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 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_4LowerLimbs()
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()
#import ipdb; ipdb.set_trace()
# ------ 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 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_4LowerLimbs()
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()
#import ipdb; ipdb.set_trace()
# ------ 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 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_4LowerLimbs()
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 CGM24(cls):
TRACKING_MARKERS = ["LASI", "RASI","RPSI", "LPSI",
"LTHI","LKNE","LTHAP","LTHAD",
"LTIB","LANK","LTIAP","LTIAD",
"LHEE","LTOE","LFMH","LVMH",
"RTHI","RKNE","RTHAP","RTHAD",
"RTIB","RANK","RTIAP","RTIAD",
"RHEE","RTOE","RFMH","RVMH"]
model=cgm2.CGM2_4LowerLimbs()
model.configure()
trackingMarkers = model.getTrackingMarkers()
np.testing.assert_equal(trackingMarkers,
TRACKING_MARKERS)
def CGM2_4_SARA_test(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.4\\Knee Calibration\\"
staticFilename = "static.c3d"
funcFilename = "functional.c3d"
gaitFilename = "gait trial 01.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,
}
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm2.CGM2_4LowerLimbs()
model.configure()
model.addAnthropoInputParameters(mp)
# --- INITIAL 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",
cgm1Behaviour=True)
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="both")
# final
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
seLeftHJCnode="LHJC_Hara",
useRightHJCnode="RHJC_Hara",
useLeftKJCnode="LKJC_mid",
useLeftAJCnode="LAJC_mid",
useRightKJCnode="RKJC_mid",
useRightAJCnode="RAJC_mid",
markerDiameter=markerDiameter).compute()
# ------ LEFT KNEE CALIBRATION -------
acqFunc = btkTools.smartReader(str(MAIN_PATH + funcFilename))
# Motion of only left
modMotionLeftKnee = modelFilters.ModelMotionFilter(
scp, acqFunc, model, pyCGM2Enums.motionMethod.Sodervisk)
modMotionLeftKnee.segmentalCompute(["Left Thigh", "Left Shank"])
# decorator
modelDecorator.KneeCalibrationDecorator(model).sara(
"Left", indexFirstFrame=831, indexLastFrame=1280)
# ----add Point into the c3d----
Or_inThigh = model.getSegment("Left Thigh").getReferential(
"TF").getNodeTrajectory("KneeFlexionOri")
axis_inThigh = model.getSegment("Left Thigh").getReferential(
"TF").getNodeTrajectory("KneeFlexionAxis")
btkTools.smartAppendPoint(acqFunc, "Left" + "_KneeFlexionOri",
Or_inThigh)
btkTools.smartAppendPoint(acqFunc, "Left" + "_KneeFlexionAxis",
axis_inThigh)
# ------ RIGHT KNEE CALIBRATION -------
# Motion of only left
modMotionRightKnee = modelFilters.ModelMotionFilter(
scp, acqFunc, model, pyCGM2Enums.motionMethod.Sodervisk)
modMotionRightKnee.segmentalCompute(["Right Thigh", "Right Shank"])
# decorator
modelDecorator.KneeCalibrationDecorator(model).sara("Right",
indexFirstFrame=61,
indexLastFrame=551)
# ----add Point into the c3d----
Or_inThigh = model.getSegment("Right Thigh").getReferential(
"TF").getNodeTrajectory("KneeFlexionOri")
axis_inThigh = model.getSegment("Right Thigh").getReferential(
"TF").getNodeTrajectory("KneeFlexionAxis")
btkTools.smartAppendPoint(acqFunc, "Right" + "_KneeFlexionOri",
Or_inThigh)
btkTools.smartAppendPoint(acqFunc, "Right" + "_KneeFlexionAxis",
axis_inThigh)
btkTools.smartWriter(acqFunc, "acqFunc-Sara.c3d")
