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_4()
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()
# ------ 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_4()
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()
# ------ 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_4()
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 calibration_GarchesFlatFoot(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"
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,
"LeftToeOffset": 0,
"RightToeOffset": 0,
}
# --- Calibration ---
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm2.CGM2_4()
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_GarchesFlatFoot.c3d")
def CGM2_4_Calibration2Dof_test(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.4\\Knee Calibration\\"
staticFilename = "static.c3d"
funcFilename = "functional.c3d"
gaitFilename = "gait trial 01.c3d"
settings = files.openJson(pyCGM2.PYCGM2_APPDATA_PATH,
"CGM2_4-pyCGM2.settings")
translators = settings["Translators"]
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)
# --store calibration parameters--
model.setStaticFilename(staticFilename)
model.setCalibrationProperty("leftFlatFoot", True)
model.setCalibrationProperty("rightFlatFoot", True)
model.setCalibrationProperty("markerDiameter", 14)
# test - no joint Range
model, acqFunc, side = kneeCalibration.calibration2Dof(
model, MAIN_PATH, funcFilename, translators, "Left", 831, 1280,
None)
# test with joint range of [20-90]
model, acqFunc, side = kneeCalibration.calibration2Dof(
model, MAIN_PATH, funcFilename, translators, "Left", 831, 1280,
[20, 90])
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 full_IK(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_4()
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_staticMotion.c3d")
def calibrate(DATA_PATH,calibrateFilenameLabelled,translators,settings,
required_mp,optional_mp,
ik_flag,leftFlatFoot,rightFlatFoot,headFlat,
markerDiameter,hjcMethod,
pointSuffix,**kwargs):
"""
Calibration of the CGM2.4
:param DATA_PATH [str]: path to your data
:param calibrateFilenameLabelled [str]: c3d file
:param translators [dict]: translators to apply
:param required_mp [dict]: required anthropometric data
:param optional_mp [dict]: optional anthropometric data (ex: LThighOffset,...)
:param ik_flag [bool]: enable the inverse kinematic solver
:param leftFlatFoot [bool]: enable of the flat foot option for the left foot
:param rightFlatFoot [bool]: enable of the flat foot option for the right foot
:param headFlat [bool]: enable of the head flat option
:param markerDiameter [double]: marker diameter (mm)
:param hjcMethod [str or list of 3 float]: method for locating the hip joint centre
:param pointSuffix [str]: suffix to add to model outputs
"""
# ---btk acquisition---
if "forceBtkAcq" in kwargs.keys():
acqStatic = kwargs["forceBtkAcq"]
else:
acqStatic = btkTools.smartReader(str(DATA_PATH+calibrateFilenameLabelled))
btkTools.checkMultipleSubject(acqStatic)
acqStatic = btkTools.applyTranslators(acqStatic,translators)
# ---check marker set used----
dcm = cgm.CGM.detectCalibrationMethods(acqStatic)
# --------------------------MODEL--------------------------------------
# ---definition---
model=cgm2.CGM2_4()
model.configure(acq=acqStatic,detectedCalibrationMethods=dcm)
model.addAnthropoInputParameters(required_mp,optional=optional_mp)
# --store calibration parameters--
model.setStaticFilename(calibrateFilenameLabelled)
model.setCalibrationProperty("leftFlatFoot",leftFlatFoot)
model.setCalibrationProperty("rightFlatFoot",rightFlatFoot)
model.setCalibrationProperty("headFlat",headFlat)
model.setCalibrationProperty("markerDiameter",markerDiameter)
# --------------------------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,
headFlat= headFlat,
markerDiameter=markerDiameter,
).compute()
# ---- Decorators -----
decorators.applyBasicDecorators(dcm, 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,
headFlat= headFlat,
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()
if "displayCoordinateSystem" in kwargs.keys() and kwargs["displayCoordinateSystem"]:
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(csp,model,finalAcqStatic)
