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 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 full_IK(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.3\\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_3.translators")
acqStatic = btkTools.applyTranslators(acqStatic, translators)
model = cgm2.CGM2_3LowerLimbs()
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_3\\cgm2_3-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_3\\cgm2_3-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, "cgm23_fullIK_Motion.c3d")
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 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 kinematicFitting_oneFile_cgmProcedure(cls):
DATA_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\LowerLimb\\subject10_S1A1_julieDataSet_noModelOutputs\\"
config = dict()
config["static"] = "StaticR010S1A1.c3d"
config["dynamicTrial"] = [
"R010S1A1Gait001.c3d", "R010S1A1Gait003.c3d",
"R010S1A1Gait004.c3d", "R010S1A1Gait005.c3d",
"R010S1A1Gait007.c3d", "R010S1A1Gait010.c3d"
]
configMP = {
"Bodymass": 64.0,
"LeftLegLength": 865.0,
"RightLegLength": 855.0,
"LeftKneeWidth": 100.0,
"RightKneeWidth": 101.0,
"LeftAnkleWidth": 69.0,
"RightAnkleWidth": 69.0
}
requiredMarkers = [
"LASI", "RASI", "LPSI", "RPSI", "RTHIAP", "RTHIAD", "RTHI", "RKNE",
"RSHN", "RTIAP", "RTIB", "RANK", "RHEE", "RTOE", "RCUN", "RD1M",
"RD5M"
]
acqStatic = btkTools.smartReader(DATA_PATH + config["static"])
# model
model = cgm2Julie.CGM2ModelInf()
model.configure()
markerDiameter = 14
mp = {
'Bodymass': configMP["Bodymass"],
'LeftLegLength': configMP["LeftLegLength"],
'RightLegLength': configMP["RightLegLength"],
'LeftKneeWidth': configMP["LeftKneeWidth"],
'RightKneeWidth': configMP["RightKneeWidth"],
'LeftAnkleWidth': configMP["LeftAnkleWidth"],
'RightAnkleWidth': configMP["RightAnkleWidth"],
}
#offset 2ndToe Joint
toe = acqStatic.GetPoint("RTOE").GetValues()[:, :].mean(axis=0)
mp["rightToeOffset"] = (toe[2] - markerDiameter / 2.0) / 2.0
model.addAnthropoInputParameters(mp)
# -----------CGM STATIC CALIBRATION--------------------
# --- Initial calibration
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(
scp, acqStatic, model,
rightFlatHindFoot=True).compute() # Initial calibration
# --- decorator
modelDecorator.KneeCalibrationDecorator(model).midCondyles(
acqStatic, leftMedialKneeLabel="LKNM", rightMedialKneeLabel="RKNM")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic,
leftMedialAnkleLabel="LMMA",
rightMedialAnkleLabel="RMMA")
# --- Updated calibration
modelFilters.ModelCalibrationFilter(scp,
acqStatic,
model,
useLeftKJCnode="LKJC_mid",
useRightKJCnode="RKJC_mid",
useLeftAJCnode="LAJC_mid",
useRightAJCnode="RAJC_mid",
rightFlatHindFoot=True).compute()
# ---- optional -update static c3d
#btkTools.smartWriter(acqStatic, "StaticCalibrated.c3d")
# -----------CGM MOTION 6dof--------------------
# --- reader and checking
acqGait = btkTools.smartReader(DATA_PATH + config["dynamicTrial"][0])
btkTools.checkMarkers(acqGait, requiredMarkers)
btkTools.isGap(acqGait, requiredMarkers)
btkTools.checkFirstAndLastFrame(acqGait, "LASI")
logging.info("dyn Acquisition ---> OK ")
# --- filters
modMotion = modelFilters.ModelMotionFilter(
scp, acqGait, model, pyCGM2Enums.motionMethod.Determinist)
modMotion.compute()
modelFilters.ModelJCSFilter(model,
acqGait).compute(description="vectoriel",
pointLabelSuffix="2_6dof")
# --- writer
#btkTools.smartWriter(acqGait, "motionCalibrated.c3d")
# ------- OPENSIM IK --------------------------------------
cgmprocedure = opensimFilters.CgmOpensimCalibrationProcedures(model)
markersetFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\draft-opensimPreProcessing\\cgm2-markerset.xml"
osimfile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\draft-opensimPreProcessing\\cgm2-model.osim"
oscf = opensimFilters.opensimCalibrationFilter(osimfile, model,
cgmprocedure)
oscf.addMarkerSet(markersetFile)
fittingOsim = oscf.build()
filename = config["dynamicTrial"][0]