#--- FINAL CALIBRATION ---
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
useLeftHJCnode="LHJC_Hara",
useRightHJCnode="RHJC_Hara",
useLeftKJCnode="KJC_Sara",
useLeftAJCnode="LAJC_mid",
useRightKJCnode="KJC_Sara",
useRightAJCnode="RAJC_mid",
markerDiameter=markerDiameter,
RotateLeftThighFlag=True,
RotateRightThighFlag=True).compute()
# save static c3d with update KJC
btkTools.smartWriter(acqStatic, "Static-SARA.c3d")
# ------ Fitting -------
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
# Motion FILTER
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", "RASI", "RPSI", "LPSI"])
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqGait,
segmentLabels=["Left HindFoot", "Right HindFoot", "Pelvis"],
angleLabels=["LFootProgress", "RFootProgress", "Pelvis"],
eulerSequences=["TOR", "TOR", "ROT"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix="cgm1_6dof")
# ------- OPENSIM IK --------------------------------------
# --- osim builder ---
cgmCalibrationprocedure = opensimFilters.CgmOpensimCalibrationProcedures(
model)
markersetFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_4\\cgm2_4-markerset.xml"
osimfile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\osim\\lowerLimb_ballsJoints.osim"
oscf = opensimFilters.opensimCalibrationFilter(
osimfile, model, cgmCalibrationprocedure)
oscf.addMarkerSet(markersetFile)
scalingOsim = oscf.build(exportOsim=False)
# --- fitting ---
#procedure
cgmFittingProcedure = opensimFilters.CgmOpensimFittingProcedure(model)
iksetupFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_4\\cgm2_4-ikSetUp_template.xml"
osrf = opensimFilters.opensimFittingFilter(iksetupFile, scalingOsim,
cgmFittingProcedure,
MAIN_PATH)
acqIK = osrf.run(acqGait,
str(MAIN_PATH + gaitFilename),
exportSetUp=False)
# -------- NEW MOTION FILTER ON IK MARKERS ------------------
modMotion_ik = modelFilters.ModelMotionFilter(
scp,
acqIK,
model,
pyCGM2Enums.motionMethod.Sodervisk,
useForMotionTest=True)
modMotion_ik.compute()
finalJcs = modelFilters.ModelJCSFilter(model, acqIK)
finalJcs.setFilterBool(False)
finalJcs.compute(description="ik", pointLabelSuffix="2_ik") #
btkTools.smartWriter(acqIK, "gait trial 01 - Fitting.c3d")
def calibrate(DATA_PATH,calibrateFilenameLabelled,translators,settings,
required_mp,optional_mp,
ik_flag,leftFlatFoot,rightFlatFoot,markerDiameter,hjcMethod,
pointSuffix):
# ---btk acquisition---
acqStatic = btkTools.smartReader(str(DATA_PATH+calibrateFilenameLabelled))
btkTools.checkMultipleSubject(acqStatic)
acqStatic = btkTools.applyTranslators(acqStatic,translators)
validFrames,vff,vlf = btkTools.findValidFrames(acqStatic,cgm2.CGM2_4LowerLimbs.TRACKING_MARKERS)
# --------------------------MODEL--------------------------------------
# ---definition---
model=cgm2.CGM2_4LowerLimbs()
model.configure()
model.addAnthropoInputParameters(required_mp,optional=optional_mp)
# --store calibration parameters--
model.setStaticFilename(calibrateFilenameLabelled)
model.setCalibrationProperty("leftFlatFoot",leftFlatFoot)
model.setCalibrationProperty("rightFlatFoot",rightFlatFoot)
model.setCalibrationProperty("markerDiameter",markerDiameter)
# ---check marker set used----
smc = cgm.CGM.checkCGM1_StaticMarkerConfig(acqStatic)
# --------------------------STATIC CALBRATION--------------------------
scp=modelFilters.StaticCalibrationProcedure(model) # load calibration procedure