csdf.setStatic(False)
csdf.display()
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model,finalAcqStatic).compute(description="vectoriel", pointLabelSuffix=pointSuffix)
# detection of traveling axis + absolute angle
if model.m_bodypart != enums.BodyPart.UpperLimb:
longitudinalAxis,forwardProgression,globalFrame = btkTools.findProgressionAxisFromPelvicMarkers(finalAcqStatic,["LASI","LPSI","RASI","RPSI"])
else:
longitudinalAxis,forwardProgression,globalFrame = btkTools.findProgressionAxisFromLongAxis(finalAcqStatic,"C7","CLAV")
if model.m_bodypart != enums.BodyPart.UpperLimb:
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)
if model.m_bodypart == enums.BodyPart.LowerLimbTrunk:
modelFilters.ModelAbsoluteAnglesFilter(model,finalAcqStatic,
segmentLabels=["Thorax"],
angleLabels=["Thorax"],
eulerSequences=["YXZ"],
globalFrameOrientation = globalFrame,
forwardProgression = forwardProgression).compute(pointLabelSuffix=pointSuffix)
if model.m_bodypart == enums.BodyPart.UpperLimb or model.m_bodypart == enums.BodyPart.FullBody:
modelFilters.ModelAbsoluteAnglesFilter(model,finalAcqStatic,
segmentLabels=["Thorax","Head"],
angleLabels=["Thorax", "Head"],
eulerSequences=["YXZ","TOR"],
globalFrameOrientation = globalFrame,
forwardProgression = forwardProgression).compute(pointLabelSuffix=pointSuffix)
# BSP model
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
if model.m_bodypart == enums.BodyPart.FullBody:
modelFilters.CentreOfMassFilter(model,finalAcqStatic).compute(pointLabelSuffix=pointSuffix)
return model, finalAcqStatic
def calibrate(DATA_PATH,calibrateFilenameLabelled,translators,weights,
required_mp,optional_mp,
ik_flag,leftFlatFoot,rightFlatFoot,headFlat,
markerDiameter,hjcMethod,
pointSuffix,**kwargs):
"""
Calibration of the CGM2.4
:param DATA_PATH [str]: path to your data
:param calibrateFilenameLabelled [str]: c3d file
:param translators [dict]: translators to apply
:param required_mp [dict]: required anthropometric data
:param optional_mp [dict]: optional anthropometric data (ex: LThighOffset,...)
:param ik_flag [bool]: enable the inverse kinematic solver
:param leftFlatFoot [bool]: enable of the flat foot option for the left foot
:param rightFlatFoot [bool]: enable of the flat foot option for the right foot
:param headFlat [bool]: enable of the head flat option
:param markerDiameter [double]: marker diameter (mm)
:param hjcMethod [str or list of 3 float]: method for locating the hip joint centre
:param pointSuffix [str]: suffix to add to model outputs
"""
detectAnomaly = False
if "anomalyException" in kwargs.keys():
anomalyException = kwargs["anomalyException"]
else:
anomalyException=False
# ---btk acquisition---
if "Fitting" in weights.keys():
weights = weights["Fitting"]["Weight"]
if "forceBtkAcq" in kwargs.keys():
acqStatic = kwargs["forceBtkAcq"]
else:
acqStatic = btkTools.smartReader((DATA_PATH+calibrateFilenameLabelled))
btkTools.checkMultipleSubject(acqStatic)
if btkTools.isPointExist(acqStatic,"SACR"):
translators["LPSI"] = "SACR"
translators["RPSI"] = "SACR"
LOGGER.logger.info("[pyCGM2] Sacrum marker detected")
acqStatic = btkTools.applyTranslators(acqStatic,translators)
trackingMarkers = cgm2.CGM2_4.LOWERLIMB_TRACKING_MARKERS + cgm2.CGM2_4.THORAX_TRACKING_MARKERS+ cgm2.CGM2_4.UPPERLIMB_TRACKING_MARKERS
actual_trackingMarkers,phatoms_trackingMarkers = btkTools.createPhantoms(acqStatic, trackingMarkers)
vff = acqStatic.GetFirstFrame()
vlf = acqStatic.GetLastFrame()
# vff,vlf = btkTools.getFrameBoundaries(acqStatic,actual_trackingMarkers)
flag = btkTools.getValidFrames(acqStatic,actual_trackingMarkers,frameBounds=[vff,vlf])
gapFlag = btkTools.checkGap(acqStatic,actual_trackingMarkers,frameBounds=[vff,vlf])
if gapFlag:
raise Exception("[pyCGM2] Calibration aborted. Gap find during interval [%i-%i]. Crop your c3d " %(vff,vlf))
# --------------------ANOMALY------------------------------
# --Check MP
adap = AnomalyDetectionProcedure.AnthropoDataAnomalyProcedure( required_mp)
adf = AnomalyFilter.AnomalyDetectionFilter(None,None,adap)
mp_anomaly = adf.run()
if mp_anomaly["ErrorState"]: detectAnomaly = True