cgmFittingProcedure = opensimFilters.CgmOpensimFittingProcedure(model)
cgmFittingProcedure.updateMarkerWeight("LASI", 100)
iksetupFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\draft-opensimPreProcessing\\ikSetUp_template.xml"
osrf = opensimFilters.opensimFittingFilter(iksetupFile, fittingOsim,
cgmFittingProcedure,
DATA_PATH)
acqIK = osrf.run(acqGait, str(DATA_PATH + filename))
# -------- NEW MOTION FILTER ON IK MARKERS ------------------
modMotion_ik = modelFilters.ModelMotionFilter(
scp, acqIK, model, pyCGM2Enums.motionMethod.Sodervisk)
modMotion_ik.compute()
finalJcs = modelFilters.ModelJCSFilter(model, acqIK)
finalJcs.setFilterBool(False)
finalJcs.compute(description="ik", pointLabelSuffix="2_ik") #
# recup du mot file
motFilename = str(DATA_PATH + config["dynamicTrial"][0][:-4] + ".mot")
comparisonOpensimVsCGM(motFilename, acqIK, "2_ik")
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_4()
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")
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, enums.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, enums.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).compute()
# save static c3d with update KJC
btkTools.smartWriter(acqStatic, "Static-SARA.c3d")
# print functional Offsets
print model.mp_computed["LeftKneeFuncCalibrationOffset"]
print model.mp_computed["RightKneeFuncCalibrationOffset"]
def sara(model, DATA_PATH, reconstructFilenameLabelled, translators, side,
beginFrame, endFrame, **kwargs):
# --- btk acquisition ----
if "forceBtkAcq" in kwargs.keys():
acqFunc = kwargs["forceBtkAcq"]
else:
acqFunc = btkTools.smartReader(
str(DATA_PATH + reconstructFilenameLabelled))
btkTools.checkMultipleSubject(acqFunc)
acqFunc = btkTools.applyTranslators(acqFunc, translators)
#---get frame range of interest---
ff = acqFunc.GetFirstFrame()
lf = acqFunc.GetLastFrame()
start, end = btkTools.getStartEndEvents(acqFunc, side)
if start is not None:
logging.info("Start event detected")
initFrame = start
else:
initFrame = beginFrame if beginFrame is not None else ff
if end is not None:
logging.info("End event detected")
endFrame = end
else:
endFrame = endFrame if endFrame is not None else lf
iff = initFrame - ff
ilf = endFrame - ff
#---motion side of the lower limb---
if side is None:
side = detectSide(acqFunc, "LANK", "RANK")
logging.info("Detected motion side : %s" % (side))
# --------------------------RESET OF THE STATIC File---------
# load btkAcq from static file
staticFilename = model.m_staticFilename
acqStatic = btkTools.smartReader(str(DATA_PATH + staticFilename))
btkTools.checkMultipleSubject(acqStatic)
acqStatic = btkTools.applyTranslators(acqStatic, translators)
# initial calibration ( i.e calibration from Calibration operation)
leftFlatFoot = model.m_properties["CalibrationParameters"]["leftFlatFoot"]
rightFlatFoot = model.m_properties["CalibrationParameters"][
"rightFlatFoot"]
markerDiameter = model.m_properties["CalibrationParameters"][
"markerDiameter"]
headFlat = model.m_properties["CalibrationParameters"]["headFlat"]
if side == "Left":
model.mp_computed["LeftKneeFuncCalibrationOffset"] = 0
if side == "Right":
model.mp_computed["RightKneeFuncCalibrationOffset"] = 0
# initial calibration ( zero previous KneeFunc offset on considered side )
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
headFlat=headFlat,
markerDiameter=markerDiameter).compute()
if model.version in ["CGM2.3", "CGM2.4", "CGM2.5"]:
if side == "Left":
thigh_markers = model.getSegment("Left Thigh").m_tracking_markers
shank_markers = model.getSegment("Left Shank").m_tracking_markers
elif side == "Right":
thigh_markers = model.getSegment("Right Thigh").m_tracking_markers
shank_markers = model.getSegment("Right Shank").m_tracking_markers
validFrames, vff, vlf = btkTools.findValidFrames(
acqFunc, thigh_markers + shank_markers)
proximalSegmentLabel = str(side + " Thigh")
distalSegmentLabel = str(side + " Shank")
# segment Motion
modMotion = modelFilters.ModelMotionFilter(
scp, acqFunc, model, enums.motionMethod.Sodervisk)