# ---initial calibration filter----
# use if all optional mp are zero
modelFilters.ModelCalibrationFilter(scp,acqStatic,model,
leftFlatFoot = leftFlatFoot, rightFlatFoot = rightFlatFoot,
markerDiameter=markerDiameter,
).compute()
# ---- Decorators -----
decorators.applyDecorators_CGM(smc, model,acqStatic,optional_mp,markerDiameter)
decorators.applyHJCDecorators(model,hjcMethod)
# ----Final Calibration filter if model previously decorated -----
if model.decoratedModel:
# initial static filter
modelFilters.ModelCalibrationFilter(scp,acqStatic,model,
leftFlatFoot = leftFlatFoot, rightFlatFoot = rightFlatFoot,
markerDiameter=markerDiameter).compute()
# ----------------------CGM MODELLING----------------------------------
# ----motion filter----
modMotion=modelFilters.ModelMotionFilter(scp,acqStatic,model,enums.motionMethod.Sodervisk,
markerDiameter=markerDiameter)
modMotion.compute()
if ik_flag:
# ---OPENSIM IK---
# --- opensim calibration Filter ---
osimfile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\osim\\lowerLimb_ballsJoints.osim" # osimfile
markersetFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_4\\cgm2_4-markerset.xml" # markerset
cgmCalibrationprocedure = opensimFilters.CgmOpensimCalibrationProcedures(model) # procedure
oscf = opensimFilters.opensimCalibrationFilter(osimfile,
model,
cgmCalibrationprocedure,
str(DATA_PATH))
oscf.addMarkerSet(markersetFile)
scalingOsim = oscf.build()
# --- opensim Fitting Filter ---
iksetupFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_4\\cgm2_4-ikSetUp_template.xml" # ik tool file
cgmFittingProcedure = opensimFilters.CgmOpensimFittingProcedure(model) # procedure
cgmFittingProcedure.updateMarkerWeight("LASI",settings["Fitting"]["Weight"]["LASI"])
cgmFittingProcedure.updateMarkerWeight("RASI",settings["Fitting"]["Weight"]["RASI"])
cgmFittingProcedure.updateMarkerWeight("LPSI",settings["Fitting"]["Weight"]["LPSI"])
cgmFittingProcedure.updateMarkerWeight("RPSI",settings["Fitting"]["Weight"]["RPSI"])
cgmFittingProcedure.updateMarkerWeight("RTHI",settings["Fitting"]["Weight"]["RTHI"])
cgmFittingProcedure.updateMarkerWeight("RKNE",settings["Fitting"]["Weight"]["RKNE"])
cgmFittingProcedure.updateMarkerWeight("RTIB",settings["Fitting"]["Weight"]["RTIB"])
cgmFittingProcedure.updateMarkerWeight("RANK",settings["Fitting"]["Weight"]["RANK"])
cgmFittingProcedure.updateMarkerWeight("RHEE",settings["Fitting"]["Weight"]["RHEE"])
cgmFittingProcedure.updateMarkerWeight("RTOE",settings["Fitting"]["Weight"]["RTOE"])
cgmFittingProcedure.updateMarkerWeight("LTHI",settings["Fitting"]["Weight"]["LTHI"])
cgmFittingProcedure.updateMarkerWeight("LKNE",settings["Fitting"]["Weight"]["LKNE"])
cgmFittingProcedure.updateMarkerWeight("LTIB",settings["Fitting"]["Weight"]["LTIB"])
cgmFittingProcedure.updateMarkerWeight("LANK",settings["Fitting"]["Weight"]["LANK"])
cgmFittingProcedure.updateMarkerWeight("LHEE",settings["Fitting"]["Weight"]["LHEE"])
cgmFittingProcedure.updateMarkerWeight("LTOE",settings["Fitting"]["Weight"]["LTOE"])
cgmFittingProcedure.updateMarkerWeight("LTHAP",settings["Fitting"]["Weight"]["LTHAP"])
cgmFittingProcedure.updateMarkerWeight("LTHAD",settings["Fitting"]["Weight"]["LTHAD"])
cgmFittingProcedure.updateMarkerWeight("LTIAP",settings["Fitting"]["Weight"]["LTIAP"])
cgmFittingProcedure.updateMarkerWeight("LTIAD",settings["Fitting"]["Weight"]["LTIAD"])
cgmFittingProcedure.updateMarkerWeight("RTHAP",settings["Fitting"]["Weight"]["RTHAP"])