# --marker presence
markersets = [cgm2.CGM2_4.LOWERLIMB_TRACKING_MARKERS, cgm2.CGM2_4.THORAX_TRACKING_MARKERS, cgm2.CGM2_4.UPPERLIMB_TRACKING_MARKERS]
for markerset in markersets:
ipdp = InspectorProcedure.MarkerPresenceDetectionProcedure( markerset)
idf = InspectorFilter.InspectorFilter(acqStatic,calibrateFilenameLabelled,ipdp)
inspector = idf.run()
# # --marker outliers
if inspector["In"] !=[]:
madp = AnomalyDetectionProcedure.MarkerAnomalyDetectionRollingProcedure(inspector["In"], plot=False, window=4,threshold = 3)
adf = AnomalyFilter.AnomalyDetectionFilter(acqStatic,calibrateFilenameLabelled,madp)
anomaly = adf.run()
anomalyIndexes = anomaly["Output"]
if anomaly["ErrorState"]: detectAnomaly = True
if detectAnomaly and anomalyException:
raise Exception ("Anomalies has been detected - Check Warning message of the log file")
# --------------------MODELLING------------------------------
# ---check marker set used----
dcm = cgm.CGM.detectCalibrationMethods(acqStatic)
# --------------------------MODEL--------------------------------------
# ---definition---
model=cgm2.CGM2_4()
model.configure(detectedCalibrationMethods=dcm)
model.addAnthropoInputParameters(required_mp,optional=optional_mp)
if dcm["Left Knee"] == enums.JointCalibrationMethod.KAD: actual_trackingMarkers.append("LKNE")
if dcm["Right Knee"] == enums.JointCalibrationMethod.KAD: actual_trackingMarkers.append("RKNE")
model.setStaticTrackingMarkers(actual_trackingMarkers)
# --store calibration parameters--
model.setStaticFilename(calibrateFilenameLabelled)
model.setCalibrationProperty("leftFlatFoot",leftFlatFoot)
model.setCalibrationProperty("rightFlatFoot",rightFlatFoot)
model.setCalibrationProperty("headFlat",headFlat)
model.setCalibrationProperty("markerDiameter",markerDiameter)
# --------------------------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,
headFlat= headFlat,
markerDiameter=markerDiameter,
).compute()
# ---- Decorators -----
decorators.applyBasicDecorators(dcm, 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,
headFlat= headFlat,
markerDiameter=markerDiameter).compute()
# ----------------------CGM MODELLING----------------------------------
# ----motion filter----
modMotion=modelFilters.ModelMotionFilter(scp,acqStatic,model,enums.motionMethod.Sodervisk,
markerDiameter=markerDiameter)
modMotion.compute()
# ----progression Frame----
progressionFlag = False
if btkTools.isPointsExist(acqStatic, ['LASI', 'RASI', 'RPSI', 'LPSI'],ignorePhantom=False):
LOGGER.logger.info("[pyCGM2] - progression axis detected from Pelvic markers ")
pfp = progressionFrame.PelvisProgressionFrameProcedure()
pff = progressionFrame.ProgressionFrameFilter(acqStatic,pfp)
pff.compute()
progressionAxis = pff.outputs["progressionAxis"]
globalFrame = pff.outputs["globalFrame"]
forwardProgression = pff.outputs["forwardProgression"]
progressionFlag = True
elif btkTools.isPointsExist(acqStatic, ['C7', 'T10', 'CLAV', 'STRN'],ignorePhantom=False) and not progressionFlag:
LOGGER.logger.info("[pyCGM2] - progression axis detected from Thoracic markers ")
pfp = progressionFrame.ThoraxProgressionFrameProcedure()
pff = progressionFrame.ProgressionFrameFilter(acqStatic,pfp)
pff.compute()
progressionAxis = pff.outputs["progressionAxis"]
globalFrame = pff.outputs["globalFrame"]
forwardProgression = pff.outputs["forwardProgression"]
else:
globalFrame = "XYZ"
progressionAxis = "X"
forwardProgression = True
LOGGER.logger.error("[pyCGM2] - impossible to detect progression axis - neither pelvic nor thoracic markers are present. Progression set to +X by default ")
# ----manage IK Targets----
ikTargets = list()
for target in weights.keys():
if target not in actual_trackingMarkers:
weights[target] = 0
LOGGER.logger.warning("[pyCGM2] - the IK targeted marker [%s] is not labelled in the acquisition [%s]"%(target,calibrateFilenameLabelled))
else:
ikTargets.append(target)
model.setStaticIkTargets(ikTargets)
if "noKinematicsCalculation" in kwargs.keys() and kwargs["noKinematicsCalculation"]:
LOGGER.logger.warning("[pyCGM2] No Kinematic calculation done for the static file")
return model, acqStatic,detectAnomaly
else:
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,
