def KadMed_TrueEquinus_leftSkinMarkers(cls):
DATA_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\kad-med-TrueEquinus-leftSkinMarkers\\"
staticFilename = "static.c3d"
markerDiameter=14
required_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
}
settings = files.openJson(pyCGM2.PYCGM2_APPDATA_PATH,"CGM1_1-pyCGM2.settings")
translators = settings["Translators"]
pointSuffix = "cgm1_6dof"
model,acqStatic = cgm1.calibrate(DATA_PATH,staticFilename,translators,
required_mp,optional_mp,
False,False,markerDiameter,
pointSuffix)
mcsp = modelFilters.ModelCoordinateSystemProcedure(model)
mcsf = modelFilters.CoordinateSystemDisplayFilter(mcsp,model,acqStatic)
mcsf.setStatic(False)
mcsf.display()
btkTools.smartWriter(acqStatic,"CGM1-KadMed-TrueEquinus-leftSkin-static.c3d")
#motion
gaitFilename="gait trial 01.c3d"
mfpa = None
momentProjection=enums.MomentProjection.Distal
acqGait = cgm1.fitting(model,DATA_PATH, gaitFilename,
translators,
markerDiameter,
pointSuffix,
mfpa,
momentProjection)
mcsp = modelFilters.ModelCoordinateSystemProcedure(model)
mcsf = modelFilters.CoordinateSystemDisplayFilter(mcsp,model,acqGait)
mcsf.setStatic(False)
mcsf.display()
#mcsp = modelFilters.ModelCoordinateSystemProcedure(model)
#modelFilters.CoordinateSystemDisplayFilter(mcsp,model,acqGait).display()
btkTools.smartWriter(acqGait, "CGM1-KadMed-TrueEquinus-leftSkin-gait.c3d")
# testings
offsetTesting(acqStatic,model,display = True, unitTesting=True)
testJointCentres(acqGait)
testRelativesAngles(acqGait,pointSuffix)
# --------------------pyCGM2 MODEL ------------------------------
model = files.loadModel(DATA_PATH,subject)
# --------------------------CHECKING -----------------------------------
# check model is the CGM1
logging.info("loaded model : %s" %(model.version ))
if model.version != "CGM1.0":
raise Exception ("%s-pyCGM2.model file was not calibrated from the CGM1.0 calibration pipeline"%model.version)
# --------------------------SESSION INFOS ------------------------------------
# translators management
translators = files.getTranslators(DATA_PATH,"CGM1.translators")
if not translators: translators = settings["Translators"]
# --------------------------MODELLING PROCESSING -----------------------
acqGait = cgm1.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,
markerDiameter,
pointSuffix,
mfpa,momentProjection)
# ----------------------SAVE-------------------------------------------
# Todo: pyCGM2 model : cpickle doesn t work. Incompatibility with Swig. ( see about BTK wrench)
# new static file
if args.fileSuffix is not None:
btkTools.smartWriter(acqGait, str(DATA_PATH+reconstructFilenameLabelled[:-4]+"-modelled-"+args.fileSuffix+".c3d"))
else:
btkTools.smartWriter(acqGait, str(DATA_PATH+reconstructFilenameLabelled[:-4]+"-modelled.c3d"))
def modelling(manager,DATA_PATH,DATA_PATH_OUT,vskFile=None):
modelVersion = manager.getModelVersion()
logging.info("model version : %s" %(modelVersion))
# --------------------------MODELLING ------------------------------------
# manage global settings and translators
if modelVersion == "CGM1.0":
translatorFiles= "CGM1.translators"
globalPyCGM2settingFile = "CGM1-pyCGM2.settings"
elif modelVersion == "CGM1.1":
translatorFiles= "CGM1_1.translators"
globalPyCGM2settingFile = "CGM1_1-pyCGM2.settings"
elif modelVersion == "CGM2.1":
translatorFiles= "CGM2_1.translators"
globalPyCGM2settingFile = "CGM2_1-pyCGM2.settings"
elif modelVersion == "CGM2.2":
translatorFiles= "CGM2_2.translators"
globalPyCGM2settingFile = "CGM2_2-pyCGM2.settings"
elif modelVersion == "CGM2.2e":
translatorFiles= "CGM2_2.translators"
globalPyCGM2settingFile = "CGM2_2-Expert-pyCGM2.settings"
elif modelVersion == "CGM2.3":
translatorFiles= "CGM2_3.translators"
globalPyCGM2settingFile = "CGM2_3-pyCGM2.settings"
elif modelVersion == "CGM2.3e":
translatorFiles= "CGM2_3.translators"
globalPyCGM2settingFile = "CGM2_3-Expert-pyCGM2.settings"
elif modelVersion == "CGM2.4":
translatorFiles= "CGM2_4.translators"