modMotion.segmentalCompute([proximalSegmentLabel, distalSegmentLabel])
# decorator
modelDecorator.KneeCalibrationDecorator(model).sara(
side, indexFirstFrame=iff, indexLastFrame=ilf)
# --------------------------FINAL CALIBRATION OF THE STATIC File---------
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
headFlat=headFlat,
markerDiameter=markerDiameter).compute()
return model, acqFunc, side
def calibration2Dof(model, DATA_PATH, reconstructFilenameLabelled, translators,
side, beginFrame, endFrame, jointRange):
acqFunc = btkTools.smartReader(str(DATA_PATH +
reconstructFilenameLabelled))
btkTools.checkMultipleSubject(acqFunc)
acqFunc = btkTools.applyTranslators(acqFunc, translators)
#---get frame range of interest---
ff = acqFunc.GetFirstFrame()
lf = acqFunc.GetLastFrame()
initFrame = beginFrame if beginFrame is not None else ff
endFrame = endFrame if endFrame is not None else lf
iff = initFrame - ff
ilf = endFrame - ff
# motion
if side is None:
side = detectSide(acqFunc, "LANK", "RANK")
logging.info("Detected motion side : %s" % (side))
if model.version in ["CGM1.0", "CGM1.1", "CGM2.1", "CGM2.2", "CGM2.2e"]:
validFrames, vff, vlf = btkTools.findValidFrames(
acqFunc, cgm.CGM1LowerLimbs.TRACKING_MARKERS)
# --------------------------RESET OF THE STATIC File---------
# load btkAcq from static file
staticFilename = model.m_staticFilename
acqStatic = btkTools.smartReader(str(DATA_PATH + staticFilename))
btkTools.checkMultipleSubject(acqStatic)
acqStatic = btkTools.applyTranslators(acqStatic, translators)
# initial calibration ( i.e calibration from Calibration operation)
leftFlatFoot = model.m_properties["CalibrationParameters"]["leftFlatFoot"]
rightFlatFoot = model.m_properties["CalibrationParameters"][
"rightFlatFoot"]
markerDiameter = model.m_properties["CalibrationParameters"][
"markerDiameter"]
if side == "Left":
# remove other functional calibration
model.mp_computed["LeftKneeFuncCalibrationOffset"] = 0
if side == "Right":
# remove other functional calibration
model.mp_computed["RightKneeFuncCalibrationOffset"] = 0
# no rotation on both thigh - re init anatonical frame
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
markerDiameter=markerDiameter).compute()
if model.version in ["CGM1.0", "CGM1.1", "CGM2.1", "CGM2.2", "CGM2.2e"]:
modMotion = modelFilters.ModelMotionFilter(
scp, acqFunc, model, enums.motionMethod.Determinist)
modMotion.compute()
elif model.version in ["CGM2.3", "CGM2.3e", "CGM2.4", "CGM2.4e"]:
if side == "Left":
thigh_markers = model.getSegment("Left Thigh").m_tracking_markers
shank_markers = model.getSegment("Left Shank").m_tracking_markers
elif side == "Right":
thigh_markers = model.getSegment("Right Thigh").m_tracking_markers
shank_markers = model.getSegment("Right Shank").m_tracking_markers
validFrames, vff, vlf = btkTools.findValidFrames(
acqFunc, thigh_markers + shank_markers)
proximalSegmentLabel = str(side + " Thigh")
distalSegmentLabel = str(side + " Shank")
# Motion
modMotion = modelFilters.ModelMotionFilter(
scp, acqFunc, model, enums.motionMethod.Sodervisk)
modMotion.segmentalCompute([proximalSegmentLabel, distalSegmentLabel])
# calibration decorators
modelDecorator.KneeCalibrationDecorator(model).calibrate2dof(
side, indexFirstFrame=iff, indexLastFrame=ilf, jointRange=jointRange)
# --------------------------FINAL CALIBRATION OF THE STATIC File---------
# ---- Calibration
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
markerDiameter=markerDiameter).compute()
return model, acqFunc, side
# --- Calibration ---
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm2.CGM2_2LowerLimbs()
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.Determinist)
modMotion.compute()
def test_lowLevel(self):
DATA_PATH = pyCGM2.TEST_DATA_PATH + "GaitModels\CGM2.3\\Hannibal-medial\\"
staticFilename = "static.c3d"
gaitFilename= "gait1.c3d"
markerDiameter=14
required_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,
'LeftShoulderOffset' : 0,
'RightShoulderOffset' : 0,
'LeftElbowWidth' : 0,
'LeftWristWidth' : 0,