cgmFittingProcedure.updateMarkerWeight("RTHAD",settings["Fitting"]["Weight"]["RTHAD"])
cgmFittingProcedure.updateMarkerWeight("RTIAP",settings["Fitting"]["Weight"]["RTIAP"])
cgmFittingProcedure.updateMarkerWeight("RTIAD",settings["Fitting"]["Weight"]["RTIAD"])
cgmFittingProcedure.updateMarkerWeight("LSMH",settings["Fitting"]["Weight"]["LSMH"])
cgmFittingProcedure.updateMarkerWeight("LFMH",settings["Fitting"]["Weight"]["LFMH"])
cgmFittingProcedure.updateMarkerWeight("LVMH",settings["Fitting"]["Weight"]["LVMH"])
cgmFittingProcedure.updateMarkerWeight("RSMH",settings["Fitting"]["Weight"]["RSMH"])
cgmFittingProcedure.updateMarkerWeight("RFMH",settings["Fitting"]["Weight"]["RFMH"])
cgmFittingProcedure.updateMarkerWeight("RVMH",settings["Fitting"]["Weight"]["RVMH"])
# cgmFittingProcedure.updateMarkerWeight("LTHL",settings["Fitting"]["Weight"]["LTHL"])
# cgmFittingProcedure.updateMarkerWeight("LTHLD",settings["Fitting"]["Weight"]["LTHLD"])
# cgmFittingProcedure.updateMarkerWeight("LPAT",settings["Fitting"]["Weight"]["LPAT"])
# cgmFittingProcedure.updateMarkerWeight("LTIBL",settings["Fitting"]["Weight"]["LTIBL"])
# cgmFittingProcedure.updateMarkerWeight("RTHL",settings["Fitting"]["Weight"]["RTHL"])
# cgmFittingProcedure.updateMarkerWeight("RTHLD",settings["Fitting"]["Weight"]["RTHLD"])
# cgmFittingProcedure.updateMarkerWeight("RPAT",settings["Fitting"]["Weight"]["RPAT"])
# cgmFittingProcedure.updateMarkerWeight("RTIBL",settings["Fitting"]["Weight"]["RTIBL"])
osrf = opensimFilters.opensimFittingFilter(iksetupFile,
scalingOsim,
cgmFittingProcedure,
str(DATA_PATH) )
acqStaticIK = osrf.run(acqStatic,str(DATA_PATH + calibrateFilenameLabelled ))
# eventual static acquisition to consider for joint kinematics
finalAcqStatic = acqStaticIK if ik_flag else acqStatic
# --- final pyCGM2 model motion Filter ---
# use fitted markers
modMotionFitted=modelFilters.ModelMotionFilter(scp,finalAcqStatic,model,enums.motionMethod.Sodervisk)
modMotionFitted.compute()
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model,finalAcqStatic).compute(description="vectoriel", pointLabelSuffix=pointSuffix)
# detection of traveling axis
longitudinalAxis,forwardProgression,globalFrame = btkTools.findProgressionAxisFromPelvicMarkers(finalAcqStatic,["LASI","RASI","RPSI","LPSI"])
# absolute angles
modelFilters.ModelAbsoluteAnglesFilter(model,finalAcqStatic,
segmentLabels=["Left Foot","Right Foot","Pelvis"],
angleLabels=["LFootProgress", "RFootProgress","Pelvis"],
eulerSequences=["TOR","TOR", "ROT"],
globalFrameOrientation = globalFrame,
forwardProgression = forwardProgression).compute(pointLabelSuffix=pointSuffix)
return model, finalAcqStatic
def full_IK(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.4\\fullBody\\"
staticFilename = "PN01OP01S01STAT.c3d"
gaitFilename = "PN01OP01S01SS01.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_4LowerLimbs()
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).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()
# ------- OPENSIM IK --------------------------------------
# --- osim builder ---
cgmCalibrationprocedure = opensimFilters.CgmOpensimCalibrationProcedures(
model)
markersetFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_4\\cgm2_4-markerset.xml"
osimfile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\osim\\lowerLimb_ballsJoints.osim"
oscf = opensimFilters.opensimCalibrationFilter(