globalPyCGM2settingFile = "CGM2_4-pyCGM2.settings"
elif modelVersion == "CGM2.4e":
translatorFiles= "CGM2_4.translators"
globalPyCGM2settingFile = "CGM2_4-Expert-pyCGM2.settings"
else:
raise Exception( "model version not known")
settings = files.openJson(pyCGM2.PYCGM2_APPDATA_PATH,globalPyCGM2settingFile)
translators = files.getTranslators(DATA_PATH,translatorFiles)
if not translators: translators = settings["Translators"]
# mp file
if vskFile is None:
logging.info("mp from pipeline file")
required_mp,optional_mp = manager.getMP()
else:
logging.warning("mp from vsk file")
vsk = vskTools.Vsk(str(DATA_PATH + vskFile))
required_mp,optional_mp = vskTools.getFromVskSubjectMp(vsk, resetFlag=True)
fileSuffix = manager.getFileSuffix()
pointSuffix = manager.getPointSuffix()
ik_flag = manager.isIkFitting()
#------calibration--------
leftFlatFoot = manager.getLeftFlatFoot()
rightFlatFoot = manager.getRightFlatFoot()
markerDiameter = manager.getMarkerDiameter()
calibrateFilenameLabelled = manager.getStaticTial()
if modelVersion == "CGM1.0":
model,finalAcqStatic = cgm1.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,required_mp,optional_mp,
leftFlatFoot,rightFlatFoot,markerDiameter,
pointSuffix)
elif modelVersion == "CGM1.1":
model,finalAcqStatic = cgm1_1.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,required_mp,optional_mp,
leftFlatFoot,rightFlatFoot,markerDiameter,
pointSuffix)
elif modelVersion == "CGM2.1":
hjcMethods = manager.getHJC()
hjcMethods["Left"] = "Hara" if hjcMethods["Left"] == [] else hjcMethods["Left"]
hjcMethods["Right"] = "Hara" if hjcMethods["Right"] == [] else hjcMethods["Right"]
model,finalAcqStatic = cgm2_1.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,required_mp,optional_mp,
leftFlatFoot,rightFlatFoot,markerDiameter,hjcMethods,
pointSuffix)
elif modelVersion == "CGM2.2":
hjcMethods = manager.getHJC()
hjcMethods["Left"] = "Hara" if hjcMethods["Left"] == [] else hjcMethods["Left"]
hjcMethods["Right"] = "Hara" if hjcMethods["Right"] == [] else hjcMethods["Right"]
model,finalAcqStatic = cgm2_2.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,settings,
required_mp,optional_mp,
True,leftFlatFoot,rightFlatFoot,markerDiameter,hjcMethods,
pointSuffix)
elif modelVersion == "CGM2.2e":
hjcMethods = manager.getHJC()
hjcMethods["Left"] = "Hara" if hjcMethods["Left"] == [] else hjcMethods["Left"]
hjcMethods["Right"] = "Hara" if hjcMethods["Right"] == [] else hjcMethods["Right"]
model,finalAcqStatic = cgm2_2e.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,settings,
required_mp,optional_mp,
True,leftFlatFoot,rightFlatFoot,markerDiameter,hjcMethods,
pointSuffix)
elif modelVersion == "CGM2.3":
hjcMethods = manager.getHJC()
hjcMethods["Left"] = "Hara" if hjcMethods["Left"] == [] else hjcMethods["Left"]
hjcMethods["Right"] = "Hara" if hjcMethods["Right"] == [] else hjcMethods["Right"]
model,finalAcqStatic = cgm2_3.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,settings,
required_mp,optional_mp,
ik_flag,leftFlatFoot,rightFlatFoot,markerDiameter,hjcMethods,
pointSuffix)
elif modelVersion == "CGM2.3e":
hjcMethods = manager.getHJC()
hjcMethods["Left"] = "Hara" if hjcMethods["Left"] == [] else hjcMethods["Left"]
hjcMethods["Right"] = "Hara" if hjcMethods["Right"] == [] else hjcMethods["Right"]
model,finalAcqStatic = cgm2_3e.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,settings,
required_mp,optional_mp,
ik_flag,leftFlatFoot,rightFlatFoot,markerDiameter,hjcMethods,
pointSuffix)
elif modelVersion == "CGM2.4":
hjcMethods = manager.getHJC()
hjcMethods["Left"] = "Hara" if hjcMethods["Left"] == [] else hjcMethods["Left"]
hjcMethods["Right"] = "Hara" if hjcMethods["Right"] == [] else hjcMethods["Right"]
model,finalAcqStatic = cgm2_4.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,settings,
required_mp,optional_mp,
ik_flag,leftFlatFoot,rightFlatFoot,markerDiameter,hjcMethods,
pointSuffix)
elif modelVersion == "CGM2.4e":
hjcMethods = manager.getHJC()