'LeftHandThickness' : 0,
'RightElbowWidth' : 0,
'RightWristWidth' : 0,
'RightHandThickness' : 0
}
optional_mp = {
'LeftTibialTorsion' : 0,
'LeftThighRotation' : 0,
'LeftShankRotation' : 0,
'RightTibialTorsion' : 0,
'RightThighRotation' : 0,
'RightShankRotation' : 0
}
# --- Calibration ---
# ---check marker set used----
acqStatic = btkTools.smartReader(DATA_PATH + staticFilename)
dcm = cgm.CGM.detectCalibrationMethods(acqStatic)
model=cgm2.CGM2_3()
model.configure(detectedCalibrationMethods=dcm)
model.addAnthropoInputParameters(required_mp,optional=optional_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(DATA_PATH + gaitFilename)
# 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_3\\cgm2_3-markerset.xml"
osimfile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\osim\\lowerLimb_ballsJoints.osim"
oscf = opensimFilters.opensimCalibrationFilter(osimfile,
model,
cgmCalibrationprocedure,
DATA_PATH)
oscf.addMarkerSet(markersetFile)
scalingOsim = oscf.build(exportOsim=False)
# --- fitting ---
#procedure
cgmFittingProcedure = opensimFilters.CgmOpensimFittingProcedure(model)
iksetupFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_3\\cgm2_3-ikSetUp_template.xml"
osrf = opensimFilters.opensimFittingFilter(iksetupFile,
scalingOsim,
cgmFittingProcedure,
DATA_PATH,
acqGait )
acqIK = osrf.run(str(DATA_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.compute(description="ik", pointLabelSuffix = "2_ik")#
btkTools.smartWriter(acqIK,"cgm23_fullIK_Motion.c3d")
def calibrate(self, aquiStatic, dictRef, dictAnatomic, options=None):
# add markers
valSACR = (aquiStatic.GetPoint("LPSI").GetValues() +
aquiStatic.GetPoint("RPSI").GetValues()) / 2.0
btkTools.smartAppendPoint(aquiStatic, "SACR", valSACR, desc="")
valMidAsis = (aquiStatic.GetPoint("LASI").GetValues() +
aquiStatic.GetPoint("RASI").GetValues()) / 2.0
btkTools.smartAppendPoint(aquiStatic, "midASIS", valMidAsis, desc="")
valLMET = (aquiStatic.GetPoint("LFMH").GetValues() +
aquiStatic.GetPoint("LVMH").GetValues()) / 2.0
btkTools.smartAppendPoint(aquiStatic, "LMET", valLMET, desc="")
valRMET = (aquiStatic.GetPoint("RFMH").GetValues() +
aquiStatic.GetPoint("RVMH").GetValues()) / 2.0
btkTools.smartAppendPoint(aquiStatic, "RMET", valRMET, desc="")
ff = aquiStatic.GetFirstFrame()
lf = aquiStatic.GetLastFrame()
frameInit = ff - ff
frameEnd = lf - ff + 1
# calibrate technical
self._calibrateTechnicalSegment(aquiStatic,
"Pelvis",
dictRef,
frameInit,
frameEnd,
options=options)
self._calibrateTechnicalSegment(aquiStatic,
"Left Thigh",
dictRef,
frameInit,
frameEnd,
options=options)
self._calibrateTechnicalSegment(aquiStatic,
"Right Thigh",
dictRef,
frameInit,
frameEnd,
options=options)
self._calibrateTechnicalSegment(aquiStatic,
"Left Shank",
dictRef,
frameInit,
frameEnd,
options=options)
self._calibrateTechnicalSegment(aquiStatic,
"Right Shank",
dictRef,
frameInit,
frameEnd,
options=options)
self._calibrateTechnicalSegment(aquiStatic,
"Left Foot",
dictRef,
frameInit,
frameEnd,
options=options)
self._calibrateTechnicalSegment(aquiStatic,
"Right Foot",
dictRef,
frameInit,
frameEnd,
options=options)
# # ---- decorator ----
modelDecorator.HipJointCenterDecorator(self).greatTrochanterOffset(
aquiStatic)
modelDecorator.KneeCalibrationDecorator(self).midCondyles(aquiStatic)
modelDecorator.AnkleCalibrationDecorator(self).midMaleolus(aquiStatic)
# calibrate anatomic
self._calibrateAnatomicalSegment(aquiStatic,
"Pelvis",
dictAnatomic,
frameInit,
frameEnd,
options=options)
self._calibrateAnatomicalSegment(aquiStatic,
"Left Thigh",
dictAnatomic,
frameInit,
frameEnd,
options=options)
self._calibrateAnatomicalSegment(aquiStatic,
"Right Thigh",
dictAnatomic,
frameInit,
frameEnd,
options=options)
self._calibrateAnatomicalSegment(aquiStatic,
"Left Shank",
dictAnatomic,
frameInit,
frameEnd,
options=options)
self._calibrateAnatomicalSegment(aquiStatic,
"Right Shank",
dictAnatomic,
frameInit,
frameEnd,
options=options)
self._calibrateAnatomicalSegment(aquiStatic,
"Left Foot",
dictAnatomic,
frameInit,
frameEnd,