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",weights["LASI"])
cgmFittingProcedure.updateMarkerWeight("RASI",weights["RASI"])
cgmFittingProcedure.updateMarkerWeight("LPSI",weights["LPSI"])
cgmFittingProcedure.updateMarkerWeight("RPSI",weights["RPSI"])
cgmFittingProcedure.updateMarkerWeight("RTHI",weights["RTHI"])
cgmFittingProcedure.updateMarkerWeight("RKNE",weights["RKNE"])
cgmFittingProcedure.updateMarkerWeight("RTIB",weights["RTIB"])
cgmFittingProcedure.updateMarkerWeight("RANK",weights["RANK"])
cgmFittingProcedure.updateMarkerWeight("RHEE",weights["RHEE"])
cgmFittingProcedure.updateMarkerWeight("RTOE",weights["RTOE"])
cgmFittingProcedure.updateMarkerWeight("LTHI",weights["LTHI"])
cgmFittingProcedure.updateMarkerWeight("LKNE",weights["LKNE"])
cgmFittingProcedure.updateMarkerWeight("LTIB",weights["LTIB"])
cgmFittingProcedure.updateMarkerWeight("LANK",weights["LANK"])
cgmFittingProcedure.updateMarkerWeight("LHEE",weights["LHEE"])
cgmFittingProcedure.updateMarkerWeight("LTOE",weights["LTOE"])
cgmFittingProcedure.updateMarkerWeight("LTHAP",weights["LTHAP"])
cgmFittingProcedure.updateMarkerWeight("LTHAD",weights["LTHAD"])
cgmFittingProcedure.updateMarkerWeight("LTIAP",weights["LTIAP"])
cgmFittingProcedure.updateMarkerWeight("LTIAD",weights["LTIAD"])
cgmFittingProcedure.updateMarkerWeight("RTHAP",weights["RTHAP"])
cgmFittingProcedure.updateMarkerWeight("RTHAD",weights["RTHAD"])
cgmFittingProcedure.updateMarkerWeight("RTIAP",weights["RTIAP"])
cgmFittingProcedure.updateMarkerWeight("RTIAD",weights["RTIAD"])
cgmFittingProcedure.updateMarkerWeight("LSMH",weights["LSMH"])
cgmFittingProcedure.updateMarkerWeight("LFMH",weights["LFMH"])
cgmFittingProcedure.updateMarkerWeight("LVMH",weights["LVMH"])
cgmFittingProcedure.updateMarkerWeight("RSMH",weights["RSMH"])
cgmFittingProcedure.updateMarkerWeight("RFMH",weights["RFMH"])
cgmFittingProcedure.updateMarkerWeight("RVMH",weights["RVMH"])
# cgmFittingProcedure.updateMarkerWeight("LTHL",weights["LTHL"])
# cgmFittingProcedure.updateMarkerWeight("LTHLD",weights["LTHLD"])
# cgmFittingProcedure.updateMarkerWeight("LPAT",weights["LPAT"])
# cgmFittingProcedure.updateMarkerWeight("LTIBL",weights["LTIBL"])
# cgmFittingProcedure.updateMarkerWeight("RTHL",weights["RTHL"])
# cgmFittingProcedure.updateMarkerWeight("RTHLD",weights["RTHLD"])
# cgmFittingProcedure.updateMarkerWeight("RPAT",weights["RPAT"])
# cgmFittingProcedure.updateMarkerWeight("RTIBL",weights["RTIBL"])
osrf = opensimFilters.opensimFittingFilter(iksetupFile,
scalingOsim,
cgmFittingProcedure,
DATA_PATH,
acqStatic,
accuracy = 1e-5)
osrf.setTimeRange(acqStatic,beginFrame = vff, lastFrame=vlf)
LOGGER.logger.info("-------INVERSE KINEMATICS IN PROGRESS----------")
try:
acqStaticIK = osrf.run(DATA_PATH + calibrateFilenameLabelled,
progressionAxis = progressionAxis ,
forwardProgression = forwardProgression)
LOGGER.logger.info("[pyCGM2] - IK solver complete")
except:
LOGGER.logger.error("[pyCGM2] - IK solver fails")
acqStaticIK = acqStatic
detectAnomaly = True
LOGGER.logger.info("-----------------------------------------------")
# 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()
if "displayCoordinateSystem" in kwargs.keys() and kwargs["displayCoordinateSystem"]:
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(csp,model,finalAcqStatic)
csdf.setStatic(False)
csdf.display()
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model,finalAcqStatic).compute(description="vectoriel", pointLabelSuffix=pointSuffix)
modelFilters.ModelAbsoluteAnglesFilter(model,finalAcqStatic,
segmentLabels=["Left Foot","Right Foot","Pelvis","Thorax","Head"],
angleLabels=["LFootProgress", "RFootProgress","Pelvis","Thorax", "Head"],
eulerSequences=["TOR","TOR", "ROT","YXZ","TOR"],
globalFrameOrientation = globalFrame,
forwardProgression = forwardProgression).compute(pointLabelSuffix=pointSuffix)
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
modelFilters.CentreOfMassFilter(model,finalAcqStatic).compute(pointLabelSuffix=pointSuffix)
btkTools.cleanAcq(finalAcqStatic)
if detectAnomaly and not anomalyException:
LOGGER.logger.error("Anomalies has been detected - Check Warning messages of the log file")
return model, finalAcqStatic,detectAnomaly