hjcMethods["Left"] = "Hara" if hjcMethods["Left"] == [] else hjcMethods["Left"]
hjcMethods["Right"] = "Hara" if hjcMethods["Right"] == [] else hjcMethods["Right"]
model,finalAcqStatic = cgm2_4e.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,settings,
required_mp,optional_mp,
ik_flag,leftFlatFoot,rightFlatFoot,markerDiameter,hjcMethods,
pointSuffix)
btkTools.smartWriter(finalAcqStatic, str(DATA_PATH_OUT+"calibrated.c3d"))
logging.info("Static Calibration -----> Done")
# knee calibration
leftEnable = manager.isKneeCalibrationEnable("Left")
rightEnable = manager.isKneeCalibrationEnable("Right")
if leftEnable:
method, trial,begin,end,jointRange = manager.getKneeCalibration("Left")
if method == "Calibration2Dof":
model,acqFunc,side = kneeCalibration.calibration2Dof(model,
DATA_PATH,trial,translators,
"Left",begin,end,jointRange)
logging.info("Left knee Calibration (Calibration2Dof) -----> Done")
elif method == "SARA":
model,acqFunc,side = kneeCalibration.sara(model,
DATA_PATH,trial,translators,
"Left",begin,end)
logging.info("Left knee Calibration (SARA) -----> Done")
if rightEnable:
method, trial,begin,end,jointRange = manager.getKneeCalibration("Right")
if method == "Calibration2Dof":
model,acqFunc,side = kneeCalibration.calibration2Dof(model,
DATA_PATH,trial,translators,
"Right",begin,end,jointRange)
logging.info("Right knee Calibration (Calibration2Dof) -----> Done")
elif method == "SARA":
model,acqFunc,side = kneeCalibration.sara(model,
DATA_PATH,trial,translators,
"Right",begin,end)
logging.info("Right knee Calibration (SARA) -----> Done")
# update mp
manager.updateMp(model)
# save settings
if manager.m_pipelineFile is not None:
manager.save(DATA_PATH,str( manager.m_pipelineFile+"-saved"))
logging.info("pipeline file -----> Save")
# Fitting
trials = manager.getFittingTrials()
momentProjection = manager.getMomentProjection()
if modelVersion not in ["CGM1.0", "CGM1.1", "CGM2.1"]:
ikwf = manager.getIkWeightFile()
if ikwf is not None:
ikWeight = files.openJson(DATA_PATH,ikwf)
settings["Fitting"]["Weight"]=ikWeight["Weight"]
for trial in trials:
mfpa = None if trial["Mfpa"] == "Auto" else trial["Mfpa"]
reconstructFilenameLabelled = trial["File"]
if modelVersion == "CGM1.0":
acqGait = cgm1.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,
markerDiameter,
pointSuffix,
mfpa,momentProjection)
elif modelVersion == "CGM1.1":
acqGait = cgm1_1.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,
markerDiameter,
pointSuffix,
mfpa,momentProjection)
elif modelVersion == "CGM2.1":
acqGait = cgm2_1.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,
markerDiameter,
pointSuffix,
mfpa,momentProjection)
elif modelVersion == "CGM2.2":
acqGait = cgm2_2.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,settings,
markerDiameter,
pointSuffix,
mfpa,
momentProjection)
elif modelVersion == "CGM2.2e":
acqGait = cgm2_2e.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,settings,
markerDiameter,
pointSuffix,
mfpa,
momentProjection)
elif modelVersion == "CGM2.3":
acqGait = cgm2_3.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,settings,
ik_flag,markerDiameter,
pointSuffix,
mfpa,
momentProjection)
elif modelVersion == "CGM2.3e":
acqGait = cgm2_3e.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,settings,
ik_flag,markerDiameter,
pointSuffix,
mfpa,
momentProjection)
elif modelVersion == "CGM2.4":
acqGait = cgm2_4.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,settings,
ik_flag,markerDiameter,
pointSuffix,
mfpa,
momentProjection)
elif modelVersion == "CGM2.4e":
acqGait = cgm2_4e.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,settings,
ik_flag,markerDiameter,
pointSuffix,
mfpa,
momentProjection)
logging.info("Fitting -----> Done")
if fileSuffix is not None:
c3dFilename = str(reconstructFilenameLabelled[:-4]+"-modelled-"+fileSuffix+".c3d")
else:
c3dFilename = str(reconstructFilenameLabelled[:-4]+"-modelled.c3d")
btkTools.smartWriter(acqGait, str(DATA_PATH_OUT+c3dFilename))
logging.info("c3d file (%s) generated" %(c3dFilename) )