options=options)
self._calibrateAnatomicalSegment(aquiStatic,
"Right Foot",
dictAnatomic,
frameInit,
frameEnd,
options=options)
# -*- coding: utf-8 -*-
import logging
from argparse import Namespace
import os
from tkFileDialog import askopenfilenames, askopenfilename
from extraction_enf import extraction_enf as extraction_enf
from extract_metaData_pycgm2 import extract_metaData_pycgm2 as extract_metaData_pycgm2
from extraction_name_enf import extraction_name_enf as extraction_name_enf
# pyCGM2 libraries
import pyCGM2
# from pyCGM2 import enums
from pyCGM2.Model.CGM2.coreApps import cgm2_1, cgmUtils
from pyCGM2.Model import modelDecorator
from pyCGM2.Tools import btkTools
from pyCGM2.Utils import files
# from pyCGM2.Eclipse import vskTools
from shutil import copy2
# test decorator
cgm2_1_DynaKad = modelDecorator.KneeCalibrationDecorator(cgm2_1).calibrate2dof('Left')
cgm2_1_DynaKad.calibrate2dof('Left')
cgm2_1_DynaKad.calibrate2dof('Right')
def CGM23_2DOF_test(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.3\\Knee Calibration\\"
staticFilename = "Static.c3d"
leftKneeFilename = "Left Knee.c3d"
rightKneeFilename = "Right Knee.c3d"
gaitFilename = "gait trial 01.c3d"
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,
}
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm2.CGM2_3()
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")
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 -------
acqLeftKnee = btkTools.smartReader(str(MAIN_PATH + leftKneeFilename))
# Motion of only left
modMotionLeftKnee = modelFilters.ModelMotionFilter(
scp, acqLeftKnee, model, enums.motionMethod.Sodervisk)
modMotionLeftKnee.segmentalCompute(["Left Thigh", "Left Shank"])
# decorator
modelDecorator.KneeCalibrationDecorator(model).calibrate2dof(
"Left", indexFirstFrame=489, indexLastFrame=1451)
# ----add Point into the c3d----
btkTools.smartWriter(acqLeftKnee, "Left Knee-2dof.c3d")
# ------ RIGHT KNEE CALIBRATION -------
acqRightKnee = btkTools.smartReader(str(MAIN_PATH + rightKneeFilename))
# Motion of only left
modMotionRightKnee = modelFilters.ModelMotionFilter(
scp, acqRightKnee, model, enums.motionMethod.Sodervisk)
modMotionRightKnee.segmentalCompute(["Right Thigh", "Right Shank"])
# decorator
modelDecorator.KneeCalibrationDecorator(model).calibrate2dof(
"Right", indexFirstFrame=25, indexLastFrame=1060)
# ----add Point into the c3d----
btkTools.smartWriter(acqRightKnee, "Right Knee-2dof.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).compute()
# save static c3d with update KJC
btkTools.smartWriter(acqStatic, "Static-2DOF.c3d")
def noIK_6dof(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.3\\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_3.translators")
acqStatic = btkTools.applyTranslators(acqStatic, translators)
model = cgm2.CGM2_3LowerLimbs()
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()
csp = modelFilters.ModelCoordinateSystemProcedure(model)
modelFilters.CoordinateSystemDisplayFilter(csp, model,
acqGait).display()
btkTools.smartWriter(acqGait, "cgm23_noIK6dof_Motion.c3d")
"TF",
sequence="ZXY",
pointLabel1="RSMH",
pointLabel2="RHEE",
pointLabel3="RVMH",
pointLabelOrigin="RHEE")
#---Initial Calibration Filter---
smf0 = modelFilters.ModelCalibrationFilter(gcp, acqStatic, bioMechModel)
smf0.setBoolOption("technicalReferentialOnly")
smf0.compute()
# ---- decorator ----
modelDecorator.HipJointCenterDecorator(bioMechModel).greatTrochanterOffset(
acqStatic)
modelDecorator.KneeCalibrationDecorator(bioMechModel).midCondyles(
acqStatic)
modelDecorator.AnkleCalibrationDecorator(bioMechModel).midMaleolus(
acqStatic)
gcp.setAnatomicalDefinition("Pelvis",
sequence="YZX",
nodeLabel1="RASI",
nodeLabel2="LASI",
nodeLabel3="SACR",
nodeLabelOrigin="midASIS")
gcp.setAnatomicalDefinition("Left Thigh",
sequence="ZXiY",
nodeLabel1="LKJC_mid",
nodeLabel2="LHJC_gt",
nodeLabel3="LKNE",
nodeLabelOrigin="LHJC_gt")
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