osimfile, model, cgmCalibrationprocedure, MAIN_PATH)
oscf.addMarkerSet(markersetFile)
scalingOsim = oscf.build(exportOsim=False)
# --- fitting ---
#procedure
cgmFittingProcedure = opensimFilters.CgmOpensimFittingProcedure(model)
iksetupFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_4\\cgm2_4-ikSetUp_template.xml"
osrf = opensimFilters.opensimFittingFilter(iksetupFile, scalingOsim,
cgmFittingProcedure,
MAIN_PATH)
acqIK = osrf.run(acqGait,
str(MAIN_PATH + gaitFilename),
exportSetUp=False)
# -------- NEW MOTION FILTER ON IK MARKERS ------------------
modMotion_ik = modelFilters.ModelMotionFilter(
scp,
acqIK,
model,
enums.motionMethod.Sodervisk,
useForMotionTest=True)
modMotion_ik.compute()
finalJcs = modelFilters.ModelJCSFilter(model, acqIK)
finalJcs.setFilterBool(False)
finalJcs.compute(description="ik", pointLabelSuffix="2_ik") #
btkTools.smartWriter(acqIK, "cgm24_fullIK_Motion.c3d")
def full_IK(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.4\\medial\\"
staticFilename = "static.c3d"
gaitFilename = "gait Trial 01.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_4LowerLimbs()
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).compute()
# ------ Fitting -------
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
# Motion FILTER
modMotion = modelFilters.ModelMotionFilter(
scp, acqGait, model, pyCGM2Enums.motionMethod.Sodervisk)
modMotion.compute()
# relative angles
modelFilters.ModelJCSFilter(model, acqGait).compute(
description="vectoriel", pointLabelSuffix="cgm1_6dof")
# absolute angles
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromPelvicMarkers(
acqGait, ["LASI", "RASI", "RPSI", "LPSI"])
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqGait,
segmentLabels=["Left Foot", "Right Foot", "Pelvis"],
angleLabels=["LFootProgress", "RFootProgress", "Pelvis"],
eulerSequences=["TOR", "TOR", "ROT"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix="cgm1_6dof")
# ---Marker decomp filter----
mtf = modelFilters.TrackingMarkerDecompositionFilter(model, acqGait)
mtf.decompose()
# ------- OPENSIM IK --------------------------------------
# --- osim builder ---
cgmCalibrationprocedure = opensimFilters.CgmOpensimCalibrationProcedures(
model)
markersetFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_4\\cgm2_4-markerset - expert.xml"
osimfile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\osim\\lowerLimb_ballsJoints.osim"
oscf = opensimFilters.opensimCalibrationFilter(
osimfile, model, cgmCalibrationprocedure, MAIN_PATH)
oscf.addMarkerSet(markersetFile)
scalingOsim = oscf.build(exportOsim=False)
# --- fitting ---
#procedure
cgmFittingProcedure = opensimFilters.CgmOpensimFittingProcedure(
model, expertMode=True)
iksetupFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_4\\cgm2_4-expert-ikSetUp_template.xml"
osrf = opensimFilters.opensimFittingFilter(iksetupFile, scalingOsim,
cgmFittingProcedure,
MAIN_PATH)
acqIK = osrf.run(acqGait,
str(MAIN_PATH + gaitFilename),
exportSetUp=False)
# -------- NEW MOTION FILTER ON IK MARKERS ------------------
modMotion_ik = modelFilters.ModelMotionFilter(
scp,
acqIK,
model,
pyCGM2Enums.motionMethod.Sodervisk,
useForMotionTest=True)
modMotion_ik.compute()
finalJcs = modelFilters.ModelJCSFilter(model, acqIK)
finalJcs.setFilterBool(False)
finalJcs.compute(description="ik", pointLabelSuffix="2_ik") #
btkTools.smartWriter(acqIK, "cgm24e_fullIK.c3d")
