDict = kinematicLabelsDict,
kineticLabelsDict = kineticLabelsDict,
subjectInfos=subjectInfo,
modelInfos=modelInfo,
experimentalInfos=experimentalInfo)
analysisFilter = analysis.AnalysisFilter()
analysisFilter.setBuilder(analysisBuilder)
analysisFilter.setInfo(model = modelInfo)
analysisFilter.build()
analysisInstance = analysisFilter.analysis
# ----INFOS-----
modelInfo={"Type":"cgm2", "hjc":"hara"}
subjectInfo={"Id":"1", "Name":"Lecter"}
experimentalInfo={"Condition":"Barefoot", "context":"block"}
exportFilter = exporter.XlsAnalysisExportFilter()
exportFilter.setAnalysisInstance(analysisInstance)
exportFilter.export("testAdvancedNan", path=DATA_PATH,excelFormat = "xls",mode="Advanced")
exportFilter2 = exporter.XlsAnalysisExportFilter()
exportFilter2.setAnalysisInstance(analysisInstance)
exportFilter2.export("testBasic2", path=DATA_PATH,excelFormat = "xls",mode="Basic")
def GpsCGM1Test(cls):
# ----DATA-----
DATA_PATH = pyCGM2.TEST_DATA_PATH + "operations\\analysis\\gps\\"
reconstructedFilenameLabelledNoExt = "gait Trial 03 - viconName"
reconstructedFilenameLabelled = reconstructedFilenameLabelledNoExt + ".c3d"
logging.info("data Path: " + DATA_PATH)
logging.info("reconstructed file: " + reconstructedFilenameLabelled)
modelledFilenames = [reconstructedFilenameLabelled]
#---- 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
#--------------------------------------------------------------------------
# ----INFOS-----
modelInfo = {"type": "S01"}
subjectInfo = None
experimentalInfo = None
pointLabelSuffix = ""
pointLabelSuffixPlus = pointLabelSuffix if pointLabelSuffix == "" else "_" + pointLabelSuffix
kinematicLabelsDict = {
'Left': [
"LHipAngles" + pointLabelSuffixPlus,
"LKneeAngles" + pointLabelSuffixPlus,
"LAnkleAngles" + pointLabelSuffixPlus,
"LFootProgressAngles" + pointLabelSuffixPlus,
"LPelvisAngles" + pointLabelSuffixPlus
],
'Right': [
"RHipAngles" + pointLabelSuffixPlus,
"RKneeAngles" + pointLabelSuffixPlus,
"RAnkleAngles" + pointLabelSuffixPlus,
"RFootProgressAngles" + pointLabelSuffixPlus,
"RPelvisAngles" + pointLabelSuffixPlus
]
}
kineticLabelsDict = {
'Left': [
"LHipMoment" + pointLabelSuffixPlus,
"LKneeMoment" + pointLabelSuffixPlus,
"LAnkleMoment" + pointLabelSuffixPlus,
"LHipPower" + pointLabelSuffixPlus,
"LKneePower" + pointLabelSuffixPlus,
"LAnklePower" + pointLabelSuffixPlus
],
'Right': [
"RHipMoment" + pointLabelSuffixPlus,
"RKneeMoment" + pointLabelSuffixPlus,
"RAnkleMoment" + pointLabelSuffixPlus,
"RHipPower" + pointLabelSuffixPlus,
"RKneePower" + pointLabelSuffixPlus,
"RAnklePower" + pointLabelSuffixPlus
]
}
analysisBuilder = analysis.GaitAnalysisBuilder(
cycles,
kinematicLabelsDict=kinematicLabelsDict,
kineticLabelsDict=kineticLabelsDict,
subjectInfos=subjectInfo,
modelInfos=modelInfo,
experimentalInfos=experimentalInfo)
analysisFilter = analysis.AnalysisFilter()
analysisFilter.setBuilder(analysisBuilder)
analysisFilter.setInfo(model=modelInfo)
analysisFilter.build()
analysisInstance = analysisFilter.analysis
## --- GPS ----
ndp = normativeDatasets.Schwartz2008("Free")
gps = scores.CGM1_GPS()
scf = scores.ScoreFilter(gps, analysisInstance, ndp)
scf.compute()
xlsExport = exporter.XlsAnalysisExportFilter()
xlsExport.setAnalysisInstance(analysisInstance)
xlsExport.export("gpsTest2", path=DATA_PATH, mode="Advanced")
def gaitProcessing(DATA_PATH, modelledFilenames, modelVersion,
modelInfo, subjectInfo, experimentalInfo,
normativeData,
pointSuffix,
outputPath=None,
outputFilename="gaitProcessing",
exportXls=False,
plot=True,
plotDisplay=True):
if outputPath is None:
outputPath= DATA_PATH
if isinstance(modelledFilenames,str) or isinstance(modelledFilenames,unicode):
modelledFilenames = [modelledFilenames]
#---- c3d manager
#--------------------------------------------------------------------------
c3dmanagerProcedure = c3dManager.UniqueC3dSetProcedure(DATA_PATH,modelledFilenames)
cmf = c3dManager.C3dManagerFilter(c3dmanagerProcedure)
cmf.enableEmg(False)
trialManager = cmf.generate()
#---- make analysis
#-----------------------------------------------------------------------
# pycgm2-filter pipeline are gathered in a single function
if modelVersion in["CGM1.0","CGM1.1","CGM2.1","CGM2.2","CGM2.2e","CGM2.3","CGM2.3e","CGM2.4","CGM2.4e"]:
if modelVersion in ["CGM2.4","CGM2.4e"]:
cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT["Left"].append("LForeFootAngles")
cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT["Right"].append("RForeFootAngles")
analysis = gaitSmartFunctions.make_analysis(trialManager,
cgm.CGM1LowerLimbs.ANALYSIS_KINEMATIC_LABELS_DICT,
cgm.CGM1LowerLimbs.ANALYSIS_KINETIC_LABELS_DICT,
modelInfo, subjectInfo, experimentalInfo,
pointLabelSuffix=pointSuffix)
#---- normative dataset
#-----------------------------------------------------------------------
if normativeData["Author"] == "Schwartz2008":
chosenModality = normativeData["Modality"]
nds = normativeDatasets.Schwartz2008(chosenModality) # modalites : "Very Slow" ,"Slow", "Free", "Fast", "Very Fast"
elif normativeData["Author"] == "Pinzone2014":
chosenModality = normativeData["Modality"]
nds = normativeDatasets.Pinzone2014(chosenModality) # modalites : "Center One" ,"Center Two"
#---- GPS
gps =scores.CGM1_GPS(pointSuffix= pointSuffix)
scf = scores.ScoreFilter(gps,analysis, nds)
scf.compute()
#---- export
#-----------------------------------------------------------------------
files.saveAnalysis(analysis,outputPath,outputFilename)
if exportXls:
exportFilter = exporter.XlsAnalysisExportFilter()
exportFilter.setAnalysisInstance(analysis)
exportFilter.export(outputFilename, path=outputPath,excelFormat = "xls",mode="Advanced")
#---- plot panels
#-----------------------------------------------------------------------
if plot:
gaitSmartFunctions.cgm_gaitPlots(modelVersion,analysis,trialManager.kineticFlag,
outputPath,outputFilename,
pointLabelSuffix=pointSuffix,
normativeDataset=nds )
if plotDisplay:
plt.show()
return analysis