# motion
gaitFilename = "MRI-US-01, 2008-08-08, 3DGA 14.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion = modelFilters.ModelMotionFilter(scp,
acqGait,
model,
enums.motionMethod.Determinist,
usePyCGM2_coordinateSystem=True)
modMotion.compute()
# calibration decorators
modelDecorator.KneeCalibrationDecorator(model).calibrate2dof("Left")
modelDecorator.KneeCalibrationDecorator(model).calibrate2dof("Right")
# final calibration
modelFilters.ModelCalibrationFilter(scp,
acqStatic,
model,
RotateLeftThigh=True,
RotateRightThigh=True).compute()
#----MOTION----
# motion with dynakadOffset
modMotion = modelFilters.ModelMotionFilter(scp,
acqGait,
model,
enums.motionMethod.Determinist,
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")
def calibration2Dof(model, DATA_PATH, reconstructFilenameLabelled, translators,
side, beginFrame, endFrame, jointRange, **kwargs):
# --- btk acquisition ----
if "forceBtkAcq" in kwargs.keys():
acqFunc = kwargs["forceBtkAcq"]
else:
acqFunc = btkTools.smartReader(
(DATA_PATH + reconstructFilenameLabelled))
btkTools.checkMultipleSubject(acqFunc)
acqFunc = btkTools.applyTranslators(acqFunc, translators)
# filtering
# -----------------------
if "fc_lowPass_marker" in kwargs.keys(
) and kwargs["fc_lowPass_marker"] != 0:
trackingMarkers = model.getTrackingMarkers(acqFunc)
fc = kwargs["fc_lowPass_marker"]
order = 4
if "order_lowPass_marker" in kwargs.keys():
order = kwargs["order_lowPass_marker"]
signal_processing.markerFiltering(acqFunc,
trackingMarkers,
order=order,
fc=fc)
#---get frame range of interest---
ff = acqFunc.GetFirstFrame()
lf = acqFunc.GetLastFrame()
# motion
if side is None:
side = detectSide(acqFunc, "LANK", "RANK")
LOGGER.logger.info("Detected motion side : %s" % (side))
start, end = btkTools.getStartEndEvents(acqFunc, side)
if start is not None:
LOGGER.logger.info("Start event detected")
initFrame = start
else:
initFrame = beginFrame if beginFrame is not None else ff
if end is not None:
LOGGER.logger.info("End event detected")
endFrame = end
else:
endFrame = endFrame if endFrame is not None else lf
iff = initFrame - ff
ilf = endFrame - ff
if model.version in ["CGM1.0", "CGM1.1", "CGM2.1", "CGM2.2"]:
validFrames, vff, vlf = btkTools.findValidFrames(
acqFunc, cgm.CGM1.LOWERLIMB_TRACKING_MARKERS)
# --------------------------RESET OF THE STATIC File---------
# load btkAcq from static file
staticFilename = model.m_staticFilename
acqStatic = btkTools.smartReader((DATA_PATH + staticFilename))
btkTools.checkMultipleSubject(acqStatic)
acqStatic = btkTools.applyTranslators(acqStatic, translators)
# initial calibration ( i.e calibration from Calibration operation)
leftFlatFoot = model.m_properties["CalibrationParameters"]["leftFlatFoot"]
rightFlatFoot = model.m_properties["CalibrationParameters"][
"rightFlatFoot"]
headFlat = model.m_properties["CalibrationParameters"]["headFlat"]
markerDiameter = model.m_properties["CalibrationParameters"][
"markerDiameter"]
if side == "Left":
# remove other functional calibration
model.mp_computed["LeftKneeFuncCalibrationOffset"] = 0
if side == "Right":
# remove other functional calibration
model.mp_computed["RightKneeFuncCalibrationOffset"] = 0
# no rotation on both thigh - re init anatonical frame
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
headFlat=headFlat,
markerDiameter=markerDiameter).compute()
if model.version in ["CGM1.0", "CGM1.1", "CGM2.1", "CGM2.2"]:
modMotion = modelFilters.ModelMotionFilter(
scp, acqFunc, model, enums.motionMethod.Determinist)
modMotion.compute()
elif model.version in ["CGM2.3", "CGM2.4", "CGM2.5"]:
if side == "Left":
thigh_markers = model.getSegment("Left Thigh").m_tracking_markers
shank_markers = model.getSegment("Left Shank").m_tracking_markers
elif side == "Right":
thigh_markers = model.getSegment("Right Thigh").m_tracking_markers
shank_markers = model.getSegment("Right Shank").m_tracking_markers
validFrames, vff, vlf = btkTools.findValidFrames(
acqFunc, thigh_markers + shank_markers)
proximalSegmentLabel = (side + " Thigh")
distalSegmentLabel = (side + " Shank")
# Motion
modMotion = modelFilters.ModelMotionFilter(
scp, acqFunc, model, enums.motionMethod.Sodervisk)
modMotion.segmentalCompute([proximalSegmentLabel, distalSegmentLabel])
# calibration decorators
modelDecorator.KneeCalibrationDecorator(model).calibrate2dof(
side, indexFirstFrame=iff, indexLastFrame=ilf, jointRange=jointRange)
# --------------------------FINAL CALIBRATION OF THE STATIC File---------
# ---- Calibration
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
headFlat=headFlat,
markerDiameter=markerDiameter).compute()
return model, acqFunc, side
if FP2 == 'right':
plateforme_mpa += 'R'
elif FP2 == 'left':
plateforme_mpa += 'L'
else:
plateforme_mpa += 'X'
reconstructFilenameLabelled = os.path.split(filename)[1]
# Fitting
# Pour le premier fichier on 'décore' le modèle pour pouvoir faire
# la méthode de dynakad (il faut que le modele ait été utilisé en dynamique)
if ind_file == 1:
acqGait = cgm2_1.fitting(model, DATA_PATH, reconstructFilenameLabelled,
translators, markerDiameter, pointSuffix,
plateforme_mpa, momentProjection)
modelDecorator.KneeCalibrationDecorator(model).calibrate2dof('Left')
modelDecorator.KneeCalibrationDecorator(model).calibrate2dof('Right')
acqGait = cgm2_1.fitting(model, DATA_PATH, reconstructFilenameLabelled,
translators, markerDiameter, pointSuffix,
plateforme_mpa, momentProjection)
# writer
if fileSuffix is not None:
c3dFilename = str(reconstructFilenameLabelled[:-4] + "-modelled-" +
fileSuffix + ".c3d")
else:
c3dFilename = str(reconstructFilenameLabelled)
btkTools.smartWriter(acqGait, str(DATA_PATH_OUT + c3dFilename))
logging.info("c3d file (%s) generated" % (c3dFilename))
def applyBasicDecorators(dcm,
model,
acqStatic,
optional_mp,
markerDiameter,
cgm1only=False):
if model.getBodyPart() != enums.BodyPart.UpperLimb:
# native but thighRotation altered in mp
if dcm["Left Knee"] == enums.JointCalibrationMethod.Basic and dcm[
"Left Ankle"] == enums.JointCalibrationMethod.Basic and optional_mp[
"LeftThighRotation"] != 0:
logging.warning(
"CASE FOUND ===> Left Side = NATIVE CGM1 + manual Thigh ")
modelDecorator.Cgm1ManualOffsets(model).compute(
acqStatic, "left", optional_mp["LeftThighRotation"],
markerDiameter, optional_mp["LeftTibialTorsion"],
optional_mp["LeftShankRotation"])
if dcm["Right Knee"] == enums.JointCalibrationMethod.Basic and dcm[
"Right Ankle"] == enums.JointCalibrationMethod.Basic and optional_mp[
"RightThighRotation"] != 0:
logging.warning(
"CASE FOUND ===> Right Side = NATIVE CGM1 + manual Thigh ")
modelDecorator.Cgm1ManualOffsets(model).compute(
acqStatic, "right", optional_mp["RightThighRotation"],
markerDiameter, optional_mp["RightTibialTorsion"],
optional_mp["RightShankRotation"])
# KAD - and Kadmed
if dcm["Left Knee"] == enums.JointCalibrationMethod.KAD:
logging.warning("CASE FOUND ===> Left Side = Knee-KAD")
modelDecorator.Kad(model, acqStatic).compute(
markerDiameter=markerDiameter, side="left")
if dcm["Left Ankle"] == enums.JointCalibrationMethod.Medial:
logging.warning("CASE FOUND ===> Left Side = Ankle-Med")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="left")
if dcm["Right Knee"] == enums.JointCalibrationMethod.KAD:
logging.warning("CASE FOUND ===> Right Side = Knee-KAD")
modelDecorator.Kad(model, acqStatic).compute(
markerDiameter=markerDiameter, side="right")
if dcm["Right Ankle"] == enums.JointCalibrationMethod.Medial:
logging.warning("CASE FOUND ===> Right Side = Ankle-Med")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="right")
if not cgm1only:
if model.getBodyPart() != enums.BodyPart.UpperLimb:
#Kad-like (KneeMed)
if dcm["Left Knee"] == enums.JointCalibrationMethod.Medial and dcm[
"Left Ankle"] == enums.JointCalibrationMethod.Basic:
modelDecorator.KneeCalibrationDecorator(model).midCondyles_KAD(
acqStatic, markerDiameter=markerDiameter, side="left")
if dcm["Right Knee"] == enums.JointCalibrationMethod.Medial and dcm[
"Right Ankle"] == enums.JointCalibrationMethod.Basic:
modelDecorator.KneeCalibrationDecorator(model).midCondyles_KAD(
acqStatic, markerDiameter=markerDiameter, side="right")
#knee and ankle Med
if dcm["Left Knee"] == enums.JointCalibrationMethod.Medial and dcm[
"Left Ankle"] == enums.JointCalibrationMethod.Medial:
logging.info(
"[pyCGM2] Left Knee : Medial - Left Ankle : Medial")
modelDecorator.KneeCalibrationDecorator(model).midCondyles(
acqStatic, markerDiameter=markerDiameter, side="left")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="left")
if dcm["Right Knee"] == enums.JointCalibrationMethod.Medial and dcm[
"Right Ankle"] == enums.JointCalibrationMethod.Medial:
logging.info(
"[pyCGM2] Right Knee : Medial - Right Ankle : Medial")
modelDecorator.KneeCalibrationDecorator(model).midCondyles(
acqStatic, markerDiameter=markerDiameter, side="right")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="right")
def applyDecorators_CGM(smc, model,acqStatic,optional_mp,markerDiameter):
# native but thighRotation altered in mp
if smc["left"] == enums.CgmStaticMarkerConfig.Native and optional_mp["LeftThighRotation"] !=0:
logging.warning("CASE FOUND ===> Left Side = NATIVE CGM1 + manual Thigh ")
modelDecorator.Cgm1ManualOffsets(model).compute(acqStatic,"left",optional_mp["LeftThighRotation"],
markerDiameter, optional_mp["LeftTibialTorsion"], optional_mp["LeftShankRotation"])
if smc["right"] == enums.CgmStaticMarkerConfig.Native and optional_mp["RightThighRotation"] !=0:
logging.warning("CASE FOUND ===> Right Side = NATIVE CGM1 + manual Thigh ")
modelDecorator.Cgm1ManualOffsets(model).compute(acqStatic,"right",optional_mp["RightThighRotation"],
markerDiameter,optional_mp["RightTibialTorsion"],optional_mp["RightShankRotation"])
# KAD
if smc["left"] == enums.CgmStaticMarkerConfig.KAD:
logging.warning("CASE FOUND ===> Left Side = KAD")
modelDecorator.Kad(model,acqStatic).compute(markerDiameter=markerDiameter, side="left")
if smc["right"] == enums.CgmStaticMarkerConfig.KAD:
logging.warning("CASE FOUND ===> Right Side = KAD")
modelDecorator.Kad(model,acqStatic).compute(markerDiameter=markerDiameter, side="right")
# KADmed
if smc["left"] == enums.CgmStaticMarkerConfig.KADmed:
logging.warning("CASE FOUND ===> Left Side = KAD+med")
modelDecorator.Kad(model,acqStatic).compute(markerDiameter=markerDiameter, side="left")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="left")
if smc["right"] == enums.CgmStaticMarkerConfig.KADmed:
logging.warning("CASE FOUND ===> Right Side = KAD+med")
modelDecorator.Kad(model,acqStatic).compute(markerDiameter=markerDiameter, side="right")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="right")
# KneeMed
if smc["left"] == enums.CgmStaticMarkerConfig.KneeMed:
logging.warning("CASE FOUND ===> Left Side = KneeMed - ankle for KJC")
modelDecorator.KneeCalibrationDecorator(model).midCondyles_KAD(acqStatic, markerDiameter=markerDiameter, side="left")
if smc["right"] == enums.CgmStaticMarkerConfig.KneeMed:
logging.warning("CASE FOUND ===> Right Side = KneeMed - ankle for KJC")
modelDecorator.KneeCalibrationDecorator(model).midCondyles_KAD(acqStatic, markerDiameter=markerDiameter, side="right")
# KneeAnkleMed
if smc["left"] == enums.CgmStaticMarkerConfig.KneeAnkleMed:
logging.warning("CASE FOUND ===> Left Side = Knee and Ankle Medial")
modelDecorator.KneeCalibrationDecorator(model).midCondyles(acqStatic, markerDiameter=markerDiameter, side="left")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="left")
if smc["right"] == enums.CgmStaticMarkerConfig.KneeAnkleMed:
logging.warning("CASE FOUND ===> Right Side = Knee and Ankle Medial")
modelDecorator.KneeCalibrationDecorator(model).midCondyles(acqStatic, markerDiameter=markerDiameter, side="right")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="right")
# AnkleMed
if smc["left"] == enums.CgmStaticMarkerConfig.AnkleMed:
logging.warning("CASE FOUND ===> Left Side = Ankle Medial")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="left")
if smc["right"] == enums.CgmStaticMarkerConfig.AnkleMed:
logging.warning("CASE FOUND ===> Right Side = Ankle Medial")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="right")
